The CDF upgrade

International Nuclear Information System (INIS)

Newman-Holmes, C.

1995-01-01

The Collider Detector at Fermilab (CDF) has been used to study proton-antiproton collisions at the Fermilab Tevatron since 1985. Over the years, the detector has evolved steadily to increase its physics capability and to keep pace with improvements to the Tevatron. Fermilab is currently building a new Main Injector accelerator which will lead to even larger luminosity values. This paper describes upgrades to CDF that will allow one to exploit the higher luminosity of the Main Injector

The CDF Silicon Vertex Trigger

International Nuclear Information System (INIS)

Dell'Orso, Mauro

2006-01-01

Motivations, design, performance and ongoing upgrade of the CDF Silicon Vertex Trigger are presented. The system provides CDF with a powerful tool for online tracking with offline quality in order to enhance the reach on B-physics and large P t -physics coupled to b quarks

MR-CDF: Managing multi-resolution scientific data

Science.gov (United States)

Salem, Kenneth

1993-01-01

MR-CDF is a system for managing multi-resolution scientific data sets. It is an extension of the popular CDF (Common Data Format) system. MR-CDF provides a simple functional interface to client programs for storage and retrieval of data. Data is stored so that low resolution versions of the data can be provided quickly. Higher resolutions are also available, but not as quickly. By managing data with MR-CDF, an application can be relieved of the low-level details of data management, and can easily trade data resolution for improved access time.

Photon production at CDF and DO/

International Nuclear Information System (INIS)

Lamoureux, J.I.

1996-01-01

Prompt photon production has been studied in bar pp collisions at √s=1.8 TeV using the CDF and DO/ detectors at Fermilab. The measured inclusive isolated photon spectrum at CDF and DO/ are used to test NLO QCD predictions. The CDF result shows that additional soft radiation (K T ) in excess of NLO QCD is required to explain the data. No new resonance is observed in the photon+jet mass spectrum from DO/ which is consistent with NLO QCD predictions. The pseudorapidity distribution of the leading jet in photon events at CDF is compared to different parton distribution sets. The angular distribution is found to be better explained by a larger Bremsstrahlung contribution. copyright 1996 American Institute of Physics

CDF results on B decays

International Nuclear Information System (INIS)

Skarha, J.E.

1995-05-01

The authors present recent CDF results on B lifetimes, B meson mass measurements, ratios of branching ratios, and rare decays. In addition, they present the first measurement of time-dependent B d mixing at CDF. Several results have been updated and a few new ones included since the workshop

Enhanced B-Raf-mediated NRF2 gene transcription and HATs-mediated NRF2 protein acetylation contributes to ABCC1-mediated chemoresistance and glutathione-mediated survival in acquired topoisomerase II poison-resistant cancer cells.

Science.gov (United States)

Chen, Huang-Hui; Chang, Hsin-Huei; Chang, Jang-Yang; Tang, Ya-Chu; Cheng, Yung-Chi; Lin, Li-Mei; Cheng, Shu-Ying; Huang, Chih-Hsiang; Sun, Man-Wu; Chen, Chiung-Tong; Kuo, Ching-Chuan

2017-12-01

Nuclear factor erythroid-2-related factor 2 (NRF2) mainly regulates transcriptional activation through antioxidant-responsive elements (AREs) present in the promoters of NRF2 target genes. Recently, we found that NRF2 was overexpressed in a KB-derived drug-resistant cancer cell panel. In this panel, KB-7D cells, which show acquired resistance to topoisomerase II (Top II) poisons, exhibited the highest NRF2 activation. To investigate whether NRF2 directly contributed to acquired resistance against Top II poisons, we manipulated NRF2 by genetic and pharmacological approaches. The result demonstrated that silencing of NRF2 by RNA interference increased the sensitivity and treatment with NRF2 activator decreased the sensitivity of KB and KB-7D cells toward Top II poisons. Further, increased B-Raf-mediated NRF2 gene transcription and HATs-mediated NRF2 protein acetylation activated NRF2 signaling in KB-7D cells. Moreover, increased binding of NRF2 to an ARE in the promoter of ATP-binding cassette subfamily C member 1 (ABCC1) directly contributed to Top II poison resistance. In addition, activation of NRF2 increased glutathione level and antioxidant capacity in KB-7D cells compared with that in KB cells; moreover, high glutathione level provided survival advantage to KB-7D cells. Our study is the first to show that aberrant NRF2 activation is via increased B-Raf-mediated NRF2 gene transcription and HATs-mediated NRF2 protein acetylation, which increases the acquired resistance and promote the survival of Top II poison-resistant cancer cells. Importantly, NRF2 downstream effectors ABCC1 and glutathione directly contribute to acquired resistance and survival, respectively. These results suggest that blockade of NRF2 signaling may enhance therapeutic efficacy and reduce the survival of Top II poison-refractory tumors in clinical. Copyright © 2017 Elsevier Inc. All rights reserved.

Quarkonia production at CDF

International Nuclear Information System (INIS)

Demina, R.

1996-08-01

We present the results of J/ψ, ψ', χ c and Υ(1S), Υ(2S), Υ(3S) production in the proton-antiproton collisions at √s = 1800 GeV measured with the CDF Detector. Contributions of different production mechanisms are discussed. 10 refs., 7 figs

Sequencing and characterization of mixed function monooxygenase genes CYP1A1 and CYP1A2 of Mink (Mustela vison) to facilitate study of dioxin-like compounds

International Nuclear Information System (INIS)

Zhang Xiaowei; Moore, Jeremy N.; Newsted, John L.; Hecker, Markus; Zwiernik, Matthew J.; Jones, Paul D.; Bursian, Steven J.

2009-01-01

As part of an ongoing effort to understand aryl hydrocarbon receptor (AhR) mediated toxicity in mink, cDNAs encoding for CYP1A1 and the CYP1A2 mixed function monooxygenases were cloned and characterized. In addition, the effects of selected dibenzofurans on the expression of these genes and the presence of their respective proteins (P4501A) were investigated, and then correlated with the catalytic activities of these proteins as measured by ethoxyresorufin O-deethylase (EROD) and methoxyresorufin O-deethylase (MROD) activities. The predicted protein sequences for CYP1A1 and CYP1A2 comprise 517 and 512 amino acid residues, respectively. The phylogenetic analysis of the mink CYP1As with protein sequences of other mammals revealed high sequence homology with sea otter, seals and the dog, with amino acid identities ranging from 89 to 95% for CYP1A1 and 81 to 93% for CYP1A2. Since exposure to both 2,3,7,8-Tetrachlorodibenzofuran (TCDF) and 2,3,4,7,8-Pentachlorodibenzofuran (PeCDF) resulted in dose-dependent increases of CYP1A1 mRNA, CYP1A2 mRNA and CYP1A protein levels an underlying AhR-mediated mechanism is suggested. The up-regulation of CYP1A mRNA in liver was more consistent to the sum adipose TEQ concentration than to the liver TEQ concentration in minks treated with TCDF or PeCDF. The result suggested that the hepatic-sequestered fraction of PeCDF was biologically inactive to the induction of CYP1A1 and CYP1A2

CDF Top Physics

Science.gov (United States)

Tartarelli, G. F.; CDF Collaboration

1996-05-01

The authors present the latest results about top physics obtained by the CDF experiment at the Fermilab Tevatron collider. The data sample used for these analysis (about 110 pb{sup{minus}1}) represents almost the entire statistics collected by CDF during four years (1992--95) of data taking. This large data size has allowed detailed studies of top production and decay properties. The results discussed here include the determination of the top quark mass, the measurement of the production cross section, the study of the kinematics of the top events and a look at top decays.

The Arabidopsis mediator complex subunits MED16, MED14, and MED2 regulate mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes.

Science.gov (United States)

Hemsley, Piers A; Hurst, Charlotte H; Kaliyadasa, Ewon; Lamb, Rebecca; Knight, Marc R; De Cothi, Elizabeth A; Steele, John F; Knight, Heather

2014-01-01

The Mediator16 (MED16; formerly termed SENSITIVE TO FREEZING6 [SFR6]) subunit of the plant Mediator transcriptional coactivator complex regulates cold-responsive gene expression in Arabidopsis thaliana, acting downstream of the C-repeat binding factor (CBF) transcription factors to recruit the core Mediator complex to cold-regulated genes. Here, we use loss-of-function mutants to show that RNA polymerase II recruitment to CBF-responsive cold-regulated genes requires MED16, MED2, and MED14 subunits. Transcription of genes known to be regulated via CBFs binding to the C-repeat motif/drought-responsive element promoter motif requires all three Mediator subunits, as does cold acclimation-induced freezing tolerance. In addition, these three subunits are required for low temperature-induced expression of some other, but not all, cold-responsive genes, including genes that are not known targets of CBFs. Genes inducible by darkness also required MED16 but required a different combination of Mediator subunits for their expression than the genes induced by cold. Together, our data illustrate that plants control transcription of specific genes through the action of subsets of Mediator subunits; the specific combination defined by the nature of the stimulus but also by the identity of the gene induced.

Electron identification at CDF

International Nuclear Information System (INIS)

Kim, Shinhong

1990-01-01

Electron identification at CDF is performed using the information of lateral and longitudinal shower spread, the track-cluster position match and the energy-momentum match. The tracking chamber with a solenoidal magnetic field at CDF is powerful for rejecting the backgrounds such as the π ± - π 0 overlaps, the π 0 /γ conversions and interactive π ± in electromagnetic calorimeter: The energy- momentum match cut can decrease the background due to the π ± - π 0 overlaps for non-isolated electrons with Et above 10 GeV by a factor of 20. The conversion electrons are identified using track information with an efficiency of 80 ± 3%. The charge of electrons from W decay can be determined in the pseudorapidity range of |η| < 1.7 at CDF. The charge determination is useful for background estimation of Drell-Yan physics and heavy flavor physics. 5 refs., 5 figs

The CDF Run II disk inventory manager

International Nuclear Information System (INIS)

Hubbard, Paul; Lammel, Stephan

2001-01-01

The Collider Detector at Fermilab (CDF) experiment records and analyses proton-antiproton interactions at a center-of-mass energy of 2 TeV. Run II of the Fermilab Tevatron started in April of this year. The duration of the run is expected to be over two years. One of the main data handling strategies of CDF for Run II is to hide all tape access from the user and to facilitate sharing of data and thus disk space. A disk inventory manager was designed and developed over the past years to keep track of the data on disk, to coordinate user access to the data, and to stage data back from tape to disk as needed. The CDF Run II disk inventory manager consists of a server process, a user and administrator command line interfaces, and a library with the routines of the client API. Data are managed in filesets which are groups of one or more files. The system keeps track of user access to the filesets and attempts to keep frequently accessed data on disk. Data that are not on disk are automatically staged back from tape as needed. For CDF the main staging method is based on the mt-tools package as tapes are written according to the ANSI standard

Level-3 Calorimetric Resolution available for the Level-1 and Level-2 CDF Triggers

CERN Document Server

Canepa, A.; Liu, T.; Cortiana, G.; Flanagan, G.; Frisch, H.; Krop, D.; Pilcher, C.; Rusu, V.; Cavaliere, V.; Greco, V.; Giannetti, P.; Piendibene, M.; Sartori, L.; Vidal, Miguel

2008-01-01

As the Tevatron luminosity increases sophisticated selections are required to be efficient in selecting rare events among a very huge background. To cope with this problem, CDF has pushed the offline calorimeter algorithm reconstruction resolution up to Level 2 and, when possible, even up to Level 1, increasing efficiency and, at the same time, keeping under control the rates. The CDF Run II Level 2 calorimeter trigger is implemented in hardware and is based on a simple algorithm that was used in Run I. This system has worked well for Run II at low luminosity. As the Tevatron instantaneous luminosity increases, the limitation due to this simple algorithm starts to become clear: some of the most important jet and MET (Missing ET) related triggers have large growth terms in cross section at higher luminosity. In this paper, we present an upgrade of the Level 2 Calorimeter system which makes the calorimeter trigger tower information available directly to a CPU allowing more sophisticated algorithms to be impleme...

The CDF SVX II detector upgrade

International Nuclear Information System (INIS)

Skarha, J.E.

1993-10-01

The proposed CDF SVX II detector upgrade for secondary vertex detection during the Fermilab Tevatron Run II collider run is described. The general design and important features of this silicon vertex detector are presented. The CDF physics goals which are addressed by this detector are also given

Novel Hematopoietic Target Genes in the NRF2-Mediated Transcriptional Pathway

Directory of Open Access Journals (Sweden)

Michelle R. Campbell

2013-01-01

Full Text Available Nuclear factor- (erythroid-derived 2 like 2 (NFE2L2, NRF2 is a key transcriptional activator of the antioxidant response pathway and is closely related to erythroid transcription factor NFE2. Under oxidative stress, NRF2 heterodimerizes with small Maf proteins and binds cis-acting enhancer sequences found near oxidative stress response genes. Using the dietary isothiocyanate sulforaphane (SFN to activate NRF2, chromatin immunoprecipitation sequencing (ChIP-seq identified several hundred novel NRF2-mediated targets beyond its role in oxidative stress. Activated NRF2 bound the antioxidant response element (ARE in promoters of several known and novel target genes involved in iron homeostasis and heme metabolism, including known targets FTL and FTH1, as well as novel binding in the globin locus control region. Five novel NRF2 target genes were chosen for followup: AMBP, ABCB6, FECH, HRG-1 (SLC48A1, and TBXAS1. SFN-induced gene expression in erythroid K562 and lymphoid cells were compared for each target gene. NRF2 silencing showed reduced expression in lymphoid, lung, and hepatic cells. Furthermore, stable knockdown of NRF2 negative regulator KEAP1 in K562 cells resulted in increased NQO1, AMBP, and TBXAS1 expression. NFE2 binding sites in K562 cells revealed similar binding profiles as lymphoid NRF2 sites in all potential NRF2 candidates supporting a role for NRF2 in heme metabolism and erythropoiesis.

The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering.

Science.gov (United States)

Henriques, Rossana; Wang, Huan; Liu, Jun; Boix, Marc; Huang, Li-Fang; Chua, Nam-Hai

2017-11-01

Circadian rhythms of gene expression are generated by the combinatorial action of transcriptional and translational feedback loops as well as chromatin remodelling events. Recently, long noncoding RNAs (lncRNAs) that are natural antisense transcripts (NATs) to transcripts encoding central oscillator components were proposed as modulators of core clock function in mammals (Per) and fungi (frq/qrf). Although oscillating lncRNAs exist in plants, their functional characterization is at an initial stage. By screening an Arabidopsis thaliana lncRNA custom-made array we identified CDF5 LONG NONCODING RNA (FLORE), a circadian-regulated lncRNA that is a NAT of CDF5. Quantitative real-time RT-PCR confirmed the circadian regulation of FLORE, whereas GUS-staining and flowering time evaluation were used to determine its biological function. FLORE and CDF5 antiphasic expression reflects mutual inhibition in a similar way to frq/qrf. Moreover, whereas the CDF5 protein delays flowering by directly repressing FT transcription, FLORE promotes it by repressing several CDFs (CDF1, CDF3, CDF5) and increasing FT transcript levels, indicating both cis and trans function. We propose that the CDF5/FLORE NAT pair constitutes an additional circadian regulatory module with conserved (mutual inhibition) and unique (function in trans) features, able to fine-tune its own circadian oscillation, and consequently, adjust the onset of flowering to favourable environmental conditions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

ERK1/2 mediates glucose-regulated POMC gene expression in hypothalamic neurons.

Science.gov (United States)

Zhang, Juan; Zhou, Yunting; Chen, Cheng; Yu, Feiyuan; Wang, Yun; Gu, Jiang; Ma, Lian; Ho, Guyu

2015-04-01

Hypothalamic glucose-sensing neurons regulate the expression of genes encoding feeding-related neuropetides POMC, AgRP, and NPY - the key components governing metabolic homeostasis. AMP-activated protein kinase (AMPK) is postulated to be the molecular mediator relaying glucose signals to regulate the expression of these neuropeptides. Whether other signaling mediator(s) plays a role is not clear. In this study, we investigated the role of ERK1/2 using primary hypothalamic neurons as the model system. The primary neurons were differentiated from hypothalamic progenitor cells. The differentiated neurons possessed the characteristic neuronal cell morphology and expressed neuronal post-mitotic markers as well as leptin-regulated orexigenic POMC and anorexigenic AgRP/NPY genes. Treatment of cells with glucose dose-dependently increased POMC and decreased AgRP/NPY expression with a concurrent suppression of AMPK phosphorylation. In addition, glucose treatment dose-dependently increased the ERK1/2 phosphorylation. Blockade of ERK1/2 activity with its specific inhibitor PD98059 partially (approximately 50%) abolished glucose-induced POMC expression, but had little effect on AgRP/NPY expression. Conversely, blockade of AMPK activity with its specific inhibitor produced a partial (approximately 50%) reversion of low-glucose-suppressed POMC expression, but almost completely blunted the low-glucose-induced AgRP/NPY expression. The results indicate that ERK1/2 mediated POMC but not AgRP/NPY expression. Confirming the in vitro findings, i.c.v. administration of PD98059 in rats similarly attenuated glucose-induced POMC expression in the hypothalamus, but again had little effect on AgRP/NPY expression. The results are indicative of a novel role of ERK1/2 in glucose-regulated POMC expression and offer new mechanistic insights into hypothalamic glucose sensing. © 2015 Society for Endocrinology.

Silicon Tracking Upgrade at CDF

International Nuclear Information System (INIS)

Kruse, M.C.

1998-04-01

The Collider Detector at Fermilab (CDF) is scheduled to begin recording data from Run II of the Fermilab Tevatron in early 2000. The silicon tracking upgrade constitutes both the upgrade to the CDF silicon vertex detector (SVX II) and the new Intermediate Silicon Layers (ISL) located at radii just beyond the SVX II. Here we review the design and prototyping of all aspects of these detectors including mechanical design, data acquisition, and a trigger based on silicon tracking

Test on 2,000 photomultipliers for the CDF endplug calorimeter upgrade

International Nuclear Information System (INIS)

Fiori, I.

1997-01-01

A systematic test of various characteristics, such as gain, dark current, maximum peak current, stability and relative quantum efficiency, has been made to evaluate about 2,000 photomultiplier tubes for the upgraded CDF Endplug calorimeters. The phototubes are Hamamatsu R4125,19mm diameter with green-extended photocathode. In this report we discuss the distribution of the major characteristics measured and the failure mode. Comparisons between independent measurements made on some of the characteristics are used to evaluate the quality of the measurement itself

Online track processor for the CDF upgrade

International Nuclear Information System (INIS)

Thomson, E. J.

2002-01-01

A trigger track processor, called the eXtremely Fast Tracker (XFT), has been designed for the CDF upgrade. This processor identifies high transverse momentum (> 1.5 GeV/c) charged particles in the new central outer tracking chamber for CDF II. The XFT design is highly parallel to handle the input rate of 183 Gbits/s and output rate of 44 Gbits/s. The processor is pipelined and reports the result for a new event every 132 ns. The processor uses three stages: hit classification, segment finding, and segment linking. The pattern recognition algorithms for the three stages are implemented in programmable logic devices (PLDs) which allow in-situ modification of the algorithm at any time. The PLDs reside on three different types of modules. The complete system has been installed and commissioned at CDF II. An overview of the track processor and performance in CDF Run II are presented

The Arabidopsis Mediator Complex Subunits MED16, MED14, and MED2 Regulate Mediator and RNA Polymerase II Recruitment to CBF-Responsive Cold-Regulated Genes[C][W][OPEN

Science.gov (United States)

Hemsley, Piers A.; Hurst, Charlotte H.; Kaliyadasa, Ewon; Lamb, Rebecca; Knight, Marc R.; De Cothi, Elizabeth A.; Steele, John F.; Knight, Heather

2014-01-01

The Mediator16 (MED16; formerly termed SENSITIVE TO FREEZING6 [SFR6]) subunit of the plant Mediator transcriptional coactivator complex regulates cold-responsive gene expression in Arabidopsis thaliana, acting downstream of the C-repeat binding factor (CBF) transcription factors to recruit the core Mediator complex to cold-regulated genes. Here, we use loss-of-function mutants to show that RNA polymerase II recruitment to CBF-responsive cold-regulated genes requires MED16, MED2, and MED14 subunits. Transcription of genes known to be regulated via CBFs binding to the C-repeat motif/drought-responsive element promoter motif requires all three Mediator subunits, as does cold acclimation–induced freezing tolerance. In addition, these three subunits are required for low temperature–induced expression of some other, but not all, cold-responsive genes, including genes that are not known targets of CBFs. Genes inducible by darkness also required MED16 but required a different combination of Mediator subunits for their expression than the genes induced by cold. Together, our data illustrate that plants control transcription of specific genes through the action of subsets of Mediator subunits; the specific combination defined by the nature of the stimulus but also by the identity of the gene induced. PMID:24415770

Recent QCD results from CDF

International Nuclear Information System (INIS)

Yun, J.C.

1990-01-01

In this paper we report recent QCD analysis with the new data taken from CDF detector. CDF recorded an integrated luminosity of 4.4 nb -1 during the 1988--1989 run at center of mass system (CMS) energy of 1.8 TeV. The major topics of this report are inclusive jet, dijet, trijet and direct photon analysis. These measurements are compared of QCD predictions. For the inclusive jet an dijet analysis, tests of quark compositeness are emphasized. 11 refs., 6 figs

Entdeckung elektroschwacher Produktion einzelner Top-Quarks mit dem CDF II Experiment; Discovery electroweak production of single top quarks with the CDF II Experiment

Energy Technology Data Exchange (ETDEWEB)

Luck, Jan [Karlsruhe Inst. of Technology (KIT) (Germany)

2009-01-01

This thesis presents a neural network search for combined as well as separate s- and t-channel single top-quark production with the CDF II experiment at the Tevatron using 3.2 fb^-1 of collision data. It is the twelfth thesis dealing with single top-quark production performed within the CDF Collaboration, whereas three have been done in Run I [53–55] and eight in Run II [23, 25, 28, 39, 56–59].

'Miniskirt' counter array at CDF II

International Nuclear Information System (INIS)

Artikov, A.; Artikov, A.

2006-01-01

Full text: Muon detection is fundamental for the most of the interesting analyses at CDF. At the course of Run II, the collaboration expects to collect hundreds of t t-bar decays yielding a muon as well as several million B-hadron events involving J/ψ → μ + μ - decays. Muon detection is also of fundamental importance in the study of W-boson properties and in the search for Higgs production associated with W or Z bosons. Considerable effort therefore went into extending the muon detector coverage for Run II, which started in March 2001. The CDF II muon detector system consists of multiple layers of drift chambers and scintillation counters, which span the pseudorapidity (|η|) range between 0 and 1.5. Detectors spanning different ranges have different geometries, and the muon scintillation counter system includes subsystems in the regions that have come to be known as the 'central' (0 pe for WLS fiber readout is smaller than for conventional readout, we can also expect an increase in the statistical contribution to the overall uncertainty. Our first concern, before adopting this solution, was therefore to ascertain that the mean timing resolution obtained under these conditions was adequate. The modifications, testing and installation of these counters within the CDF Upgrade Project are described in detail. The timing characteristics of MSX' counters are also investigated using cosmic muons. The measurements show that the time resolution does not exceed 2.2 ns. (author)

Indirectly cooled large thin superconducting CDF solenoid

International Nuclear Information System (INIS)

Kondo, Kunitaka; Mori, Shigeki; Yoshizaki, Ryozo; Saito, Ryusei; Asano, Katsuhiko.

1985-01-01

The manufacturing technique of the indirectly cooled large thin superconducting solenoid for the collider detector facility (CDF solenoid) has been studied through cooperation of University of Tsukuba and the National Laboratory for High Energy Physics of the Ministry of Education of Japan, and the Fermi National Accelerator Laboratory in the U.S. Fabrication and testing of the solenoid has recently been completed by Hitachi. The CDF solenoid has a large-sized thin structure for meeting the requirement by experiments to be applied. Hitachi has thus developed a variety of new technologies including the design standard, coil cooling method, material selection, and manufacturing technique in accordance with experimental data, which were confirmed in a series of analyses and tests made on various prototypes. The CDF solenoid, built using Hitachi's new technologies, is of the world's top class among equipment of this type. This paper outlines the design criteria for the major components employed in the CDF solenoid and the test results of the solenoid. (author)

B physics with the CDF Run II upgrade

International Nuclear Information System (INIS)

DeJongh, F.

1996-01-01

During the Run 1 data taking period, from 1992 through 1995, CDF has acquired 110 pb -1 of p anti p collisions at a center of mass energy of 1,800 GeV. This data has provided many results on B physics, and provides a basis for extrapolating to Run 2, which is scheduled to start in 1999 after major upgrades to both the accelerator and detector. The authors present herein a summary of Run 1 results relevant to an analysis of the CP asymmetry in B → J/ψK s , the CDF upgrade plans for Run 2, and some of the main B physics goals related to the exploration of the origin of CP violation

Search for supersymmetry with like-sign lepton-tau events at CDF.

Science.gov (United States)

Aaltonen, T; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Appel, J A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Auerbach, B; Aurisano, A; Azfar, F; Badgett, W; Bae, T; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauce, M; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Bland, K R; Blumenfeld, B; Bocci, A; Bodek, A; Bortoletto, D; Boudreau, J; Boveia, A; Brigliadori, L; Bromberg, C; Brucken, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Bussey, P; Butti, P; Buzatu, A; Calamba, A; Camarda, S; Campanelli, M; Canelli, F; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Cho, K; Chokheli, D; Ciocci, M A; Clark, A; Clarke, C; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Cremonesi, M; Cruz, D; Cuevas, J; Culbertson, R; d'Ascenzo, N; Datta, M; De Barbaro, P; Demortier, L; Deninno, M; d'Errico, M; Devoto, F; Di Canto, A; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dorigo, M; Driutti, A; Ebina, K; Edgar, R; Elagin, A; Erbacher, R; Errede, S; Esham, B; Eusebi, R; Farrington, S; Fernández Ramos, J P; Field, R; Flanagan, G; Forrest, R; Franklin, M; Freeman, J C; Frisch, H; Funakoshi, Y; Garfinkel, A F; Garosi, P; Gerberich, H; Gerchtein, E; Giagu, S; Giakoumopoulou, V; Gibson, K; Ginsburg, C M; Giokaris, N; Giromini, P; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldin, D; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González López, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gramellini, E; Grinstein, S; Grosso-Pilcher, C; Group, R C; Guimaraes da Costa, J; Hahn, S R; Han, J Y; Happacher, F; Hara, K; Hare, M; Harr, R F; Harrington-Taber, T; Hatakeyama, K; Hays, C; Heinrich, J; Herndon, M; Hocker, A; Hong, Z; Hopkins, W; Hou, S; Hughes, R E; Husemann, U; Hussein, M; Huston, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kambeitz, M; Kamon, T; Karchin, P E; Kasmi, A; Kato, Y; Ketchum, W; Keung, J; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y J; Kim, Y K; Kimura, N; Kirby, M; Knoepfel, K; Kondo, K; Kong, D J; Konigsberg, J; Kotwal, A V; Kreps, M; Kroll, J; Kruse, M; Kuhr, T; Kurata, M; Laasanen, A T; Lammel, S; Lancaster, M; Lannon, K; Latino, G; Lee, H S; Lee, J S; Leo, S; Leone, S; Lewis, J D; Limosani, A; Lipeles, E; Lister, A; Liu, H; Liu, Q; Liu, T; Lockwitz, S; Loginov, A; Lucà, A; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; Madrak, R; Maestro, P; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, P; Martínez, M; Matera, K; Mattson, M E; Mazzacane, A; Mazzanti, P; McNulty, R; Mehta, A; Mehtala, P; Mesropian, C; Miao, T; Mietlicki, D; Mitra, A; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M J; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakano, I; Napier, A; Nett, J; Neu, C; Nigmanov, T; Nodulman, L; Noh, S Y; Norniella, O; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Ortolan, L; Pagliarone, C; Palencia, E; Palni, P; Papadimitriou, V; Parker, W; Pauletta, G; Paulini, M; Paus, C; Phillips, T J; Piacentino, G; Pianori, E; Pilot, J; Pitts, K; Plager, C; Pondrom, L; Poprocki, S; Potamianos, K; Pranko, A; Prokoshin, F; Ptohos, F; Punzi, G; Ranjan, N; Redondo Fernández, I; Renton, P; Rescigno, M; Rimondi, F; Ristori, L; Robson, A; Rodriguez, T; Rolli, S; Ronzani, M; Roser, R; Rosner, J L; Ruffini, F; Ruiz, A; Russ, J; Rusu, V; Sakumoto, W K; Sakurai, Y; Santi, L; Sato, K; Saveliev, V; Savoy-Navarro, A; Schlabach, P; Schmidt, E E; Schwarz, T; Scodellaro, L; Scuri, F; Seidel, S; Seiya, Y; Semenov, A; Sforza, F; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shochet, M; Shreyber-Tecker, I; Simonenko, A; Sinervo, P; Sliwa, K; Smith, J R; Snider, F D; Song, H; Sorin, V; Stancari, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Sudo, Y; Sukhanov, A; Suslov, I; Takemasa, K; Takeuchi, Y; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thomson, E; Thukral, V; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Trovato, M; Ukegawa, F; Uozumi, S; Vázquez, F; Velev, G; Vellidis, C; Vernieri, C; Vidal, M; Vilar, R; Vizán, J; Vogel, M; Volpi, G; Wagner, P; Wallny, R; Wang, S M; Warburton, A; Waters, D; Wester, W C; Whiteson, D; Wicklund, A B; Wilbur, S; Williams, H H; Wilson, J S; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, H; Wright, T; Wu, X; Wu, Z; Yamamoto, K; Yamato, D; Yang, T; Yang, U K; Yang, Y C; Yao, W-M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Zanetti, A M; Zeng, Y; Zhou, C; Zucchelli, S

2013-05-17

We present a search for chargino-neutralino associated production using like electric charge dilepton events collected by the CDF II detector at the Fermilab Tevatron in proton-antiproton collisions at sqrt[s] = 1.96 TeV. One lepton is identified as the hadronic decay of a tau lepton, while the other is an electron or muon. In data corresponding to 6.0 fb(-1) of integrated luminosity, we obtain good agreement with standard model predictions and set limits on the chargino-neutralino production cross section for simplified gravity- and gauge-mediated models. As an example, assuming that the chargino and neutralino decays to taus dominate, in the simplified gauge-mediated model we exclude cross sections greater than 300 fb at 95% credibility level for chargino and neutralino masses of 225 GeV/c(2). This analysis is the first to extend the LHC searches for electroweak supersymmetric production of gauginos to high tanβ and slepton next-to-lightest supersymmetric particle scenarios.

CDF [Collider Detector at Fermilab] detector simulation

International Nuclear Information System (INIS)

Freeman, J.

1987-12-01

The Collider Detector at Fermilab (CDF) uses several different simulation programs, each tuned for specific applications. The programs rely heavily on the extensive test beam data that CDF has accumulated. Sophisticated shower parameterizations are used, yielding enormous gains in speed over full cascade programs. 3 refs., 5 figs

Minimum bias and underlying event studies at CDF

International Nuclear Information System (INIS)

Moggi, Niccolo

2010-01-01

Soft, non-perturbative, interactions are poorly understood from the theoretical point of view even though they form a large part of the hadronic cross section at the energies now available. We review the CDF studies on minimum-bias ad underlying event in p(bar p) collisions at 2 TeV. After proposing an operative definition of 'underlying event', we present part of a systematic set of measurements carried out by the CDF Collaboration with the goal to provide data to test and improve the QCD models of hadron collisions. Different analysis strategies of the underlying event and possible event topologies are discussed. Part of the CDF minimum-bias results are also presented: in this sample, that represent the full inelastic cross-section, we can test simultaneously our knowledge of all the components that concur to form hadronic interactions. Comparisons with MonteCarlo simulations are always shown along with the data. These measurements will also contribute to more precise estimates of the soft QCD background of high-p T observables.

Operational Experience, Improvements, and Performance of the CDF Run II Silicon Vertex Detector

CERN Document Server

Aaltonen, T; Boveia, A.; Brau, B.; Bolla, G; Bortoletto, D; Calancha, C; Carron, S.; Cihangir, S.; Corbo, M.; Clark, D.; Di Ruzza, B.; Eusebi, R.; Fernandez, J.P.; Freeman, J.C.; Garcia, J.E.; Garcia-Sciveres, M.; Gonzalez, O.; Grinstein, S.; Hartz, M.; Herndon, M.; Hill, C.; Hocker, A.; Husemann, U.; Incandela, J.; Issever, C.; Jindariani, S.; Junk, T.R.; Knoepfel, K.; Lewis, J.D.; Martinez-Ballarin, R.; Mathis, M.; Mattson, M.; Merkel, P; Mondragon, M.N.; Moore, R.; Mumford, J.R.; Nahn, S.; Nielsen, J.; Nelson, T.K.; Pavlicek, V.; Pursley, J.; Redondo, I.; Roser, R.; Schultz, K.; Spalding, J.; Stancari, M.; Stanitzki, M.; Stuart, D.; Sukhanov, A.; Tesarek, R.; Treptow, K.; Wallny, R.; Worm, S.

2013-01-01

The Collider Detector at Fermilab (CDF) pursues a broad physics program at Fermilab's Tevatron collider. Between Run II commissioning in early 2001 and the end of operations in September 2011, the Tevatron delivered 12 fb-1 of integrated luminosity of p-pbar collisions at sqrt(s)=1.96 TeV. Many physics analyses undertaken by CDF require heavy flavor tagging with large charged particle tracking acceptance. To realize these goals, in 2001 CDF installed eight layers of silicon microstrip detectors around its interaction region. These detectors were designed for 2--5 years of operation, radiation doses up to 2 Mrad (0.02 Gy), and were expected to be replaced in 2004. The sensors were not replaced, and the Tevatron run was extended for several years beyond its design, exposing the sensors and electronics to much higher radiation doses than anticipated. In this paper we describe the operational challenges encountered over the past 10 years of running the CDF silicon detectors, the preventive measures undertaken, an...

Eurogrid: a new glideinWMS based portal for CDF data analysis

Science.gov (United States)

Amerio, S.; Benjamin, D.; Dost, J.; Compostella, G.; Lucchesi, D.; Sfiligoi, I.

2012-12-01

The CDF experiment at Fermilab ended its Run-II phase on September 2011 after 11 years of operations and 10 fb-1 of collected data. CDF computing model is based on a Central Analysis Farm (CAF) consisting of local computing and storage resources, supported by OSG and LCG resources accessed through dedicated portals. At the beginning of 2011 a new portal, Eurogrid, has been developed to effectively exploit computing and disk resources in Europe: a dedicated farm and storage area at the TIER-1 CNAF computing center in Italy, and additional LCG computing resources at different TIER-2 sites in Italy, Spain, Germany and France, are accessed through a common interface. The goal of this project is to develop a portal easy to integrate in the existing CDF computing model, completely transparent to the user and requiring a minimum amount of maintenance support by the CDF collaboration. In this paper we will review the implementation of this new portal, and its performance in the first months of usage. Eurogrid is based on the glideinWMS software, a glidein based Workload Management System (WMS) that works on top of Condor. As CDF CAF is based on Condor, the choice of the glideinWMS software was natural and the implementation seamless. Thanks to the pilot jobs, user-specific requirements and site resources are matched in a very efficient way, completely transparent to the users. Official since June 2011, Eurogrid effectively complements and supports CDF computing resources offering an optimal solution for the future in terms of required manpower for administration, support and development.

High ET jet cross sections at CDF

International Nuclear Information System (INIS)

Flaugher, B.

1996-08-01

The inclusive jet cross section for p anti p collisions at √s = 1.8 TeV as measured by the CDF collaboration will be presented. Preliminary CDF measurements of the Σ E T cross section at √s = 1.8 TeV and the central inclusive jet cross section at √s = 0.630 TeV will also be shown

Searches for new phenomena at CDF

International Nuclear Information System (INIS)

Wilson, P.J.

1997-07-01

We present recent results of searches for new physics in 110 pb - 1 of p anti p collisions at √s = 1800 GeV using the CDF detector. Presented are searches for third generation leptoquarks, charged and neutral Higgs bosons and the supersymmetric partner of the top quark (t). A search for new physics in diphoton events tests some models attempting to explain the CDF ''eeγγE T '' event. Finding no signal in any of these channels, production limits are presented

Jet physics at CDF

International Nuclear Information System (INIS)

Melese, P.

1997-05-01

We present high E T jet measurements from CDF at the Fermilab Tevatron Collider. The incfilusive jet cross section at √s = 1800 GeV with ∼ 5 times more data is compared to the published CDF results, preliminary D0 results, and next-to-leading order QCD predictions. The summation E T cross section is also compared to QCD predictions and the dijet angular distribution is used to place a limit on quark compositeness. The inclusive jet cross section at √s = 630 GeV is compared with that at 1800 GeV to test the QCD predictions for the scaling of jet cross sections with √s. Finally, we present momentum distributions of charged particles in jets and compare them to Modified Leading Log Approximation predictions

The CDF II eXtremely fast tracker upgrade

Energy Technology Data Exchange (ETDEWEB)

Abulencia, A.; Azzurri, P.; Cochran, E.; Dittmann, J.; Donati, S.; Efron, J.; Erbacher, R.; Errede, D.; Fedorko, I.; Flanagan, G.; Forrest, R.; /Illinois U., Urbana

2006-09-01

The CDF II Extremely Fast Tracker is the trigger track processor which reconstructs charged particle tracks in the transverse plane of the CDF II central outer tracking chamber. The system is now being upgraded to perform a three dimensional track reconstruction. A review of the upgrade is presented here.

Search for new phenomena with the CDF detector

International Nuclear Information System (INIS)

Azzi, P.

1997-05-01

We present the results of the searches for new phenomena in pp collisions at √s=1.8 TeV with the CDF detector using the full data sample of 110 pb -1 collected between 1992 and 1995. We have searched for new physics in events with two photons, testing some of the hypotheses proposed to explain the appearance of the CDF eeγγ E T event. New results on the search for a heavy neutral scalar object, charged Higgs bosons (H ± ) and the scalar top quark are presented. Finally we summarize the CDF results on the search for third generation leptoquarks

Search for the top quark with CDF

International Nuclear Information System (INIS)

Barbaro-Galtieri, A.

1991-01-01

During the 1988--89 Tevatron Collider run the CDF detector has collected data for an integrated luminosity of 4.4 pb -1 . The sample has been used to search for the top quark in several topologies. Preliminary results show that a top mass below 89 GeV is excluded at the 95% confidence level, thus extending the limit of 77 GeV previously published by CDF. 14 refs., 8 figs

Combination of the CDF and D0 Effective Leptonic Electroweak Mixing Angles

Energy Technology Data Exchange (ETDEWEB)

The Tevatron Electroweak Working Group

2016-07-31

CDF and D0 have measured the effective leptonic weak mixing angle $sin^2 \\theta^{lept}_{eff}$ , using their full Tevatron datasets. This note describes the Tevatron combination of these measurements, and the zfitter standard model-based inference of the on-shell electroweak mixing angle $sin^2 \\theta_W$, or equivalently, the W-boson mass. The combination of CDF and D0 results yields: $sin^2 \\theta^{lept}_ {eff}$ = 0.23179 ± 0.00035, and $sin^2 \\theta_W$ = 0.22356 ± 0.00035, or equivalently, $M_W$(indirect) = 80.351 ± 0.018 GeV/$c^2$.

Visualizing NetCDF Files by Using the EverVIEW Data Viewer

Science.gov (United States)

Conzelmann, Craig; Romañach, Stephanie S.

2010-01-01

Over the past few years, modelers in South Florida have started using Network Common Data Form (NetCDF) as the standard data container format for storing hydrologic and ecologic modeling inputs and outputs. With its origins in the meteorological discipline, NetCDF was created by the Unidata Program Center at the University Corporation for Atmospheric Research, in conjunction with the National Aeronautics and Space Administration and other organizations. NetCDF is a portable, scalable, self-describing, binary file format optimized for storing array-based scientific data. Despite attributes which make NetCDF desirable to the modeling community, many natural resource managers have few desktop software packages which can consume NetCDF and unlock the valuable data contained within. The U.S. Geological Survey and the Joint Ecosystem Modeling group, an ecological modeling community of practice, are working to address this need with the EverVIEW Data Viewer. Available for several operating systems, this desktop software currently supports graphical displays of NetCDF data as spatial overlays on a three-dimensional globe and views of grid-cell values in tabular form. An included Open Geospatial Consortium compliant, Web-mapping service client and charting interface allows the user to view Web-available spatial data as additional map overlays and provides simple charting visualizations of NetCDF grid values.

Performance of the CDF Silicon VerteX detector

International Nuclear Information System (INIS)

Schneider, O.

1992-11-01

The current status of the online and offline performance of the CDF Silicon VerteX detector is presented. So far, at low radiation dose, the device delivers good quality data. After the latest alignment using collision data, a spatial resolution of 13 pm is achieved in the transverse plane, demonstrating that CDF has a powerful tool to detect b decay vertices

CDF experience with monte carlo production using LCG grid

International Nuclear Information System (INIS)

Griso, S P; Lucchesi, D; Compostella, G; Sfiligoi, I; Cesini, D

2008-01-01

The upgrades of the Tevatron collider and CDF detector have considerably increased the demand on computing resources, in particular for Monte Carlo production. This has forced the collaboration to move beyond the usage of dedicated resources and start exploiting the Grid. The CDF Analysis Farm (CAF) model has been reimplemented into LcgCAF in order to access Grid resources by using the LCG/EGEE middleware. Many sites in Italy and in Europe are accessed through this portal by CDF users mainly to produce Monte Carlo data but also for other analysis jobs. We review here the setup used to submit jobs to Grid sites and retrieve the output, including CDF-specific configuration of some Grid components. We also describe the batch and interactive monitor tools developed to allow users to verify the jobs status during their lifetime in the Grid environment. Finally we analyze the efficiency and typical failure modes of the current Grid infrastructure reporting the performances of different parts of the system used

The CDF muon system

International Nuclear Information System (INIS)

LeCompte, T.J.; Papadimitriou, V.

1993-01-01

The authors describe the characteristics of the CDF muon system and their experience with it. They explain how the trigger works and how they identify muons offline. They also describe the future upgrades of the system and their trigger plans for Run IB and beyond

Collider detector at Fermilab - CDF. Progress report

International Nuclear Information System (INIS)

Theriot, D.

1985-06-01

CDF, the Collider Detector at Fermilab, is a collaboration of almost 180 physicists from ten US universities (University of Chicago, Brandeis University, Harvard University, University of Illinois, University of Pennsylvania, Purdue University, Rockefeller University, Rutgers University, Texas A and M University, and University of Wisconsin), three US DOE supported national laboratories (Fermilab, Argonne National Laboratory, and Lawrence Berkeley Laboratory), Italy (Frascati National Laboratory and University of Pisa), and Japan (KEK National Laboratory and University of Tsukuba). The primary physics goal for CDF is to study the general features of proton-antiproton collisions at 2 TeV center-of-mass energy. On general grounds, we expect that parton subenergies in the range 50 to 500 GeV will provide the most interesting physics at this energy. Work at the present CERN Collider has already demonstrated the richness of the 100 GeV scale in parton subenergies. 7 refs., 14 figs

Collider Detector (CDF) at FERMILAB: an overview

International Nuclear Information System (INIS)

Theriot, D.

1984-07-01

CDF, the Collider Detector at Fermilab, is a collaboration of almost 150 physicists from ten US universities (University of Chicago, Brandeis University, Harvard University, University of Illinois, University of Pennsylvania, Purdue University, Rockefeller University, Rutgers University, Texas A and M University, and University of Wisconsin), three US DOE supported national laboratories (Fermilab, Argonne National Laboratory, and Lawrence Berkeley Laboratory), Italy (Frascati Laboratory and University of Pisa), and Japan (KEK National Laboratory and Unversity of Tsukuba). The primary physics goal for CDF is to study the general features of proton-antiproton collisions at 2 TeV center-of-mass energy. On general grounds, we expect that parton subenergies in the range 50 to 500 GeV will provide the most interesting physics at this energy. Work at the present CERN Collider has already demonstrated the richness of the 100 GeV scale in parton subenergies

E2F1-mediated transcriptional inhibition of the plasminogen activator inhibitor type 1 gene

DEFF Research Database (Denmark)

Koziczak, M; Müller, H; Helin, K

2001-01-01

but independent of binding to pocket-binding proteins, suggesting a novel mechanism for E2F-mediated negative gene regulation [Koziczak, M., Krek, W. & Nagamine, Y. (2000) Mol. Cell. Biol. 20, 2014-2022]. However, it remains to be seen whether endogenous E2F can exert a similar effect. We report here that down....... These results all indicate that endogenous E2F can directly repress the PAI-1 gene. DNase I hypersensitive-site analysis of the PAI-1 promoter suggested the involvement of conformation changes in chromatin structure of the PAI-1 promoter. 5' deletion analysis of the PAI-1 promoter showed that multiple sites...

J/ψ and Υ production at CDF

International Nuclear Information System (INIS)

Liss, T.

1990-01-01

Characteristics of J/ψ and Υ produced at the Tevatron and detected in the dimuon channel at CDF are reviewed. The masses of the J/ψ and Υ are measured to be 3.096 ± 0.001 GeV/c 2 and 9.469 ± 0.010 GeV/c 2 respectively. These mass measurements are used to determine the systematic uncertainty on the momentum scale in the central tracking chamber. 2 refs., 14 figs

The CDF II eXtremely Fast Tracker Upgrade

CERN Document Server

Fedorko, I; Errede, D; Gerberich, H; Junk, T; Kasten, M; Levine, S; Mokos, R; Pitts, K; Rogers, E; Veramendi, G; Azzurri, P; Donati, S; Staveris-Polykalas, A; Cochran, E; Efron, J; Gartner, J; Hughes, R; Johnson, M; Kilminster, B; Lannon, K; McKim, J; Olivito, D; Parks, B; Slaunwhite, J; Winer, B; Dittmann, J; Hewamanage, S; Krumnack, N; Wilson, J S; Erbacher, R; Forrest, R; Ivanov, A; Soha, A; Flanagan, G; Jones, T; Holm, S; Klein, R; Schmidt, E E; Scott, L; Shaw, T; Wilson, P J

2008-01-01

The CDF II eXtremely Fast Tracker (XFT) is the trigger processor which reconstructs charged particle tracks in the transverse plane of the central tracking chamber. The XFT tracks are also extrapolated to the electromagnetic calorimeter and muon chambers to generate trigger electron and muon candidates. The XFT is crucial for the entire CDF II physics program: it detects high pT leptons from W/Z and heavy flavor decays and, in conjunction with the Level 2 processors, it identifies secondary vertices from beauty decays. The XFT has thus been crucial for the recent measurement of the oscilation and Σb discovery. The increase of the Tevatron instantaneous luminosity demanded an upgrade of the system to cope with the higher occupancy of the chamber. In the upgraded XFT, three dimensional tracking reduces the level of fake tracks and measures the longitudinal track parameters, which strongly reinforce the trigger selections. This allows to mantain the trigger perfectly efficient at the record luminosities 2–3·...

Common Data Format (CDF) and Coordinated Data Analysis Web (CDAWeb)

Science.gov (United States)

Candey, Robert M.

2010-01-01

The Coordinated Data Analysis Web (CDAWeb) data browsing system provides plotting, listing and open access v ia FTP, HTTP, and web services (REST, SOAP, OPeNDAP) for data from mo st NASA Heliophysics missions and is heavily used by the community. C ombining data from many instruments and missions enables broad resear ch analysis and correlation and coordination with other experiments a nd missions. Crucial to its effectiveness is the use of a standard se lf-describing data format, in this case, the Common Data Format (CDF) , also developed at the Space Physics Data facility , and the use of metadata standa rds (easily edited with SKTeditor ). CDAweb is based on a set of IDL routines, CDAWlib . . The CDF project also maintains soft ware and services for translating between many standard formats (CDF. netCDF, HDF, FITS, XML) .

NCWin — A Component Object Model (COM) for processing and visualizing NetCDF data

Science.gov (United States)

Liu, Jinxun; Chen, J.M.; Price, D.T.; Liu, S.

2005-01-01

NetCDF (Network Common Data Form) is a data sharing protocol and library that is commonly used in large-scale atmospheric and environmental data archiving and modeling. The NetCDF tool described here, named NCWin and coded with Borland C + + Builder, was built as a standard executable as well as a COM (component object model) for the Microsoft Windows environment. COM is a powerful technology that enhances the reuse of applications (as components). Environmental model developers from different modeling environments, such as Python, JAVA, VISUAL FORTRAN, VISUAL BASIC, VISUAL C + +, and DELPHI, can reuse NCWin in their models to read, write and visualize NetCDF data. Some Windows applications, such as ArcGIS and Microsoft PowerPoint, can also call NCWin within the application. NCWin has three major components: 1) The data conversion part is designed to convert binary raw data to and from NetCDF data. It can process six data types (unsigned char, signed char, short, int, float, double) and three spatial data formats (BIP, BIL, BSQ); 2) The visualization part is designed for displaying grid map series (playing forward or backward) with simple map legend, and displaying temporal trend curves for data on individual map pixels; and 3) The modeling interface is designed for environmental model development by which a set of integrated NetCDF functions is provided for processing NetCDF data. To demonstrate that the NCWin can easily extend the functions of some current GIS software and the Office applications, examples of calling NCWin within ArcGIS and MS PowerPoint for showing NetCDF map animations are given.

Remote data monitoring for CDF

International Nuclear Information System (INIS)

Kippenhan, H.A. Jr.; Lidinsky, W.; Roediger, G.

1995-11-01

Remote data monitoring from the physicists' home institutions has become an important issue in large international experiments to ensure high performance of the detectors and high quality of data and scientific results. The CDF experiment is a collaboration of 450 physicists from 36 institutions in the U.S., Japan, Canada, Italy and Taiwan. Future experiments at Fermilab, CERN and elsewhere will be even larger, and will be performed over a period of order 10 years. The ability of collaborators at remote sites to monitor the increasingly complex detectors and feed the results back into the data acquisition process will be of great importance We report on the status and performance of remote monitoring from Japan of the CDF experiment in Batavia Illinois. We also discuss feasibilities for modest Remote Control Rooms

CDF tau triggers, analysis and other developments

International Nuclear Information System (INIS)

J. R. Smith

2003-01-01

This note is a write-up of contribution made by the author to the HCP2002 conference. It has two principal subjects. The first subject concerns the CDF τ triggers, τ-cone algorithms and τ physics analysis. τ physics is going to be very important in Run II because τ's can extend SUSY searches at large tan β in particular, τ's will help in the searches for (tilde χ) 1 ± (tilde χ) 2 0 , MSSM Higgs and other non Standard Model (SM) processes. Also, τ events are important for various Standard Model processes including Precision Electroweak, t(bar t), and SM Higgs searches. τ triggers are installed and operating at CDF. The second subject of this contribution to the HCP2002 conference concerns the algorithms of backwards differentiation abstracted from their usual setting inside of Automatic Differentiation software packages. Backwards differentiation (reverse-mode differentiation) provides a useful means for optimizing many kinds of problems

Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment.

Science.gov (United States)

Eyboulet, Fanny; Cibot, Camille; Eychenne, Thomas; Neil, Helen; Alibert, Olivier; Werner, Michel; Soutourina, Julie

2013-12-01

Mediator is a large multiprotein complex conserved in all eukaryotes. The crucial function of Mediator in transcription is now largely established. However, we found that this complex also plays an important role by connecting transcription with DNA repair. We identified a functional contact between the Med17 Mediator subunit and Rad2/XPG, the 3' endonuclease involved in nucleotide excision DNA repair. Genome-wide location analyses revealed that Rad2 is associated with RNA polymerase II (Pol II)- and Pol III-transcribed genes and telomeric regions in the absence of exogenous genotoxic stress. Rad2 occupancy of Pol II-transcribed genes is transcription-dependent. Genome-wide Rad2 occupancy of class II gene promoters is well correlated with that of Mediator. Furthermore, UV sensitivity of med17 mutants is correlated with reduced Rad2 occupancy of class II genes and concomitant decrease of Mediator interaction with Rad2 protein. Our results suggest that Mediator is involved in DNA repair by facilitating Rad2 recruitment to transcribed genes.

The CDF central and endwall hadron calorimeter

International Nuclear Information System (INIS)

Bertolucci, S.; Cordelli, M.; Eposito, B.; Curatolo, M.; Giromini, P.; Miscetti, S.; Sansoni, A.; Barnes, V.E.; Di Virgilio, A.; Garfinkel, A.F.; Kuhlmann, S.E.; Laasanen, A.T.

1988-01-01

The CDF central and endwall hadron calorimeter covers the polar region between 30 0 and 150 0 and a full 2π in azimuth. It consists of 48 steel-scintillator central modules with 2.5 cm sampling and 48 steel-scintillator endwall modules with 5.0 cm sampling. A general description of the detector is given. Calibration techniques and performance are discussed. Some results of the test beam studies are shown. (orig.)

Observation of Single Top Quark production with the Cdf 2. Experiment

International Nuclear Information System (INIS)

Lueck, J.

2010-01-01

We present the observation of electroweak single top-quark production using up to 3.2 fb -1 of data collected by the Cdf experiment. Lepton plus jets candidate events are classified by four parallel analysis techniques: one likelihood discriminant, one matrix-element discriminant, one decision-tree discriminant, and one neural-network discriminant. These outputs are combined with a super discriminant based on a neural-network analysis in order to improve the expected sensitivity. In conjunction with one neural-network discriminant using a complementary dataset of Met plus jets events with a veto on identified leptons we observe a signal consistent with the standard model but inconsistent with the background-only model by 5.0 standard deviations, with a median expected sensitivity in excess of 5.9 standard deviations.

Log(s) physics results from CDF

International Nuclear Information System (INIS)

1989-01-01

The Collider Detector at Fermilab (CDF) is a large, azimuthally symmetric detector designed to study bar pp interactions at the Fermilab Tevatron Collider. Results are presented from data taken with a minimum bias trigger at √s = 630 and 1800 GeV during the 1987 run. The topics include the current analysis of dn/dη and some very preliminary results on short range pseudorapidity correlations and Bose-Einstein correlations. 7 refs., 5 figs., 2 tabs

Characterization of emission properties of Er3+ ions in TeO2-CdF2-WO3 glasses.

Science.gov (United States)

Bilir, G; Mustafaoglu, N; Ozen, G; DiBartolo, B

2011-12-01

TeO(2)-CdF(2)-WO(3) glasses with various compositions and Er(3+) concentrations were prepared by conventional melting method. Their optical properties were studied by measuring the absorption, luminescence spectra and the decay patterns at room temperature. From the optical absorption spectra the Judd-Ofelt parameters (Ω(t)), transition probabilities, branching ratios of various transitions, and radiative lifetimes were calculated. The absorption and emission cross-section spectra of the (4)I(15/2) to (4)I(13/2) transition of erbium were determined. Emission quantum efficiencies and the average critical distance R(0) which provides a measure for the strength of cross relaxation were determined. Copyright © 2011 Elsevier B.V. All rights reserved.

Germline stem cell gene PIWIL2 mediates DNA repair through relaxation of chromatin.

Directory of Open Access Journals (Sweden)

De-Tao Yin

Full Text Available DNA damage response (DDR is an intrinsic barrier of cell to tumorigenesis initiated by genotoxic agents. However, the mechanisms underlying the DDR are not completely understood despite of extensive investigation. Recently, we have reported that ectopic expression of germline stem cell gene PIWIL2 is associated with tumor stem cell development, although the underlying mechanisms are largely unknown. Here we show that PIWIL2 is required for the repair of DNA-damage induced by various types of genotoxic agents. Upon ultraviolet (UV irradiation, silenced PIWIL2 gene in normal human fibroblasts was transiently activated after treatment with UV light. This activation was associated with DNA repair, because Piwil2-deficienct mouse embryonic fibroblasts (mili(-/- MEFs were defective in cyclobutane pyrimidine dimers (CPD repair after UV treatment. As a result, the UV-treated mili(-/- MEFs were more susceptible to apoptosis, as characterized by increased levels of DNA damage-associated apoptotic proteins, such as active caspase-3, cleaved Poly (ADP-ribose polymerase (PARP and Bik. The impaired DNA repair in the mili(-/- MEFs was associated with the reductions of histone H3 acetylation and chromatin relaxation, although the DDR pathway downstream chromatin relaxation appeared not to be directly affected by Piwil2. Moreover, guanine-guanine (Pt-[GG] and double strand break (DSB repair were also defective in the mili(-/- MEFs treated by genotoxic chemicals Cisplatin and ionizing radiation (IR, respectively. The results indicate that Piwil2 can mediate DNA repair through an axis of Piwil2 → histone acetylation → chromatin relaxation upstream DDR pathways. The findings reveal a new role for Piwil2 in DNA repair and suggest that Piwil2 may act as a gatekeeper against DNA damage-mediated tumorigenesis.

Membrane fusion inducers, chloroquine and spermidine increase lipoplex-mediated gene transfection

International Nuclear Information System (INIS)

Wong-Baeza, Carlos; Bustos, Israel; Serna, Manuel; Tescucano, Alonso; Alcantara-Farfan, Veronica; Ibanez, Miguel; Montanez, Cecilia; Wong, Carlos; Baeza, Isabel

2010-01-01

Gene transfection into mammalian cells can be achieved with viral and non-viral vectors. Non-viral vectors, such as cationic lipids that form lipoplexes with DNA, are safer and more stable than viral vectors, but their transfection efficiencies are lower. Here we describe that the simultaneous treatment with a membrane fusion inducer (chlorpromazine or procainamide) plus the lysosomotropic agent chloroquine increases lipoplex-mediated gene transfection in human (HEK293 and C-33 A) and rat (PC12) cell lines (up to 9.2-fold), as well as in situ in BALB/c mice spleens and livers (up to 6-fold); and that the polyamine spermidine increases lipoplex-mediated gene transfection and expression in cell cultures. The use of these four drugs provides a novel, safe and relatively inexpensive way to considerably increase lipoplex-mediated gene transfection efficiency.

Electron paramagnetic resonance and optical absorption of uranium ions diluted in CdF2 single crystals

International Nuclear Information System (INIS)

Pereira, J.J.C.R.

1976-08-01

The electron paramagnetic resonance (EPR) has been studied in conection with the optical absortion spectra of Uranium ions diluted in CdF 2 single crystals. Analyses of the EPR and optical absorption spectra obtained experimentally, and a comparison with known results in the isomorfic CaF 2 , SrF 2 and BaF 2 , allowed the identification of two paramagnetic centers associated with Uranium ions. These are the U(2+) ion in cubic symmetry having the triplet γ 5 as ground state, and the U(3+) ion in cubic symmetry having the dublet γ 6 as ground state. (Author) [pt

Double boson production at CDF

International Nuclear Information System (INIS)

Neuberger, D.

1996-07-01

New measurements of boson pair production in p anti p collisions have been performed by the CDF collaboration using a data sample of approximately 110 pb -1 . The cross sections for WW and WZ production are measured in the pure leptonic decay channel to σ(p anti p → WZ) = 3.2 +5.0 -3. 2 pb and σ(p anti p → W + W - ) = 10.2 +6.5 -5.3 pb, respectively. Limits on anomalous coupling parameters are set in the searches for WW and WZ production. Assuming an energy scale of Λ FF = 2 TeV, we find for the WWZ and WWγ couplings at 95% CL: -0.4 < λ < 0.3 (δκ 0) and -0.5 < δκ < 0.5 (λ = 0)

TLR2-dependent inhibition of macrophage responses to IFN-gamma is mediated by distinct, gene-specific mechanisms.

Directory of Open Access Journals (Sweden)

Sarah A Benson

2009-07-01

Full Text Available Mycobacterium tuberculosis uses multiple mechanisms to avoid elimination by the immune system. We have previously shown that M. tuberculosis can inhibit selected macrophage responses to IFN-gamma through TLR2-dependent and -independent mechanisms. To specifically address the role of TLR2 signaling in mediating this inhibition, we stimulated macrophages with the specific TLR2/1 ligand Pam(3CSK(4 and assayed responses to IFN-gamma. Pam(3CSK(4 stimulation prior to IFN-gamma inhibited transcription of the unrelated IFN-gamma-inducible genes, CIITA and CXCL11. Surface expression of MHC class II and secretion of CXCL11 were greatly reduced as well, indicating that the reduction in transcripts had downstream effects. Inhibition of both genes required new protein synthesis. Using chromatin immunoprecipitation, we found that TLR2 stimulation inhibited IFN-gamma-induced RNA polymerase II binding to the CIITA and CXCL11 promoters. Furthermore, TATA binding protein was unable to bind the TATA box of the CXCL11 promoter, suggesting that assembly of transcriptional machinery was disrupted. However, TLR2 stimulation affected chromatin modifications differently at each of the inhibited promoters. Histone H3 and H4 acetylation was reduced at the CIITA promoter but unaffected at the CXCL11 promoter. In addition, NF-kappaB signaling was required for inhibition of CXCL11 transcription, but not for inhibition of CIITA. Taken together, these results indicate that TLR2-dependent inhibition of IFN-gamma-induced gene expression is mediated by distinct, gene-specific mechanisms that disrupt binding of the transcriptional machinery to the promoters.

CDF silicon vertex tracker: tevatron run II preliminary results

International Nuclear Information System (INIS)

Ashmanskas, W.; Belforte, S.; Budagov, Yu.

2002-01-01

The Online Silicon Vertex Tracker (SVT) is the unique new trigger processor dedicated to the 2-D reconstruction of charged particle trajectories at Level 2 of the CDF trigger. The SVT has been successfully built, installed and operated during the 2000 and 20001 CDF data taking runs. The performance of the SVT is already very close to the design. The SVT is able to find tracks and calculate their impact parameter with high precision (σ d = 35 μm). It is possible to correct the beam position offset and give the beam position feedback to accelerator in real time. In fact, the beam position is calculated online every few seconds with an accuracy of 1 to 5 μm. The beam position is continuously sent to the accelerator control. By using trigger tracks, parent particles such as K S 's and D 0 's are reconstructed, proving that the SVT is ready to be used for physics studies

The CDF calorimeter upgrade for RunIIb

CERN Document Server

Huston, J; Kuhlmann, S; Lami, S; Miller, R; Paoletti, R; Turini, N; Ukegawa, F

2004-01-01

The physics program at the Fermilab Tevatron Collider will continue to explore the high energy elementary particle physics until the LHC commissioning. The upgrade of the CDF calorimeter opens a new window for improving the jet energy resolution, important in finding various signals such as Higgs by correcting the energy loss in the dead material and adding information in the jet algorithms using charged particles. It plays an important role in soft electron tagging of b- jets and photon identification in SUSY. The upgrade of the CDF calorimeter includes: a) the replacement of slow gas detector on the front face of the Central Calorimeter with Preshower (CPR) based on 2cm thick scintillator tiles segmented in eta and Phi and read out by WLS fibers running into a groove on the surface of each tiles. The WLS fibers are placed to clear fibers after leaving the tiles; b) the replacement of the Central Crack Chamber (CCR) with 5mm thick scintillator tiles read with the same technique: To finalize the design parame...

Beauty baryons: Recent CDF results

International Nuclear Information System (INIS)

Tseng, J.

1996-12-01

Using data collected between 1992 and 1995 at the Fermilab Tevatron, CDF has searched for the Λ b baryon through both semileptonic and hadronic decay channels. This presentation reviews measurements of the Λ b mass, lifetime, and production and decay rates performed with this data

CDF-XL: computing cumulative distribution functions of reaction time data in Excel.

Science.gov (United States)

Houghton, George; Grange, James A

2011-12-01

In experimental psychology, central tendencies of reaction time (RT) distributions are used to compare different experimental conditions. This emphasis on the central tendency ignores additional information that may be derived from the RT distribution itself. One method for analysing RT distributions is to construct cumulative distribution frequency plots (CDFs; Ratcliff, Psychological Bulletin 86:446-461, 1979). However, this method is difficult to implement in widely available software, severely restricting its use. In this report, we present an Excel-based program, CDF-XL, for constructing and analysing CDFs, with the aim of making such techniques more readily accessible to researchers, including students (CDF-XL can be downloaded free of charge from the Psychonomic Society's online archive). CDF-XL functions as an Excel workbook and starts from the raw experimental data, organised into three columns (Subject, Condition, and RT) on an Input Data worksheet (a point-and-click utility is provided for achieving this format from a broader data set). No further preprocessing or sorting of the data is required. With one click of a button, CDF-XL will generate two forms of cumulative analysis: (1) "standard" CDFs, based on percentiles of participant RT distributions (by condition), and (2) a related analysis employing the participant means of rank-ordered RT bins. Both analyses involve partitioning the data in similar ways, but the first uses a "median"-type measure at the participant level, while the latter uses the mean. The results are presented in three formats: (i) by participants, suitable for entry into further statistical analysis; (ii) grand means by condition; and (iii) completed CDF plots in Excel charts.

Freud-2/CC2D1B mediates dual repression of the serotonin-1A receptor gene.

Science.gov (United States)

Hadjighassem, Mahmoud R; Galaraga, Kimberly; Albert, Paul R

2011-01-01

The serotonin-1A (5-HT1A) receptor functions as a pre-synaptic autoreceptor in serotonin neurons that regulates their activity, and is also widely expressed on non-serotonergic neurons as a post-synaptic heteroreceptor to mediate serotonin action. The 5-HT1A receptor gene is strongly repressed by a dual repressor element (DRE), which is recognized by two proteins: Freud-1/CC2D1A and another unknown protein. Here we identify mouse Freud-2/CC2D1B as the second repressor of the 5-HT1A-DRE. Freud-2 shares 50% amino acid identity with Freud-1, and contains conserved structural domains. Mouse Freud-2 bound specifically to the rat 5-HT1A-DRE adjacent to, and partially overlapping, the Freud-1 binding site. By supershift assay using nuclear extracts from L6 myoblasts, Freud-2-DRE complexes were distinguished from Freud-1-DRE complexes. Freud-2 mRNA and protein were detected throughout mouse brain and peripheral tissues. Freud-2 repressed 5-HT1A promoter-reporter constructs in a DRE-dependent manner in non-neuronal (L6) or 5-HT1A-expressing neuronal (NG108-15, RN46A) cell models. In NG108-15 cells, knockdown of Freud-2 using a specific short-interfering RNA reduced endogenous Freud-2 protein levels and decreased Freud-2 bound to the 5-HT1A-DRE as detected by chromatin immunoprecipitation assay, but increased 5-HT1A promoter activity and 5-HT1A protein levels. Taken together, these data show that Freud-2 is the second component that, with Freud-1, mediates dual repression of the 5-HT1A receptor gene at the DRE. © 2010 The Authors. European Journal of Neuroscience © 2010 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Top physics at CDF

Energy Technology Data Exchange (ETDEWEB)

Hughes, R.E. [Univ. of Rochester, NY (United States)

1997-01-01

We report on top physics results using a 100 pb{sup -1} data sample of p{bar p} collisions at {radical}s = 1.8 TeV collected with the Collider Detector at Fermilab (CDF). We have identified top signals in a variety of decay channels, and used these channels to extract a measurement of the top mass and production cross section. A subset of the data (67 pb{sup -1}) is used to determine M{sub top} = 176 {+-} 8(stat) {+-} 10(syst) and {sigma}(tt) = 7.6 {sub -2.0}{sup +2.4} pb. We present studies of the kinematics of t{bar t} events and extract the first direct measurement of V{sub tb}. Finally, we indicate prospects for future study of top physics at the Tevatron.

Positive-negative-selection-mediated gene targeting in rice

Directory of Open Access Journals (Sweden)

Zenpei eShimatani

2015-01-01

Full Text Available Gene targeting (GT refers to the designed modification of genomic sequence(s through homologous recombination (HR. GT is a powerful tool both for the study of gene function and for molecular breeding. However, in transformation of higher plants, non-homologous end joining (NHEJ occurs overwhelmingly in somatic cells, masking HR-mediated GT. Positive-negative selection (PNS is an approach for finding HR-mediated GT events because it can eliminate NHEJ effectively by expression of a negative-selection marker gene. In rice—a major crop worldwide—reproducible PNS-mediated GT of endogenous genes has now been successfully achieved. The procedure is based on strong PNS using diphtheria toxin A-fragment as a negative marker, and has succeeded in the directed modification of several endogenous rice genes in various ways. In addition to gene knock-outs and knock-ins, a nucleotide substitution in a target gene was also achieved recently. This review presents a summary of the development of the rice PNS system, highlighting its advantages. Different types of gene modification and gene editing aimed at developing new plant breeding technology (NPBT based on PNS are discussed.

Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

Science.gov (United States)

Kagey, Michael H.; Newman, Jamie J.; Bilodeau, Steve; Zhan, Ye; Orlando, David A.; van Berkum, Nynke L.; Ebmeier, Christopher C.; Goossens, Jesse; Rahl, Peter B.; Levine, Stuart S.; Taatjes, Dylan J.; Dekker, Job; Young, Richard A.

2010-01-01

Summary Transcription factors control cell specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. We report here that Mediator and Cohesin physically and functionally connect the enhancers and core promoters of active genes in embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with Cohesin, which can form rings that connect two DNA segments. The Cohesin loading factor Nipbl is associated with Mediator/Cohesin complexes, providing a means to load Cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by Mediator and Cohesin. Mediator and Cohesin occupy different promoters in different cells, thus generating cell-type specific DNA loops linked to the gene expression program of each cell. PMID:20720539

CDF End Plug calorimeter Upgrade Project

International Nuclear Information System (INIS)

Apollinari, G.; de Barbaro, P.; Mishina, M.

1994-01-01

We report on the status of the CDF End Plug Upgrade Project. In this project, the CDF calorimeters in the end plug and the forward regions will be replaced by a single scintillator based calorimeter. After an extensive R ampersand D effort on the tile/fiber calorimetry, we have now advanced to a construction phase. We review the results of the R ampersand D leading to the final design of the calorimeters and the development of tooling devised for this project. The quality control program of the production of the electromagnetic and hadronic calorimeters is described. A shower maximum detector for the measurement of the shower centroid and the shower profile of electrons, γ and π 0 has been designed. Its performance requirements, R ampersand D results and mechanical design are discussed

Prospects of physics at CDF with the SVX

International Nuclear Information System (INIS)

Dell'Agnello, S.

1991-09-01

During next physics run CDF will strongly enhance its heavy flavor tagging capabilities with the installation of a silicon vertex detector (SVX), that will allow precise measurements of secondary decay vertices in the plane transverse to the beam (impact parameter resolution ≅ 12 μm). We expect this detector to have a significant impact on b-physics (cτ B ≅ 350 μm) and top search. In the following we will discuss CDF prospects for top search and for CP violation asymmetry measurements in the B-sector. 16 refs., 5 figs., 1 tabs

The performance of the CDF luminosity monitor

CERN Document Server

Acosta, D; Konigsberg, J; Korytov, A; Mitselmakher, G; Necula, V; Nomerotski, A; Pronko, A; Sukhanov, A; Safonov, A; Tsybychev, D; Wang, S M; Wong, M

2002-01-01

We describe the initial performance of the detector used for the luminosity measurement in the CDF experiment in Run II at the Tevatron. The detector consists of low-mass gaseous Cherenkov counters with high light yield (approx 100 photoelectrons) and monitors the process of inelastic pp-bar scattering. It allows for several methods of precise luminosity measurements at peak instantaneous luminosities of 2x10 sup 3 sup 2 cm sup - sup 2 s sup - sup 1 , corresponding to an average of six pp-bar interactions per bunch crossing.

[Small interfering RNA-mediated COX-2 gene silencing enhances chemosensitivity of KB/VCR cells by suppressing MDR-1 gene expression and P-glycoprotein activity].

Science.gov (United States)

Mo, Xianchao; Li, Weizhong

2014-05-01

To investigate the effect of small interfering RNA (siRNA)-mediated COX-2 gene silencing in enhancing the chemosensitivity of KB/VCR cell lines. KB/VCR cells were trasnfected with COX-2 siRNA were examined for expressions of COX-2 and MDR-1 mRNAs with RT-PCR and for Rho-123 accumulation using flow cytometry. MTT assay was used to analyze the proliferation of the transfected KB/VCR cells. Compared with the negative and blank control groups, COX-2 siRNA transfection resulted in significant growth inhibition of KB/VCR cells exposed to vincristine (PKB/VCR cells. COX-2 gene silencing can enhance the chemosensitivity of KB/VCR cells to vincristine, the mechanism of which may involve down-regulated MDR-1 gene expression and inhibition of P-glycoprotein activity.

C/EBPβ Mediates Growth Hormone-Regulated Expression of Multiple Target Genes

Science.gov (United States)

Cui, Tracy X.; Lin, Grace; LaPensee, Christopher R.; Calinescu, Anda-Alexandra; Rathore, Maanjot; Streeter, Cale; Piwien-Pilipuk, Graciela; Lanning, Nathan; Jin, Hui; Carter-Su, Christin; Qin, Zhaohui S.

2011-01-01

Regulation of c-Fos transcription by GH is mediated by CCAAT/enhancer binding protein β (C/EBPβ). This study examines the role of C/EBPβ in mediating GH activation of other early response genes, including Cyr61, Btg2, Socs3, Zfp36, and Socs1. C/EBPβ depletion using short hairpin RNA impaired responsiveness of these genes to GH, as seen for c-Fos. Rescue with wild-type C/EBPβ led to GH-dependent recruitment of the coactivator p300 to the c-Fos promoter. In contrast, rescue with C/EBPβ mutated at the ERK phosphorylation site at T188 failed to induce GH-dependent recruitment of p300, indicating that ERK-mediated phosphorylation of C/EBPβ at T188 is required for GH-induced recruitment of p300 to c-Fos. GH also induced the occupancy of phosphorylated C/EBPβ and p300 on Cyr61, Btg2, and Socs3 at predicted C/EBP-cAMP response element-binding protein motifs in their promoters. Consistent with a role for ERKs in GH-induced expression of these genes, treatment with U0126 to block ERK phosphorylation inhibited their GH-induced expression. In contrast, GH-dependent expression of Zfp36 and Socs1 was not inhibited by U0126. Thus, induction of multiple early response genes by GH in 3T3-F442A cells is mediated by C/EBPβ. A subset of these genes is regulated similarly to c-Fos, through a mechanism involving GH-stimulated ERK 1/2 activation, phosphorylation of C/EBPβ, and recruitment of p300. Overall, these studies suggest that C/EBPβ, like the signal transducer and activator of transcription proteins, regulates multiple genes in response to GH. PMID:21292824

VE-Cadherin-Mediated Epigenetic Regulation of Endothelial Gene Expression.

Science.gov (United States)

Morini, Marco F; Giampietro, Costanza; Corada, Monica; Pisati, Federica; Lavarone, Elisa; Cunha, Sara I; Conze, Lei L; O'Reilly, Nicola; Joshi, Dhira; Kjaer, Svend; George, Roger; Nye, Emma; Ma, Anqi; Jin, Jian; Mitter, Richard; Lupia, Michela; Cavallaro, Ugo; Pasini, Diego; Calado, Dinis P; Dejana, Elisabetta; Taddei, Andrea

2018-01-19

The mechanistic foundation of vascular maturation is still largely unknown. Several human pathologies are characterized by deregulated angiogenesis and unstable blood vessels. Solid tumors, for instance, get their nourishment from newly formed structurally abnormal vessels which present wide and irregular interendothelial junctions. Expression and clustering of the main endothelial-specific adherens junction protein, VEC (vascular endothelial cadherin), upregulate genes with key roles in endothelial differentiation and stability. We aim at understanding the molecular mechanisms through which VEC triggers the expression of a set of genes involved in endothelial differentiation and vascular stabilization. We compared a VEC-null cell line with the same line reconstituted with VEC wild-type cDNA. VEC expression and clustering upregulated endothelial-specific genes with key roles in vascular stabilization including claudin-5 , vascular endothelial-protein tyrosine phosphatase ( VE-PTP ), and von Willebrand factor ( vWf ). Mechanistically, VEC exerts this effect by inhibiting polycomb protein activity on the specific gene promoters. This is achieved by preventing nuclear translocation of FoxO1 (Forkhead box protein O1) and β-catenin, which contribute to PRC2 (polycomb repressive complex-2) binding to promoter regions of claudin-5 , VE-PTP , and vWf . VEC/β-catenin complex also sequesters a core subunit of PRC2 (Ezh2 [enhancer of zeste homolog 2]) at the cell membrane, preventing its nuclear translocation. Inhibition of Ezh2/VEC association increases Ezh2 recruitment to claudin-5 , VE-PTP , and vWf promoters, causing gene downregulation. RNA sequencing comparison of VEC-null and VEC-positive cells suggested a more general role of VEC in activating endothelial genes and triggering a vascular stability-related gene expression program. In pathological angiogenesis of human ovarian carcinomas, reduced VEC expression paralleled decreased levels of claudin-5 and VE-PTP. These

$t\\bar{t}$ Production in Multijet Events at CDF (RunII)

Energy Technology Data Exchange (ETDEWEB)

Gresele, Ambra Alessia [Univ. of Bologna (Italy)

2003-03-14

This thesis describes the all hadronic $t\\bar{t}$ analysis on the ~100 pb-1 of data collected so far by the CDF experiment (chapter 2 and chapter 3) in the $p\\bar{p}$ collisions at √s = 2 TeV of Tevatron (Fermilab).

CDF GlideinWMS usage in Grid computing of high energy physics

International Nuclear Information System (INIS)

Zvada, Marian; Sfiligoi, Igor; Benjamin, Doug

2010-01-01

Many members of large science collaborations already have specialized grids available to advance their research in the need of getting more computing resources for data analysis. This has forced the Collider Detector at Fermilab (CDF) collaboration to move beyond the usage of dedicated resources and start exploiting Grid resources. Nowadays, CDF experiment is increasingly relying on glidein-based computing pools for data reconstruction. Especially, Monte Carlo production and user data analysis, serving over 400 users by central analysis farm middleware (CAF) on the top of Condor batch system and CDF Grid infrastructure. Condor is designed as distributed architecture and its glidein mechanism of pilot jobs is ideal for abstracting the Grid computing by making a virtual private computing pool. We would like to present the first production use of the generic pilot-based Workload Management System (glideinWMS), which is an implementation of the pilot mechanism based on the Condor distributed infrastructure. CDF Grid computing uses glideinWMS for its data reconstruction on the FNAL campus Grid, user analysis and Monte Carlo production across Open Science Grid (OSG). We review this computing model and setup used including CDF specific configuration within the glideinWMS system which provides powerful scalability and makes Grid computing working like in a local batch environment with ability to handle more than 10000 running jobs at a time.

Mechanical design of the CDF SVX II silicon vertex detector

International Nuclear Information System (INIS)

Skarha, J.E.

1994-08-01

A next generation silicon vertex detector is planned at CDF for the 1998 Tevatron collider run with the Main Injector. The SVX II silicon vertex detector will allow high luminosity data-taking, enable online triggering of secondary vertex production, and greatly increase the acceptance for heavy flavor physics at CDF. The design specifications, geometric layout, and early mechanical prototyping work for this detector are discussed

Top-quark mass measurement from dilepton events at CDF II.

Science.gov (United States)

Abulencia, A; Acosta, D; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Ambrose, D; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arguin, J-F; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Bachacou, H; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Bedeschi, F; Behari, S; Belforte, S; Bellettini, G; Bellinger, J; Belloni, A; Ben-Haim, E; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bishai, M; Blair, R E; Blocker, C; Bloom, K; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Bourov, S; Boveia, A; Brau, B; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carron, S; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chapman, J; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Chu, P H; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciljak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Connolly, A; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Cruz, A; Cuevas, J; Culbertson, R; Cyr, D; DaRonco, S; D'Auria, S; D'Onofrio, M; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; Dell'Orso, M; Demers, S; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Dionisi, C; Dittmann, J; Dituro, P; Dörr, C; Dominguez, A; Donati, S; Donega, M; Dong, P; Donini, J; Dorigo, T; Dube, S; Ebina, K; Efron, J; Ehlers, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Flores-Castillo, L R; Foland, A; Forrester, S; Foster, G W; Franklin, M; Freeman, J C; Fujii, Y; Furic, I; Gajjar, A; Gallinaro, M; Galyardt, J; Garcia, J E; Garcia Sciverez, M; Garfinkel, A F; Gay, C; Gerberich, H; Gerchtein, E; Gerdes, D; Giagu, S; Giannetti, P; Gibson, A; Gibson, K; Ginsburg, C; Giolo, K; Giordani, M; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Gotra, Y; Goulianos, K; Gresele, A; Griffiths, M; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Haber, C; Hahn, S R; Hahn, K; Halkiadakis, E; Hamilton, A; Han, B-Y; Handler, R; Happacher, F; Hara, K; Hare, M; Harper, S; Harr, R F; Harris, R M; Hatakeyama, K; Hauser, J; Hays, C; Hayward, H; Heijboer, A; Heinemann, B; Heinrich, J; Hennecke, M; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Huston, J; Ikado, K; Incandela, J; Introzzi, G; Iori, M; Ishizawa, Y; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jensen, H; Jeon, E J; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kamon, T; Kang, J; Karagoz-Unel, M; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, M S; Kim, S B; Kim, S H; Kim, Y K; Kirby, M; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kobayashi, H; Kondo, K; Kong, D J; Konigsberg, J; Kordas, K; Korytov, A; Kotwal, A V; Kovalev, A; Kraus, J; Kravchenko, I; Kreps, M; Kreymer, A; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kuhlmann, S E; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecci, C; LeCompte, T; Lee, J; Lee, J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Li, K; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Liss, T M; Lister, A; Litvintsev, D O; Liu, T; Liu, Y; Lockyer, N S; Loginov, A; Loreti, M; Loverre, P; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Maki, T; Maksimovic, P; Manca, G; Margaroli, F; Marginean, R; Marino, C; Martin, A; Martin, M; Martin, V; Martínez, M; Maruyama, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McGivern, D; McIntyre, P; McNamara, P; McNulty, R; Mehta, A; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; von der Mey, M; Miao, T; Miladinovic, N; Miles, J; Miller, R; Miller, J S; Mills, C; Milnik, M; Miquel, R; Miscetti, S; Mitselmakher, G; Miyamoto, A; Moggi, N; Mohr, B; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Mulhearn, M; Muller, Th; Mumford, R; Murat, P; Nachtman, J; Nahn, S; Nakano, I; Napier, A; Naumov, D; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nigmanov, T; Nodulman, L; Norniella, O; Ogawa, T; Oh, S H; Oh, Y D; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Paoletti, R; Papadimitriou, V; Papikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pitts, K; Plager, C; Pondrom, L; Pope, G; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Rakitin, A; Rappoccio, S; Ratnikov, F; Reisert, B; Rekovic, V; van Remortel, N; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Rinnert, K; Ristori, L; Robertson, W J; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Rott, C; Ruiz, A; Russ, J; Rusu, V; Ryan, D; Saarikko, H; Sabik, S; Safonov, A; Sakumoto, W K; Salamanna, G; Salto, O; Saltzberg, D; Sanchez, C; Santi, L; Sarkar, S; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Semeria, F; Sexton-Kennedy, L; Sfiligoi, I; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sill, A; Sinervo, P; Sisakyan, A; Sjolin, J; Skiba, A; Slaughter, A J; Sliwa, K; Smirnov, D; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sumorok, K; Sun, H; Suzuki, T; Taffard, A; Tafirout, R; Takashima, R; Takeuchi, Y; Takikawa, K; Tanaka, M; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Tether, S; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tollefson, K; Tomura, T; Tonelli, D; Tönnesmann, M; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuchiya, R; Tsuno, S; Turini, N; Ukegawa, F; Unverhau, T; Uozumi, S; Usynin, D; Vacavant, L; Vaiciulis, A; Vallecorsa, S; Varganov, A; Vataga, E; Velev, G; Veramendi, G; Veszpremi, V; Vickey, T; Vidal, R; Vila, I; Vilar, R; Vollrath, I; Volobouev, I; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wallny, R; Walter, T; Wan, Z; Wang, M J; Wang, S M; Warburton, A; Ward, B; Waschke, S; Waters, D; Watts, T; Weber, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Worm, S; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, Y; Yang, C; Yang, U K; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zetti, F; Zhang, X; Zhou, J; Zucchelli, S

2006-04-21

We report a measurement of the top-quark mass using events collected by the CDF II detector from pp collisions at square root of s = 1.96 TeV at the Fermilab Tevatron. We calculate a likelihood function for the top-quark mass in events that are consistent with tt --> bl(-)nu(l)bl'+ nu'(l) decays. The likelihood is formed as the convolution of the leading-order matrix element and detector resolution functions. The joint likelihood is the product of likelihoods for each of 33 events collected in 340 pb(-1) of integrated luminosity, yielding a top-quark mass M(t) = 165.2 +/- 6.1(stat) +/- 3.4(syst) GeV/c2. This first application of a matrix-element technique to tt --> bl+ nu(l)bl'- nu(l') decays gives the most precise single measurement of M(t) in dilepton events. Combined with other CDF run II measurements using dilepton events, we measure M(t) = 167.9 +/- 5.2(stat) +/- 3.7(syst) GeV/c2.

Non-host Plant Resistance against Phytophthora capsici Is Mediated in Part by Members of the I2 R Gene Family in Nicotiana spp.

Science.gov (United States)

Vega-Arreguín, Julio C; Shimada-Beltrán, Harumi; Sevillano-Serrano, Jacobo; Moffett, Peter

2017-01-01

The identification of host genes associated with resistance to Phytophthora capsici is crucial to developing strategies of control against this oomycete pathogen. Since there are few sources of resistance to P. capsici in crop plants, non-host plants represent a promising source of resistance genes as well as excellent models to study P. capsici - plant interactions. We have previously shown that non-host resistance to P. capsici in Nicotiana spp. is mediated by the recognition of a specific P. capsici effector protein, PcAvr3a1 in a manner that suggests the involvement of a cognate disease resistance (R) genes. Here, we have used virus-induced gene silencing (VIGS) and transgenic tobacco plants expressing dsRNA in Nicotiana spp. to identify candidate R genes that mediate non-host resistance to P. capsici . Silencing of members of the I2 multigene family in the partially resistant plant N. edwardsonii and in the resistant N. tabacum resulted in compromised resistance to P. capsici . VIGS of two other components required for R gene-mediated resistance, EDS1 and SGT1 , also enhanced susceptibility to P. capsici in N. edwardsonii , as well as in the susceptible plants N. benthamiana and N. clevelandii . The silencing of I2 family members in N. tabacum also compromised the recognition of PcAvr3a1. These results indicate that in this case, non-host resistance is mediated by the same components normally associated with race-specific resistance.

Luminosity monitoring and measurement at CDF

International Nuclear Information System (INIS)

Cronin-Hennessy, D.; Beretvas, A.; Derwent, P.F.

2000-01-01

Using two telescopes of beam-beam counters, CDF (Collider Detector at Fermilab) has measured the luminosity to an accuracy of 4.1% (3.6%) in run Ib (Ia). For run Ib (Ia) the average luminosity was 9.1(3.3)x10 30 cm -2 s -1 . For a typical data set the integrated luminosity was 86.47 (19.65) pb -1 in run Ib (Ia) resulting in a total integrated luminosity of 106.1±4.1 pb -1 . This paper shows how we have determined the accuracy of our results

Recent CDF results

International Nuclear Information System (INIS)

Conway, J.S.

1996-07-01

Preliminary results form the CDF detector, based on analysis of data collected in Run 1a and Run 1b at the Tevatron, totaling 110 pb - 1 integrated luminosity, place new limits on the masses and couplings of new particles including charged Higgs bosons, supersymmetric gauge particles and quarks, and new vector bosons. One of the observed events, having an e + e - pair, two photons, and large missing energy would not occur with significant rate in the Standard Model, leading to speculation regarding its origin and the possible existence of related events

Recent results of high p(T) physics at the CDF II

Energy Technology Data Exchange (ETDEWEB)

Tsuno, Soushi; /Okayama U.

2005-02-01

The Tevatron Run II program has been in progress since 2001. The CDF experiment has accumulated roughly five times as much data as did Run I, with much improved detectors. Preliminary results from the CDF experiment are presented. The authors focus on recent high p{sub T} physics results in the Tevatron Run II program.

Ectopic Expression of Homeobox Gene NKX2-1 in Diffuse Large B-Cell Lymphoma Is Mediated by Aberrant Chromatin Modifications

Science.gov (United States)

Nagel, Stefan; Ehrentraut, Stefan; Tomasch, Jürgen; Quentmeier, Hilmar; Meyer, Corinna; Kaufmann, Maren; Drexler, Hans G.; MacLeod, Roderick A. F.

2013-01-01

Homeobox genes encode transcription factors ubiquitously involved in basic developmental processes, deregulation of which promotes cell transformation in multiple cancers including hematopoietic malignancies. In particular, NKL-family homeobox genes TLX1, TLX3 and NKX2-5 are ectopically activated by chromosomal rearrangements in T-cell neoplasias. Here, using transcriptional microarray profiling and RQ-PCR we identified ectopic expression of NKL-family member NKX2-1, in a diffuse large B-cell lymphoma (DLBCL) cell line SU-DHL-5. Moreover, in silico analysis demonstrated NKX2-1 overexpression in 5% of examined DLBCL patient samples. NKX2-1 is physiologically expressed in lung and thyroid tissues where it regulates differentiation. Chromosomal and genomic analyses excluded rearrangements at the NKX2-1 locus in SU-DHL-5, implying alternative activation. Comparative expression profiling implicated several candidate genes in NKX2-1 regulation, variously encoding transcription factors, chromatin modifiers and signaling components. Accordingly, siRNA-mediated knockdown and overexpression studies confirmed involvement of transcription factor HEY1, histone methyltransferase MLL and ubiquitinated histone H2B in NKX2-1 deregulation. Chromosomal aberrations targeting MLL at 11q23 and the histone gene cluster HIST1 at 6p22 which we observed in SU-DHL-5 may, therefore, represent fundamental mutations mediating an aberrant chromatin structure at NKX2-1. Taken together, we identified ectopic expression of NKX2-1 in DLBCL cells, representing the central player in an oncogenic regulative network compromising B-cell differentiation. Thus, our data extend the paradigm of NKL homeobox gene deregulation in lymphoid malignancies. PMID:23637834

First paper from Tevatron Run II submitted by CDF collaboration

CERN Multimedia

2003-01-01

"Scientists of the Collider Detector at Fermilab submitted today (March 19) the first scientific publication of Collider Run II to the science journal Physical Review D. The paper titled "Measurement of the Mass Difference m(Ds+)-m(D+) at CDF II" summarizes the results of an analysis carried out by CDF scientists Christoph Paus and Ivan Furic, MIT, describing the mass measurement of particles containing charm quarks" (1 page).

miRNA-mediated functional changes through co-regulating function related genes.

Directory of Open Access Journals (Sweden)

Jie He

Full Text Available BACKGROUND: MicroRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation. RESULTS: To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1. CONCLUSIONS: With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.

Measurement of ttbar forward-backward asymmetry at CDF

CERN Multimedia

CERN. Geneva

2011-01-01

Early measurements of the forward-backward ttbar production asymmetry at CDF and D0 suggested significant asymmetries that have been interpreted as evidence for exotic gluon partners or new t-channel interactions. We present new measurements performed with 5 fb-1 of Tevatron ppbar collisions at Ecm = 1.96 TeV, recorded and analyzed at CDF. Significant inclusive asymmetries are observed in both the lepton+jets and the dilepton decay modes of the ttbar pair. In the dilepton mode, the asymmetry is observed in the reconstructed top rapidity, and in the lepton rapidity difference, which is independent of any top reconstruction. In the lepton plus jets sample, the full reconstruction of the top kinematics is used to measure the dependence of the asymmetry on the tt bar rapidity difference Delta(y) and the invariant mass M_(ttbar ) of the ttbar system. The asymmetry is found to be most significant at large Delta(y) and M_(ttbar) . For M_(ttbar) > 450 GeV/c2, the parton-level asymmetry in the t-tbar rest frame is...

Top mass measurement at CDF

International Nuclear Information System (INIS)

Rolli, S.

1996-06-01

We present the measurement of the top quark mass using L = 110 pb -1 data sample of pp collisions at √s = 1.8 TeV collected with the Collider Detector at Fermilab (CDF). We show the results for the different channels and discuss with some emphasis the determination of the systematic uncertainties. 7 refs., 10 figs., 5 tabs

Beautiful physics at CDF

International Nuclear Information System (INIS)

Bauer, G.

1998-01-01

B-physics with p anti p collisions at CDF is reviewed, including production cross sections, masses, and decay properties. with a focus on lifetime and mixing measurements. A two-component lifetime fit of B 0 s → l + D - s X results in the limit ΔΓ s /Γ s s . From our five B 0 d -anti B 0 d oscillation analyses, we highlight the use of ''same side'' flavor tagging

Experimental research on treating hepatic carcinoma by arterial injection of liposome mediated p53 genes

Energy Technology Data Exchange (ETDEWEB)

Guangyu, Zhu; Qin, Lu; Gaojun, Teng; Jinhe, Guo; Hui, Yu; Gang, Deng; Shicheng, He; Wen, Fang; Guozhao, Li; Xiaoying, Wei [Zhongda Hospital, Southeast Univ., Nanjing (China)

2007-02-15

Objective: To investigate the transfection and expression of p53 genes mediated by liposome and its feasibility in treatment of liver cancer by transcatheter arterial injection on rabbit VX2 hepatocarcinoma model. Methods: pCMV-myc-p53 plasmids, LipofectAMINE and p53-LipofectAMINE complex were infused into tumor's feeding artery of rabbit VX2 hepatocarcinoma model, respectively, and then protein of cancer tissue was extracted, followed by measuring gene transfection and expression by western blot and immunohistochemistry, p53-LipofectAMlNE complex in different doses were infused into tumor's feeding artery of rabbit VX2 hepatocarcinoma model with the gene transfection and expression detected by the same way. Results: Liposome-mediated p53 gene injected through catheter could be successfully transfected and expressed in the cancer tissue of rabbit VX2 hepatocarcinoma model, with transfection efficiency higher than the gene delivery alone. The efficiency and the gene dose has dose-effect relationship. Conclusions: Treatment of liver cancer by transcatheter arterial injection of p53 genes mediated by liposome is a feasible and effective method, with wide prospect of application. (authors)

Experimental research on treating hepatic carcinoma by arterial injection of liposome mediated p53 genes

International Nuclear Information System (INIS)

Zhu Guangyu; Lu Qin; Teng Gaojun; Guo Jinhe; Yu Hui; Deng Gang; He Shicheng; Fang Wen; Li Guozhao; Wei Xiaoying

2007-01-01

Objective: To investigate the transfection and expression of p53 genes mediated by liposome and its feasibility in treatment of liver cancer by transcatheter arterial injection on rabbit VX2 hepatocarcinoma model. Methods: pCMV-myc-p53 plasmids, LipofectAMINE and p53-LipofectAMINE complex were infused into tumor's feeding artery of rabbit VX2 hepatocarcinoma model, respectively, and then protein of cancer tissue was extracted, followed by measuring gene transfection and expression by western blot and immunohistochemistry, p53-LipofectAMlNE complex in different doses were infused into tumor's feeding artery of rabbit VX2 hepatocarcinoma model with the gene transfection and expression detected by the same way. Results: Liposome-mediated p53 gene injected through catheter could be successfully transfected and expressed in the cancer tissue of rabbit VX2 hepatocarcinoma model, with transfection efficiency higher than the gene delivery alone. The efficiency and the gene dose has dose-effect relationship. Conclusions: Treatment of liver cancer by transcatheter arterial injection of p53 genes mediated by liposome is a feasible and effective method, with wide prospect of application. (authors)

Diethylstilbestrol (DES)-stimulated hormonal toxicity is mediated by ERα alteration of target gene methylation patterns and epigenetic modifiers (DNMT3A, MBD2, and HDAC2) in the mouse seminal vesicle.

Science.gov (United States)

Li, Yin; Hamilton, Katherine J; Lai, Anne Y; Burns, Katherine A; Li, Leping; Wade, Paul A; Korach, Kenneth S

2014-03-01

Diethylstilbestrol (DES) is a synthetic estrogen associated with adverse effects on reproductive organs. DES-induced toxicity of the mouse seminal vesicle (SV) is mediated by estrogen receptor α (ERα), which alters expression of seminal vesicle secretory protein IV (Svs4) and lactoferrin (Ltf) genes. We examined a role for nuclear receptor activity in association with DNA methylation and altered gene expression. We used the neonatal DES exposure mouse model to examine DNA methylation patterns via bisulfite conversion sequencing in SVs of wild-type (WT) and ERα-knockout (αERKO) mice. The DNA methylation status at four specific CpGs (-160, -237, -306, and -367) in the Svs4 gene promoter changed during mouse development from methylated to unmethylated, and DES prevented this change at 10 weeks of age in WT SV. At two specific CpGs (-449 and -459) of the Ltf gene promoter, DES altered the methylation status from methylated to unmethylated. Alterations in DNA methylation of Svs4 and Ltf were not observed in αERKO SVs, suggesting that changes of methylation status at these CpGs are ERα dependent. The methylation status was associated with the level of gene expression. In addition, gene expression of three epigenetic modifiers-DNMT3A, MBD2, and HDAC2-increased in the SV of DES-exposed WT mice. DES-induced hormonal toxicity resulted from altered gene expression of Svs4 and Ltf associated with changes in DNA methylation that were mediated by ERα. Alterations in gene expression of DNMT3A, MBD2, and HDAC2 in DES-exposed male mice may be involved in mediating the changes in methylation status in the SV. Li Y, Hamilton KJ, Lai AY, Burns KA, Li L, Wade PA, Korach KS. 2014. Diethylstilbestrol (DES)-stimulated hormonal toxicity is mediated by ERα alteration of target gene methylation patterns and epigenetic modifiers (DNMT3A, MBD2, and HDAC2) in the mouse seminal vesicle. Environ Health Perspect 122:262-268; http://dx.doi.org/10.1289/ehp.1307351.

Search for supersymmetric particles at CDF

International Nuclear Information System (INIS)

Wagner, R.G.

1989-01-01

Analyses of events with large unbalanced transverse energy from the 1987 and 1988-89 CDF data runs have set limits on the masses of supersymmetric squarks and gluinos. In a simple model with a stable photino as the lightest supersymmetric particle, the 1987 data with an integrated luminosity of 25.3 nb -1 have excluded at the 90% CL, squarks of mass less than 73 GeV/c 2 and gluinos of mass less than 74 GeV/c 2 . Preliminary results from an analysis of 1 pb -1 of data from the current 1988-89 run imply that the existence of a squark of mass less than 150 GeV/c 2 is unlikely. 4 refs., 2 fig., 1 tab

Long term data preservation for CDF at INFN-CNAF

International Nuclear Information System (INIS)

Amerio, S; Chiarelli, L; Dell'Agnello, L; Girolamo, D De; Gregori, D; Pezzi, M; Prosperini, A; Ricci, P; Rosso, F; Zani, S

2014-01-01

Long-term preservation of experimental data (intended as both raw and derived formats) is one of the emerging requirements coming from scientific collaborations. Within the High Energy Physics community the Data Preservation in High Energy Physics (DPHEP) group coordinates this effort. CNAF is not only one of the Tier-1s for the LHC experiments, it is also a computing center providing computing and storage resources to many other HEP and non-HEP scientific collaborations, including the CDF experiment. After the end of data taking in 2011, CDF is now facing the challenge to both preserve the large amount of data produced during several years of data taking and to retain the ability to access and reuse it in the future. CNAF is heavily involved in the CDF Data Preservation activities, in collaboration with the Fermilab National Laboratory (FNAL) computing sector. At the moment about 4 PB of data (raw data and analysis-level ntuples) are starting to be copied from FNAL to the CNAF tape library and the framework to subsequently access the data is being set up. In parallel to the data access system, a data analysis framework is being developed which allows to run the complete CDF analysis chain in the long term future, from raw data reprocessing to analysis-level ntuple production. In this contribution we illustrate the technical solutions we put in place to address the issues encountered as we proceeded in this activity.

PHYTOREMEDIATION OF DREDGED SEDIMENTS: A CASE STUDY AT THE JONES ISLAND CDF

Science.gov (United States)

The Jones Island Confined Disposal Facility (CDF) is a 44 acre in-lake area that receives dredged material from Milwaukee Harbor and the surrounding waterways. Some of those materials are contaminated with industrial waste and urban run-off. The CDF is nearing the end of its desi...

Jet physics at CDF Run II

Energy Technology Data Exchange (ETDEWEB)

Safonov, A.; /UC, Davis

2004-12-01

The latest results on jet physics at CDF are presented and discussed. Particular attention is paid to studies of the inclusive jet cross section using 177 pb{sup -1} of Run II data. Also discussed is a study of gluon and quark jet fragmentation.

VE-Cadherin–Mediated Epigenetic Regulation of Endothelial Gene Expression

Science.gov (United States)

Morini, Marco F.; Giampietro, Costanza; Corada, Monica; Pisati, Federica; Lavarone, Elisa; Cunha, Sara I.; Conze, Lei L.; O’Reilly, Nicola; Joshi, Dhira; Kjaer, Svend; George, Roger; Nye, Emma; Ma, Anqi; Jin, Jian; Mitter, Richard; Lupia, Michela; Cavallaro, Ugo; Pasini, Diego; Calado, Dinis P.

2018-01-01

Rationale: The mechanistic foundation of vascular maturation is still largely unknown. Several human pathologies are characterized by deregulated angiogenesis and unstable blood vessels. Solid tumors, for instance, get their nourishment from newly formed structurally abnormal vessels which present wide and irregular interendothelial junctions. Expression and clustering of the main endothelial-specific adherens junction protein, VEC (vascular endothelial cadherin), upregulate genes with key roles in endothelial differentiation and stability. Objective: We aim at understanding the molecular mechanisms through which VEC triggers the expression of a set of genes involved in endothelial differentiation and vascular stabilization. Methods and Results: We compared a VEC-null cell line with the same line reconstituted with VEC wild-type cDNA. VEC expression and clustering upregulated endothelial-specific genes with key roles in vascular stabilization including claudin-5, vascular endothelial-protein tyrosine phosphatase (VE-PTP), and von Willebrand factor (vWf). Mechanistically, VEC exerts this effect by inhibiting polycomb protein activity on the specific gene promoters. This is achieved by preventing nuclear translocation of FoxO1 (Forkhead box protein O1) and β-catenin, which contribute to PRC2 (polycomb repressive complex-2) binding to promoter regions of claudin-5, VE-PTP, and vWf. VEC/β-catenin complex also sequesters a core subunit of PRC2 (Ezh2 [enhancer of zeste homolog 2]) at the cell membrane, preventing its nuclear translocation. Inhibition of Ezh2/VEC association increases Ezh2 recruitment to claudin-5, VE-PTP, and vWf promoters, causing gene downregulation. RNA sequencing comparison of VEC-null and VEC-positive cells suggested a more general role of VEC in activating endothelial genes and triggering a vascular stability-related gene expression program. In pathological angiogenesis of human ovarian carcinomas, reduced VEC expression paralleled decreased

ttm-1 encodes CDF transporters that excrete zinc from intestinal cells of C. elegans and act in a parallel negative feedback circuit that promotes homeostasis.

Directory of Open Access Journals (Sweden)

Hyun Cheol Roh

2013-05-01

Full Text Available Zinc is an essential metal involved in a wide range of biological processes, and aberrant zinc metabolism is implicated in human diseases. The gastrointestinal tract of animals is a critical site of zinc metabolism that is responsible for dietary zinc uptake and distribution to the body. However, the role of the gastrointestinal tract in zinc excretion remains unclear. Zinc transporters are key regulators of zinc metabolism that mediate the movement of zinc ions across membranes. Here, we identified a comprehensive list of 14 predicted Cation Diffusion Facilitator (CDF family zinc transporters in Caenorhabditis elegans and demonstrated that zinc is excreted from intestinal cells by one of these CDF proteins, TTM-1B. The ttm-1 locus encodes two transcripts, ttm-1a and ttm-1b, that use different transcription start sites. ttm-1b expression was induced by high levels of zinc specifically in intestinal cells, whereas ttm-1a was not induced by zinc. TTM-1B was localized to the apical plasma membrane of intestinal cells, and analyses of loss-of-function mutant animals indicated that TTM-1B promotes zinc excretion into the intestinal lumen. Zinc excretion mediated by TTM-1B contributes to zinc detoxification. These observations indicate that ttm-1 is a component of a negative feedback circuit, since high levels of cytoplasmic zinc increase ttm-1b transcript levels and TTM-1B protein functions to reduce the level of cytoplasmic zinc. We showed that TTM-1 isoforms function in tandem with CDF-2, which is also induced by high levels of cytoplasmic zinc and reduces cytoplasmic zinc levels by sequestering zinc in lysosome-related organelles. These findings define a parallel negative feedback circuit that promotes zinc homeostasis and advance the understanding of the physiological roles of the gastrointestinal tract in zinc metabolism in animals.

Diffractive dijet and W production in CDF

International Nuclear Information System (INIS)

Goulianos, K.

1998-01-01

Results on diffractive dijet and W-boson production from CDF are reviewed and compared with predictions based on factorization of the diffractive structure function of the proton measured in deep inelastic scattering at HERA

v-src induction of the TIS10/PGS2 prostaglandin synthase gene is mediated by an ATF/CRE transcription response element.

Science.gov (United States)

Xie, W; Fletcher, B S; Andersen, R D; Herschman, H R

1994-10-01

We recently reported the cloning of a mitogen-inducible prostaglandin synthase gene, TIS10/PGS2. In addition to growth factors and tumor promoters, the v-src oncogene induces TIS10/PGS2 expression in 3T3 cells. Deletion analysis, using luciferase reporters, identifies a region between -80 and -40 nucleotides 5' of the TIS10/PGS2 transcription start site that mediates pp60v-src induction in 3T3 cells. This region contains the sequence CGTCACGTG, which includes overlapping ATF/CRE (CGTCA) and E-box (CACGTG) sequences. Gel shift-oligonucleotide competition experiments with nuclear extracts from cells stably transfected with a temperature-sensitive v-src gene demonstrate that the CGTCACGTG sequence can bind proteins at both the ATF/CRE and E-box sequences. Dominant-negative CREB and Myc proteins that bind DNA, but do not transactivate, block v-src induction of a luciferase reporter driven by the first 80 nucleotides of the TIS10/PGS2 promoter. Mutational analysis distinguishes which TIS10/PGS2 cis-acting element mediates pp60v-src induction. E-box mutation has no effect on the fold induction in response to pp60v-src. In contrast, ATF/CRE mutation attenuates the pp60v-src response. Antibody supershift and methylation interference experiments demonstrate that CREB and at least one other ATF transcription factor in these extracts bind to the TIS10/PGS2 ATF/CRE element. Expression of a dominant-negative ras gene also blocks TIS10/PGS2 induction by v-src. Our data suggest that Ras mediates pp60v-src activation of an ATF transcription factor, leading to induced TIS10/PGS2 expression via the ATF/CRE element of the TIS10/PGS2 promoter. This is the first description of v-src activation of gene expression via an ATF/CRE element.

Application of quantitative time-lapse imaging (QTLI) for evaluation of Mrp2-based drug–drug interaction induced by liver metabolites

International Nuclear Information System (INIS)

Nakanishi, Takeo; Ikenaga, Miho; Fukuda, Hajime; Matsunaga, Norikazu; Tamai, Ikumi

2012-01-01

We previously reported a quantitative time-lapse imaging (QTLI)-based analysis method to assess drug–drug interactions (DDI) at multidrug resistance-associated protein 2 (Mrp2) in rat sandwich-cultured hepatocyte (SCH) system, utilizing the fluorescent Mrp2 substrate, 5-(and 6)-carboxy-2′,7′-dichlorofluorescein (CDF). Here, we aimed to examine the feasibility of using QTLI to evaluate DDI involving drug metabolite(s) generated in hepatocytes. We used estradiol (E2) and bilirubin as model compounds; both are not substrates of MRP2, whereas their hepatic metabolites, estradiol-17β-glucuronide (E17G) or bilirubin glucuronides, are known to be its substrates as well as inhibitors. When rat SCHs were pre-exposed with E2, fluorescence of CDF accumulated in bile canaliculi decreased depending upon both the duration of pre-exposure and the concentration of extracellular E2. The decrease corresponded with the increase in intracellular concentration of E17G in hepatocytes. Furthermore, cytotoxicity of vinblastine, a substrate of MRP2, was enhanced in SCHs treated with E2. Similarly, CDF accumulated in bile canaliculi was significantly reduced in rat SCHs pre-exposed with bilirubin. In conclusion, these results suggest that phase II biotransformation of a competitor is reflected in alteration of MRP2-mediated CDF transport detected in QTLI. The QTLI might provide a convenient platform to evaluate transporter-based DDIs involving hepatic metabolites of drug candidates without the need to identify the metabolites. -- Highlights: ► Mrp2-mediated CDF transport is inhibited by E2, but not E17G in vesicle study. ► Both E2 and E17G do not compromise CDF formation from CDFDA in hepatocytes. ► CDF accumulation in bile canaliculi is inhibited by E2 or E17G in QTLI. ► Increasing exposure to E2 decreases CDF accumulation in bile canaliculi in QTLI. ► QTLI is feasible to assess Mrp2-based DDI involving drug metabolite in hepatocytes.

Application of quantitative time-lapse imaging (QTLI) for evaluation of Mrp2-based drug–drug interaction induced by liver metabolites

Energy Technology Data Exchange (ETDEWEB)

Nakanishi, Takeo; Ikenaga, Miho; Fukuda, Hajime; Matsunaga, Norikazu; Tamai, Ikumi, E-mail: tamai@p.kanazawa-w.ac.jp

2012-09-01

We previously reported a quantitative time-lapse imaging (QTLI)-based analysis method to assess drug–drug interactions (DDI) at multidrug resistance-associated protein 2 (Mrp2) in rat sandwich-cultured hepatocyte (SCH) system, utilizing the fluorescent Mrp2 substrate, 5-(and 6)-carboxy-2′,7′-dichlorofluorescein (CDF). Here, we aimed to examine the feasibility of using QTLI to evaluate DDI involving drug metabolite(s) generated in hepatocytes. We used estradiol (E2) and bilirubin as model compounds; both are not substrates of MRP2, whereas their hepatic metabolites, estradiol-17β-glucuronide (E17G) or bilirubin glucuronides, are known to be its substrates as well as inhibitors. When rat SCHs were pre-exposed with E2, fluorescence of CDF accumulated in bile canaliculi decreased depending upon both the duration of pre-exposure and the concentration of extracellular E2. The decrease corresponded with the increase in intracellular concentration of E17G in hepatocytes. Furthermore, cytotoxicity of vinblastine, a substrate of MRP2, was enhanced in SCHs treated with E2. Similarly, CDF accumulated in bile canaliculi was significantly reduced in rat SCHs pre-exposed with bilirubin. In conclusion, these results suggest that phase II biotransformation of a competitor is reflected in alteration of MRP2-mediated CDF transport detected in QTLI. The QTLI might provide a convenient platform to evaluate transporter-based DDIs involving hepatic metabolites of drug candidates without the need to identify the metabolites. -- Highlights: ► Mrp2-mediated CDF transport is inhibited by E2, but not E17G in vesicle study. ► Both E2 and E17G do not compromise CDF formation from CDFDA in hepatocytes. ► CDF accumulation in bile canaliculi is inhibited by E2 or E17G in QTLI. ► Increasing exposure to E2 decreases CDF accumulation in bile canaliculi in QTLI. ► QTLI is feasible to assess Mrp2-based DDI involving drug metabolite in hepatocytes.

Bombyx mori E26 transformation-specific 2 (BmEts2), an Ets family protein, represses Bombyx mori Rels (BmRels)-mediated promoter activation of antimicrobial peptide genes in the silkworm Bombyx mori.

Science.gov (United States)

Tanaka, H; Sagisaka, A; Suzuki, N; Yamakawa, M

2016-10-01

E26 transformation-specific (Ets) family transcription factors are known to play roles in various biological phenomena, including immunity, in vertebrates. However, the mechanisms by which Ets proteins contribute to immunity in invertebrates remain poorly understood. In this study, we identified a cDNA encoding BmEts2, which is a putative orthologue of Drosophila Yan and human translocation-ets-leukemia/Ets-variant gene 6, from the silkworm Bombyx mori. Expression of the BmEts2 gene was significantly increased in the fat bodies of silkworm larvae in response to injection with Escherichia coli and Staphylococcus aureus. BmEts2 overexpression dramatically repressed B. mori Rels (BmRels)-mediated promoter activation of antimicrobial peptide genes in silkworm cells. Conversely, gene knockdown of BmEts2 significantly enhanced BmRels activity. In addition, two κB sites located on the 5' upstream region of cecropin B1 were found to be involved in the repression of BmRels-mediated promoter activation. Protein-competition analysis further demonstrated that BmEts2 competitively inhibited binding of BmRels to κB sites. Overall, BmEts2 acts as a repressor of BmRels-mediated transactivation of antimicrobial protein genes by inhibiting the binding of BmRels to κB sites. © 2016 The Royal Entomological Society.

Intravascular local gene transfer mediated by protein-coated metallic stent.

Science.gov (United States)

Yuan, J; Gao, R; Shi, R; Song, L; Tang, J; Li, Y; Tang, C; Meng, L; Yuan, W; Chen, Z

2001-10-01

To assess the feasibility, efficiency and selectivity of adenovirus-mediated gene transfer to local arterial wall by protein-coated metallic stent. A replication-defective recombinant adenovirus carrying the Lac Z reporter gene for nuclear-specific beta-galactosidase (Ad-beta gal) was used in this study. The coating for metallic stent was made by immersing it in a gelatin solution containing crosslinker. The coated stents were mounted on a 4.0 or 3.0 mm percutaneous transluminal coronary angioplasty (PTCA) balloon and submersed into a high-titer Ad-beta gal viral stock (2 x 10(10) pfu/ml) for 3 min, and then implanted into the carotid arteries in 4 mini-swines and into the left anterior descending branch of the coronary artery in 2 mini-swines via 8F large lumen guiding catheters. The animals were sacrificed 7 (n = 4), 14 (n = 1) and 21 (n = 1) days after implantation, respectively. The beta-galactosidase expression was assessed by X-gal staining. The results showed that the expression of transgene was detected in all animal. In 1 of carotid artery with an intact intima, the beta-gal expression was limited to endothelial cells. In vessels with denuded endothelium, gene expression was found in the sub-intima, media and adventitia. The transfection efficiency of medial smooth muscle cells was 38.6%. In 2 animals sacrificed 7 days after transfection, a microscopic examination of X-gal-stained samples did not show evidence of transfection in remote organs and arterial segments adjacent to the treated arterial site. Adenovirus-mediated arterial gene transfer to endothelial, smooth muscle cells and adventitia by protein-coated metallic stent is feasible. The transfection efficiency is higher. The coated stent may act as a good carrier of adenovirus-mediated gene transfer and have a potential to prevent restenosis following PTCA.

The upgraded CDF front end electronics for calorimetry

Energy Technology Data Exchange (ETDEWEB)

Drake, G.; Frei, D.; Hahn, S.R.; Nelson, C.A.; Segler, S.L.; Stuermer, W.

1991-11-01

The front end electronics used in the calorimetry of the CDF detector has been upgraded to meet system requirements for higher expected luminosity. A fast digitizer utilizing a 2 {mu}Sec, 16 bit ADC has been designed and built. Improvements to the front end trigger circuitry have been implemented, including the production of 900 new front end modules. Operational experience with the previous system is presented, with discussion of the problems and performance goals.

The upgraded CDF front end electronics for calorimetry

International Nuclear Information System (INIS)

Drake, G.; Frei, D.; Hahn, S.R.; Nelson, C.A.; Segler, S.L.; Stuermer, W.

1991-11-01

The front end electronics used in the calorimetry of the CDF detector has been upgraded to meet system requirements for higher expected luminosity. A fast digitizer utilizing a 2 μSec, 16 bit ADC has been designed and built. Improvements to the front end trigger circuitry have been implemented, including the production of 900 new front end modules. Operational experience with the previous system is presented, with discussion of the problems and performance goals

Ionizing and ultraviolet radiation enhances the efficiency of DNA mediated gene transfer in vitro

International Nuclear Information System (INIS)

Perez, C.F.

1984-08-01

The enhancement effects of ionizing and non-ionizing radiation on the efficiency of DNA mediated gene transfer were studied. Confluent Rat-2 cells were transfected with purified SV40 viral DNA, irradiated with either X-rays or ultraviolet, trypsinized, plated, and assayed for the formation of foci on Rat-2 monolayers. Both ionizing and ultraviolet radiation enhanced the frequency of A-gene transformants/survivor compared to unirradiated transfected cells. These enhancements were non-linear and dose dependent. A recombinant plasmid, pOT-TK5, was constructed that contained the SV40 virus A-gene and the Herpes Simplex virus (HSV) thymidine kinase (TK) gene. Confluent Rat-2 cells transfected with pOT-TK5 DNA and then immediately irradiated with either X-rays or 330 MeV/amu argon particles at the Berkeley Bevalac showed a higher frequency of HAT + colonies/survivor than unirradiated transfected cells. Rat-2 cells transfected with the plasmid, pTK2, containing only the HSV TK-gene were enhanced for TK-transformation by both X-rays and ultraviolet radiation. The results demonstrate that radiation enhancement of the efficiency of DNA mediated gene transfer is not explained by increased nuclear uptake of the transfected DNA. Radiation increases the competence of the transfected cell population for genetic transformation. Three models for this increased competence are presented. The targeted integration model, the inducible recombination model, the partition model, and the utilization of DNA mediated gene transfer for DNA repair studies are discussed. 465 references

Ionizing and ultraviolet radiation enhances the efficiency of DNA mediated gene transfer in vitro

Energy Technology Data Exchange (ETDEWEB)

Perez, C.F.

1984-08-01

The enhancement effects of ionizing and non-ionizing radiation on the efficiency of DNA mediated gene transfer were studied. Confluent Rat-2 cells were transfected with purified SV40 viral DNA, irradiated with either X-rays or ultraviolet, trypsinized, plated, and assayed for the formation of foci on Rat-2 monolayers. Both ionizing and ultraviolet radiation enhanced the frequency of A-gene transformants/survivor compared to unirradiated transfected cells. These enhancements were non-linear and dose dependent. A recombinant plasmid, pOT-TK5, was constructed that contained the SV40 virus A-gene and the Herpes Simplex virus (HSV) thymidine kinase (TK) gene. Confluent Rat-2 cells transfected with pOT-TK5 DNA and then immediately irradiated with either X-rays or 330 MeV/amu argon particles at the Berkeley Bevalac showed a higher frequency of HAT/sup +/ colonies/survivor than unirradiated transfected cells. Rat-2 cells transfected with the plasmid, pTK2, containing only the HSV TK-gene were enhanced for TK-transformation by both X-rays and ultraviolet radiation. The results demonstrate that radiation enhancement of the efficiency of DNA mediated gene transfer is not explained by increased nuclear uptake of the transfected DNA. Radiation increases the competence of the transfected cell population for genetic transformation. Three models for this increased competence are presented. The targeted integration model, the inducible recombination model, the partition model, and the utilization of DNA mediated gene transfer for DNA repair studies are discussed. 465 references.

Co-regulation of the atrial natriuretic factor and cardiac myosin light chain-2 genes during alpha-adrenergic stimulation of neonatal rat ventricular cells. Identification of cis sequences within an embryonic and a constitutive contractile protein gene which mediate inducible expression.

Science.gov (United States)

Knowlton, K U; Baracchini, E; Ross, R S; Harris, A N; Henderson, S A; Evans, S M; Glembotski, C C; Chien, K R

1991-04-25

To study the mechanisms which mediate the transcriptional activation of cardiac genes during alpha adrenergic stimulation, the present study examined the regulated expression of three cardiac genes, a ventricular embryonic gene (atrial natriuretic factor, ANF), a constitutively expressed contractile protein gene (cardiac MLC-2), and a cardiac sodium channel gene. alpha 1-Adrenergic stimulation activates the expression and release of ANF from neonatal ventricular cells. As assessed by RNase protection analyses, treatment with alpha-adrenergic agonists increases the steady-state levels of ANF mRNA by greater than 15-fold. However, a rat cardiac sodium channel gene mRNA is not induced, indicating that alpha-adrenergic stimulation does not lead to an increase in the expression of all cardiac genes. Studies employing a series of rat ANF luciferase and rat MLC-2 luciferase fusion genes identify 315- and 92-base pair cis regulatory sequences within an embryonic gene (ANF) and a constitutively expressed contractile protein gene (MLC-2), respectively, which mediate alpha-adrenergic-inducible gene expression. Transfection of various ANF luciferase reporters into neonatal rat ventricular cells demonstrated that upstream sequences which mediate tissue-specific expression (-3003 to -638) can be segregated from those responsible for inducibility. The lack of inducibility of a cardiac Na+ channel gene, and the segregation of ANF gene sequences which mediate cardiac specific from those which mediate inducible expression, provides further insight into the relationship between muscle-specific and inducible expression during cardiac myocyte hypertrophy. Based on these results, a testable model is proposed for the induction of embryonic cardiac genes and constitutively expressed contractile protein genes and the noninducibility of a subset of cardiac genes during alpha-adrenergic stimulation of neonatal rat ventricular cells.

The CDF Silicon Vertex Detector

International Nuclear Information System (INIS)

Tkaczyk, S.; Carter, H.; Flaugher, B.

1993-01-01

A silicon strip vertex detector was designed, constructed and commissioned at the CDF experiment at the Tevatron collider at Fermilab. The mechanical design of the detector, its cooling and monitoring are presented. The front end electronics employing a custom VLSI chip, the readout electronics and various components of the SVX system are described. The system performance and the experience with the operation of the

Host genes involved in Agrobacterium-mediated transformation

NARCIS (Netherlands)

Soltani, Jalal

2009-01-01

Agrobacterium is the nature’s genetic engineer that can transfer genes across the kingdom barriers to both prokaryotic and eukaryotic host cells. The host genes which are involved in Agrobacterium-mediated transformatiom (AMT) are not well known. Here, I studied in a systematic way to identify the

Characteristics of nobiletin-mediated alteration of gene expression in cultured cell lines

Energy Technology Data Exchange (ETDEWEB)

Nemoto, Kiyomitsu, E-mail: nemoto@u-shizuoka-ken.ac.jp [Department of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan); Ikeda, Ayaka; Yoshida, Chiaki; Kimura, Junko; Mori, Junki [Department of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan); Fujiwara, Hironori [Department of Anti-Dementia Functional Food Development, Research Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, 6-6-7 Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Yokosuka, Akihito; Mimaki, Yoshihiro [Department of Medicinal Pharmacognosy, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji 192-0392 (Japan); Ohizumi, Yasushi [Department of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan); Department of Anti-Dementia Functional Food Development, Research Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, 6-6-7 Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Laboratory of Kampo Medicines, Yokohama College of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066 (Japan); Degawa, Masakuni [Department of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 (Japan)

2013-02-15

Highlights: ► Nobiletin-mediated alterations of gene expression were examined with DNA microarrays. ► Three organ-derived cell lines were treated with 100 μM nobiletin for 24 h. ► In all cell lines, 3 endoplasmic reticulum stress-responsive genes were up-regulated. ► Some cell cycle-regulating and oxidative stress-promoting genes were down-regulated. ► These alterations may contribute to nobiletin-mediated biological effects. -- Abstract: Nobiletin, a polymethoxylated flavonoid that is highly contained in the peels of citrus fruits, exerts a wide variety of beneficial effects, including anti-proliferative effects in cancer cells, repressive effects in hyperlipidemia and hyperglycemia, and ameliorative effects in dementia at in vitro and in vivo levels. In the present study, to further understand the mechanisms of these actions of nobiletin, the nobiletin-mediated alterations of gene expression in three organ-derived cell lines – 3Y1 rat fibroblasts, HuH-7 human hepatocarcinoma cells, and SK-N-SH human neuroblastoma cells – were first examined with DNA microarrays. In all three cell lines, treatments with nobiletin (100 μM) for 24 h resulted in more than 200% increases in the expression levels of five genes, including the endoplasmic reticulum stress-responsive genes Ddit3, Trib3, and Asns, and in less than 50% decreases in the expression levels of seven genes, including the cell cycle-regulating genes Ccna2, Ccne2, and E2f8 and the oxidative stress-promoting gene Txnip. It was also confirmed that in each nobiletin-treated cell line, the levels of the DDIT3 (DNA-damage-inducible transcript 3, also known as CHOP and GADD153) and ASNS (asparagine synthetase) proteins were increased, while the level of the TXNIP (thioredoxin-interacting protein, also known as VDUP1 and TBP-2) protein was decreased. All these findings suggest that nobiletin exerts a wide variety of biological effects, at least partly, through induction of endoplasmic reticulum stress and

EWS/FLI mediates transcriptional repression via NKX2.2 during oncogenic transformation in Ewing's sarcoma.

Directory of Open Access Journals (Sweden)

Leah A Owen

2008-04-01

Full Text Available EWS/FLI is a master regulator of Ewing's sarcoma formation. Gene expression studies in A673 Ewing's sarcoma cells have demonstrated that EWS/FLI downregulates more genes than it upregulates, suggesting that EWS/FLI, and/or its targets, function as transcriptional repressors. One critical EWS/FLI target, NKX2.2, is a transcription factor that contains both transcriptional activation and transcriptional repression domains, raising the possibility that it mediates portions of the EWS/FLI transcriptional signature. We now report that microarray analysis demonstrated that the transcriptional profile of NKX2.2 consists solely of downregulated genes, and overlaps with the EWS/FLI downregulated signature, suggesting that NKX2.2 mediates oncogenic transformation via transcriptional repression. Structure-function analysis revealed that the DNA binding and repressor domains in NKX2.2 are required for oncogenesis in Ewing's sarcoma cells, while the transcriptional activation domain is completely dispensable. Furthermore, blockade of TLE or HDAC function, two protein families thought to mediate the repressive function of NKX2.2, inhibited the transformed phenotype and reversed the NKX2.2 transcriptional profile in Ewing's sarcoma cells. Whole genome localization studies (ChIP-chip revealed that a significant portion of the NKX2.2-repressed gene expression signature was directly mediated by NKX2.2 binding. These data demonstrate that the transcriptional repressive function of NKX2.2 is necessary, and sufficient, for the oncogenic phenotype of Ewing's sarcoma, and suggest a therapeutic approach to this disease.

Transcription factor CREB is involved in CaSR-mediated cytoskeleton gene expression.

Science.gov (United States)

Huang, Shuaishuai; Ren, Yu; Wang, Ping; Li, Yanyuan; Wang, Xue; Zhuang, Haihui; Fang, Rong; Wang, Yuduo; Liu, Ningsheng; Hehir, Michael; Zhou, Jeff X

2015-03-01

Our previous studies illustrated that a steady increase of intracellular calcium concentration ([Ca2+]i) was important for maintaining microtubules (MTs) rearrangement in apoptotic cells. However, little is known about the effect of calcium sensing receptor (CaSR)-mediated increase in [Ca2+]i on cytoskeleton gene expression. We examined the impact of taxol or CaSR agonist/antagonist on the regulation of [Ca2+]i concentration, cytoskeleton arrangement, phosphorylated CREB and cytoskeleton gene expressions in HeLa cells with dominant negative plasmid of CREB (PM). This study demonstrated that Gdcl3 (a specific CaSR agonist) evoked a rapid increase of [Ca2+]i, formed a rigid bundle of MTs which surrounded the nucleus and decreased the cytoskeleton gene expressions in HeLa cells. These effects were rescued by addition of NPS2390 (a specific CaSR antagonist). Moreover, CaSR activity affected cytoskeleton gene expression through transcription factor CREB. Histoscores of pCREB immunoreactivity in tissues of cervical adenocarcinoma, renal clear cell carcinoma, and diffuse large B-cell lymphoma were markedly increased compared with non malignant tissue. These data demonstrate, for the first time, that CaSR-mediated increase in [Ca2+]i probably modulate cytoskeleton organization and gene expression via transcription factor. © 2014 Wiley Periodicals, Inc.

CDF run II run control and online monitor

International Nuclear Information System (INIS)

Arisawa, T.; Ikado, K.; Badgett, W.; Chlebana, F.; Maeshima, K.; McCrory, E.; Meyer, A.; Patrick, J.; Wenzel, H.; Stadie, H.; Wagner, W.; Veramendi, G.

2001-01-01

The authors discuss the CDF Run II Run Control and online event monitoring system. Run Control is the top level application that controls the data acquisition activities across 150 front end VME crates and related service processes. Run Control is a real-time multi-threaded application implemented in Java with flexible state machines, using JDBC database connections to configure clients, and including a user friendly and powerful graphical user interface. The CDF online event monitoring system consists of several parts: the event monitoring programs, the display to browse their results, the server program which communicates with the display via socket connections, the error receiver which displays error messages and communicates with Run Control, and the state manager which monitors the state of the monitor programs

Signature-based global searches at CDF

International Nuclear Information System (INIS)

Hocker, James Andrew

2008-01-01

Data collected in Run II of the Fermilab Tevatron are searched for indications of new electroweak scale physics. Rather than focusing on particular new physics scenarios, CDF data are analyzed for discrepancies with respect to the Standard Model prediction. Gross features of the data, mass bumps, and significant excesses of events with large summed transverse momentum are examined in a model-independent and quasi-model-independent approach. This global search for new physics in over three hundred exclusive final states in 2 fb -1 of p(bar p) collisions at √s = 1.96 TeV reveals no significant indication of physics beyond the Standard Model

Antimetastatic gene expression profiles mediated by retinoic acid receptor beta 2 in MDA-MB-435 breast cancer cells

International Nuclear Information System (INIS)

Wallden, Brett; Emond, Mary; Swift, Mari E; Disis, Mary L; Swisshelm, Karen

2005-01-01

The retinoic acid receptor beta 2 (RARβ2) gene modulates proliferation and survival of cultured human breast cancer cells. Previously we showed that ectopic expression of RARβ2 in a mouse xenograft model prevented metastasis, even in the absence of the ligand, all-trans retinoic acid. We investigated both cultured cells and xenograft tumors in order to delineate the gene expression profiles responsible for an antimetastatic phenotype. RNA from MDA-MB-435 human breast cancer cells transduced with RARβ2 or empty retroviral vector (LXSN) was analyzed using Agilent Human 1A Oligo microarrays. The one hundred probes with the greatest differential intensity (p < 0.004, jointly) were determined by selecting the top median log ratios from eight-paired microarrays. Validation of differences in expression was done using Northern blot analysis and quantitative RT-PCR (qRT-PCR). We determined expression of selected genes in xenograft tumors. RARβ2 cells exhibit gene profiles with overrepresentation of genes from Xq28 (p = 2 × 10 -8 ), a cytogenetic region that contains a large portion of the cancer/testis antigen gene family. Other functions or factors impacted by the presence of exogenous RARβ2 include mediators of the immune response and transcriptional regulatory mechanisms. Thirteen of fifteen (87%) of the genes evaluated in xenograft tumors were consistent with differences we found in the cell cultures (p = 0.007). Antimetastatic RARβ2 signalling, direct or indirect, results in an elevation of expression for genes such as tumor-cell antigens (CTAG1 and CTAG2), those involved in innate immune response (e.g., RIG-I/DDX58), and tumor suppressor functions (e.g., TYRP1). Genes whose expression is diminished by RARβ2 signalling include cell adhesion functions (e.g, CD164) nutritional or metabolic processes (e.g., FABP6), and the transcription factor, JUN

SVT: an online silicon vertex tracker for the CDF upgrade

International Nuclear Information System (INIS)

Bardi, A.; Belforte, S.; Berryhill, J.

1997-07-01

The SVT is an online tracker for the CDF upgrade which will reconstruct 2D tracks using information from the Silicon VerteX detector (SVXII) and Central Outer Tracker (COT). The precision measurement of the track impact parameter will then be used to select and record large samples of B hadrons. We discuss the overall architecture, algorithms, and hardware implementation of the system

v-src Induction of the TIS10/PGS2 prostaglandin synthase gene is mediated by an ATF/CRE transcription response element

Energy Technology Data Exchange (ETDEWEB)

Xie, W.; Fletcher, B.S.; Andersen, R.D.; Herschman, H.R. [Univ. of California, Los Angeles, CA (United States)

1994-10-01

The authors recently reported the cloning of a mitogen-inducible prostaglandin synthase gene, TIS10/PGS2. In addition to growth factor and tumor promoters, the v-src oncogene induces TIS10/PGS2 expression in 3T3 cells. Deletion analysis, using luciferase reporters, identifies a region between -80 and -40 nucleotides 5{prime} of the TIS10/PGS2 transcription start site that mediates pp60{sup v-src} induction in 3T3 cells. This region contains the sequence CGTCACGTG, which includes overlapping ATF/CRE (CGTCA) and E-box (CACGTG) sequences. Gel shift-oligonucleotide competition experiments with nuclear extracts from cells stably transfected with a temperature-sensitive v-src gene demonstrate that the CGTCACGTG sequence can bind proteins at both the AFT/CRE and E-box sequences. Dominant-negative CREB and Myc proteins that bind DNA, but do not transactivate, block v-src induction of a luciferase reporter driven by the first 80 nucleotides of the TIS10/PGS2 promoter. Mutational analysis distinguishes which TIS10/PGS2 cis-acting element mediates pp60{sup v-src} induction. E-box mutation has no effect on the fold induction in response to pp60{sup v-src}. In contrast, ATF/CRE mutation attenuates the pp{sup v-src} response. Antibody supershift and methylation interference experiments demonstrate that CREB and at least one other ATF transcription factor in these extracts bind to the TIS10/PGS2 ATF/CRE element. Expression of a dominant-negative ras gene also blocks TIS10/PGS2 induction by v-src. The data suggest that Ras mediates pp60{sup v-src} activation of an ATF transcription factor, leading to induced TIS10/PGS2 expression via the ATF/CRE element of the TIS10/PGS2 promoter. This is the first description of v-src activation of gene expression via an ATF/CRE element. 64 refs., 8 figs.

Ultrasound-mediated interferon β gene transfection inhibits growth of malignant melanoma

International Nuclear Information System (INIS)

Yamaguchi, Kazuki; Feril, Loreto B.; Tachibana, Katsuro; Takahashi, Akira; Matsuo, Miki; Endo, Hitomi; Harada, Yoshimi; Nakayama, Juichiro

2011-01-01

Highlights: → Successful ultrasound-mediated transfection of melanoma (C32) cells with IFN-β genes both in vitro and in vivo. → Ultrasound-mediated IFN-β transfection inhibited proliferation of melanoma cells in vitro. → Ultrasound-mediated IFN-β transfection inhibited melanoma tumor growth in vivo. -- Abstract: We investigated the effects of ultrasound-mediated transfection (sonotransfection) of interferon β (IFN-β) gene on melanoma (C32) both in vitro and in vivo. C32 cells were sonotransfected with IFN-β in vitro. Subcutaneous C32 tumors in mice were sonicated weekly immediately after intra-tumor injection with IFN-β genes mixed with microbubbles. Successful sonotransfection with IFN-β gene in vitro was confirmed by ELISA, which resulted in C32 growth inhibition. In vivo, the growth ratio of tumors transfected with IFN-β gene was significantly lower than the other experimental groups. These results may lead to a new method of treatment against melanoma and other hard-to-treat cancers.

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

Science.gov (United States)

Luisier, Raphaëlle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik

2014-01-01

Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and β-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesis. PMID:24464994

Isolated prompt photon production at CDF

International Nuclear Information System (INIS)

Maas, P.A.

1992-11-01

This note describes measurements of isolated prompt photon production at √s = 1.8 TeV using the CDF experiment. The measurements are compared to recent NLO QCD calculations, including recently obtained parton distribution functions. Qualitatively, the QCD calculation with the new parton distribution functions agrees better with the data than the previous parton distribution functions

B physics at CDF

International Nuclear Information System (INIS)

Donati, S.

1998-09-01

B physics results from the CDF Collaboration based on data collected during the 1992-1996 Tevatron run are presented. In particular, we report the discovery of the B c meson in the semileptonic decay B c → J/ψlνX, updates of b hadrons lifetime measurements, with a description of the B s lifetime measurement, the B 0 d - anti B 0 d mixing results and the limits set on rare B decay branching ratios. Current results are used to extrapolate B physics prospects for the future high luminosity run II

The CDF silicon vertex trigger for B-mesons physics study

International Nuclear Information System (INIS)

Belforte, S.; Donati, S.; Ristori, L.; Spinella, F.; Budagov, Yu.; Chlachidze, G.; Glagolev, V.; Semenov, A.; Sisakyan, A.; Punzi, G.

2001-01-01

The CDF scientific program includes particularly the study of some key topics of the Standard Model: 1) constraint of the CKM matrix: CP violation in B sector (B 0 → π + π - ) and B s mixing (B s 0 → D s - π + , B s 0 → D s - π + π - π + ); 2) t-quark physics (t → Wb); and processes beyond the Standard Model - e.g., Higgs searching (MSSM) in the H → b bar b mode. All the above processes have the common feature - the presence of b-quarks (B-mesons). B hadrons of sufficiently high transverse momentum are characterized by a large mean value of distribution of the impact parameter with respect to the beam axis. That means events containing this kind of particles can be recognized and separated from non-long-lived background simply by cutting on the track's impact parameter. The upgraded CDF is equipped by the so-called Silicon Vertex Tracker (SVT), a unique electronic device for real time track reconstruction using the data from two CDF track detectors: the silicon strip vertex detector and drift chamber. The SVT is a level-2 trigger which within 10 μs reconstructs the tracks and obtains the transverse momentum (p t ), azimuthal angle (φ) and impact parameter (d) with 30 μm precision. The simulation studies show the background reduction by factor 1000 for B 0 π + π - by demand d > 100 μm for at least two tracks. This trigger is the first one of this sort ever used for hadron collider experiments: it enables to trigger on the secondary vertex, which opens the unique new opportunities in the heavy quark physics study. The basic logic, architecture and perspectives of SVT application are briefly described

Co-factors necessary for PPAR mediated transactivation of endogenous target genes

DEFF Research Database (Denmark)

Grøntved, Lars; Nielsen, Ronni; Stunnenberg, Henk

of endogenous target gene in different cell types are elusive. To mutually compare the ability of the PPAR subtypes to activate endogenous target genes in a given cell, PPARa, PPARb/d and PPARg2 were HA tagged and rapidly, equally and synchronously expressed using adenoviral delivery. Within a few hours after...... subtype specific activation of target genes. Accumulating evidence suggests that transcriptional co-factors can function as master regulators for nuclear receptors and impose promoter selectivity. To study co-factor necessity for PPAR mediated transactivation of endogenous target genes, specific co...

Enhancing the CDF's B physics program with a faster data acquisition system

International Nuclear Information System (INIS)

Maksimovic, Petar

2011-01-01

The physics program of Run II at the Tevatron includes precision electroweak measurements such as the determination of the top quark and W boson masses; bottom and charm physics including the determination of the B s and D 0 mixing parameters; studies of the strong interaction; and searches for the Higgs particle, supersymmetric particles, hidden space-time dimensions and quark substructure. All of these measurements benefit from a high-resolution tracking detector. Most of them rely heavily on the efficient identification of heavy flavored B hadrons by detection of displaced secondary vertices, and are enhanced by the capability to trigger on tracks not coming from the primary vertex. This is uniquely provided by CDF's finely-segmented silicon detectors surrounding the interaction region. Thus CDF experiment's physics potential critically depends on the performance of its silicon detectors. The CDF silicon detectors were designed to operate up to 2-3 fb -1 of accumulated pji collisions, with an upgrade planned thereafter. However, the upgrade project was canceled in 2003 and Run II has been extended through 2011, with an expected total delivered integrated luminosity of 12 fb -1 or more. Several preventive measures were taken to keep the original detector operational and maintain its performance. The most important of these are the decrease in the operating temperature of the detector, which reduces the impact of radiation exposure, and measures to minimize damage due to integrated radiation dose, thermal cycles, and wire bond resonance conditions. Despite these measures the detectors operating conditions continue to change with issues arising from radiation damage to the sensors, aging infrastructure and electronics. These, together with the basic challenges posed by the inaccessibility of the detector volume and large number (about 750 thousand) of readout channels, make the silicon detector operations the single most complex and high priority job in the CDF

Scaling behavior of jet production at CDF

International Nuclear Information System (INIS)

Behrends, S.

1992-11-01

Inclusive jet cross-sections have been measured in bar pp collisions at √s = 546 and 1800 GeV, using the CDF detector at the Fermilab Tevatron. The ratio of jet cross-sections is compared to predictions from simple scaling and 0(α s 3 ) QCD

Search for Bs Oscillations at CDF II

International Nuclear Information System (INIS)

Menzemer, Stephanie

2006-01-01

We report updated results in the search for Bs flavor oscillations performed at CDF II. We analyze a dataset of approximately 355 pb-1 from proton-antiproton collisions at a center-of-mass energy of 1.96 TeV collected in 2002-2004 with the CDF II detector at the Tevatron Collider. Samples of both fully reconstructed Bs → Ds(3)π, and partially reconstructed, Bs → DslX, decays have been studied. A combination of opposite side tagging algorithms has been used to determine the flavor of the Bs mesons at production time. Information about the oscillation frequency of the system, Δms, is obtained by performing an amplitude scan of the data, from which an exclusion limit Δms ≥ 8.6 ps -1 (at 95% C.L.), with a measured sensitivity of 13.0 ps-1 has been derived; Combination with previously available measurements increases the world exclusion limit from 14.5 ps-1 to 16.6 ps-1 (at 95% C.L.)

Differential modulation of expression of nuclear receptor mediated genes by tris(2-butoxyethyl) phosphate (TBOEP) on early life stages of zebrafish (Danio rerio)

Energy Technology Data Exchange (ETDEWEB)

Ma, Zhiyuan, E-mail: zhiyuan_nju@163.com [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Yu, Yijun, E-mail: yjun.yu@gmail.com [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Tang, Song [School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3 (Canada); Liu, Hongling, E-mail: hlliu@nju.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Su, Guanyong; Xie, Yuwei [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Giesy, John P. [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3 (Canada); Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B3 (Canada); Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region (Hong Kong); Hecker, Markus [School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3 (Canada); Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3 (Canada); Yu, Hongxia [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023 (China)

2015-12-15

Highlights: • Effects of TBOEP on expression of genes of several nuclear hormone receptors and their relationship with adverse effect pathways in zebrafish. • TBOEP was neither an agonist nor antagonist of AR or AhR as determined by use of in vitro mammalian cell-based receptor transactivation assays. • Modulation of ER- and MR-dependent pathways allowed for development of feasible receptor-mediated, critical mechanisms of toxic action. - Abstract: As one substitute for phased-out brominated flame retardants (BFRs), tris(2-butoxyethyl) phosphate (TBOEP) is frequently detected in aquatic organisms. However, knowledge about endocrine disrupting mechanisms associated with nuclear receptors caused by TBOEP remained restricted to results from in vitro studies with mammalian cells. In the study, results of which are presented here, embryos/larvae of zebrafish (Danio rerio) were exposed to 0.02, 0.1 or 0.5 μM TBOEP to investigate expression of genes under control of several nuclear hormone receptors (estrogen receptors (ERs), androgen receptor (AR), thyroid hormone receptor alpha (TRα), mineralocorticoid receptor (MR), glucocorticoid receptor (GR), aryl hydrocarbon (AhR), peroxisome proliferator-activated receptor alpha (PPARα), and pregnane × receptor (P × R)) pathways at 120 hpf. Exposure to 0.5 μM TBOEP significantly (p < 0.05, one-way analysis of variance) up-regulated expression of estrogen receptors (ERs, er1, er2a, and er2b) genes and ER-associated genes (vtg4, vtg5, pgr, ncor, and ncoa3), indicating TBOEP modulates the ER pathway. In contrast, expression of most genes (mr, 11βhsd, ube2i,and adrb2b) associated with the mineralocorticoid receptor (MR) pathway were significantly down-regulated. Furthermore, in vitro mammalian cell-based (MDA-kb2 and H4IIE-luc) receptor transactivation assays, were also conducted to investigate possible agonistic or antagonistic effects on AR- and AhR-mediated pathways. In mammalian cells, none of these pathways were

Tracking in the trigger from the CDF experience to CMS upgrade

CERN Document Server

Palla, F

2007-01-01

Precise tracking information in the online selection of interesting physics events is extremely beneficial at hadron colliders. The CDF experiment at the Tevatron, has shown for the first time the impact of the tracking in triggers, allowing to achieve unprecedented precision in B-physics measurements. The CMS experiment at LHC will largely make use of tracking information at high level trigger, after the Level-1 acceptance. The increased luminosity of the Super-LHC collider will impose to CMS a drastic revision of the Level-1 trigger strategy, incorporating the tracker information at the first stage of the selection. After a review of the CDF and CMS approaches we will discuss several possible Level-1 tracker based concepts for the upgraded CMS detector at Super-LHC. One approach is based on associative memories, which has already been demonstrated in CDF. It makes use of binary readout in the front end electronics, followed by transfer of the full granularity data off detector using optical links to dedicat...

Scaling behavior of jet production at CDF

Energy Technology Data Exchange (ETDEWEB)

Behrends, S. [Brandeis Univ., Waltham, MA (United States). Dept. of Physics; The CDF Collaboration

1992-11-01

Inclusive jet cross-sections have been measured in {bar p}p collisions at {radical}s = 546 and 1800 GeV, using the CDF detector at the Fermilab Tevatron. The ratio of jet cross-sections is compared to predictions from simple scaling and 0({alpha}{sub s{sup 3}}) QCD.

Design and production of a new surface mount charge-integrating amplifier for CDF

Energy Technology Data Exchange (ETDEWEB)

Nelson, C.; Drake, G.

1991-12-31

We present our experiences in designing and producing 26,000 new charge-integrating amplifiers for CDF, using surface-mount components. The new amplifiers were needed to instrument 920 new 24-channel CDF RABBIT boards, which are replacing an older design rendered obsolete by increases in the collision rate. Important design considerations were frequency response, physical size and cost. 5 refs.

Design and production of a new surface mount charge-integrating amplifier for CDF

International Nuclear Information System (INIS)

Nelson, C.; Drake, G.

1991-01-01

We present our experiences in designing and producing 26,000 new charge-integrating amplifiers for CDF, using surface-mount components. The new amplifiers were needed to instrument 920 new 24-channel CDF RABBIT boards, which are replacing an older design rendered obsolete by increases in the collision rate. Important design considerations were frequency response, physical size and cost. 5 refs

Area-Specific Cell Stimulation via Surface-Mediated Gene Transfer Using Apatite-Based Composite Layers

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Yushin Yazaki

2015-04-01

Full Text Available Surface-mediated gene transfer systems using biocompatible calcium phosphate (CaP-based composite layers have attracted attention as a tool for controlling cell behaviors. In the present study we aimed to demonstrate the potential of CaP-based composite layers to mediate area-specific dual gene transfer and to stimulate cells on an area-by-area basis in the same well. For this purpose we prepared two pairs of DNA–fibronectin–apatite composite (DF-Ap layers using a pair of reporter genes and pair of differentiation factor genes. The results of the area-specific dual gene transfer successfully demonstrated that the cells cultured on a pair of DF-Ap layers that were adjacently placed in the same well showed specific gene expression patterns depending on the gene that was immobilized in theunderlying layer. Moreover, preliminary real-time PCR results indicated that multipotential C3H10T1/2 cells may have a potential to change into different types of cells depending on the differentiation factor gene that was immobilized in the underlying layer, even in the same well. Because DF-Ap layers have a potential to mediate area-specific cell stimulation on their surfaces, they could be useful in tissue engineering applications.

Epigenetic involvement of Alien/ESET complex in thyroid hormone-mediated repression of E2F1 gene expression and cell proliferation

International Nuclear Information System (INIS)

Hong, Wei; Li, Jinru; Wang, Bo; Chen, Linfeng; Niu, Wenyan; Yao, Zhi; Baniahmad, Aria

2011-01-01

Highlights: ► Corepressor Alien interacts with histone methyltransferase ESET in vivo. ► Alien/ESET complex is recruited to nTRE of T3-responsive gene by liganded TRβ1. ► ESET-mediated H3K9 methylation is required for liganded TRβ1-repressed transcription. ► ESET is involved in T3-repressed G1/S phase transition and proliferation. -- Abstract: The ligand-bound thyroid hormone receptor (TR) is known to repress via a negative TRE (nTRE) the expression of E2F1, a key transcription factor that controls the G1/S phase transition. Alien has been identified as a novel interacting factor of E2F1 and acts as a corepressor of E2F1. The detailed molecular mechanism by which Alien inhibits E2F1 gene expression remains unclear. Here, we report that the histone H3 lysine 9 (H3K9) methyltransferase (HMT) ESET is an integral component of the corepressor Alien complex and the Alien/ESET complex is recruited to both sites, the E2F1 and the nTRE site of the E2F1 gene while the recruitment to the negative thyroid hormone response element (nTRE) is induced by the ligand-bound TRβ1 within the E2F1 gene promoter. We show that, overexpression of ESET promotes, whereas knockdown of ESET releases, the inhibition of TRβ1-regulated gene transcription upon T3 stimulation; and H3K9 methylation is required for TRβ1-repressed transcription. Furthermore, depletion of ESET impairs thyroid hormone-repressed proliferation as well as the G1/S transition of the cell cycle. Taken together, our data indicate that ESET is involved in TRβ1-mediated transcription repression and provide a molecular basis of thyroid hormone-induced repression of proliferation.

Causal relationship between the AHSG gene and BMD through fetuin-A and BMI: multiple mediation analysis.

Science.gov (United States)

Sritara, C; Thakkinstian, A; Ongphiphadhanakul, B; Chailurkit, L; Chanprasertyothin, S; Ratanachaiwong, W; Vathesatogkit, P; Sritara, P

2014-05-01

Using mediation analysis, a causal relationship between the AHSG gene and bone mineral density (BMD) through fetuin-A and body mass index (BMI) mediators was suggested. Fetuin-A, a multifunctional protein of hepatic origin, is associated with bone mineral density. It is unclear if this association is causal. This study aimed at clarification of this issue. A cross-sectional study was conducted among 1,741 healthy workers from the Electricity Generating Authority of Thailand (EGAT) cohort. The alpha-2-Heremans-Schmid glycoprotein (AHSG) rs2248690 gene was genotyped. Three mediation models were constructed using seemingly unrelated regression analysis. First, the ln[fetuin-A] group was regressed on the AHSG gene. Second, the BMI group was regressed on the AHSG gene and the ln[fetuin-A] group. Finally, the BMD model was constructed by fitting BMD on two mediators (ln[fetuin-A] and BMI) and the independent AHSG variable. All three analyses were adjusted for confounders. The prevalence of the minor T allele for the AHSG locus was 15.2%. The AHSG locus was highly related to serum fetuin-A levels (P Multiple mediation analyses showed that AHSG was significantly associated with BMD through the ln[fetuin-A] and BMI pathway, with beta coefficients of 0.0060 (95% CI 0.0038, 0.0083) and 0.0030 (95% CI 0.0020, 0.0045) at the total hip and lumbar spine, respectively. About 27.3 and 26.0% of total genetic effects on hip and spine BMD, respectively, were explained by the mediation effects of fetuin-A and BMI. Our study suggested evidence of a causal relationship between the AHSG gene and BMD through fetuin-A and BMI mediators.

Co-Introduced Functional CCR2 Potentiates In Vivo Anti-Lung Cancer Functionality Mediated by T Cells Double Gene-Modified to Express WT1-Specific T-Cell Receptor

Science.gov (United States)

Asai, Hiroaki; Fujiwara, Hiroshi; An, Jun; Ochi, Toshiki; Miyazaki, Yukihiro; Nagai, Kozo; Okamoto, Sachiko; Mineno, Junichi; Kuzushima, Kiyotaka; Shiku, Hiroshi; Inoue, Hirofumi; Yasukawa, Masaki

2013-01-01

Background and Purpose Although gene-modification of T cells to express tumor-related antigen-specific T-cell receptor (TCR) or chimeric antigen receptor (CAR) has clinically proved promise, there still remains room to improve the clinical efficacy of re-directed T-cell based antitumor adoptive therapy. In order to achieve more objective clinical responses using ex vivo-expanded tumor-responsive T cells, the infused T cells need to show adequate localized infiltration into the tumor. Methodology/Principal Findings Human lung cancer cells variously express a tumor antigen, Wilms' Tumor gene product 1 (WT1), and an inflammatory chemokine, CCL2. However, CCR2, the relevant receptor for CCL2, is rarely expressed on activated T-lymphocytes. A HLA-A2402+ human lung cancer cell line, LK79, which expresses high amounts of both CCL2 and WT1 mRNA, was employed as a target. Normal CD8+ T cells were retrovirally gene-modified to express both CCR2 and HLA-A*2402-restricted and WT1235–243 nonapeptide-specific TCR as an effector. Anti-tumor functionality mediated by these effector cells against LK79 cells was assessed both in vitro and in vivo. Finally the impact of CCL2 on WT1 epitope-responsive TCR signaling mediated by the effector cells was studied. Introduced CCR2 was functionally validated using gene-modified Jurkat cells and human CD3+ T cells both in vitro and in vivo. Double gene-modified CD3+ T cells successfully demonstrated both CCL2-tropic tumor trafficking and cytocidal reactivity against LK79 cells in vitro and in vivo. CCL2 augmented the WT1 epitope-responsive TCR signaling shown by relevant luciferase production in double gene-modified Jurkat/MA cells to express luciferase and WT1-specific TCR, and CCL2 also dose-dependently augmented WT1 epitope-responsive IFN-γ production and CD107a expression mediated by these double gene-modifiedCD3+ T cells. Conclusion/Significance Introduction of the CCL2/CCR2 axis successfully potentiated in vivo anti-lung cancer

Co-introduced functional CCR2 potentiates in vivo anti-lung cancer functionality mediated by T cells double gene-modified to express WT1-specific T-cell receptor.

Directory of Open Access Journals (Sweden)

Hiroaki Asai

Full Text Available BACKGROUND AND PURPOSE: Although gene-modification of T cells to express tumor-related antigen-specific T-cell receptor (TCR or chimeric antigen receptor (CAR has clinically proved promise, there still remains room to improve the clinical efficacy of re-directed T-cell based antitumor adoptive therapy. In order to achieve more objective clinical responses using ex vivo-expanded tumor-responsive T cells, the infused T cells need to show adequate localized infiltration into the tumor. METHODOLOGY/PRINCIPAL FINDINGS: Human lung cancer cells variously express a tumor antigen, Wilms' Tumor gene product 1 (WT1, and an inflammatory chemokine, CCL2. However, CCR2, the relevant receptor for CCL2, is rarely expressed on activated T-lymphocytes. A HLA-A2402(+ human lung cancer cell line, LK79, which expresses high amounts of both CCL2 and WT1 mRNA, was employed as a target. Normal CD8(+ T cells were retrovirally gene-modified to express both CCR2 and HLA-A*2402-restricted and WT1(235-243 nonapeptide-specific TCR as an effector. Anti-tumor functionality mediated by these effector cells against LK79 cells was assessed both in vitro and in vivo. Finally the impact of CCL2 on WT1 epitope-responsive TCR signaling mediated by the effector cells was studied. Introduced CCR2 was functionally validated using gene-modified Jurkat cells and human CD3(+ T cells both in vitro and in vivo. Double gene-modified CD3(+ T cells successfully demonstrated both CCL2-tropic tumor trafficking and cytocidal reactivity against LK79 cells in vitro and in vivo. CCL2 augmented the WT1 epitope-responsive TCR signaling shown by relevant luciferase production in double gene-modified Jurkat/MA cells to express luciferase and WT1-specific TCR, and CCL2 also dose-dependently augmented WT1 epitope-responsive IFN-γ production and CD107a expression mediated by these double gene-modified CD3(+ T cells. CONCLUSION/SIGNIFICANCE: Introduction of the CCL2/CCR2 axis successfully potentiated in

Silencing SlMED18, tomato Mediator subunit 18 gene, restricts internode elongation and leaf expansion.

Science.gov (United States)

Wang, Yunshu; Hu, Zongli; Zhang, Jianling; Yu, XiaoHui; Guo, Jun-E; Liang, Honglian; Liao, Changguang; Chen, Guoping

2018-02-19

Mediator complex, a conserved multi-protein, is necessary for controlling RNA polymerase II (Pol II) transcription in eukaryotes. Given little is known about them in tomato, a tomato Mediator subunit 18 gene was isolated and named SlMED18. To further explore the function of SlMED18, the transgenic tomato plants targeting SlMED18 by RNAi-mediated gene silencing were generated. The SlMED18-RNAi lines exhibited multiple developmental defects, including smaller size and slower growth rate of plant and significantly smaller compound leaves. The contents of endogenous bioactive GA 3 in SlMED18 silenced lines were slightly less than that in wild type. Furthermore, qRT-PCR analysis indicated that expression of gibberellins biosynthesis genes such as SlGACPS and SlGA20x2, auxin transport genes (PIN1, PIN4, LAX1 and LAX2) and several key regulators, KNOX1, KNOX2, PHAN and LANCEOLATE(LA), which involved in the leaf morphogenesis were significantly down-regulated in SlMED18-RNAi lines. These results illustrated that SlMED18 plays an essential role in regulating plant internode elongation and leaf expansion in tomato plants and it acts as a key positive regulator of gibberellins biosynthesis and signal transduction as well as auxin proper transport signalling. These findings are the basis for understanding the function of the individual Mediator subunits in tomato.

CLCA2 as a p53-Inducible Senescence Mediator

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Chizu Tanikawa

2012-02-01

Full Text Available p53 is a tumor suppressor gene that is frequently mutated in multiple cancer tissues. Activated p53 protein regulates its downstream genes and subsequently inhibits malignant transformation by inducing cell cycle arrest, apoptosis, DNA repair, and senescence. However, genes involved in the p53-mediated senescence pathway are not yet fully elucidated. Through the screening of two genome-wide expression profile data sets, one for cells in which exogenous p53 was introduced and the other for senescent fibroblasts, we have identified chloride channel accessory 2 (CLCA2 as a p53-inducible senescence-associated gene. CLCA2 was remarkably induced by replicative senescence as well as oxidative stress in a p53-dependent manner. We also found that ectopically expressed CLCA2 induced cellular senescence, and the down-regulation of CLCA2 by small interfering RNA caused inhibition of oxidative stress-induced senescence. Interestingly, the reduced expression of CLCA2 was frequently observed in various kinds of cancers including prostate cancer, whereas its expression was not affected in precancerous prostatic intraepithelial neoplasia. Thus, our findings suggest a crucial role of p53/CLCA2-mediated senescence induction as a barrier for malignant transformation.

B-physics at CDF and prospects for the next run

International Nuclear Information System (INIS)

Wenzel, H.

1991-09-01

Current CDF b-physics results are presented. The analysis is based on data corresponding to an integrated luminosity of 4.4 pb -1 recorded with the CDF detector in 88--89 at the Fermilab Tevatron p bar p collider (√ bar s = 1.8 TeV). Preliminary results include the differential cross section dPt / dσ(b) , some reconstructed exclusive B-decays, a limit for the rare decay B 0 → μ + μ - and a measurement of B bar B-mixing parameters. Finally we will discuss the prospects concerning b-physics for the next data run which will start in February 1992. 12 refs., 8 figs

The CDF level-3 trigger

International Nuclear Information System (INIS)

Devlin, T.

1993-01-01

The Collider Detector at Fermilab (CDF) has been operating at the Tevatron and collecting data on proton-antiproton interactions with collision rates above 250,000 Hz. Three levels of filtering select events for data logging at a rate of about 4 Hz. The Level 3 trigger provides most of the capabilities of the offline production programs for event reconstruction and physics analysis. The type of physics triggers, application of cuts, and combinations of logical requirements for event selection are controlled at run time by a trigger table using a syntax fully integrated with the Level 1 and Level 2 hardware triggers. The level 3 software operates in 48 RISC/UNIX processors (over 1000 mips) served by four 20-MByte/sec data buses for input, output and control. The system architecture, debugging, code validation, error reporting, analysis capabilities and performance will be described

Genistein and Glyceollin Effects on ABCC2 (MRP2 and ABCG2 (BCRP in Caco-2 Cells

Directory of Open Access Journals (Sweden)

Chandler Schexnayder

2015-12-01

Full Text Available The goal of the present study was to determine the effects of glyceollins on intestinal ABCC2 (ATP Binding Cassette C2, multidrug resistance protein 2, MRP2 and ABCG2 (ATP Binding Cassette G2, breast cancer resistance protein, BCRP function using the Caco-2 cell intestinal epithelial cell model. Glyceollins are soy-derived phytoestrogens that demonstrate anti-proliferative activity in several sources of cancer cells. 5 (and 6-carboxy-2′,7′-dichloroflourescein (CDF was used as a prototypical MRP2 substrate; whereas BODIPY-prazosin provided an indication of BCRP function. Comparison studies were conducted with genistein. Glyceollins were shown to inhibit MRP2-mediated CDF transport, with activity similar to the MRP2 inhibitor, MK-571. They also demonstrated concentration-dependent inhibition BCRP-mediated efflux of BODIPY-prazosin, with a potency similar to that of the recognized BCRP inhibitor, Ko143. In contrast, genistein did not appear to alter MRP2 activity and even provided a modest increase in BCRP efflux of BODIPY-prazosin. In particular, glyceollin inhibition of these two important intestinal efflux transporters suggests the potential for glyceollin to alter the absorption of other phytochemicals with which it might be co-administered as a dietary supplement, as well as alteration of the absorption of pharmaceuticals that may be administered concomitantly.

Identification, evolution and functional characterization of two Zn CDF-family transporters of the ectomycorrhizal fungus Suillus luteus.

Science.gov (United States)

Ruytinx, Joske; Coninx, Laura; Nguyen, Hoai; Smisdom, Nick; Morin, Emmanuelle; Kohler, Annegret; Cuypers, Ann; Colpaert, Jan V

2017-08-01

Two genes, SlZnT1 and SlZnT2, encoding Cation Diffusion Facilitator (CDF) family transporters were isolated from Suillus luteus mycelium by genome walking. Both gene models are very similar and phylogenetic analysis indicates that they are most likely the result of a recent gene duplication event. Comparative sequence analysis of the deduced proteins predicts them to be Zn transporters. This function was confirmed by functional analysis in yeast for SlZnT1. SlZnT1 was able to restore growth of the highly Zn sensitive yeast mutant Δzrc1 and localized to the vacuolar membrane. Transformation of Δzrc1 yeast cells with SlZnT1 resulted in an increased accumulation of Zn compared to empty vector transformed Δzrc1 yeast cells and equals Zn accumulation in wild type yeast cells. We were not able to express functional SlZnT2 in yeast. In S. luteus, both SlZnT genes are constitutively expressed whatever the external Zn concentrations. A labile Zn pool was detected in the vacuoles of S. luteus free-living mycelium. Therefore we conclude that SlZnT1 is indispensable for maintenance of Zn homeostasis by transporting excess Zn into the vacuole. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Structural basis for the differential effects of CaBP1 and calmodulin on CaV1.2 calcium-dependent inactivation

Science.gov (United States)

Findeisen, Felix; Minor, Daniel L.

2010-01-01

Calcium-binding protein 1 (CaBP1), a calmodulin (CaM) homolog, endows certain voltage-gated calcium channels (CaVs) with unusual properties. CaBP1 inhibits CaV1.2 calcium-dependent inactivation (CDI) and introduces calcium-dependent facilitation (CDF). Here, we show that the ability of CaBP1 to inhibit CaV1.2 CDI and induce CDF arises from interaction between the CaBP1 N-lobe and interlobe linker residue Glu94. Unlike CaM, where functional EF hands are essential for channel modulation, CDI inhibition does not require functional CaBP1 EF-hands. Furthermore, CaBP1-mediated CDF has different molecular requirements than CaM-mediated CDF. Overall, the data show that CaBP1 comprises two structural modules having separate functions: similar to CaM, the CaBP1 C-lobe serves as a high-affinity anchor that binds the CaV1.2 IQ domain at a site that overlaps with the Ca2+/CaM C-lobe site, whereas the N-lobe/linker module houses the elements required for channel modulation. Discovery of this division provides the framework for understanding how CaBP1 regulates CaVs. PMID:21134641

Nipbl and mediator cooperatively regulate gene expression to control limb development.

Directory of Open Access Journals (Sweden)

Akihiko Muto

2014-09-01

Full Text Available Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS, the most common "cohesinopathy". It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb, knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions.

A verilog simulation of the CDF DAQ system

Energy Technology Data Exchange (ETDEWEB)

Schurecht, K.; Harris, R. (Fermi National Accelerator Lab., Batavia, IL (United States)); Sinervo, P.; Grindley, R. (Toronto Univ., ON (Canada). Dept. of Physics)

1991-11-01

A behavioral simulation of the CDF data acquisition system was written in the Verilog modeling language in order to investigate the effects of various improvements to the existing system. This system is modeled as five separate components that communicate with each other via Fastbus interrupt messages. One component of the system, the CDF event builder, is modeled in substantially greater detail due to its complex structure. This simulation has been verified by comparing its performance with that of the existing DAQ system. Possible improvements to the existing systems were studied using the simulation, and the optimal upgrade path for the system was chosen on the basis of these studies. The overall throughput of the modified system is estimated to be double that of the existing setup. Details of this modeling effort will be discussed, including a comparison of the modeled and actual performance of the existing system.

A verilog simulation of the CDF DAQ system

International Nuclear Information System (INIS)

Schurecht, K.; Harris, R.; Sinervo, P.; Grindley, R.

1991-11-01

A behavioral simulation of the CDF data acquisition system was written in the Verilog modeling language in order to investigate the effects of various improvements to the existing system. This system is modeled as five separate components that communicate with each other via Fastbus interrupt messages. One component of the system, the CDF event builder, is modeled in substantially greater detail due to its complex structure. This simulation has been verified by comparing its performance with that of the existing DAQ system. Possible improvements to the existing systems were studied using the simulation, and the optimal upgrade path for the system was chosen on the basis of these studies. The overall throughput of the modified system is estimated to be double that of the existing setup. Details of this modeling effort will be discussed, including a comparison of the modeled and actual performance of the existing system

Tensor decomposition-based unsupervised feature extraction identifies candidate genes that induce post-traumatic stress disorder-mediated heart diseases.

Science.gov (United States)

Taguchi, Y-H

2017-12-21

Although post-traumatic stress disorder (PTSD) is primarily a mental disorder, it can cause additional symptoms that do not seem to be directly related to the central nervous system, which PTSD is assumed to directly affect. PTSD-mediated heart diseases are some of such secondary disorders. In spite of the significant correlations between PTSD and heart diseases, spatial separation between the heart and brain (where PTSD is primarily active) prevents researchers from elucidating the mechanisms that bridge the two disorders. Our purpose was to identify genes linking PTSD and heart diseases. In this study, gene expression profiles of various murine tissues observed under various types of stress or without stress were analyzed in an integrated manner using tensor decomposition (TD). Based upon the obtained features, ∼ 400 genes were identified as candidate genes that may mediate heart diseases associated with PTSD. Various gene enrichment analyses supported biological reliability of the identified genes. Ten genes encoding protein-, DNA-, or mRNA-interacting proteins-ILF2, ILF3, ESR1, ESR2, RAD21, HTT, ATF2, NR3C1, TP53, and TP63-were found to be likely to regulate expression of most of these ∼ 400 genes and therefore are candidate primary genes that cause PTSD-mediated heart diseases. Approximately 400 genes in the heart were also found to be strongly affected by various drugs whose known adverse effects are related to heart diseases and/or fear memory conditioning; these data support the reliability of our findings. TD-based unsupervised feature extraction turned out to be a useful method for gene selection and successfully identified possible genes causing PTSD-mediated heart diseases.

More loosely bound hadron molecules at CDF?

CERN Document Server

Bignamini, C; Piccinini, F; Polosa, A D; Riquer, V; Sabelli, C

2010-01-01

In a recent paper we have proposed a method to estimate the prompt production cross section of X(3872) at the Tevatron assuming that this particle is a loosely bound molecule of a D and a D*bar meson. Under this hypothesis we find that it is impossible to explain the high prompt production cross section found by CDF at sigma(X(3872)) \\sim 30-70 nb as our theoretical prediction is about 300 times smaller than the measured one. Following our work, Artoisenet and Braaten, have suggested that final state interactions in the DD*bar system might be so strong to push the result we obtained for the cross section up to the experimental value. Relying on their conclusions we show that the production of another very narrow loosely bound molecule, the X_s=D_s D_s*bar, could be similarly enhanced. X_s should then be detectable at CDF with a mass of 4080 MeV and a prompt production cross section of sigma(X_s) \\sim 1-3 nb.

HvCKX2 gene silencing by biolistic or Agrobacterium-mediated transformation in barley leads to different phenotypes.

Science.gov (United States)

Zalewski, Wojciech; Orczyk, Wacław; Gasparis, Sebastian; Nadolska-Orczyk, Anna

2012-11-07

CKX genes encode cytokinin dehydrogenase enzymes (CKX), which metabolize cytokinins in plants and influence developmental processes. The genes are expressed in different tissues and organs during development; however, their exact role in barley is poorly understood. It has already been proven that RNA interference (RNAi)-based silencing of HvCKX1 decreased the CKX level, especially in those organs which showed the highest expression, i.e. developing kernels and roots, leading to higher plant productivity and higher mass of the roots [1]. The same type of RNAi construct was applied to silence HvCKX2 and analyze the function of the gene. Two cultivars of barley were transformed with the same silencing and selection cassettes by two different methods: biolistic and via Agrobacterium. The mean Agrobacterium-mediated transformation efficiency of Golden Promise was 3.47% (±2.82). The transcript level of HvCKX2 in segregating progeny of T(1) lines was decreased to 34%. The reduction of the transcript in Agrobacterium-derived plants resulted in decreased CKX activity in the developing and developed leaves as well as in 7 DAP (days after pollination) spikes. The final phenotypic effect was increased productivity of T(0) plants and T(1) lines. Higher productivity was the result of the higher number of seeds and higher grain yield. It was also correlated with the higher 1000 grain weight, increased (by 7.5%) height of the plants and higher (from 0.5 to 2) numbers of spikes. The transformation efficiency of Golden Promise after biolistic transformation was more than twice as low compared to Agrobacterium. The transcript level in segregating progeny of T(1) lines was decreased to 24%. Otherwise, the enzyme activity found in the leaves of the lines after biolistic transformation, especially in cv. Golden Promise, was very high, exceeding the relative level of the control lines. These unbalanced ratios of the transcript level and the activity of the CKX enzyme negatively

Gold nanoparticle mediated laser transfection for efficient siRNA mediated gene knock down.

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Dag Heinemann

Full Text Available Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types.

Gold nanoparticle mediated laser transfection for efficient siRNA mediated gene knock down.

Science.gov (United States)

Heinemann, Dag; Schomaker, Markus; Kalies, Stefan; Schieck, Maximilian; Carlson, Regina; Murua Escobar, Hugo; Ripken, Tammo; Meyer, Heiko; Heisterkamp, Alexander

2013-01-01

Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types.

Gold Nanoparticle Mediated Laser Transfection for Efficient siRNA Mediated Gene Knock Down

Science.gov (United States)

Heinemann, Dag; Schomaker, Markus; Kalies, Stefan; Schieck, Maximilian; Carlson, Regina; Escobar, Hugo Murua; Ripken, Tammo; Meyer, Heiko; Heisterkamp, Alexander

2013-01-01

Laser based transfection methods have proven to be an efficient and gentle alternative to established molecule delivery methods like lipofection or electroporation. Among the laser based methods, gold nanoparticle mediated laser transfection bears the major advantage of high throughput and easy usability. This approach uses plasmon resonances on gold nanoparticles unspecifically attached to the cell membrane to evoke transient and spatially defined cell membrane permeabilization. In this study, we explore the parameter regime for gold nanoparticle mediated laser transfection for the delivery of molecules into cell lines and prove its suitability for siRNA mediated gene knock down. The developed setup allows easy usage and safe laser operation in a normal lab environment. We applied a 532 nm Nd:YAG microchip laser emitting 850 ps pulses at a repetition rate of 20.25 kHz. Scanning velocities of the laser spot over the sample of up to 200 mm/s were tested without a decline in perforation efficiency. This velocity leads to a process speed of ∼8 s per well of a 96 well plate. The optimal particle density was determined to be ∼6 particles per cell using environmental scanning electron microscopy. Applying the optimized parameters transfection efficiencies of 88% were achieved in canine pleomorphic adenoma ZMTH3 cells using a fluorescent labeled siRNA while maintaining a high cell viability of >90%. Gene knock down of d2-EGFP was demonstrated and validated by fluorescence repression and western blot analysis. On basis of our findings and established mathematical models we suppose a mixed transfection mechanism consisting of thermal and multiphoton near field effects. Our findings emphasize that gold nanoparticle mediated laser transfection provides an excellent tool for molecular delivery for both, high throughput purposes and the transfection of sensitive cells types. PMID:23536802

A comparison of CRISPR/Cas9 and siRNA-mediated ALDH2 gene silencing in human cell lines.

Science.gov (United States)

Wang, Fei; Guo, Tao; Jiang, Hongmei; Li, Ruobi; Wang, Ting; Zeng, Ni; Dong, Guanghui; Zeng, Xiaowen; Li, Daochuan; Xiao, Yongmei; Hu, Qiansheng; Chen, Wen; Xing, Xiumei; Wang, Qing

2018-06-01

Gene knockdown and knockout using RNAi and CRISPR/Cas9 allow for efficient evaluation of gene function, but it is unclear how the choice of technology can influence the results. To compare the phenotypes obtained using siRNA and CRISPR/Cas9 technologies, aldehyde dehydrogenase 2 (ALDH2) was selected as an example. In this study, we constructed one HepG2 cell line with a homozygous mutation in the fifth exon of ALDH2 (ALDH2-KO1 cell) using the eukaryotic CRISPR/Cas9 expression system followed by the limited dilution method and one HepG2 cell line with different mutations in the ALDH2 gene (ALDH2-KO2 cell) using the lentivirus CRISPR/Cas9 system. Additionally, one ALDH2-knockdown (KD) HepG2 cell line was created using siRNA. The reproducibility of these methods was further verified in the HEK293FT cell line. We found that the mRNA expression level of ALDH2 was significantly decreased and the protein expression level of ALDH2 was completely abolished in the ALDH2-KO cell lines, but not in ALDH2-KD cells. Furthermore, the functional activity of ALDH2 was also markedly disrupted in the two ALDH2-KO cell lines compared with ALDH2-KD and wild-type cells. The lack of ALDH2 expression mediated by CRIPSR/Cas9 resulted in a more dramatic increase in the cellular susceptibility to chemical-induced reactive oxygen species generation, cytotoxicity, apoptosis, and inflammation, especially at low concentrations compared with ALDH2-KD and WT cells. Therefore, we consider the gene knockout cell line created by CRISPR/Cas9 to be a more useful tool for identifying the function of a gene.

Operation and performance of the silicon vertex detector (SVX') at CDF

International Nuclear Information System (INIS)

Singh, P.P.

1994-10-01

The authors describe the operation and performance of the Silicon Vertex Detector (SVX'), which replaced the CDF SVX detector for run lb of the Fermilab Tevatron Collider. The new features of the SVX' include AC coupled readout, Field OXide Field Effect Transistor (FOXFET) biasing and radiation hard front end electronics. The authors expect the detector to survive beyond the 100 pb -1 of data taking anticipated for the present CDF physics run. Preliminary results from the collider data show that the detector has a resolution of about 12 μm. This provides a powerful tool to do top and bottom physics

The Mediator Complex MED15 Subunit Mediates Activation of Downstream Lipid-Related Genes by the WRINKLED1 Transcription Factor.

Science.gov (United States)

Kim, Mi Jung; Jang, In-Cheol; Chua, Nam-Hai

2016-07-01

The Mediator complex is known to be a master coordinator of transcription by RNA polymerase II, and this complex is recruited by transcription factors (TFs) to target promoters for gene activation or repression. The plant-specific TF WRINKLED1 (WRI1) activates glycolysis-related and fatty acid biosynthetic genes during embryogenesis. However, no Mediator subunit has yet been identified that mediates WRI1 transcriptional activity. Promoter-β-glucuronidase fusion experiments showed that MEDIATOR15 (MED15) is expressed in the same cells in the embryo as WRI1. We found that the Arabidopsis (Arabidopsis thaliana) MED15 subunit of the Mediator complex interacts directly with WRI1 in the nucleus. Overexpression of MED15 or WRI1 increased transcript levels of WRI1 target genes involved in glycolysis and fatty acid biosynthesis; these genes were down-regulated in wild-type or WRI1-overexpressing plants by silencing of MED15 However, overexpression of MED15 in the wri1 mutant also increased transcript levels of WRI1 target genes, suggesting that MED15 also may act with other TFs to activate downstream lipid-related genes. Chromatin immunoprecipitation assays confirmed the association of MED15 with six WRI1 target gene promoters. Additionally, silencing of MED15 resulted in reduced fatty acid content in seedlings and mature seeds, whereas MED15 overexpression increased fatty acid content in both developmental stages. Similar results were found in wri1 mutant and WRI1 overexpression lines. Together, our results indicate that the WRI1/MED15 complex transcriptionally regulates glycolysis-related and fatty acid biosynthetic genes during embryogenesis. © 2016 American Society of Plant Biologists. All Rights Reserved.

Structural basis for the differential effects of CaBP1 and calmodulin on Ca(V)1.2 calcium-dependent inactivation.

Science.gov (United States)

Findeisen, Felix; Minor, Daniel L

2010-12-08

Calcium-binding protein 1 (CaBP1), a calmodulin (CaM) homolog, endows certain voltage-gated calcium channels (Ca(V)s) with unusual properties. CaBP1 inhibits Ca(V)1.2 calcium-dependent inactivation (CDI) and introduces calcium-dependent facilitation (CDF). Here, we show that the ability of CaBP1 to inhibit Ca(V)1.2 CDI and induce CDF arises from interaction between the CaBP1 N-lobe and interlobe linker residue Glu94. Unlike CaM, where functional EF hands are essential for channel modulation, CDI inhibition does not require functional CaBP1 EF hands. Furthermore, CaBP1-mediated CDF has different molecular requirements than CaM-mediated CDF. Overall, the data show that CaBP1 comprises two structural modules having separate functions: similar to CaM, the CaBP1 C-lobe serves as a high-affinity anchor that binds the Ca(V)1.2 IQ domain at a site that overlaps with the Ca²+/CaM C-lobe site, whereas the N-lobe/linker module houses the elements required for channel modulation. Discovery of this division provides the framework for understanding how CaBP1 regulates Ca(V)s. Copyright © 2010 Elsevier Ltd. All rights reserved.

The RASNIK real-time relative alignment monitor for the CDF inner tracking detectors

International Nuclear Information System (INIS)

Goldstein, David; Saltzberg, David

2003-01-01

We describe the design and operation of the RASNIK optical relative alignment system designed for and installed on the CDF inner tracking detectors. The system provides low-cost minute-by-minute alignment monitoring with submicron precision. To reduce ambiguities, we modified the original three-element RASNIK design to a two-element one. Since the RASNIKs are located within 10-40 cm of the beam line, the systems were built from low-mass and radiation-hard components and are operated in a mode which reduces damage from radiation. We describe the data-acquisition system, which has been running without interruption since before the CDF detector was rolled into its collision hall in March 2001. We evaluate what has been learned about sources of detector motion from almost 2 years of RASNIK data and discuss possible improvements to the system

Strategies to regulate transcription factor-mediated gene positioning and interchromosomal clustering at the nuclear periphery.

Science.gov (United States)

Randise-Hinchliff, Carlo; Coukos, Robert; Sood, Varun; Sumner, Michael Chas; Zdraljevic, Stefan; Meldi Sholl, Lauren; Garvey Brickner, Donna; Ahmed, Sara; Watchmaker, Lauren; Brickner, Jason H

2016-03-14

In budding yeast, targeting of active genes to the nuclear pore complex (NPC) and interchromosomal clustering is mediated by transcription factor (TF) binding sites in the gene promoters. For example, the binding sites for the TFs Put3, Ste12, and Gcn4 are necessary and sufficient to promote positioning at the nuclear periphery and interchromosomal clustering. However, in all three cases, gene positioning and interchromosomal clustering are regulated. Under uninducing conditions, local recruitment of the Rpd3(L) histone deacetylase by transcriptional repressors blocks Put3 DNA binding. This is a general function of yeast repressors: 16 of 21 repressors blocked Put3-mediated subnuclear positioning; 11 of these required Rpd3. In contrast, Ste12-mediated gene positioning is regulated independently of DNA binding by mitogen-activated protein kinase phosphorylation of the Dig2 inhibitor, and Gcn4-dependent targeting is up-regulated by increasing Gcn4 protein levels. These different regulatory strategies provide either qualitative switch-like control or quantitative control of gene positioning over different time scales. © 2016 Randise-Hinchliff et al.

Introduction to HOBIT, a b-jet identification tagger at the CDF experiment optimized for light Higgs boson searches

Energy Technology Data Exchange (ETDEWEB)

Freeman, J.; Junk, T.; Kirby, M.; Oksuzian, Y.; Phillips, T. J.; Snider, F. D.; Trovato, M.; Vizan, J.; Yao, W. M.

2013-01-01

We present the development and validation of the Higgs Optimized b Identification Tagger (HOBIT), a multivariate b-jet identification algorithm optimized for Higgs boson searches at the CDF experiment at the Fermilab Tevatron. At collider experiments, b taggers allow one to distinguish particle jets containing B hadrons from other jets; these algorithms have been used for many years with great success at CDF. HOBIT has been designed specifically for use in searches for light Higgs bosons decaying via H ! b\\bar{b}. This fact combined with the extent to which HOBIT synthesizes and extends the best ideas of previous taggers makes HOBIT unique among CDF b-tagging algorithms. Employing feed-forward neural network architectures, HOBIT provides an output value ranging from approximately -1 ("light-jet like") to 1 ("b-jet like"); this continuous output value has been tuned to provide maximum sensitivity in light Higgs boson search analyses. When tuned to the equivalent light jet rejection rate, HOBIT tags 54% of b jets in simulated 120 GeV/c2 Higgs boson events compared to 39% for SecVtx, the most commonly used b tagger at CDF. We present features of the tagger as well as its characterization in the form of b-jet finding efficiencies and false (light-jet) tag rates.

Rpi-blb2-Mediated Hypersensitive Cell Death Caused by Phytophthora infestans AVRblb2 Requires SGT1, but not EDS1, NDR1, Salicylic Acid-, Jasmonic Acid-, or Ethylene-Mediated Signaling

Directory of Open Access Journals (Sweden)

Sang-Keun Oh

2014-09-01

Full Text Available Potato Rpi-blb2 encodes a protein with a coiled-coil-nucleotide binding site and leucine-rich repeat (CC-NBS-LRR motif that recognizes the Phytophthora infestans AVRblb2 effector and triggers hypersensitive cell death (HCD. To better understand the components required for Rpi-blb2-mediated HCD in plants, we used virus-induced gene silencing to repress candidate genes in Rpi-blb2-transgenic Nicotiana benthamiana plants and assayed the plants for AVRblb2 effector. Rpi-blb2 triggers HCD through NbSGT1-mediated pathways, but not NbEDS1- or NbNDR1-mediated pathways. In addition, the role of salicylic acid (SA, jasmonic acid (JA, and ethylene (ET in Rpi-blb2-mediated HCD were analyzed by monitoring of the responses of NbICS1-, NbCOI1-, or NbEIN2-silenced or Rpi-blb2::NahG-transgenic plants. Rpi-blb2-mediated HCD in response to AVRblb2 was not associated with SA accumulation. Thus, SA affects Rpi-blb2-mediated resistance against P. infestans, but not Rpi-blb2-mediated HCD in response to AVRblb2. Additionally, JA and ET signaling were not required for Rpi-blb2-mediated HCD in N. benthamiana. Taken together, these findings suggest that NbSGT1 is a unique positive regulator of Rpi-blb2-mediated HCD in response to AVRblb2, but EDS1, NDR1, SA, JA, and ET are not required.

Follistatin allows efficient retroviral-mediated gene transfer into rat liver

International Nuclear Information System (INIS)

Borgnon, Josephine; Djamouri, Fatima; Lorand, Isabelle; Rico, Virginie Di; Loux, Nathalie; Pages, Jean-Christophe; Franco, Dominique; Capron, Frederique; Weber, Anne

2005-01-01

Retroviral vectors are widely used tools for gene therapy. However, in vivo gene transfer is only effective in dividing cells, which, in liver, requires a regenerative stimulus. Follistatin is effective in promoting liver regeneration after 90% and 70% hepatectomy in rats. We studied its efficacy on liver regeneration and retroviral-mediated gene delivery in 50% hepatectomized rats. When human recombinant follistatin was infused into the portal vein immediately after 50% hepatectomy, hepatocyte proliferation was significantly higher than in control 50% hepatectomized rats. A single injection of virus particles administered 23 h after follistatin infusion resulted in more than 20% gene transduction efficiency in hepatocytes compared to 3% in control rats. It is concluded that a single injection of follistatin induces onset of proliferation in 50% hepatectomized rats and allows efficient retroviral-mediated gene transfer to the liver

Epigenetic involvement of Alien/ESET complex in thyroid hormone-mediated repression of E2F1 gene expression and cell proliferation

Energy Technology Data Exchange (ETDEWEB)

Hong, Wei, E-mail: hongwei@tijmu.edu.cn [Department of Immunology, Tianjin Medical University, 300070 Tianjin (China); College of Basic Medicine, Tianjin Medical University, 300070 Tianjin (China); Li, Jinru; Wang, Bo [College of Basic Medicine, Tianjin Medical University, 300070 Tianjin (China); Chen, Linfeng [Department of Medical Oncology, Harvard Medical School, Dana Farber Cancer Institute, Boston, 02115 MA (United States); Niu, Wenyan; Yao, Zhi [Department of Immunology, Tianjin Medical University, 300070 Tianjin (China); Baniahmad, Aria, E-mail: aban@mti.uni-jena.de [Institute for Human Genetics, Jena University Hospital, 07740 Jena (Germany)

2011-12-02

Highlights: Black-Right-Pointing-Pointer Corepressor Alien interacts with histone methyltransferase ESET in vivo. Black-Right-Pointing-Pointer Alien/ESET complex is recruited to nTRE of T3-responsive gene by liganded TR{beta}1. Black-Right-Pointing-Pointer ESET-mediated H3K9 methylation is required for liganded TR{beta}1-repressed transcription. Black-Right-Pointing-Pointer ESET is involved in T3-repressed G1/S phase transition and proliferation. -- Abstract: The ligand-bound thyroid hormone receptor (TR) is known to repress via a negative TRE (nTRE) the expression of E2F1, a key transcription factor that controls the G1/S phase transition. Alien has been identified as a novel interacting factor of E2F1 and acts as a corepressor of E2F1. The detailed molecular mechanism by which Alien inhibits E2F1 gene expression remains unclear. Here, we report that the histone H3 lysine 9 (H3K9) methyltransferase (HMT) ESET is an integral component of the corepressor Alien complex and the Alien/ESET complex is recruited to both sites, the E2F1 and the nTRE site of the E2F1 gene while the recruitment to the negative thyroid hormone response element (nTRE) is induced by the ligand-bound TR{beta}1 within the E2F1 gene promoter. We show that, overexpression of ESET promotes, whereas knockdown of ESET releases, the inhibition of TR{beta}1-regulated gene transcription upon T3 stimulation; and H3K9 methylation is required for TR{beta}1-repressed transcription. Furthermore, depletion of ESET impairs thyroid hormone-repressed proliferation as well as the G1/S transition of the cell cycle. Taken together, our data indicate that ESET is involved in TR{beta}1-mediated transcription repression and provide a molecular basis of thyroid hormone-induced repression of proliferation.

Recent Trends of Polymer Mediated Liposomal Gene Delivery System

Directory of Open Access Journals (Sweden)

Shyamal Kumar Kundu

2014-01-01

Full Text Available Advancement in the gene delivery system have resulted in clinical successes in gene therapy for patients with several genetic diseases, such as immunodeficiency diseases, X-linked adrenoleukodystrophy (X-ALD blindness, thalassemia, and many more. Among various delivery systems, liposomal mediated gene delivery route is offering great promises for gene therapy. This review is an attempt to depict a portrait about the polymer based liposomal gene delivery systems and their future applications. Herein, we have discussed in detail the characteristics of liposome, importance of polymer for liposome formulation, gene delivery, and future direction of liposome based gene delivery as a whole.

The functions of Mediator in Candida albicans support a role in shaping species-specific gene expression.

Directory of Open Access Journals (Sweden)

Nathalie Uwamahoro

Full Text Available The Mediator complex is an essential co-regulator of RNA polymerase II that is conserved throughout eukaryotes. Here we present the first study of Mediator in the pathogenic fungus Candida albicans. We focused on the Middle domain subunit Med31, the Head domain subunit Med20, and Srb9/Med13 from the Kinase domain. The C. albicans Mediator shares some roles with model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, such as functions in the response to certain stresses and the role of Med31 in the expression of genes regulated by the activator Ace2. The C. albicans Mediator also has additional roles in the transcription of genes associated with virulence, for example genes related to morphogenesis and gene families enriched in pathogens, such as the ALS adhesins. Consistently, Med31, Med20, and Srb9/Med13 contribute to key virulence attributes of C. albicans, filamentation, and biofilm formation; and ALS1 is a biologically relevant target of Med31 for development of biofilms. Furthermore, Med31 affects virulence of C. albicans in the worm infection model. We present evidence that the roles of Med31 and Srb9/Med13 in the expression of the genes encoding cell wall adhesins are different between S. cerevisiae and C. albicans: they are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans. This suggests that Mediator subunits regulate adhesion in a distinct manner between these two distantly related fungal species.

A Final Review of the Performance of the CDF Run II Data Acquisition System

CERN Multimedia

CERN. Geneva

2012-01-01

The CDF Collider Detector at Fermilab ceased data collection on September 30, 2011 after over twenty five years of operation. We review the performance of the CDF Run II data acquisition systems over the last ten of these years while recording nearly 10 fb-1 of proton-antiproton collisions with a high degree of efficiency. Technology choices in the online control and configuration systems and front-end embedded processing have impacted the efficiency and quality of the data accumulated by CDF, and have had to perform over a large range of instantaneous luminosity values and trigger rates. We identify significant sources of problems and successes. In particular, we present our experience computing and acquiring data in a radiation environment, and attempt to correlate system technical faults with radiation dose rate and technology choices.

A Final Review of the Performance of the CDF Run II Data Acquisition System

International Nuclear Information System (INIS)

Badgett, W

2012-01-01

The CDF Collider Detector at Fermilab ceased data collection on September 30, 2011 after over twenty-five years of operation. We review the performance of the CDF Run II data acquisition systems over the last ten of these years while recording nearly 10 inverse femtobarns of proton-antiproton collisions with a high degree of efficiency - exceeding 83%. Technology choices in the online control and configuration systems and front-end embedded processing have impacted the efficiency and quality of the data accumulated by CDF, and have had to perform over a large range of instantaneous luminosity values and trigger rates. We identify significant sources of problems and successes. In particular, we present our experience computing and acquiring data in a radiation environment, and attempt to correlate system technical faults with radiation dose rate and technology choices.

Gene structure and expression characteristic of a novel odorant receptor gene cluster in the parasitoid wasp Microplitis mediator (Hymenoptera: Braconidae).

Science.gov (United States)

Wang, S-N; Shan, S; Zheng, Y; Peng, Y; Lu, Z-Y; Yang, Y-Q; Li, R-J; Zhang, Y-J; Guo, Y-Y

2017-08-01

Odorant receptors (ORs) expressed in the antennae of parasitoid wasps are responsible for detection of various lipophilic airborne molecules. In the present study, 107 novel OR genes were identified from Microplitis mediator antennal transcriptome data. Phylogenetic analysis of the set of OR genes from M. mediator and Microplitis demolitor revealed that M. mediator OR (MmedOR) genes can be classified into different subfamilies, and the majority of MmedORs in each subfamily shared high sequence identities and clear orthologous relationships to M. demolitor ORs. Within a subfamily, six MmedOR genes, MmedOR98, 124, 125, 126, 131 and 155, shared a similar gene structure and were tightly linked in the genome. To evaluate whether the clustered MmedOR genes share common regulatory features, the transcription profile and expression characteristics of the six closely related OR genes were investigated in M. mediator. Rapid amplification of cDNA ends-PCR experiments revealed that the OR genes within the cluster were transcribed as single mRNAs, and a bicistronic mRNA for two adjacent genes (MmedOR124 and MmedOR98) was also detected in female antennae by reverse transcription PCR. In situ hybridization experiments indicated that each OR gene within the cluster was expressed in a different number of cells. Moreover, there was no co-expression of the two highly related OR genes, MmedOR124 and MmedOR98, which appeared to be individually expressed in a distinct population of neurons. Overall, there were distinct expression profiles of closely related MmedOR genes from the same cluster in M. mediator. These data provide a basic understanding of the olfactory coding in parasitoid wasps. © 2017 The Royal Entomological Society.

Dysregulation of RNA Mediated Gene Expression in Motor Neuron Diseases.

Science.gov (United States)

Gonçalves, Inês do Carmo G; Rehorst, Wiebke A; Kye, Min Jeong

2016-01-01

Recent findings indicate an important role for RNA-mediated gene expression in motor neuron diseases, including ALS (amyotrophic lateral sclerosis) and SMA (spinal muscular atrophy). ALS, also known as Lou Gehrig's disease, is an adult-onset progressive neurodegenerative disorder, whereby SMA or "children's Lou Gehrig's disease" is considered a pediatric neurodevelopmental disorder. Despite the difference in genetic causes, both ALS and SMA share common phenotypes; dysfunction/loss of motor neurons that eventually leads to muscle weakness and atrophy. With advanced techniques in molecular genetics and cell biology, current data suggest that these two distinct motor neuron diseases share more than phenotypes; ALS and SMA have similar cellular pathological mechanisms including mitochondrial dysfunction, oxidative stress and dysregulation in RNA-mediated gene expression. Here, we will discuss the current findings on these two diseases with specific focus on RNA-mediated gene regulation including miRNA expression, pre-mRNA processing and RNA binding proteins.

The Agricultural Antibiotic Carbadox Induces Phage-mediated Gene Transfer in Salmonella

Directory of Open Access Journals (Sweden)

Bradley L. Bearson

2014-02-01

Full Text Available Antibiotics are used for disease therapeutic or preventative effects in humans and animals, as well as for enhanced feed conversion efficiency in livestock. Antibiotics can also cause undesirable effects in microbial populations, including selection for antibiotic resistance, enhanced pathogen invasion, and stimulation of horizontal gene transfer. Carbadox is a veterinary antibiotic used in the U.S. during the starter phase of swine production for improved feed efficiency and control of swine dysentery and bacterial swine enteritis. Carbadox has been shown in vitro to induce phage-encoded Shiga toxin in Shiga toxin-producing Escherichia coli and a phage-like element transferring antibiotic resistance genes in Brachyspira hyodysenteriae, but the effect of carbadox on prophages in other bacteria is unknown. This study examined carbadox exposure on prophage induction and genetic transfer in Salmonella enterica serovar Typhimurium, a human foodborne pathogen that frequently colonizes swine without causing disease. S. Typhimurium LT2 exposed to carbadox induced prophage production, resulting in bacterial cell lysis and release of virions that were visible by electron microscopy. Carbadox induction of phage-mediated gene transfer was confirmed by monitoring the transduction of a sodCIII::neo cassette in the Fels-1 prophage from LT2 to a recipient Salmonella strain. Furthermore, carbadox frequently induced generalized transducing phages in multidrug-resistant phage type DT104 and DT120 isolates, resulting in the transfer of chromosomal and plasmid DNA that included antibiotic resistance genes. Our research indicates that exposure of Salmonella to carbadox induces prophages that can transfer virulence and antibiotic resistance genes to susceptible bacterial hosts. Carbadox-induced, phage-mediated gene transfer could serve as a contributing factor in bacterial evolution during animal production, with prophages being a reservoir for bacterial fitness

Improving the Acceptance in the Single Top Quark Analysis using 7.5 fb$^{-1}$ of CDF data

Energy Technology Data Exchange (ETDEWEB)

Ronzani, Manfredi [Pisa U.

2012-01-01

The Top quark was observed at the Fermilab Tevatron by the CDF and D0 collaboration in 1995 via strong production of top quarks pairs at center-of-mass energy of √s=1.8 Tev, using 60 pb−1 of data [1]. Standard Model of elementary particles predicts top quark to be produced individually via electroweak interactions in three different channels (s, t and Wt). This is defined as ”single top” (from now on also ST). ST was observed by CDF collaboration in 2009 at center-of-mass energy of √s=1.96 Tev using 3.2 fb−1 of p¯p collected data [2]. This thesis concerns the upgrade of this measurement using 7.5 fb−1 of data.

Precision top-quark mass measurements at CDF

Czech Academy of Sciences Publication Activity Database

Aaltonen, T.; Gonzalez, B.A.; Amerio, S.; Lysák, Roman

2012-01-01

Roč. 109, č. 15 (2012), "152003-1"-"152003-7" ISSN 0031-9007 R&D Projects: GA MŠk LC527 Institutional research plan: CEZ:AV0Z10100502 Keywords : top mass * top pair production * dijet mass spectrum * CDF * Batavia TEVATRON Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 7.943, year: 2012 http://arxiv.org/abs/arXiv:1207.6758

Mediator Recruitment to Heat Shock Genes Requires Dual Hsf1 Activation Domains and Mediator Tail Subunits Med15 and Med16*

Science.gov (United States)

Kim, Sunyoung; Gross, David S.

2013-01-01

The evolutionarily conserved Mediator complex is central to the regulation of gene transcription in eukaryotes because it serves as a physical and functional interface between upstream regulators and the Pol II transcriptional machinery. Nonetheless, its role appears to be context-dependent, and the detailed mechanism by which it governs the expression of most genes remains unknown. Here we investigate Mediator involvement in HSP (heat shock protein) gene regulation in the yeast Saccharomyces cerevisiae. We find that in response to thermal upshift, subunits representative of each of the four Mediator modules (Head, Middle, Tail, and Kinase) are rapidly, robustly, and selectively recruited to the promoter regions of HSP genes. Their residence is transient, returning to near-background levels within 90 min. Hsf1 (heat shock factor 1) plays a central role in recruiting Mediator, as indicated by the fact that truncation of either its N- or C-terminal activation domain significantly reduces Mediator occupancy, whereas removal of both activation domains abolishes it. Likewise, ablation of either of two Mediator Tail subunits, Med15 or Med16, reduces Mediator recruitment to HSP promoters, whereas deletion of both abolishes it. Accompanying the loss of Mediator, recruitment of RNA polymerase II is substantially diminished. Interestingly, Mediator antagonizes Hsf1 occupancy of non-induced promoters yet facilitates enhanced Hsf1 association with activated ones. Collectively, our observations indicate that Hsf1, via its dual activation domains, recruits holo-Mediator to HSP promoters in response to acute heat stress through cooperative physical and/or functional interactions with the Tail module. PMID:23447536

A Study of NetCDF as an Approach for High Performance Medical Image Storage

International Nuclear Information System (INIS)

Magnus, Marcone; Prado, Thiago Coelho; Von Wangenhein, Aldo; De Macedo, Douglas D J; Dantas, M A R

2012-01-01

The spread of telemedicine systems increases every day. The systems and PACS based on DICOM images has become common. This rise reflects the need to develop new storage systems, more efficient and with lower computational costs. With this in mind, this article discusses a study for application in NetCDF data format as the basic platform for storage of DICOM images. The study case comparison adopts an ordinary database, the HDF5 and the NetCDF to storage the medical images. Empirical results, using a real set of images, indicate that the time to retrieve images from the NetCDF for large scale images has a higher latency compared to the other two methods. In addition, the latency is proportional to the file size, which represents a drawback to a telemedicine system that is characterized by a large amount of large image files.

A measurement of the b bar b cross section at CDF

International Nuclear Information System (INIS)

Yu, I.

1994-08-01

We report a measurement of the b bar b cross section at CDF from the 1992--1993 run of the Tevatron Collider. Dimuon events from inclusive b → μ decays of b bar b pairs are used to obtain the cross section as a function of P T (b 1 ) and P T (b 2 ). The results are compared to the predictions of next-to-leading order QCD and are found to be consistent

Efficient Oligo nucleotide mediated CRISPR-Cas9 Gene Editing in Aspergilli

DEFF Research Database (Denmark)

Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Kogle, Martin Engelhard

2018-01-01

CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool to assess protospacer....... niger, and in A. oryzae indicating that this type of repair may be wide spread in filamentous fungi. Importantly, we demonstrate that by using single-stranded oligo nucleotides for CRISPR-Cas9 mediated gene editing it is possible to introduce specific point mutations as well gene deletions...

Agrobacterium-mediated gene transfer in plants and biosafety considerations.

Science.gov (United States)

Mehrotra, Shweta; Goyal, Vinod

2012-12-01

Agrobacterium, the natures' genetic engineer, has been used as a vector to create transgenic plants. Agrobacterium-mediated gene transfer in plants is a highly efficient transformation process which is governed by various factors including genotype of the host plant, explant, vector, plasmid, bacterial strain, composition of culture medium, tissue damage, and temperature of co-cultivation. Agrobacterium has been successfully used to transform various economically and horticulturally important monocot and dicot species by standard tissue culture and in planta transformation techniques like floral or seedling infilteration, apical meristem transformation, and the pistil drip methods. Monocots have been comparatively difficult to transform by Agrobacterium. However, successful transformations have been reported in the last few years based on the adjustment of the parameters that govern the responses of monocots to Agrobacterium. A novel Agrobacterium transferred DNA-derived nanocomplex method has been developed which will be highly valuable for plant biology and biotechnology. Agrobacterium-mediated genetic transformation is known to be the preferred method of creating transgenic plants from a commercial and biosafety perspective. Agrobacterium-mediated gene transfer predominantly results in the integration of foreign genes at a single locus in the host plant, without associated vector backbone and is also known to produce marker free plants, which are the prerequisites for commercialization of transgenic crops. Research in Agrobacterium-mediated transformation can provide new and novel insights into the understanding of the regulatory process controlling molecular, cellular, biochemical, physiological, and developmental processes occurring during Agrobacterium-mediated transformation and also into a wide range of aspects on biological safety of transgenic crops to improve crop production to meet the demands of ever-growing world's population.

A multiple mediator analysis approach to quantify the effects of the ADH1B and ALDH2 genes on hepatocellular carcinoma risk.

Science.gov (United States)

Shih, Stephannie; Huang, Yen-Tsung; Yang, Hwai-I

2018-06-01

Previous work suggested a genetic component affecting the risk of hepatocellular carcinoma (HCC) and mediation analyses have elucidated potential indirect pathways of these genetic effects. Specifically, the effects of alcohol dehydrogenase (ADH1B) and aldehyde dehydrogenase (ALDH2) genes on HCC risk vary based on alcohol consumption habits. However, alcohol consumption may not be the only mediator in the identified pathway: factors related to alcohol consumption may contribute to the same indirect pathway. Thus, we developed a multimediator model to quantify the genetic effects on HCC risk through sequential dichotomous mediators under the counterfactual framework. Our method provided a closed form formula for the mediation effects through different indirect paths, which requires no assumption for the rarity of outcome. In simulation studies of a finite sample, we presented the utility of the method with the variance of the effects estimated using the delta method and bootstrapping. We applied our method to data from participants in Taiwan (580 cases and 3,207 controls) and quantified the mediation effects of single nucleotide polymorphisms (SNPs) in the ADH1B and ALDH2 genes on HCC through alcohol consumption (yes/no) and high alanine transaminase (ALT) levels (greater than or equal to 45 U/L or below 45 U/L). Assuming a dominant risk model, we identified that the SNPs' effects through alcohol consumption is more significant than through ALT levels on HCC risk. This new method provides insight to the magnitude of various casual mechanisms as a closed form solution and can be readily applied in other genomic studies. © 2018 WILEY PERIODICALS, INC.

DNA-mediated gene transfer into ataxia-telangiectasia cells

International Nuclear Information System (INIS)

Crescenzi, M.; Pulciani, S.; Carbonari, M.; Tedesco, L.; Russo, G.; Gaetano, C.; Fiorilli, M.

1986-01-01

The complete description of the genetic lesion(s) underlying the AT mutation might, therefore, highlight not only a DNA-repair pathwa, but also an important aspect of the physiology of lymphocytes. DNA-mediated gene transfer into eukaryotic cells has proved a powerful tool for the molecular cloning of certain mammalian genes. The possibility to clone a given gene using this technology depends, basically, on the availability of a selectable marker associated with the expression of the transfected gene in the recipient cell. Recently, a human DNA repair gene has been cloned in CHO mutant cells by taking advantage of the increased resistance to ultraviolet radiation of the transformants. As a preliminary step toward the molecular cloning of the AT gene(s), the authors have attempted to confer radioresistance to AT cells by transfection with normal human DNA

Host-Induced Gene Silencing of Rice Blast Fungus Magnaporthe oryzae Pathogenicity Genes Mediated by the Brome Mosaic Virus.

Science.gov (United States)

Zhu, Lin; Zhu, Jian; Liu, Zhixue; Wang, Zhengyi; Zhou, Cheng; Wang, Hong

2017-09-26

Magnaporthe oryzae is a devastating plant pathogen, which has a detrimental impact on rice production worldwide. Despite its agronomical importance, some newly-emerging pathotypes often overcome race-specific disease resistance rapidly. It is thus desirable to develop a novel strategy for the long-lasting resistance of rice plants to ever-changing fungal pathogens. Brome mosaic virus (BMV)-induced RNA interference (RNAi) has emerged as a useful tool to study host-resistance genes for rice blast protection. Planta-generated silencing of targeted genes inside biotrophic pathogens can be achieved by expression of M. oryzae -derived gene fragments in the BMV-mediated gene silencing system, a technique termed host-induced gene silencing (HIGS). In this study, the effectiveness of BMV-mediated HIGS in M. oryzae was examined by targeting three predicted pathogenicity genes, MoABC1, MoMAC1 and MoPMK1 . Systemic generation of fungal gene-specific small interfering RNA (siRNA) molecules induced by inoculation of BMV viral vectors inhibited disease development and reduced the transcription of targeted fungal genes after subsequent M. oryzae inoculation. Combined introduction of fungal gene sequences in sense and antisense orientation mediated by the BMV silencing vectors significantly enhanced the efficiency of this host-generated trans-specific RNAi, implying that these fungal genes played crucial roles in pathogenicity. Collectively, our results indicated that BMV-HIGS system was a great strategy for protecting host plants against the invasion of pathogenic fungi.

Enhancement of plasmid-mediated stable gene expression by ...

African Journals Online (AJOL)

ARL

2012-06-12

Jun 12, 2012 ... production and faithful translation and processing of proteins (Baldi et al., ..... deeper understanding of the interaction of cellular factors and regulatory DNA .... mediated transgene expression in the rat brain. Gene Ther., 7: ...

Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

Science.gov (United States)

Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-01-01

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

Charmless b-hadrons decays at CDF

International Nuclear Information System (INIS)

Morello, Michael Joseph

2008-01-01

We present CDF results on the branching fractions and time-integrated direct CP asymmetries for Bd, Bs and Lb decay modes into pairs of charmless charged hadrons (pions, kaons and protons). The data-set for these measurements amounts to 1fb -1 of p(bar p) collisions at a center of mass energy 1.96TeV. We report on the first observation of the Bs->Kpi, Lb-ppi and Lb->pK decay modes and on the measurement of their branching fractions and direct CP asymmetries

Top decay physics at CDF and measurement of the CKM element Vtb

International Nuclear Information System (INIS)

LeCompte, T.J.

1995-01-01

Now that the top quark's existence has been firmly established by the CDF and D0 experiments 1,2) , we begin to measure its properties. Branching fractions are of particular interest in the case of the t quark, since they probe the couplings of the top quark to gauge bosons and other quarks, and because ''the top quark is the only quark with reasonable mass'' 3) . Because the top quark is the only quark with mass comparable to the electroweak scale, its decays, particularly non-standard decays, might shed some light on what makes the top quark different from lighter quarks, and the role it plays in electroweak symmetry breaking. This paper describes some recent measurements on the decay of the top quark using the CDF detector, a general purpose detector designed to study p bar p collisions at √s=1.8 TeV; it has been described in detail elsewhere 4,1) . The analyses presented use 100-110 pb- 1 of data collected between 1992 and 1995 at the Fermilab TeVatron

Architecture and development of the CDF hardware event builder

International Nuclear Information System (INIS)

Shaw, T.M.; Booth, A.W.; Bowden, M.

1989-01-01

A hardware Event Builder (EVB) has been developed for use at the Collider Detector experiment at Fermi National Accelerator (CDF). the Event builder presently consists of five FASTBUS modules and has the task of reading out the front end scanners, reformatting the data into YBOS bank structure, and transmitting the data to a Level 3 (L3) trigger system which is composed of multiple VME processing nodes. The Event Builder receives its instructions from a VAX based Buffer Manager (BFM) program via a Unibus Processor Interface (UPI). The Buffer Manager instructs the Event Builder to read out one of the four CDF front end buffers. The Event Builder then informs the Buffer Manager when the event has been formatted and then is instructed to push it up to the L3 trigger system. Once in the L3 system, a decision is made as to whether to write the event to tape

Gene therapy for C-26 colon cancer using heparin-polyethyleneimine nanoparticle-mediated survivin T34A

Directory of Open Access Journals (Sweden)

Zhang L

2011-10-01

Full Text Available Ling Zhang1,*, Xiang Gao1,2,*, Ke Men1, BiLan Wang1, Shuang Zhang1, Jinfeng Qiu1, Meijuan Huang1, MaLing Gou1, Ning Huang2, ZhiYong Qian1, Xia Zhao1, YuQuan Wei11State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, 2Department of Pathophysiology, College of Preclinical and Forensic Medical Sciences, Sichuan University, Chengdu, People’s Republic of China*These authors contributed equally to this workBackground: Gene therapy provides a novel method for the prevention and treatment of cancer, but the clinical application of gene therapy is restricted, mainly because of the absence of an efficient and safe gene delivery system. Recently, we developed a novel nonviral gene carrier, ie, heparin-polyethyleneimine (HPEI nanoparticles for this purpose.Methods and results: HPEI nanoparticles were used to deliver plasmid-expressing mouse survivin-T34A (ms-T34A to treat C-26 carcinoma in vitro and in vivo. According to the in vitro studies, HPEI nanoparticles could efficiently transfect the pGFP report gene into C-26 cells, with a transfection efficiency of 30.5% ± 2%. Moreover, HPEI nanoparticle-mediated ms-T34A could efficiently inhibit the proliferation of C-26 cells by induction of apoptosis in vitro. Based on the in vivo studies, HPEI nanoparticles could transfect the Lac-Z report gene into C-26 cells in vivo. Intratumoral injection of HPEI nanoparticle-mediated ms-T34A significantly inhibited growth of subcutaneous C-26 carcinoma in vivo by induction of apoptosis and inhibition of angiogenesis.Conclusion: This research suggests that HPEI nanoparticle-mediated ms-T34A may have a promising role in C-26 colon carcinoma therapy.Keywords: gene therapy, mouse survivin-T34A, colon cancer, polyethyleneimine, nanoparticles, cancer therapy

Performance and system flexibility of the CDF Hardware Event Builder

Energy Technology Data Exchange (ETDEWEB)

Shaw, T.M.; Schurecht, K. (Fermi National Accelerator Lab., Batavia, IL (United States)); Sinervo, P. (Toronto Univ., ON (Canada). Dept. of Physics)

1991-11-01

The CDF Hardware Event Builder (1) is a flexible system which is built from a combination of three different 68020-based single width Fastbus modules. The system may contain as few as three boards or as many as fifteen, depending on the specific application. Functionally, the boards receive a command to read out the raw event data from a set of Fastbus based data buffers ( scanners''), reformat data and then write the data to a Level 3 trigger/processing farm which will decide to throw the event away or to write it to tape. The data acquisition system at CDF will utilize two nine board systems which will allow an event rate of up to 35 Hz into the Level 3 trigger. This paper will present detailed performance factors, system and individual board architecture, and possible system configurations.

Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis.

Directory of Open Access Journals (Sweden)

Xinan Yang

Full Text Available Identification and characterization of crucial gene target(s that will allow focused therapeutics development remains a challenge. We have interrogated the putative therapeutic targets associated with the transcription factor Grainy head-like 2 (GRHL2, a critical epithelial regulatory factor. We demonstrate the possibility to define the molecular functions of critical genes in terms of their personalized expression profiles, allowing appropriate functional conclusions to be derived. A novel methodology, relative expression analysis with gene-set pairs (RXA-GSP, is designed to explore the potential clinical utility of cancer-biology discovery. Observing that Grhl2-overexpression leads to increased metastatic potential in vitro, we established a model assuming Grhl2-induced or -inhibited genes confer poor or favorable prognosis respectively for cancer metastasis. Training on public gene expression profiles of 995 breast cancer patients, this method prioritized one gene-set pair (GRHL2, CDH2, FN1, CITED2, MKI67 versus CTNNB1 and CTNNA3 from all 2717 possible gene-set pairs (GSPs. The identified GSP significantly dichotomized 295 independent patients for metastasis-free survival (log-rank tested p = 0.002; severe empirical p = 0.035. It also showed evidence of clinical prognostication in another independent 388 patients collected from three studies (log-rank tested p = 3.3e-6. This GSP is independent of most traditional prognostic indicators, and is only significantly associated with the histological grade of breast cancer (p = 0.0017, a GRHL2-associated clinical character (p = 6.8e-6, Spearman correlation, suggesting that this GSP is reflective of GRHL2-mediated events. Furthermore, a literature review indicates the therapeutic potential of the identified genes. This research demonstrates a novel strategy to integrate both biological experiments and clinical gene expression profiles for extracting and elucidating the genomic

Identification of certain cancer-mediating genes using Gaussian ...

Indian Academy of Sciences (India)

2015-09-29

Sep 29, 2015 ... mance of GFI is compared with 19 exiting cluster validity indices. The results .... Using k-means algorithm on human lung expression data, we have found ... of possible genes that mediate the development of a cancer. In other ...

Lifetime of B hadrons from CDF

International Nuclear Information System (INIS)

Miao, Ting.

1996-08-01

A review of the lifetimes of B hadrons measured by the CDF collaboration at Fermilab is presented. The data corresponds to 110 pb -1 of p anti p collisions at √s = 1.8 TeV. The inclusive B hadron lifetime is measured using a high statistics sample of B → J/ΨΧ decays. Species specific lifetimes of the B + , B 0 , B 0 s , and Λ 0 b are determined using both fully reconstructed decays and partially reconstructed decays consisting of a lepton associated with a charm hadron

Searching for new physics at CDF

Energy Technology Data Exchange (ETDEWEB)

Shreyber, Irina; /Moscow, ITEP

2006-11-01

We present recent results on searches for physics beyond the Standard Model obtained from the analysis of 1 fb{sup -1} of data collected at the Tevatron Collider by the CDF Collaboration. We report on model-independent studies for anomalous production of {ell}{gamma} + X, {ell}{gamma}bE{sub T} and {gamma}{gamma} + E{sub T}, Standard Model t{bar t}{gamma} production. We also present results for the Randall-Sundrum Gravitons, the same-sign dileptons and the trileptons searches. No significant excess of data over the predicted background is observed.

Charm and beauty production at CDF

Energy Technology Data Exchange (ETDEWEB)

Bishai, M.; /Brookhaven

2005-01-01

Using the data samples collected with the CDF Run II detector during 2002 and early 2003, new measurements of the production cross sections of charm and beauty hadrons at {radical}s = 1960 GeV are presented. New measurements of the cross sections of centrally produced b-hadrons and J/{psi} mesons down to zero transverse momenta have been carried out. The large charm signals made available by the silicon vertex track trigger have enabled the measurement of the cross sections of D{sup 0}, D*, D{sup {+-}}, and D{sub s} mesons.

Environmental factors influencing gene transfer agent (GTA mediated transduction in the subtropical ocean.

Directory of Open Access Journals (Sweden)

Lauren D McDaniel

Full Text Available Microbial genomic sequence analyses have indicated widespread horizontal gene transfer (HGT. However, an adequate mechanism accounting for the ubiquity of HGT has been lacking. Recently, high frequencies of interspecific gene transfer have been documented, catalyzed by Gene Transfer Agents (GTAs of marine α-Proteobacteria. It has been proposed that the presence of bacterial genes in highly purified viral metagenomes may be due to GTAs. However, factors influencing GTA-mediated gene transfer in the environment have not yet been determined. Several genomically sequenced strains containing complete GTA sequences similar to Rhodobacter capsulatus (RcGTA, type strain were screened to ascertain if they produced putative GTAs, and at what abundance. Five of nine marine strains screened to date spontaneously produced virus-like particles (VLP's in stationary phase. Three of these strains have demonstrated gene transfer activity, two of which were documented by this lab. These two strains Roseovarius nubinhibens ISM and Nitratireductor 44B9s, were utilized to produce GTAs designated RnGTA and NrGTA and gene transfer activity was verified in culture. Cell-free preparations of purified RnGTA and NrGTA particles from marked donor strains were incubated with natural microbial assemblages to determine the level of GTA-mediated gene transfer. In conjunction, several ambient environmental parameters were measured including lysogeny indicated by prophage induction. GTA production in culture systems indicated that approximately half of the strains produced GTA-like particles and maximal GTA counts ranged from 10-30% of host abundance. Modeling of GTA-mediated gene transfer frequencies in natural samples, along with other measured environmental variables, indicated a strong relationship between GTA mediated gene transfer and the combined factors of salinity, multiplicity of infection (MOI and ambient bacterial abundance. These results indicate that GTA-mediated

Enhancing the CDF's B physics program with a faster data acquisition system.

Energy Technology Data Exchange (ETDEWEB)

Dr. Petar Maksimovic

2011-03-02

The physics program of Run II at the Tevatron includes precision electroweak measurements such as the determination of the top quark and W boson masses; bottom and charm physics including the determination of the B{sub s} and D{sup 0} mixing parameters; studies of the strong interaction; and searches for the Higgs particle, supersymmetric particles, hidden space-time dimensions and quark substructure. All of these measurements benefit from a high-resolution tracking detector. Most of them rely heavily on the efficient identification of heavy flavored B hadrons by detection of displaced secondary vertices, and are enhanced by the capability to trigger on tracks not coming from the primary vertex. This is uniquely provided by CDF's finely-segmented silicon detectors surrounding the interaction region. Thus CDF experiment's physics potential critically depends on the performance of its silicon detectors. The CDF silicon detectors were designed to operate up to 2-3 fb{sup -1} of accumulated pji collisions, with an upgrade planned thereafter. However, the upgrade project was canceled in 2003 and Run II has been extended through 2011, with an expected total delivered integrated luminosity of 12 fb{sup -1} or more. Several preventive measures were taken to keep the original detector operational and maintain its performance. The most important of these are the decrease in the operating temperature of the detector, which reduces the impact of radiation exposure, and measures to minimize damage due to integrated radiation dose, thermal cycles, and wire bond resonance conditions. Despite these measures the detectors operating conditions continue to change with issues arising from radiation damage to the sensors, aging infrastructure and electronics. These, together with the basic challenges posed by the inaccessibility of the detector volume and large number (about 750 thousand) of readout channels, make the silicon detector operations the single most complex and

The Mediator subunit SFR6/MED16 controls defence gene expression mediated by salicylic acid and jasmonate responsive pathways.

Science.gov (United States)

Wathugala, Deepthi L; Hemsley, Piers A; Moffat, Caroline S; Cremelie, Pieter; Knight, Marc R; Knight, Heather

2012-07-01

• Arabidopsis SENSITIVE TO FREEZING6 (SFR6) controls cold- and drought-inducible gene expression and freezing- and osmotic-stress tolerance. Its identification as a component of the MEDIATOR transcriptional co-activator complex led us to address its involvement in other transcriptional responses. • Gene expression responses to Pseudomonas syringae, ultraviolet-C (UV-C) irradiation, salicylic acid (SA) and jasmonic acid (JA) were investigated in three sfr6 mutant alleles by quantitative real-time PCR and susceptibility to UV-C irradiation and Pseudomonas infection were assessed. • sfr6 mutants were more susceptible to both Pseudomonas syringae infection and UV-C irradiation. They exhibited correspondingly weaker PR (pathogenesis-related) gene expression than wild-type Arabidopsis following these treatments or after direct application of SA, involved in response to both UV-C and Pseudomonas infection. Other genes, however, were induced normally in the mutants by these treatments. sfr6 mutants were severely defective in expression of plant defensin genes in response to JA; ectopic expression of defensin genes was provoked in wild-type but not sfr6 by overexpression of ERF5. • SFR6/MED16 controls both SA- and JA-mediated defence gene expression and is necessary for tolerance of Pseudomonas syringae infection and UV-C irradiation. It is not, however, a universal regulator of stress gene transcription and is likely to mediate transcriptional activation of specific regulons only. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Field distribution and DNA transport in solid tumors during electric field-mediated gene delivery.

Science.gov (United States)

Henshaw, Joshua W; Yuan, Fan

2008-02-01

Gene therapy has a great potential in cancer treatment. However, the efficacy of cancer gene therapy is currently limited by the lack of a safe and efficient means to deliver therapeutic genes into the nucleus of tumor cells. One method under investigation for improving local gene delivery is based on the use of pulsed electric field. Despite repeated demonstration of its effectiveness in vivo, the underlying mechanisms behind electric field-mediated gene delivery remain largely unknown. Without a thorough understanding of these mechanisms, it will be difficult to further advance the gene delivery. In this review, the electric field-mediated gene delivery in solid tumors will be examined by following individual transport processes that must occur in vivo for a successful gene transfer. The topics of examination include: (i) major barriers for gene delivery in the body, (ii) distribution of electric fields at both cell and tissue levels during the application of external fields, and (iii) electric field-induced transport of genes across each of the barriers. Through this approach, the review summarizes what is known about the mechanisms behind electric field-mediated gene delivery and what require further investigations in future studies.

Adaptor Protein Complex 2 (AP-2) Mediated, Clathrin Dependent Endocytosis, And Related Gene Activities, Are A Prominent Feature During Maturation Stage Amelogenesis

Science.gov (United States)

LACRUZ, Rodrigo S.; BROOKES, Steven J.; WEN, Xin; JIMENEZ, Jaime M.; VIKMAN, Susanna; HU, Ping; WHITE, Shane N.; LYNGSTADAAS, S. Petter; OKAMOTO, Curtis T.; SMITH, Charles E.; PAINE, Michael L.

2012-01-01

Molecular events defining enamel matrix removal during amelogenesis are poorly understood. Early reports have suggested that adaptor proteins (AP) participate in ameloblast-mediated endocytosis. Enamel formation involves the secretory and maturation stages, with an increase in resorptive function during the latter. Here, using real time PCR, we show that the expression of clathrin and adaptor protein subunits are up-regulated in maturation stage rodent enamel organ cells. AP-2 is the most up-regulated of the four distinct adaptor protein complexes. Immunolocalization confirms the presence of AP-2 and clathrin in ameloblasts with strongest reactivity at the apical pole. These data suggest that the resorptive functions of enamel cells involve AP-2 mediated, clathrin dependent endocytosis, thus implying the likelihood of a specific membrane-bound receptor(s) of enamel matrix protein debris. The mRNA expression of other endocytosis-related gene products is also up-regulated during maturation including: lysosomal-associated membrane protein 1 (Lamp1), cluster of differentiation 63 and 68 (Cd63 and Cd68), ATPase, H+ transporting, lysosomal V0 subunit D2 (Atp6v0d2), ATPase, H+ transporting, lysosomal V1 subunit B2 (Atp6v1b2), chloride channel, voltage-sensitive 7 (Clcn7) and cathepsin K (Ctsk). Immunohistological data confirms the expression of a number of these proteins in maturation stage ameloblasts. The enamel of Cd63-null mice was also examined. Despite increased mRNA and protein expression in the enamel organ during maturation, the enamel of Cd63-null mice appeared normal. This may suggest inherent functional redundancies between Cd63 and related gene products, such as Lamp1 and Cd68. Ameloblast-like LS8 cells treated with the enamel matrix protein complex Emdogain® showed up-regulation of AP-2 and clathrin subunits, further supporting the existence of a membrane-bound receptor regulated pathway for the endocytosis of enamel matrix proteins. These data together

A study of tau decays of the W boson at CDF [Collider Detector at Fermilab

International Nuclear Information System (INIS)

Gladney, L.D.

1990-01-01

A report is given of a search for tau decays of the W boson in p bar p collisions at √s = 1.8 TeV using the Collider Detector at Fermilab (CDF). A description of a hardware trigger specifically designed to enhance the number of events with tau decays is presented along with the results of a preliminary analysis of data taken during the 1988--89 run of CDF. 10 refs., 4 figs

PHOX2B-mediated regulation of ALK expression: in vitro identification of a functional relationship between two genes involved in neuroblastoma.

Directory of Open Access Journals (Sweden)

Tiziana Bachetti

Full Text Available BACKGROUND: Neuroblastoma (NB is a severe pediatric tumor originating from neural crest derivatives and accounting for 15% of childhood cancer mortality. The heterogeneous and complex genetic etiology has been confirmed with the identification of mutations in two genes, encoding for the receptor tyrosine kinase Anaplastic Lymphoma Kinase (ALK and the transcription factor Paired-like Homeobox 2B (PHOX2B, in a limited proportion of NB patients. Interestingly, these two genes are overexpressed in the great majority of primary NB samples and cell lines. These observations led us to test the hypothesis of a regulatory or functional relationship between ALK and PHOX2B underlying NB pathogenesis. METHODOLOGY/PRINCIPAL FINDINGS: Following this possibility, we first confirmed a striking correlation between the transcription levels of ALK, PHOX2B and its direct target PHOX2A in a panel of NB cell lines. Then, we manipulated their expression in NB cell lines by siRNA-mediated knock-down and forced over-expression of each gene under analysis. Surprisingly, PHOX2B- and PHOX2A-directed siRNAs efficiently downregulated each other as well as ALK gene and, consistently, the enhanced expression of PHOX2B in NB cells yielded an increment of ALK protein. We finally demonstrated that PHOX2B drives ALK gene transcription by directly binding its promoter, which therefore represents a novel PHOX2B target. CONCLUSIONS/SIGNIFICANCE: These findings provide a compelling explanation of the concurrent involvement of these two genes in NB pathogenesis and are going to foster a better understanding of molecular interactions at the base of the disease. Moreover, this work opens new perspectives for NBs refractory to conventional therapies that may benefit from the design of novel therapeutic RNAi-based approaches for multiple gene targets.

Study of Exclusive Final States at CDF

International Nuclear Information System (INIS)

Pinfold, James

2008-01-01

We present the current status of the searches, using the CDF detector at the Tevatron, for the exclusive processes: pp-bar →p(e + e - )p-bar and pp-bar →p(μ + μ - )p-bar , produced via two photon interactions; pp-bar →p(γγ)p-bar and pp-bar →p(J/ψ+γ)p-bar , from double pomeron exchange; and, pp-bar →p(J/ψ(→μ + μ - ))p-bar ; from photon-pomeron fusion

Phosphatidylinositol 3-kinase is essential for kit ligand-mediated survival, whereas interleukin-3 and flt3 ligand induce expression of antiapoptotic Bcl-2 family genes

DEFF Research Database (Denmark)

Karlsson, Richard; Engström, Maria; Jönsson, Maria

2003-01-01

Cytokines such as interleukin 3 (IL-3), kit ligand (KL), and flt3 ligand (FL) promote survival of hematopoietic stem cells and myeloid progenitor cells. In many cell types, members of the Bcl-2 gene family are major regulators of survival, but the mediating mechanisms are not fully understood....... Using two myeloid progenitor cell lines, FDCP-mix and FDC-P1, as well as primary mouse bone marrow progenitors, we demonstrate that KL-mediated survival is dependent on the activation of phosphatidylinositol-3 (PI-3) kinase. The inhibitor LY294002 was able to completely abolish survival mediated by KL...

Software development tools for the CDF MX scanner

Energy Technology Data Exchange (ETDEWEB)

Stuermer, W.; Turner, K.; Littleton-Sestini, S.

1991-11-01

This paper discuses the design of the high level assembler and diagnostic control program developed for the MX, a high speed, custom designed computer used in the CDF data acquisition system at Fermilab. These programs provide a friendly productive environment for the development of software on the MX. Details of their implementation and special features, and some of the lessons learned during their development are included.

Software development tools for the CDF MX scanner

International Nuclear Information System (INIS)

Stuermer, W.; Turner, K.; Littleton-Sestini, S.

1991-11-01

This paper discuses the design of the high level assembler and diagnostic control program developed for the MX, a high speed, custom designed computer used in the CDF data acquisition system at Fermilab. These programs provide a friendly productive environment for the development of software on the MX. Details of their implementation and special features, and some of the lessons learned during their development are included

Cholecystokinin-2 receptor mediated gene expression in neuronal PC12 cells

DEFF Research Database (Denmark)

Hansen, Thomas v O; Borup, Rehannah; Marstrand, Troels

2007-01-01

could be identified. Comparison with forskolin- and nerve growth factor (NGF)-treated PC12 cells showed that CCK induced a separate set of target genes. Taken together, we propose that neuronal CCK may have a role in the regulation of the circadian rhythm, the metabolism of cerebral cholesterol...... of neuronal CCK are incompletely understood. To identify genes regulated by neuronal CCK, we generated neuronal PC12 cells stably expressing the CCK-2 receptor (CCK-2R) and treated the cells with sulphated CCK-8 for 2-16 h, before the global expression profile was examined. The changes in gene expression...... peaked after 2 h, with 67 differentially expressed transcripts identified. A pathway analysis indicated that CCK was implicated in the regulation of the circadian clock system, the plasminogen system and cholesterol metabolism. But transcripts encoding proteins involved in dopamine signaling, ornithine...

hTERT promoter mediating gene therapy in laryngeal squamous carcinomas cells in vitro

International Nuclear Information System (INIS)

Liao Zhengkai; Zhou Yunfeng; Zhou Fuxiang; Luo Zhiguo; Xiong Jie; Bao Jie; Xie Conghua; Liu Shiquan

2007-01-01

Objective: To investigate the relationship among hTERT promoter activity, hTERT mRNA expression, and telomerase activity (TA) in laryngeal squamous carcinomas cell lines, and to evaluate the usefulness of hTERT promoter mediated gene therapy. Methods: After plasmids pGL3-hTERTp were transfected, hTEBT promoter activity, hTERT mRNA expression and TA were determined by luciferase assay, RT-PCR and TRAP-PCR-ELISA, respectively. Plasmid phTERTp-HRP was constructed and transfected, HRP expression was determined by RT-PCR and competent peroxidase activity was confirmed by enzyme activity assay. The cytotoxicity and radiosensitivity of phTERTp-HRP/IAA were determined by clonogenic assay. Results: The relative levels of hTERT promoter activity, hTERT mRNA expression and TA in Hep2R cells were 1.37-fold, 1.43-fold and 1.81-fold compared with Hep2R cells, hTERT promoter activity was closely associated with hTERT mRNA expression and TA levels (P SF 2 ) was 1.24 (Hep2R cells) and 1.20 (Hep 2cells), the parameter a of with or without IAA incubation were 0.090, 0.020 (Hep2R)and 0.099, 0.042 (Hep2). Conclusions: hTERT promoter is applicable in mediating gene therapy in different radiosensitive laryngeal squamous carcinomas cells. hTERTp-HRP/IAA gene therapy may be a promising supplementary method for radiotherapy of laryngeal squamous-cell carcinomas. (authors)

v-src induction of the TIS10/PGS2 prostaglandin synthase gene is mediated by an ATF/CRE transcription response element.

OpenAIRE

Xie, W; Fletcher, B S; Andersen, R D; Herschman, H R

1994-01-01

We recently reported the cloning of a mitogen-inducible prostaglandin synthase gene, TIS10/PGS2. In addition to growth factors and tumor promoters, the v-src oncogene induces TIS10/PGS2 expression in 3T3 cells. Deletion analysis, using luciferase reporters, identifies a region between -80 and -40 nucleotides 5' of the TIS10/PGS2 transcription start site that mediates pp60v-src induction in 3T3 cells. This region contains the sequence CGTCACGTG, which includes overlapping ATF/CRE (CGTCA) and E...

Bifidobacterial recombinant thymidine kinase-ganciclovir gene therapy system induces FasL and TNFR2 mediated antitumor apoptosis in solid tumors

International Nuclear Information System (INIS)

Wang, Changdong; Ma, Yongping; Hu, Qiongwen; Xie, Tingting; Wu, Jiayan; Zeng, Fan; Song, Fangzhou

2016-01-01

Directly targeting therapeutic suicide gene to a solid tumor is a hopeful approach for cancer gene therapy. Treatment of a solid tumor by an effective vector for a suicide gene remains a challenge. Given the lack of effective treatments, we constructed a bifidobacterial recombinant thymidine kinase (BF-rTK) -ganciclovir (GCV) targeting system (BKV) to meet this requirement and to explore antitumor mechanisms. Bifidobacterium (BF) or BF-rTK was injected intratumorally with or without ganciclovir in a human colo320 intestinal xenograft tumor model. The tumor tissues were analyzed using apoptosis antibody arrays, real time PCR and western blot. The colo320 cell was analyzed by the gene silencing method. Autophagy and necroptosis were also detected in colo320 cell. Meanwhile, three human digestive system xenograft tumor models (colorectal cancer colo320, gastric cancer MKN-45 and liver cancer SSMC-7721) and a breast cancer (MDA-MB-231) model were employed to validate the universality of BF-rTK + GCV in solid tumor gene therapy. The survival rate was evaluated in three human cancer models after the BF-rTK + GCV intratumor treatment. The analysis of inflammatory markers (TNF-α) in tumor indicated that BF-rTK + GCV significantly inhibited TNF-α expression. The results suggested that BF-rTK + GCV induced tumor apoptosis without autophagy and necroptosis occurrence. The apoptosis was transduced by multiple signaling pathways mediated by FasL and TNFR2 and mainly activated the mitochondrial control of apoptosis via Bid and Bim, which was rescued by silencing Bid or/and Bim. However, BF + GCV only induced apoptosis via Fas/FasL signal pathway accompanied with increased P53 expression. We further found that BF-rTK + GCV inhibited the expression of the inflammatory maker of TNF-α. However, BF-rTK + GCV did not result in necroptosis and autophagy. BF-rTK + GCV induced tumor apoptosis mediated by FasL and TNFR2 through the mitochondrial control of apoptosis via Bid and Bim

Measurement of low $p_{T}$ $D^{0}$ meson production cross section at CDF II

Energy Technology Data Exchange (ETDEWEB)

Mussini, Manuel [Univ. of Bologna (Italy)

2011-05-01

In this thesis we present a study of the production of D⁰ meson in the low transverse momentum region. In particular the inclusive differential production cross section of the D⁰ meson (in the two-body decay channel D⁰ → K^-π⁺) is obtained extending the published CDF II measurement to p_T as low as 1.5 GeV/c. This study is performed at the Tevatron Collider at Fermilab with the CDF II detector.

Depletion of Mediator Kinase Module Subunits Represses Superenhancer-Associated Genes in Colon Cancer Cells.

Science.gov (United States)

Kuuluvainen, Emilia; Domènech-Moreno, Eva; Niemelä, Elina H; Mäkelä, Tomi P

2018-06-01

In cancer, oncogene activation is partly mediated by acquired superenhancers, which therefore represent potential targets for inhibition. Superenhancers are enriched for BRD4 and Mediator, and both BRD4 and the Mediator MED12 subunit are disproportionally required for expression of superenhancer-associated genes in stem cells. Here we show that depletion of Mediator kinase module subunit MED12 or MED13 together with MED13L can be used to reduce expression of cancer-acquired superenhancer genes, such as the MYC gene, in colon cancer cells, with a concomitant decrease in proliferation. Whereas depletion of MED12 or MED13/MED13L caused a disproportional decrease of superenhancer gene expression, this was not seen with depletion of the kinases cyclin-dependent kinase 9 (CDK8) and CDK19. MED12-MED13/MED13L-dependent superenhancer genes were coregulated by β-catenin, which has previously been shown to associate with MED12. Importantly, β-catenin depletion caused reduced binding of MED12 at the MYC superenhancer. The effect of MED12 or MED13/MED13L depletion on cancer-acquired superenhancer gene expression was more specific than and partially distinct from that of BRD4 depletion, with the most efficient inhibition seen with combined targeting. These results identify a requirement of MED12 and MED13/MED13L for expression of acquired superenhancer genes in colon cancer, implicating these Mediator subunits as potential therapeutic targets for colon cancer, alone or together with BRD4. Copyright © 2018 American Society for Microbiology.

Beauty production at CDF

International Nuclear Information System (INIS)

Shears, Tara

2008-01-01

A review of recent measurements of beauty production, based on proton antiproton collision data at √s = 1.96 TeV and using the CDF detector, is given. Previous measurements of beauty (b) quark production at the Tevatron, carried out at centre-of-mass energies √s = 1.8 TeV, have shown discrepancies when compared to Next to Leading Order (NLO) predictions [1]. Improved predictions and experimental procedures have reduced this discrepancy [2]. Improved parton density functions, better fragmentation functions and more complete theoretical calculations have improved theoretical accuracy. Experimentally, measurements of beauty production at √s = 1.96 TeV are now presented in terms of b hadrons or B mesons, to avoid problems unfolding back to the quark level. In this review [3] measurements of inclusive beauty (where one beauty jet or hadron is reconstructed in the event), and beauty + X (where X can be a boson or another beauty jet or hadron), production will be presented: inclusive beauty jet cross-section; semi and fully reconstructed B meson cross-section; beauty dijet cross-section; semi-reconstructed B B meson cross-section; Z boson + beauty jet cross-section. More information concerning other measurements of heavy quark production can be found elsewhere [4

Jet studies at CDF/D0 collaborations

International Nuclear Information System (INIS)

Bartalini, P.

1994-01-01

Both CDF and D0 collaboration measure inclusive jet cross section, energy flow and observe color coherence effects in p-barp collisions at √s 1800 GeV. The results on new compositeness limit using inclusive jet cross section and energy flow within a jet are described. Data are in good agreement with next to leading order QCD calculations. Color coherence effects are demonstrated by measuring spatial correlations between soft and leading jets in multi jet events. (author). 14 refs., 3 figs

Recombinant adenovirus-mediated gene transfer suppresses experimental arthritis

Directory of Open Access Journals (Sweden)

E. Quattrocchi

2011-09-01

Full Text Available Collagen Induced Arthritis (CIA is a widely studied animal model to develop and test novel therapeutic approaches for treating Rheumatoid Arthritis (RA in humans. Soluble Cytotoxic T-Lymphocyte Antigen 4 (CTLA4-Ig, which binds B7 molecule on antigen presenting cells and blocks CD28 mediated T-lymphocyte activation, has been shown to ameliorate experimental autoimmune diseases such as lupus, diabetes and CIA. Objective of our research was to investigate in vivo the effectiveness of blocking the B7/CD28 T-lymphocyte co-stimulatory pathway, utilizing a gene transfer technology, as a therapeutic strategy against CIA. Replication-deficient adenoviruses encoding a chimeric CTLA4-Ig fusion protein, or β-galactosidase as control, have been injected intravenously once at arthritis onset. Disease activity has been monitored by the assessment of clinical score, paw thickness and type II collagen (CII specific cellular and humoral immune responses for 21 days. The adenovirally delivered CTLA4-Ig fusion protein at a dose of 2×108 pfu suppressed established CIA, whereas the control β-galactosidase did not significantly affect the disease course. CII-specific lymphocyte proliferation, IFNg production and anti-CII antibodies were significantly reduced by CTLA4-Ig treatment. Our results demonstrate that blockade of the B7/CD28 co-stimulatory pathway by adenovirus-mediated CTLA4-Ig gene transfer is effective in treating established CIA suggesting its potential in treating RA.

Tyrosine kinase chromosomal translocations mediate distinct and overlapping gene regulation events

International Nuclear Information System (INIS)

Kim, Hani; Gillis, Lisa C; Jarvis, Jordan D; Yang, Stuart; Huang, Kai; Der, Sandy; Barber, Dwayne L

2011-01-01

Leukemia is a heterogeneous disease commonly associated with recurrent chromosomal translocations that involve tyrosine kinases including BCR-ABL, TEL-PDGFRB and TEL-JAK2. Most studies on the activated tyrosine kinases have focused on proximal signaling events, but little is known about gene transcription regulated by these fusions. Oligonucleotide microarray was performed to compare mRNA changes attributable to BCR-ABL, TEL-PDGFRB and TEL-JAK2 after 1 week of activation of each fusion in Ba/F3 cell lines. Imatinib was used to control the activation of BCR-ABL and TEL-PDGFRB, and TEL-JAK2-mediated gene expression was examined 1 week after Ba/F3-TEL-JAK2 cells were switched to factor-independent conditions. Microarray analysis revealed between 800 to 2000 genes induced or suppressed by two-fold or greater by each tyrosine kinase, with a subset of these genes commonly induced or suppressed among the three fusions. Validation by Quantitative PCR confirmed that eight genes (Dok2, Mrvi1, Isg20, Id1, gp49b, Cxcl10, Scinderin, and collagen Vα1(Col5a1)) displayed an overlapping regulation among the three tested fusion proteins. Stat1 and Gbp1 were induced uniquely by TEL-PDGFRB. Our results suggest that BCR-ABL, TEL-PDGFRB and TEL-JAK2 regulate distinct and overlapping gene transcription profiles. Many of the genes identified are known to be involved in processes associated with leukemogenesis, including cell migration, proliferation and differentiation. This study offers the basis for further work that could lead to an understanding of the specificity of diseases caused by these three chromosomal translocations

Numerical Modeling of Wave Overtopping of Buffalo Harbor Confined Disposal Facility (CDF4)

Science.gov (United States)

2017-10-01

navigation channel , and harbor complex. Though there are anecdotal claims and debris indicating possible sediment movement, there has been no evidence of...littoral sediments inside the disposal area, into the channel and harbor, and other adjacent areas to the CDF4. 1.4 Study plan 1.4.1 Purpose There...locations. 2.4 Maintenance dredging data The need for maintenance dredging arises from sedimentation in the navigation channels , which impedes

Regulation of DNA Damage Response by Estrogen Receptor β-Mediated Inhibition of Breast Cancer Associated Gene 2

Directory of Open Access Journals (Sweden)

Yuan-Hao Lee

2015-04-01

Full Text Available Accumulating evidence suggests that ubiquitin E3 ligases are involved in cancer development as their mutations correlate with genomic instability and genetic susceptibility to cancer. Despite significant findings of cancer-driving mutations in the BRCA1 gene, estrogen receptor (ER-positive breast cancers progress upon treatment with DNA damaging-cytotoxic therapies. In order to understand the underlying mechanism by which ER-positive breast cancer cells develop resistance to DNA damaging agents, we employed an estrogen receptor agonist, Erb-041, to increase the activity of ERβ and negatively regulate the expression and function of the estrogen receptor α (ERα in MCF-7 breast cancer cells. Upon Erb-041-mediated ERα down-regulation, the transcription of an ERα downstream effector, BCA2 (Breast Cancer Associated gene 2, correspondingly decreased. The ubiquitination of chromatin-bound BCA2 was induced by ultraviolet C (UVC irradiation but suppressed by Erb-041 pretreatment, resulting in a blunted DNA damage response. Upon BCA2 silencing, DNA double-stranded breaks increased with Rad51 up-regulation and ataxia telangiectasia mutated (ATM activation. Mechanistically, UV-induced BCA2 ubiquitination and chromatin binding were found to promote DNA damage response and repair via the interaction of BCA2 with ATM, γH2AX and Rad51. Taken together, this study suggests that Erb-041 potentiates BCA2 dissociation from chromatin and co-localization with Rad51, resulting in inhibition of homologous recombination repair.

DMPD: Signalling pathways mediating type I interferon gene expression. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 17904888 Signalling pathways mediating type I interferon gene expression. Edwards M...hways mediating type I interferon gene expression. PubmedID 17904888 Title Signalling pathways...R, Slater L, Johnston SL. Microbes Infect. 2007 Sep;9(11):1245-51. Epub 2007 Jul 1. (.png) (.svg) (.html) (.csml) Show Signalling pat

Hadronic final states in high -pT QCD at CDF

Energy Technology Data Exchange (ETDEWEB)

Matera, Keith [University of Illinois, Urbana-Champaign

2013-11-18

The heavy quark content of gauge boson events is of great interest to studies of QCD. These events probe the gluon and heavy-quark parton distribution functions of the proton, and also provide a measurement of the rate of final state gluon splitting to heavy flavor. In addition, gauge boson plus heavy quark events are representative of backgrounds to Higgs, single top, and supersymmetric particle searches. Recent work with the CDF II detector at the Fermilab Tevatron has measured the cross-section of several gauge boson plus heavy flavor production processes, including the first Tevatron observation of specific charm process p{p bar} → W +c. Results are found to be in agreement with NLO predictions that include an enhanced rate of g → {cc bar}/bb splitting. Lastly, a new analysis promises to probe a lower pT (c) region than has been previously explored, by fully reconstructing D* → D0(Kπ)π decays in the full CDF dataset (9.7 fb-1).

Negative regulation of RIG-I-mediated antiviral signaling by TRK-fused gene (TFG) protein

International Nuclear Information System (INIS)

Lee, Na-Rae; Shin, Han-Bo; Kim, Hye-In; Choi, Myung-Soo; Inn, Kyung-Soo

2013-01-01

Highlights: •TRK-fused gene product (TFG) interacts with TRIM25 upon viral infection. •TFG negatively regulates RIG-I mediated antiviral signaling. •TFG depletion leads to enhanced viral replication. •TFG act downstream of MAVS. -- Abstract: RIG-I (retinoic acid inducible gene I)-mediated antiviral signaling serves as the first line of defense against viral infection. Upon detection of viral RNA, RIG-I undergoes TRIM25 (tripartite motif protein 25)-mediated K63-linked ubiquitination, leading to type I interferon (IFN) production. In this study, we demonstrate that TRK-fused gene (TFG) protein, previously identified as a TRIM25-interacting protein, binds TRIM25 upon virus infection and negatively regulates RIG-I-mediated type-I IFN signaling. RIG-I-mediated IFN production and nuclear factor (NF)-κB signaling pathways were upregulated by the suppression of TFG expression. Furthermore, vesicular stomatitis virus (VSV) replication was significantly inhibited by small inhibitory hairpin RNA (shRNA)-mediated knockdown of TFG, supporting the suppressive role of TFG in RIG-I-mediated antiviral signaling. Interestingly, suppression of TFG expression increased not only RIG-I-mediated signaling but also MAVS (mitochondrial antiviral signaling protein)-induced signaling, suggesting that TFG plays a pivotal role in negative regulation of RNA-sensing, RIG-I-like receptor (RLR) family signaling pathways

Search for high-mass resonances decaying to dimuons at CDF.

Science.gov (United States)

Aaltonen, T; Adelman, J; Akimoto, T; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burke, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cordelli, M; Cortiana, G; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'Orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heijboer, A; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Hussein, M; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, E; Lee, H S; Lee, S W; Leone, S; Lewis, J D; Lin, C-S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lucchesi, D; Luci, C; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlok, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Pagan Griso, S; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Würthwein, F; Wynne, S M; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zhang, X; Zheng, Y; Zucchelli, S

2009-03-06

We present a search for high-mass neutral resonances using dimuon data corresponding to an integrated luminosity of 2.3 fb(-1) collected in pp[over ] collisions at sqrt[s]=1.96 TeV by the CDF II detector at the Fermilab Tevatron. No significant excess above the standard model expectation is observed in the dimuon invariant-mass spectrum. We set 95% confidence level upper limits on sigmaBR(pp-->X-->micromicro), where X is a boson with spin-0, 1, or 2. Using these cross section limits, we determine lower mass limits on sneutrinos in R-parity-violating supersymmetric models, Z' bosons, and Kaluza-Klein gravitons in the Randall-Sundrum model.

Isolation, identification and in silico analysis of alpha-amylase gene of Aspergillus niger strain CSA35 obtained from cassava undergoing spoilage

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Oghenetega J. Avwioroko

2018-07-01

Full Text Available In this investigation, a gene (CDF_Amyl encoding extracellular α-amylase in Aspergillus niger strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α-amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40, respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product had a hydrophobicity score of − 0.43 but no transmembrane helix. The CDF_Amyl protein was subcellularly localized in the secretory pathway, an indication of its release into extracellular space after secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find applications in biotechnological, food and pharmaceutical industries where cloning and further modification of this gene would be required for product development and improvement.

Evidence of correlation between TGFBR2 gene expression mediated by NF-kB signaling pathways and Kawasaki disease in children.

Science.gov (United States)

Gao, Qinling; Yuan, Shuhua; Yuan, Dawei

2017-09-15

We explored the correlation between the TGFBR2 gene that is mediated by NF-kb signaling pathways and the pathogenesis of Kawasaki disease in children. In this study, 43 children with Kawasaki disease from April 2014 to January 2016 at our hospital were selected as the observation group, and 42 healthy children were selected as the control group. The mRNA expression levels of NF-kb gene and TGFBR2 gene in different groups were detected using fluorescence quantitative PCR. The protein expression levels of the NF-kb and TGFBR2 were detected using enzyme-linked immunosorbent assay (ELISA) in different groups. The expression levels of NF-kb and TGFBR2 in the observation group and the control group were detected using immunohistochemistry. Compared to the control group, the mRNA expression levels of NF-kb and TGFBR2 were 12.3 times and 27.5 times as high as those in the control group respectively and there were significant differences between the two groups (pkb and TGFBR2 in the control group (0.87±0.12, 1.25±0.18) ug/l and those in the observation group (3.27±0.17, 8.16±0.22) ug/l (pkB and TGFBR2 in children with Kawasaki disease were significantly higher than those in healthy subjects (pkB signaling pathways.

Gene expression profiling associated with angiotensin II type 2 receptor-induced apoptosis in human prostate cancer cells.

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Nana Pei

Full Text Available Increased expression of angiotensin II type 2 receptor (AT2R induces apoptosis in numerous tumor cell lines, with either Angiotensin II-dependent or Angiotensin II-independent regulation, but its molecular mechanism remains poorly understood. Here, we used PCR Array analysis to determine the gene and microRNA expression profiles in human prostate cancer cell lines transduced with AT2R recombinant adenovirus. Our results demonstrated that AT2R over expression leads to up-regulation of 6 apoptosis-related genes (TRAIL-R2, BAG3, BNIPI, HRK, Gadd45a, TP53BP2, 2 cytokine genes (IL6 and IL8 and 1 microRNA, and down-regulation of 1 apoptosis-related gene TNFSF10 and 2 cytokine genes (BMP6, BMP7 in transduced DU145 cells. HRK was identified as an up-regulated gene in AT2R-transduced PC-3 cells by real-time RT-PCR. Next, we utilized siRNAs to silence the up-regulated genes to further determine their roles on AT2R overexpression mediated apoptosis. The results showed downregulation of Gadd45a reduced the apoptotic effect by ∼30% in DU145 cells, downregulation of HRK reduced AT2R-mediated apoptosis by more than 50% in PC-3 cells, while downregulation of TRAIL-R2 enhanced AT2R-mediated apoptosis more than 4 times in DU145 cells. We also found that the effects on AT2R-mediated apoptosis caused by downregulation of Gadd45a, TRAIL-R2 and HRK were independent in activation of p38 MAPK, p44/42 MAPK and p53. Taken together, our results demonstrated that TRAIL-R2, Gadd45a and HRK may be novel target genes for further study of the mechanism of AT2R-mediated apoptosis in prostate cancer cells.

Construction of the CDF silicon vertex detector

International Nuclear Information System (INIS)

Skarha, J.; Barnett, B.; Boswell, C.; Snider, F.; Spies, A.; Tseng, J.; Vejcik, S.; Carter, H.; Flaugher, B.; Gonzales, B.; Hrycyk, M.; Nelson, C.; Segler, S.; Shaw, T.; Tkaczyk, S.; Turner, K.; Wesson, T.; Carithers, W.; Ely, R.; Haber, C.; Holland, S.; Kleinfelder, S.; Merrick, T.; Schneider, O.; Wester, W.; Wong, M.; Amidei, D.; Derwent, P.; Gold, M.; Matthews, J.; Bacchetta, N.; Bisello, D.; Busetto, G.; Castro, A.; Loreti, M.; Pescara, L.; Bedeschi, F.; Bolognesi, V.; Dell'Agnello, S.; Galeotti, S.; Mariotti, M.; Menzione, A.; Punzi, G.; Raffaelli, F.; Risotri, L.; Tartarelli, F.; Turini, N.; Wenzel, H.; Zetti, F.; Bailey, M.; Garfinkel, A.; Shaw, N.; Tipton, P.; Watts, G.

1992-04-01

Technical details and methods used in constructing the CDF silicon vertex detector are presented. This description includes a discussion of the foam-carbon fiber composite structure used to silicon microstrip detectors and the procedure for achievement of 5 μm detector alignment. The construction of the beryllium barrel structure, which houses the detector assemblies, is also described. In addition, the 10 μm placement accuracy of the detectors in the barrel structure is discussed and the detector cooling and mounting systems are described. 12 refs

Jet shapes at D0 and CDF

International Nuclear Information System (INIS)

Streets, K.T.

1995-05-01

The distribution of the transverse energy in jets has been measured in p bar p collisions at √s = 1.8 TeV at the Fermilab Tevatron collider using the CDF and DO detectors. This measurement of the jet shape is made as a function of jet transverse energy in both experiments and as a function of the jet pseudorapidity in the D0 experiment. Comparisons to Monte Carlo simulations and next-to-leading order partonic QCD calculations, Ο(α s 3 ), are presented

Constitutively active RAS signaling reduces 1,25 dihydroxyvitamin D-mediated gene transcription in intestinal epithelial cells by reducing vitamin D receptor expression.

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DeSmet, Marsha L; Fleet, James C

2017-10-01

High vitamin D status is associated with reduced colon cancer risk but these studies ignore the diversity in the molecular etiology of colon cancer. RAS activating mutations are common in colon cancer and they activate pro-proliferative signaling pathways. We examined the impact of RAS activating mutations on 1,25 dihydroxyvitamin D (1,25(OH) 2 D)-mediated gene expression in cultured colon and intestinal cell lines. Transient transfection of Caco-2 cells with a constitutively active mutant K-RAS (G12 V) significantly reduced 1,25(OH) 2 D-induced activity of both a human 25-hydroxyvitamin D, 24 hydroxyase (CYP24A1) promoter-luciferase and an artificial 3X vitamin D response element (VDRE) promoter-luciferase reporter gene. Young Adult Mouse Colon (YAMC) and Rat Intestinal Epithelial (RIE) cell lines with stable expression of mutant H-RAS had suppressed 1,25(OH) 2 D-mediated induction of CYP24A1 mRNA. The RAS effects were associated with lower Vitamin D receptor (VDR) mRNA and protein levels in YAMC and RIE cells and they could be partially reversed by VDR overexpression. RAS-mediated suppression of VDR levels was not due to either reduced VDR mRNA stability or increased VDR gene methylation. However, chromatin accessibility to the VDR gene at the proximal promoter (-300bp), an enhancer region at -6kb, and an enhancer region located in exon 3 was significantly reduced in RAS transformed YAMC cells (YAMC-RAS). These data show that constitutively active RAS signaling suppresses 1,25(OH) 2 D-mediated gene transcription in colon epithelial cells by reducing VDR gene transcription but the mechanism for this suppression is not yet known. These data suggest that cancers with RAS-activating mutations may be less responsive to vitamin D mediated treatment or chemoprevention. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gene therapy strategy for long-term myocardial protection using adeno-associated virus-mediated delivery of heme oxygenase gene.

Science.gov (United States)

Melo, Luis G; Agrawal, Reitu; Zhang, Lunan; Rezvani, Mojgan; Mangi, Abeel A; Ehsan, Afshin; Griese, Daniel P; Dell'Acqua, Giorgio; Mann, Michael J; Oyama, Junichi; Yet, Shaw-Fang; Layne, Matthew D; Perrella, Mark A; Dzau, Victor J

2002-02-05

Ischemia and oxidative stress are the leading mechanisms for tissue injury. An ideal strategy for preventive/protective therapy would be to develop an approach that could confer long-term transgene expression and, consequently, tissue protection from repeated ischemia/reperfusion injury with a single administration of a therapeutic gene. In the present study, we used recombinant adeno-associated virus (rAAV) as a vector for direct delivery of the cytoprotective gene heme oxygenase-1 (HO-1) into the rat myocardium, with the purpose of evaluating this strategy as a therapeutic approach for long-term protection from ischemia-induced myocardial injury. Human HO-1 gene (hHO-1) was delivered to normal rat hearts by intramyocardial injection. AAV-mediated transfer of the hHO-1 gene 8 weeks before acute coronary artery ligation and release led to a dramatic reduction (>75%) in left ventricular myocardial infarction. The reduction in infarct size was accompanied by decreases in myocardial lipid peroxidation and in proapoptotic Bax and proinflammatory interleukin-1beta protein abundance, concomitant with an increase in antiapoptotic Bcl-2 protein level. This suggested that the transgene exerts its cardioprotective effects in part by reducing oxidative stress and associated inflammation and apoptotic cell death. This study documents the beneficial therapeutic effect of rAAV-mediated transfer, before myocardial injury, of a cytoprotective gene that confers long-term myocardial protection from ischemia/reperfusion injury. Our data suggest that this novel "pre-event" gene transfer approach may provide sustained tissue protection from future repeated episodes of injury and may be beneficial as preventive therapy for patients with or at risk of developing coronary ischemic events.

Search for Penguin Decays of $B$ Mesons at CDF

Energy Technology Data Exchange (ETDEWEB)

Kordas, Kostas [McGill U.

2000-01-01

Using a data sample of integrated luminosity $\\int$ Ldt = 28.9 $\\pm$ 1.2 $pb^{-1}$ of proton antiproton collisions at a center-of-mass energy $\\sqrt{s}$ = 1.8 TeV collected with the CDF detector at the Fermilab Tevatron collider, we searched for "penguin" radiative decays of $B^0_d$ and $B^0_s$ mesons which involve the flavor-changing neutral-current transition of a $b$ quark into an $s$ quark with the emission of a photon, $b \\to s\\gamma$ . Speciffcally, we searched for the decays $B^0_d \\to K^{*0}$, $K^{*0} \\to K^+ \\pi^-$ and $B^0_s \\to \\phi\\gamma, \\phi \\to K^+ K^-$, as well as for the charge conjugate chains....

The measurement of the W boson mass from CDF

International Nuclear Information System (INIS)

1994-06-01

Recent results from LEP experiments have substantially improved the knowledge of the Z boson. However, hadron colliders remain the only source of direct measurements of the W boson. There have been measurements of the W boson mass from the UA2 and CDF collaborations. The W mass continues to be a subject of great interest in testing the Standard Model. Here, the authors have made a preliminary determination of the W boson mass M W = 80.38 ± 0.23 GeV/c 2 from a combined analysis of W → eν and W → μν in anti pp collisions at √s = 1.8 TeV. The electron data alone yields M W = 80.47 ± 0.15(stat.) ± 0.25(syst.) GeV/c 2 , while the muon data gives M W = 80.29 ± 0.20(stat.) ± 0.24(syst.) GeV/c 2

Up-regulation of integrin β3 in radioresistant pancreatic cancer impairs adenovirus-mediated gene therapy

International Nuclear Information System (INIS)

Egami, Takuya; Ohuchida, Kenoki; Yasui, Takaharu; Onimaru, Manabu; Toma, Hiroki; Sato, Norihiro; Tanaka, Masao; Mizumoto, Kazuhiro; Matsumoto, Kunio

2009-01-01

Adenovirus-mediated gene therapy is a promising approach for the treatment of pancreatic cancer. We previously reported that radiation enhanced adenovirus-mediated gene expression in pancreatic cancer, suggesting that adenoviral gene therapy might be more effective in radioresistant pancreatic cancer cells. In the present study, we compared the transduction efficiency of adenovirus-delivered genes in radiosensitive and radioresistant cells, and investigated the underlying mechanisms. We used an adenovirus expressing the hepatocyte growth factor antagonist, NK4 (Ad-NK4), as a representative gene therapy. We established two radioresistant human pancreatic cancer cell lines using fractionated irradiation. Radiosensitive and radioresistant pancreatic cancer cells were infected with Ad-NK4, and NK4 levels in the cells were measured. In order to investigate the mechanisms responsible for the differences in the transduction efficiency between these cells, we measured expression of the genes mediating adenovirus infection and endocytosis. The results revealed that NK4 levels in radioresistant cells were significantly lower (P<0.01) than those in radiosensitive cells, although there were no significant differences in adenovirus uptake between radiosensitive cells and radioresistant cells. Integrin β3 was up-regulated and the Coxsackie virus and adenovirus receptor was down-regulated in radioresistant cells, and inhibition of integrin β3 promoted adenovirus gene transfer. These results suggest that inhibition of integrin β3 in radioresistant pancreatic cancer cells could enhance adenovirus-mediated gene therapy. (author)

Radiochemotherapy of hepatocarcinoma via lentivirus-mediated transfer of human sodium iodide symporter gene and herpes simplex virus thymidine kinase gene

Energy Technology Data Exchange (ETDEWEB)

Chen Libo, E-mail: libochen888@hotmail.com [Department of Nuclear Medicine, Shanghai Sixth People' s Hospital, Shanghai Jiao Tong University, Shanghai 200233 (China); Guo Guoying [Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Liu Tianjing; Guo Lihe [Division of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Zhu Ruisen [Department of Nuclear Medicine, Shanghai Sixth People' s Hospital, Shanghai Jiao Tong University, Shanghai 200233 (China)

2011-07-15

Herpes simplex virus thymidine kinase (HSV-TK) gene/ganciclovir (GCV) system has been widely used as a traditional gene therapy modality, and the sodium/iodide symporter gene (NIS) has been found to be a novel therapeutic gene. Since the therapeutic effects of radioiodine therapy or prodrug chemotherapy on cancers following NIS or HSV-TK gene transfer need to be enhanced, this study was designed to investigate the feasibility of radiochemotherapy for hepatocarcinoma via coexpression of NIS gene and HSV-TK gene. Methods: HepG2 cells were stably transfected with NIS, TK and GFP gene via recombinant lentiviral vector and named HepG2/NTG. Gene expression was examined by reverse transcriptase polymerase chain reaction, fluorescence imaging and iodide uptake. The therapeutic effects were assessed by MTT assay and clonogenic assay. Results: HepG2/NTG cells concentrated {sup 125}I{sup -} up to 76-fold higher than the wild-type cells within 20 min, and the efflux happened with a T{sub 1/2eff} of less than 10 min. The iodide uptake in HepG2/NTG cells was specifically inhibited by sodium perchlorate. Dose-dependent toxicity to HepG2/NTG cells by either GCV or {sup 131}I was revealed by clonogenic assay and MTT assay, respectively. The survival rate of HepG2/NTG cells decreased to 49.7%{+-}2.5%, 43.4%{+-}2.8% and 8.6%{+-}1.2% after exposure to {sup 131}I, GCV and combined therapy, respectively. Conclusion: We demonstrate that radiochemotherapy of hepatocarcinoma via lentiviral-mediated coexpression of NIS gene and HSV-TK gene leads to stronger killing effect than single treatment, and in vivo studies are needed to verify these findings.

Radiochemotherapy of hepatocarcinoma via lentivirus-mediated transfer of human sodium iodide symporter gene and herpes simplex virus thymidine kinase gene

International Nuclear Information System (INIS)

Chen Libo; Guo Guoying; Liu Tianjing; Guo Lihe; Zhu Ruisen

2011-01-01

Herpes simplex virus thymidine kinase (HSV-TK) gene/ganciclovir (GCV) system has been widely used as a traditional gene therapy modality, and the sodium/iodide symporter gene (NIS) has been found to be a novel therapeutic gene. Since the therapeutic effects of radioiodine therapy or prodrug chemotherapy on cancers following NIS or HSV-TK gene transfer need to be enhanced, this study was designed to investigate the feasibility of radiochemotherapy for hepatocarcinoma via coexpression of NIS gene and HSV-TK gene. Methods: HepG2 cells were stably transfected with NIS, TK and GFP gene via recombinant lentiviral vector and named HepG2/NTG. Gene expression was examined by reverse transcriptase polymerase chain reaction, fluorescence imaging and iodide uptake. The therapeutic effects were assessed by MTT assay and clonogenic assay. Results: HepG2/NTG cells concentrated 125 I - up to 76-fold higher than the wild-type cells within 20 min, and the efflux happened with a T 1/2eff of less than 10 min. The iodide uptake in HepG2/NTG cells was specifically inhibited by sodium perchlorate. Dose-dependent toxicity to HepG2/NTG cells by either GCV or 131 I was revealed by clonogenic assay and MTT assay, respectively. The survival rate of HepG2/NTG cells decreased to 49.7%±2.5%, 43.4%±2.8% and 8.6%±1.2% after exposure to 131 I, GCV and combined therapy, respectively. Conclusion: We demonstrate that radiochemotherapy of hepatocarcinoma via lentiviral-mediated coexpression of NIS gene and HSV-TK gene leads to stronger killing effect than single treatment, and in vivo studies are needed to verify these findings.

Advances in ultrasound-targeted microbubble-mediated gene therapy for liver fibrosis.

Science.gov (United States)

Huang, Cuiyuan; Zhang, Hong; Bai, Ruidan

2017-07-01

Hepatic fibrosis develops as a wound-healing scar in response to acute and chronic liver inflammation and can lead to cirrhosis in patients with chronic hepatitis B and C. The condition arises due to increased synthesis and reduced degradation of extracellular matrix (ECM) and is a common pathological sequela of chronic liver disease. Excessive deposition of ECM in the liver causes liver dysfunction, ascites, and eventually upper gastrointestinal bleeding as well as a series of complications. However, fibrosis can be reversed before developing into cirrhosis and has thus been the subject of extensive researches particularly at the gene level. Currently, therapeutic genes are imported into the damaged liver to delay or prevent the development of liver fibrosis by regulating the expression of exogenous genes. One technique of gene delivery uses ultrasound targeting of microbubbles combined with therapeutic genes where the time and intensity of the ultrasound can control the release process. Ultrasound irradiation of microbubbles in the vicinity of cells changes the permeability of the cell membrane by its cavitation effect and enhances gene transfection. In this paper, recent progress in the field is reviewed with emphasis on the following aspects: the types of ultrasound microbubbles, the construction of an ultrasound-mediated gene delivery system, the mechanism of ultrasound microbubble-mediated gene transfer and the application of ultrasound microbubbles in the treatment of liver fibrosis.

Advances in ultrasound-targeted microbubble-mediated gene therapy for liver fibrosis

Directory of Open Access Journals (Sweden)

Cuiyuan Huang

2017-07-01

Full Text Available Hepatic fibrosis develops as a wound-healing scar in response to acute and chronic liver inflammation and can lead to cirrhosis in patients with chronic hepatitis B and C. The condition arises due to increased synthesis and reduced degradation of extracellular matrix (ECM and is a common pathological sequela of chronic liver disease. Excessive deposition of ECM in the liver causes liver dysfunction, ascites, and eventually upper gastrointestinal bleeding as well as a series of complications. However, fibrosis can be reversed before developing into cirrhosis and has thus been the subject of extensive researches particularly at the gene level. Currently, therapeutic genes are imported into the damaged liver to delay or prevent the development of liver fibrosis by regulating the expression of exogenous genes. One technique of gene delivery uses ultrasound targeting of microbubbles combined with therapeutic genes where the time and intensity of the ultrasound can control the release process. Ultrasound irradiation of microbubbles in the vicinity of cells changes the permeability of the cell membrane by its cavitation effect and enhances gene transfection. In this paper, recent progress in the field is reviewed with emphasis on the following aspects: the types of ultrasound microbubbles, the construction of an ultrasound-mediated gene delivery system, the mechanism of ultrasound microbubble–mediated gene transfer and the application of ultrasound microbubbles in the treatment of liver fibrosis.

Precision top-quark mass measurement at CDF.

Science.gov (United States)

Aaltonen, T; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Appel, J A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Auerbach, B; Aurisano, A; Azfar, F; Badgett, W; Bae, T; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauce, M; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Bisello, D; Bizjak, I; Bland, K R; Blumenfeld, B; Bocci, A; Bodek, A; Bortoletto, D; Boudreau, J; Boveia, A; Brigliadori, L; Bromberg, C; Brucken, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Calamba, A; Calancha, C; Camarda, S; Campanelli, M; Campbell, M; Canelli, F; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chung, W H; Chung, Y S; Ciocci, M A; Clark, A; Clarke, C; Compostella, G; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Crescioli, F; Cuevas, J; Culbertson, R; Dagenhart, D; d'Ascenzo, N; Datta, M; de Barbaro, P; Dell'Orso, M; Demortier, L; Deninno, M; Devoto, F; d'Errico, M; Di Canto, A; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Dorigo, M; Dorigo, T; Ebina, K; Elagin, A; Eppig, A; Erbacher, R; Errede, S; Ershaidat, N; Eusebi, R; Farrington, S; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Funakoshi, Y; Furic, I; Gallinaro, M; Garcia, J E; Garfinkel, A F; Garosi, P; Gerberich, H; Gerchtein, E; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Ginsburg, C M; Giokaris, N; Giromini, P; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldin, D; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Grinstein, S; Grosso-Pilcher, C; Group, R C; Guimaraes da Costa, J; Hahn, S R; Halkiadakis, E; Hamaguchi, A; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harr, R F; Hatakeyama, K; Hays, C; Heck, M; Heinrich, J; Herndon, M; Hewamanage, S; Hocker, A; Hopkins, W; Horn, D; Hou, S; Hughes, R E; Hurwitz, M; Husemann, U; Hussain, N; Hussein, M; Huston, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kamon, T; Karchin, P E; Kasmi, A; Kato, Y; Ketchum, W; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kim, Y J; Kimura, N; Kirby, M; Klimenko, S; Knoepfel, K; Kondo, K; Kong, D J; Konigsberg, J; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Kruse, M; Krutelyov, V; Kuhr, T; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; LeCompte, T; Lee, E; Lee, H S; Lee, J S; Lee, S W; Leo, S; Leone, S; Lewis, J D; Limosani, A; Lin, C-J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, H; Liu, Q; Liu, T; Lockwitz, S; Loginov, A; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; Madrak, R; Maeshima, K; Maestro, P; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Martínez, M; Mastrandrea, P; Matera, K; Mattson, M E; Mazzacane, A; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Mesropian, C; Miao, T; Mietlicki, D; Mitra, A; Miyake, H; Moed, S; Moggi, N; Mondragon, M N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakano, I; Napier, A; Nett, J; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Noh, S Y; Norniella, O; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Ortolan, L; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Paramonov, A A; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pilot, J; Pitts, K; Plager, C; Pondrom, L; Poprocki, S; Potamianos, K; Prokoshin, F; Pranko, A; Ptohos, F; Punzi, G; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Rescigno, M; Riddick, T; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Ruffini, F; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Sakurai, Y; Santi, L; Sato, K; Saveliev, V; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Seidel, S; Seiya, Y; Semenov, A; Sforza, F; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shochet, M; Shreyber-Tecker, I; Simonenko, A; Sinervo, P; Sliwa, K; Smith, J R; Snider, F D; Soha, A; Sorin, V; Song, H; Squillacioti, P; Stancari, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Sudo, Y; Sukhanov, A; Suslov, I; Takemasa, K; Takeuchi, Y; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thome, J; Thompson, G A; Thomson, E; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Trovato, M; Ukegawa, F; Uozumi, S; Varganov, A; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vila, I; Vilar, R; Vizán, J; Vogel, M; Volpi, G; Wagner, P; Wagner, R L; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Wester, W C; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Wick, F; Williams, H H; Wilson, J S; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, H; Wright, T; Wu, X; Wu, Z; Yamamoto, K; Yamato, D; Yang, T; Yang, U K; Yang, Y C; Yao, W-M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanetti, A; Zeng, Y; Zhou, C; Zucchelli, S

2012-10-12

We present a precision measurement of the top-quark mass using the full sample of Tevatron √s = 1.96 TeV proton-antiproton collisions collected by the CDF II detector, corresponding to an integrated luminosity of 8.7 fb(-1). Using a sample of tt¯ candidate events decaying into the lepton+jets channel, we obtain distributions of the top-quark masses and the invariant mass of two jets from the W boson decays from data. We then compare these distributions to templates derived from signal and background samples to extract the top-quark mass and the energy scale of the calorimeter jets with in situ calibration. The likelihood fit of the templates from signal and background events to the data yields the single most-precise measurement of the top-quark mass, M(top)=172.85±0.71(stat)±0.85(syst) GeV/c(2).

Color coherence in multijet events at CDF

International Nuclear Information System (INIS)

Meschi, E.

1992-11-01

Results of a search for an evidence of color coherence in CDF bar pp → 3jet + X data from the 1988--89 run high statistics inclusive jet sample (4.2pb -1 of integrated luminosity) are presented. We study the geometric correlation between the third jet (regarded as the product of ''soft' branchings in the Leading Log Approximation) and the second one, in comparison to Isajet and Herwig shower Monte Carlos predictions. A geometric variable for this correlation is found which is sensitive to interference: the qualitative agreement of Herwig (with coherent shower development) to the data distribution, contrasted to the disagreement of Isajet (independent development) is consistent with the observation of a color interference effect. Further evidence for this interpretation comes from ''switching off'' interference in Herwig by means of a proper event selection, which yields a distribution much similar to the Isajet one

Recent results on QCD at the Tevatron (CDF and D0)

International Nuclear Information System (INIS)

Meschi, E.

1993-11-01

In the last run the Tevatron collider delivered an integrated luminosity of 29.9 pb -1 to CDF and D0. We describe here some preliminary result from analyses of relevant QCD processes in the 1992--1993 data from the two experiments

Gene Expression by PBMC in Primary Sclerosing Cholangitis: Evidence for Dysregulation of Immune Mediated Genes

Directory of Open Access Journals (Sweden)

Christopher A. Aoki

2006-01-01

Full Text Available Primary sclerosing cholangitis (PSC is a chronic disease of the bile ducts characterized by an inflammatory infiltrate and obliterative fibrosis. The precise role of the immune system in the pathogenesis of PSC remains unknown. We used RNA microarray analysis to identify immune-related genes and pathways that are differentially expressed in PSC. Messenger RNA (mRNA from peripheral blood mononuclear cells (PBMC was isolated from both patients with PSC and age and sex matched healthy controls. Samples from 5 PSC patients and 5 controls were analyzed by microarray and based upon rigorous statistical analysis of the data, relevant genes were chosen for confirmation by RT-PCR in 10 PSC patients and 10 controls. Using unsupervised hierarchical clustering, gene expression in PSC was statistically different from our control population. Interestingly, genes within the IL-2 receptor beta, IL-6 and MAP Kinase pathways were found to be differently expressed in patients with PSC compared to controls. Further, individual genes, TNF-α induced protein 6 (TNFaip6 and membrane-spanning 4-domains, subfamily A (ms4a were found to be upregulated in PSC while similar to Mothers against decapentaplegic homolog 5 (SMAD 5 was downregulated. In conclusion, several immune-related pathways and genes were differentially expressed in PSC compared to control patients, giving further evidence that this disease is systemic and immune-mediated.

Inclusive Jet Production from Pbar P Collisions at SQRTS=630 GEV in the Cdf Detector

Science.gov (United States)

Akopian, Alexander

1996-05-01

We present a preliminary analysis of the inclusive jet cross section from pbar p collisions at √ s= 630 GeV, measured using the CDF detector. We compare these results with previous CDF measurements at 546 and 1800 GeV. ^Supported by U.S. DOE under Contract No. DE-FG02-91ER-40651. Supported by the U.S. Department of Energy; the National Science Foundation; the Istituto Nazionale di Fisica Nucleare, Italy; the Ministry of Science, Culture and Education of Japan; the A.P. Sloan Foundation, and the Alexander von Humboldt-Stiftung.

The Ve-mediated resistance response of the tomato to Verticillium dahliae involves H2O2, peroxidase and lignins and drives PAL gene expression

Directory of Open Access Journals (Sweden)

Merino Fuencisla

2010-10-01

Full Text Available Abstract Background Verticillium dahliae is a fungal pathogen that infects a wide range of hosts. The only known genes for resistance to Verticillium in the Solanaceae are found in the tomato (Solanum lycopersicum Ve locus, formed by two linked genes, Ve1 and Ve2. To characterize the resistance response mediated by the tomato Ve gene, we inoculated two nearly isogenic tomato lines, LA3030 (ve/ve and LA3038 (Ve/Ve, with V. dahliae. Results We found induction of H2O2 production in roots of inoculated plants, followed by an increase in peroxidase activity only in roots of inoculated resistant plants. Phenylalanine-ammonia lyase (PAL activity was also increased in resistant roots 2 hours after inoculation, while induction of PAL activity in susceptible roots was not seen until 48 hours after inoculation. Phenylpropanoid metabolism was also affected, with increases in ferulic acid, p-coumaric acid, vanillin and p-hydroxybenzaldehyde contents in resistant roots after inoculation. Six tomato PAL cDNA sequences (PAL1 - PAL6 were found in the SolGenes tomato EST database. RT-PCR analysis showed that these genes were expressed in all organs of the plant, albeit at different levels. Real-time RT-PCR indicated distinct patterns of expression of the different PAL genes in V. dahliae-inoculated roots. Phylogenetic analysis of 48 partial PAL cDNAs corresponding to 19 plant species grouped angiosperm PAL sequences into four clusters, suggesting functional differences among the six tomato genes, with PAL2 and PAL6 presumably involved in lignification, and the remaining PAL genes implicated in other biological processes. An increase in the synthesis of lignins was found 16 and 28 days after inoculation in both lines; this increase was greater and faster to develop in the resistant line. In both resistant and susceptible inoculated plants, an increase in the ratio of guaiacyl/syringyl units was detected 16 days after inoculation, resulting from the lowered amount

Comparison of agrobacterium mediated wheat and barley transformation with nucleoside diphosphate kinase 2 (NDPK2) gene

International Nuclear Information System (INIS)

Waheed, U.; Shah, M.M.; Smedley, M.; Harwood, W.

2016-01-01

An efficient and reliable transformation system is imperative for improvement of important crop species like barley and wheat. Wheat transformation is complex due to larger genome size and polyploidy while barley has a limitation of genotypic dependency. The objective of current study was to compare the relative transformation efficiency of wheat and barley using specific expression vector pBRACT 214-NDPK2 constructed through gateway cloning carrying Nucleoside Diphosphate Kinase 2 (NDPK2) gene. The vector was used to compare the transformation response in both crops using immature embryos through Agrobacterium mediated transformation. Both wheat and barley showed different responses towards callus induction and regeneration. Immature embryos of 1.5 to 2 mm in diameter was found optimum for wheat callus induction while 1 to 1.5 mm for barley. Both embryogenic and non-embryogenic calli were found in wheat with significantly greater tendency for embryogenecity in barley. The overall regeneration response was found different for all transformed wheat and barley cultivars. Wheat cultivars showed good response initially that drastically slowed down in later stages with the exception of Fielder that reached to the green shoots with good roots. The barley transformed lines showed good regeneration response as compared to wheat. PCR analysis of putative transformants using genomic DNA showed a maximum of 27% transformation efficiency in barely. No true transformation response was obtained in all cultivars of wheat used in this study. The protocol developed for wheat and barley transformation will greatly be helpful in crop improvement programme through genetic engineering especially in diploid relatives of cereals. (author)

Generation of TALE nickase-mediated gene-targeted cows expressing human serum albumin in mammary glands.

Science.gov (United States)

Luo, Yan; Wang, Yongsheng; Liu, Jun; Cui, Chenchen; Wu, Yongyan; Lan, Hui; Chen, Qi; Liu, Xu; Quan, Fusheng; Guo, Zekun; Zhang, Yong

2016-02-08

Targeting exogenous genes at milk protein loci via gene-targeting technology is an ideal strategy for producing large quantities of pharmaceutical proteins. Transcription-activator-like effector (TALE) nucleases (TALENs) are an efficient genome-editing tool. However, the off-target effects may lead to unintended gene mutations. In this study, we constructed TALENs and TALE nickases directed against exon 2 of the bovine β-lactoglobulin (BLG) locus. The nickases can induce a site-specific DNA single-strand break, without inducing double-strand break and nonhomologous end joining mediated gene mutation, and lower cell apoptosis rate than TALENs. After co-transfecting the bovine fetal fibroblasts with human serum albumin (HSA) gene-targeting vector and TALE nickase expression vectors, approximately 4.8% (40/835) of the cell clones contained HSA at BLG locus. Unexpectedly, one homozygous gene-targeted cell clone (1/835, 0.1%) was obtained by targeting both alleles of BLG in a single round of transfection. The recombinant protein mimicking the endogenous BLG was highly expressed and correctly folded in the mammary glands of the targeted cows, and the expression level of HSA was significantly increased in the homozygous targeted cows. Results suggested that the combination of TALE nickase-mediated gene targeting and somatic cell nuclear transfer is a feasible and safe approach in producing gene-targeted livestock.

The Long Term Data Preservation (LTDP) project at INFN CNAF: CDF use case

International Nuclear Information System (INIS)

Amerio, S; Chiarelli, L; Dell'Agnello, L; Gregori, D; Pezzi, M; Ricci, P; Rosso, F; Zani, S

2015-01-01

In the last years the problem of preservation of scientific data has become one of the most important topics inside international scientific communities. In particular the long term preservation of experimental data, raw and all related derived formats including calibration information, is one of the emerging requirements within the High Energy Physics (HEP) community for experiments that have already concluded the data taking phase. The DPHEP group (Data Preservation in HEP) coordinates the local teams within the whole collaboration and the different Tiers (computing centers). The INFN-CNAF Tier-1 is one of the reference sites for data storage and computing in the LHC community but it also offers resources to many other HEP and non-HEP collaborations. In particular the CDF experiment has used the INFN-CNAF Tier-1 resources for many years and after the end of data taking in 2011, it is now facing the challenge to both preserve the large amount of data produced during several years and to retain the ability to access and reuse the whole amount of it in the future. According to this task the CDF Italian collaboration, together with the INFN-CNAF computing center, has developed and is now implementing a long term future data preservation project in collaboration with Fermilab (FNAL) computing sector. The project comprises the copy of all CDF raw data and user level ntuples (about 4 PB) at the INFN-CNAF site and the setup of a framework which will allow to access and analyze the data in the long term future. A portion of the 4 PB of data (raw data and analysis-level ntuples) are currently being copied from FNAL to the INFN-CNAF tape library backend and a system to allow data access is being setup. In addition to this data access system, a data analysis framework is being developed in order to run the complete CDF analysis chain in the long term future, from raw data reprocessing to analysis-level ntuples production and analysis. In this contribution we first illustrate

Study of the top quark electric charge at the cdf experiment

International Nuclear Information System (INIS)

Bartos, P.

2011-01-01

We report on the measurement of the top quark electric charge using the jet charge tagging method on events containing a single lepton collected by the CDF II detector at Fermilab between February 2002 and February 2010 at the center-of-mass energy ps = 1.96 TeV . There are three main components to this measurement: determining the charge of the W (using the charge of the lepton), pairing the W with the b-jet to ensure that they are from the same top decay branch and finally determining the charge of the b-jet using the Jet Charge algorithm. We found, on a sample of 5.6 fb -1 of data, that the p-value under the standard model hypothesis is equal to 13.4%, while the p-value under the exotic model hypothesis is equal to 0.014%. Using the a priori criteria generally accepted by the CDF collaboration, we can say that the result is consistent with the standard model, while we exclude an exotic quark hypothesis with 95% confidence. Using the Bayesian approach, we obtain for the Bayes factor (2 · ln(BF)) a value of 19.6, that favors very strongly the SM hypothesis over the XM one. The presented method has the highest sensitivity to the top quark electric charge among the presented so far top quark charge analysis. (author)

Study of the top quark electric charge at the CDF experiment

Energy Technology Data Exchange (ETDEWEB)

Bartos, Pavol [Comenius Univ., Bratislava (Slovakia)

2011-01-01

We report on the measurement of the top quark electric charge using the jet charge tagging method on events containing a single lepton collected by the CDF II detector at Fermilab between February 2002 and February 2010 at the center-of-mass energy √s = 1.96 TeV. There are three main components to this measurement: determining the charge of the W (using the charge of the lepton), pairing the W with the b-jet to ensure that they are from the same top decay branch and finally determining the charge of the b-jet using the Jet Charge algorithm. We found, on a sample of 5.6 fb^-1 of data, that the p-value under the standard model hypothesis is equal to 13.4%, while the p-value under the exotic model hypothesis is equal to 0.014%. Using the a priori criteria generally accepted by the CDF collaboration, we can say that the result is consistent with the standard model, while we exclude an exotic quark hypothesis with 95% confidence. Using the Bayesian approach, we obtain for the Bayes factor (2ln(BF)) a value of 19.6, that favors very strongly the SM hypothesis over the XM one. The presented method has the highest sensitivity to the top quark electric charge among the presented so far top quark charge analysis.

A Precise Measurement of the W Boson Mass with CDF

CERN Multimedia

CERN. Geneva

2012-01-01

The W boson mass measurement probes quantum corrections to the W propagator, such as those arising from supersymmetric particles or Higgs bosons. The new measurement from CDF is more precise than the previous world average, providing a stringent constraint on the mass of the Higgs boson in the context of the Standard Model. I describe this measurement, performed with 2.2/fb of data using 1.1 million candidates in the electron and muon decay channels, with three kinematic fits in each channel. The measurement uses in-situ calibrations from cosmic rays, J/psi and Upsilon data, and W- and Z-boson decays, with multiple cross-checks including independent determinations of the Z boson mass in both channels. The W-boson mass is measured to be 80387 +- 19 MeV/c^2.

Precise measurement of the $W$-boson mass with the CDF II detector

Energy Technology Data Exchange (ETDEWEB)

Aaltonen, T.; /Helsinki Inst. of Phys.; Alvarez Gonzalez, B.; /Oviedo U. /Cantabria Inst. of Phys.; Amerio, S.; /INFN, Padua; Amidei, D.; /Michigan U.; Anastassov, A.; /Northwestern U. /Fermilab; Annovi, A.; /Frascati; Antos, J.; /Comenius U.; Apollinari, G.; /Fermilab; Appel, J.A.; /Fermilab; Arisawa, T.; /Waseda U.; Artikov, A.; /Dubna, JINR /Texas A-M

2012-03-01

We have measured the W-boson mass M{sub W} using data corresponding to 2.2 fb{sup -1} of integrated luminosity collected in p{bar p} collisions at {radical}s = 1.96 TeV with the CDF II detector at the Fermilab Tevatron collider. Samples consisting of 470 126 W {yields} e{nu} candidates and 624 708 W {yields} {mu}{nu} candidates yield the measurement M{sub W} = 80 387 {+-} 12{sub stat} {+-} 15{sub syst} = 80 387 {+-} 19 MeV/c{sup 2}. This is the most precise measurement of the W-boson mass to date and significantly exceeds the precision of all previous measurements combined.

The CDF SVX II upgrade for the Tevatron Run II

International Nuclear Information System (INIS)

Bortoletto, Daniela

1997-01-01

A microstrip silicon detector SVX II has been proposed for the upgrade of CDF to be installed in 1999 for Run II of the Tevatron. Three barrels of five layers of double-sided silicon microstrip detectors will cover the interaction region. A description of the project status will be presented. Emphasis will be given to the R and D program for silicon sensors which includes capacitance minimization, the study of coupling capacitor integrity, the operation of the detectors in conjunction with the SVXH and SVX2 readout chips in two beam tests and the determination of the detectors performance deterioration due to radiation damage

Di-jet production by double pomeron exchange in CDF

International Nuclear Information System (INIS)

Albrow, M.G.

1998-05-01

We have studied events with a high-x F antiproton and two central jets with E T > 7 GeV in CDF, in p anti p collisions at √s = 1800 GeV. We find an excess of events with a rapidity gap at least 3.5 units wide in the proton direction, which we interpret as di-jet production in double pomeron exchange events

3D Porous Chitosan-Alginate Scaffolds as an In Vitro Model for Evaluating Nanoparticle-Mediated Tumor Targeting and Gene Delivery to Prostate Cancer.

Science.gov (United States)

Wang, Kui; Kievit, Forrest M; Florczyk, Stephen J; Stephen, Zachary R; Zhang, Miqin

2015-10-12

Cationic nanoparticles (NPs) for targeted gene delivery are conventionally evaluated using 2D in vitro cultures. However, this does not translate well to corresponding in vivo studies because of the marked difference in NP behavior in the presence of the tumor microenvironment. In this study, we investigated whether prostate cancer (PCa) cells cultured in three-dimensional (3D) chitosan-alginate (CA) porous scaffolds could model cationic NP-mediated gene targeted delivery to tumors in vitro. We assessed in vitro tumor cell proliferation, formation of tumor spheroids, and expression of marker genes that promote tumor malignancy in CA scaffolds. The efficacy of NP-targeted gene delivery was evaluated in PCa cells in 2D cultures, PCa tumor spheroids grown in CA scaffolds, and PCa tumors in a mouse TRAMP-C2 flank tumor model. PCa cells cultured in CA scaffolds grew into tumor spheroids and displayed characteristics of higher malignancy as compared to those in 2D cultures. Significantly, targeted gene delivery was only observed in cells cultured in CA scaffolds, whereas cells cultured on 2D plates showed no difference in gene delivery between targeted and nontarget control NPs. In vivo NP evaluation confirmed targeted gene delivery, indicating that only CA scaffolds correctly modeled NP-mediated targeted delivery in vivo. These findings suggest that CA scaffolds serve as a better in vitro platform than 2D cultures for evaluation of NP-mediated targeted gene delivery to PCa.

RNA-mediated epigenetic heredity requires the cytosine methyltransferase Dnmt2.

Directory of Open Access Journals (Sweden)

Jafar Kiani

2013-05-01

Full Text Available RNA-mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and the modulation of the Sox9 gene, resulting in an overgrowth phenotype. We now report that expression of the Dnmt2 RNA methyltransferase is required for the establishment and hereditary maintenance of both paramutations. Our data show that the Kit paramutant phenotype was not transmitted to the progeny of Dnmt2(-/- mice and that the Sox9 paramutation was also not established in Dnmt2(-/- embryos. Similarly, RNA from Dnmt2-negative Kit heterozygotes did not induce the paramutant phenotype when microinjected into Dnmt2-deficient fertilized eggs and microinjection of the miR-124 microRNA failed to induce the characteristic giant phenotype. In agreement with an RNA-mediated mechanism of inheritance, no change was observed in the DNA methylation profiles of the Kit locus between the wild-type and paramutant mice. RNA bisulfite sequencing confirmed Dnmt2-dependent tRNA methylation in mouse sperm and also indicated Dnmt2-dependent cytosine methylation in Kit RNA in paramutant embryos. Together, these findings uncover a novel function of Dnmt2 in RNA-mediated epigenetic heredity.

A Measurement of the B⁰$\\bar{B}$⁰ mixing Using Muon Pairs at CDF

Energy Technology Data Exchange (ETDEWEB)

Meschi, E. [Scuola Normale Superiore (SNS), Pisa (Italy)

1995-10-01

This thesis concerns the experimental study of B mesons (mesons containing a b quark) produced in proton-antiproton collisions at center of mass energy of 1800 GeV. This work has been performed within the CDF collaboration. CDF is a general purpose detector located at Fermilab, in Batavia, which exploits the Fermilab proton-antiproton collider.

Bs Physics at LEP, SLD, and CDF Delta m_s and Delta Gamma_s

CERN Document Server

Boix, G

2001-01-01

The current status of the experimental knowledge of $\\Bs$ meson physics is reviewed. Results from LEP and CDF on the width difference $\\dgs$ are presented, the corresponding average is found to be in good agreement with the present theoretical estimation. The $\\Bs$ oscillations have not yet been resolved, despite the progress recently achieved by SLD and ALEPH. The world combination, including results from the LEP experiments, SLD and CDF, is presented, together with the expected and observed lower limit on the $\\Bs$ oscillation frequency. A tantalizing hint of an oscillation is observed around $\\dms\\sim17 \\psin$, near future results could increase the significance of this hint.

Culture as a mediator of gene-environment interaction: Cultural consonance, childhood adversity, a 2A serotonin receptor polymorphism, and depression in urban Brazil.

Science.gov (United States)

Dressler, William W; Balieiro, Mauro C; Ferreira de Araújo, Luiza; Silva, Wilson A; Ernesto Dos Santos, José

2016-07-01

Research on gene-environment interaction was facilitated by breakthroughs in molecular biology in the late 20th century, especially in the study of mental health. There is a reliable interaction between candidate genes for depression and childhood adversity in relation to mental health outcomes. The aim of this paper is to explore the role of culture in this process in an urban community in Brazil. The specific cultural factor examined is cultural consonance, or the degree to which individuals are able to successfully incorporate salient cultural models into their own beliefs and behaviors. It was hypothesized that cultural consonance in family life would mediate the interaction of genotype and childhood adversity. In a study of 402 adult Brazilians from diverse socioeconomic backgrounds, conducted from 2011 to 2014, the interaction of reported childhood adversity and a polymorphism in the 2A serotonin receptor was associated with higher depressive symptoms. Further analysis showed that the gene-environment interaction was mediated by cultural consonance in family life, and that these effects were more pronounced in lower social class neighborhoods. The findings reinforce the role of the serotonergic system in the regulation of stress response and learning and memory, and how these processes in turn interact with environmental events and circumstances. Furthermore, these results suggest that gene-environment interaction models should incorporate a wider range of environmental experience and more complex pathways to better understand how genes and the environment combine to influence mental health outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

TPL-2 Regulates Macrophage Lipid Metabolism and M2 Differentiation to Control TH2-Mediated Immunopathology

Science.gov (United States)

Entwistle, Lewis J.; Khoury, Hania; Papoutsopoulou, Stamatia; Mahmood, Radma; Mansour, Nuha R.; Ching-Cheng Huang, Stanley; Pearce, Edward J.; Pedro S. de Carvalho, Luiz; Ley, Steven C.

2016-01-01

Persistent TH2 cytokine responses following chronic helminth infections can often lead to the development of tissue pathology and fibrotic scarring. Despite a good understanding of the cellular mechanisms involved in fibrogenesis, there are very few therapeutic options available, highlighting a significant medical need and gap in our understanding of the molecular mechanisms of TH2-mediated immunopathology. In this study, we found that the Map3 kinase, TPL-2 (Map3k8; Cot) regulated TH2-mediated intestinal, hepatic and pulmonary immunopathology following Schistosoma mansoni infection or S. mansoni egg injection. Elevated inflammation, TH2 cell responses and exacerbated fibrosis in Map3k8 –/–mice was observed in mice with myeloid cell-specific (LysM) deletion of Map3k8, but not CD4 cell-specific deletion of Map3k8, indicating that TPL-2 regulated myeloid cell function to limit TH2-mediated immunopathology. Transcriptional and metabolic assays of Map3k8 –/–M2 macrophages identified that TPL-2 was required for lipolysis, M2 macrophage activation and the expression of a variety of genes involved in immuno-regulatory and pro-fibrotic pathways. Taken together this study identified that TPL-2 regulated TH2-mediated inflammation by supporting lipolysis and M2 macrophage activation, preventing TH2 cell expansion and downstream immunopathology and fibrosis. PMID:27487182

Diversification of the Primary Antibody Repertoire by AID-Mediated Gene Conversion.

Science.gov (United States)

Lanning, Dennis K; Knight, Katherine L

2015-01-01

Gene conversion, mediated by activation-induced cytidine deaminase (AID), has been found to contribute to generation of the primary antibody repertoire in several vertebrate species. Generation of the primary antibody repertoire by gene conversion of immunoglobulin (Ig) genes occurs primarily in gut-associated lymphoid tissues (GALT) and is best described in chicken and rabbit. Here, we discuss current knowledge of the mechanism of gene conversion as well as the contribution of the microbiota in promoting gene conversion of Ig genes. Finally, we propose that the antibody diversification strategy used in GALT species, such as chicken and rabbit, is conserved in a subset of human and mouse B cells.

Ultrasound-mediated vascular gene transfection by cavitation of endothelial-targeted cationic microbubbles.

Science.gov (United States)

Xie, Aris; Belcik, Todd; Qi, Yue; Morgan, Terry K; Champaneri, Shivam A; Taylor, Sarah; Davidson, Brian P; Zhao, Yan; Klibanov, Alexander L; Kuliszewski, Michael A; Leong-Poi, Howard; Ammi, Azzdine; Lindner, Jonathan R

2012-12-01

Ultrasound-mediated gene delivery can be amplified by acoustic disruption of microbubble carriers that undergo cavitation. We hypothesized that endothelial targeting of microbubbles bearing cDNA is feasible and, through optimizing proximity to the vessel wall, increases the efficacy of gene transfection. Contrast ultrasound-mediated gene delivery is a promising approach for site-specific gene therapy, although there are concerns with the reproducibility of this technique and the safety when using high-power ultrasound. Cationic lipid-shelled decafluorobutane microbubbles bearing a targeting moiety were prepared and compared with nontargeted microbubbles. Microbubble targeting efficiency to endothelial adhesion molecules (P-selectin or intercellular adhesion molecule [ICAM]-1) was tested using in vitro flow chamber studies, intravital microscopy of tumor necrosis factor-alpha (TNF-α)-stimulated murine cremaster muscle, and targeted contrast ultrasound imaging of P-selectin in a model of murine limb ischemia. Ultrasound-mediated transfection of luciferase reporter plasmid charge coupled to microbubbles in the post-ischemic hindlimb muscle was assessed by in vivo optical imaging. Charge coupling of cDNA to the microbubble surface was not influenced by the presence of targeting ligand, and did not alter the cavitation properties of cationic microbubbles. In flow chamber studies, surface conjugation of cDNA did not affect attachment of targeted microbubbles at microvascular shear stresses (0.6 and 1.5 dyne/cm(2)). Attachment in vivo was also not affected by cDNA according to intravital microscopy observations of venular adhesion of ICAM-1-targeted microbubbles and by ultrasound molecular imaging of P-selectin-targeted microbubbles in the post-ischemic hindlimb in mice. Transfection at the site of high acoustic pressures (1.0 and 1.8 MPa) was similar for control and P-selectin-targeted microbubbles but was associated with vascular rupture and hemorrhage. At 0.6 MPa

Search for a Higgs boson decaying to two W bosons at CDF.

Science.gov (United States)

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burke, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cordelli, M; Cortiana, G; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heijboer, A; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kusakabe, Y; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, E; Lee, H S; Lee, S W; Leone, S; Lewis, J D; Lin, C-S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lucchesi, D; Luci, C; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlok, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Griso, S Pagan; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Rekovic, V; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester Iii, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Würthwein, F; Wynne, S M; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zhang, X; Zheng, Y; Zucchelli, S

2009-01-16

We present a search for a Higgs boson decaying to two W bosons in pp[over ] collisions at sqrt[s]=1.96 TeV center-of-mass energy. The data sample corresponds to an integrated luminosity of 3.0 fb;(-1) collected with the CDF II detector. We find no evidence for production of a Higgs boson with mass between 110 and 200 GeV/c;(2), and determine upper limits on the production cross section. For the mass of 160 GeV/c;(2), where the analysis is most sensitive, the observed (expected) limit is 0.7 pb (0.9 pb) at 95% Bayesian credibility level which is 1.7 (2.2) times the standard model cross section.

Jet studies at all rapidities from D0 and CDF

International Nuclear Information System (INIS)

Varelas, N.

1996-08-01

We present results on measurements of jet shapes, color coherence, and topology of multijet events from p anti p collisions at √s = TeV at the Fermilab Tevatron collider using the CDF and D null detectors. The data are compared to next-to-leading order QCD calculations, or to predictions of parton shower based Monte Carlo models

DREAM mediates cAMP-dependent, Ca2+-induced stimulation of GFAP gene expression and regulates cortical astrogliogenesis.

Science.gov (United States)

Cebolla, Beatriz; Fernández-Pérez, Antonio; Perea, Gertrudis; Araque, Alfonso; Vallejo, Mario

2008-06-25

In the developing mouse brain, once the generation of neurons is mostly completed during the prenatal period, precisely coordinated signals act on competent neural precursors to direct their differentiation into astrocytes, which occurs mostly after birth. Among these signals, those provided by neurotrophic cytokines and bone morphogenetic proteins appear to have a key role in triggering the neurogenic to gliogenic switch and in regulating astrocyte numbers. In addition, we have reported previously that the neurotrophic peptide pituitary adenylate cyclase-activating polypeptide (PACAP) is able to promote astrocyte differentiation of cortical precursors via activation of a cAMP-dependent pathway. Signals acting on progenitor cells of the developing cortex to generate astrocytes activate glial fibrillary acidic protein (GFAP) gene expression, but the transcriptional mechanisms that regulate this activation are unclear. Here, we identify the previously known transcriptional repressor downstream regulatory element antagonist modulator (DREAM) as an activator of GFAP gene expression. We found that DREAM occupies specific sites on the GFAP promoter before and after differentiation is initiated by exposure of cortical progenitor cells to PACAP. PACAP raises intracellular calcium concentration via a mechanism that requires cAMP, and DREAM-mediated transactivation of the GFAP gene requires the integrity of calcium-binding domains. Cortical progenitor cells from dream(-/-) mice fail to express GFAP in response to PACAP. Moreover, the neonatal cortex of dream(-/-) mice exhibits a reduced number of astrocytes and increased number of neurons. These results identify the PACAP-cAMP-Ca(2+)-DREAM cascade as a new pathway to activate GFAP gene expression during astrocyte differentiation.

Measurement of the forward-backward asymmetry of top-quark and antiquark pairs using the full CDF Run II data set

Science.gov (United States)

Aaltonen, T.; Amerio, S.; Amidei, D.; Anastassov, A.; Annovi, A.; Antos, J.; Apollinari, G.; Appel, J. A.; Arisawa, T.; Artikov, A.; Asaadi, J.; Ashmanskas, W.; Auerbach, B.; Aurisano, A.; Azfar, F.; Badgett, W.; Bae, T.; Barbaro-Galtieri, A.; Barnes, V. E.; Barnett, B. A.; Barria, P.; Bartos, P.; Bauce, M.; Bedeschi, F.; Behari, S.; Bellettini, G.; Bellinger, J.; Benjamin, D.; Beretvas, A.; Bhatti, A.; Bland, K. R.; Blumenfeld, B.; Bocci, A.; Bodek, A.; Bortoletto, D.; Boudreau, J.; Boveia, A.; Brigliadori, L.; Bromberg, C.; Brucken, E.; Budagov, J.; Budd, H. S.; Burkett, K.; Busetto, G.; Bussey, P.; Butti, P.; Buzatu, A.; Calamba, A.; Camarda, S.; Campanelli, M.; Canelli, F.; Carls, B.; Carlsmith, D.; Carosi, R.; Carrillo, S.; Casal, B.; Casarsa, M.; Castro, A.; Catastini, P.; Cauz, D.; Cavaliere, V.; Cerri, A.; Cerrito, L.; Chen, Y. C.; Chertok, M.; Chiarelli, G.; Chlachidze, G.; Cho, K.; Chokheli, D.; Clark, A.; Clarke, C.; Convery, M. E.; Conway, J.; Corbo, M.; Cordelli, M.; Cox, C. A.; Cox, D. J.; Cremonesi, M.; Cruz, D.; Cuevas, J.; Culbertson, R.; d'Ascenzo, N.; Datta, M.; de Barbaro, P.; Demortier, L.; Deninno, M.; D'Errico, M.; Devoto, F.; Di Canto, A.; Di Ruzza, B.; Dittmann, J. R.; Donati, S.; D'Onofrio, M.; Dorigo, M.; Driutti, A.; Ebina, K.; Edgar, R.; Erbacher, R.; Errede, S.; Esham, B.; Farrington, S.; Fernández Ramos, J. P.; Field, R.; Flanagan, G.; Forrest, R.; Franklin, M.; Freeman, J. C.; Frisch, H.; Funakoshi, Y.; Galloni, C.; Garfinkel, A. F.; Garosi, P.; Gerberich, H.; Gerchtein, E.; Giagu, S.; Giakoumopoulou, V.; Gibson, K.; Ginsburg, C. M.; Giokaris, N.; Giromini, P.; Glagolev, V.; Glenzinski, D.; Gold, M.; Goldin, D.; Golossanov, A.; Gomez, G.; Gomez-Ceballos, G.; Goncharov, M.; González López, O.; Gorelov, I.; Goshaw, A. T.; Goulianos, K.; Gramellini, E.; Grosso-Pilcher, C.; Guimaraes da Costa, J.; Hahn, S. R.; Han, J. Y.; Happacher, F.; Hara, K.; Hare, M.; Harr, R. F.; Harrington-Taber, T.; Hatakeyama, K.; Hays, C.; Heinrich, J.; Herndon, M.; Hocker, A.; Hong, Z.; Hopkins, W.; Hou, S.; Hughes, R. E.; Husemann, U.; Hussein, M.; Huston, J.; Introzzi, G.; Iori, M.; Ivanov, A.; James, E.; Jang, D.; Jayatilaka, B.; Jeon, E. J.; Jindariani, S.; Jones, M.; Joo, K. K.; Jun, S. Y.; Junk, T. R.; Kambeitz, M.; Kamon, T.; Karchin, P. E.; Kasmi, A.; Kato, Y.; Ketchum, W.; Keung, J.; Kilminster, B.; Kim, D. H.; Kim, H. S.; Kim, J. E.; Kim, M. J.; Kim, S. H.; Kim, S. B.; Kim, Y. J.; Kim, Y. K.; Kimura, N.; Kirby, M.; Kondo, K.; Kong, D. J.; Konigsberg, J.; Kotwal, A. V.; Kreps, M.; Kroll, J.; Kruse, M.; Kuhr, T.; Kurata, M.; Laasanen, A. T.; Lammel, S.; Lancaster, M.; Lannon, K.; Latino, G.; Lee, H. S.; Lee, J. S.; Leo, S.; Leone, S.; Lewis, J. D.; Limosani, A.; Lipeles, E.; Lister, A.; Liu, Q.; Liu, T.; Lockwitz, S.; Loginov, A.; Lucchesi, D.; Lucà, A.; Lueck, J.; Lujan, P.; Lukens, P.; Lungu, G.; Lys, J.; Lysak, R.; Madrak, R.; Maestro, P.; Malik, S.; Manca, G.; Manousakis-Katsikakis, A.; Marchese, L.; Margaroli, F.; Marino, P.; Matera, K.; Mattson, M. E.; Mazzacane, A.; Mazzanti, P.; McNulty, R.; Mehta, A.; Mehtala, P.; Mesropian, C.; Miao, T.; Mietlicki, D.; Mitra, A.; Miyake, H.; Moed, S.; Moggi, N.; Moon, C. S.; Moore, R.; Morello, M. J.; Mukherjee, A.; Muller, Th.; Murat, P.; Mussini, M.; Nachtman, J.; Nagai, Y.; Naganoma, J.; Nakano, I.; Napier, A.; Nett, J.; Nigmanov, T.; Nodulman, L.; Noh, S. Y.; Norniella, O.; Oakes, L.; Oh, S. H.; Oh, Y. D.; Okusawa, T.; Orava, R.; Ortolan, L.; Pagliarone, C.; Palencia, E.; Palni, P.; Papadimitriou, V.; Parker, W.; Pauletta, G.; Paulini, M.; Paus, C.; Phillips, T. J.; Piacentino, G.; Pianori, E.; Pilot, J.; Pitts, K.; Plager, C.; Pondrom, L.; Poprocki, S.; Potamianos, K.; Pranko, A.; Prokoshin, F.; Ptohos, F.; Punzi, G.; Redondo Fernández, I.; Renton, P.; Rescigno, M.; Rimondi, F.; Ristori, L.; Robson, A.; Rodriguez, T.; Rolli, S.; Ronzani, M.; Roser, R.; Rosner, J. L.; Ruffini, F.; Ruiz, A.; Russ, J.; Rusu, V.; Sakumoto, W. K.; Sakurai, Y.; Santi, L.; Sato, K.; Saveliev, V.; Savoy-Navarro, A.; Schlabach, P.; Schmidt, E. E.; Schwarz, T.; Scodellaro, L.; Scuri, F.; Seidel, S.; Seiya, Y.; Semenov, A.; Sforza, F.; Shalhout, S. Z.; Shears, T.; Shepard, P. F.; Shimojima, M.; Shochet, M.; Shreyber-Tecker, I.; Simonenko, A.; Sliwa, K.; Smith, J. R.; Snider, F. D.; Song, H.; Sorin, V.; St. Denis, R.; Stancari, M.; Stentz, D.; Strologas, J.; Sudo, Y.; Sukhanov, A.; Suslov, I.; Takemasa, K.; Takeuchi, Y.; Tang, J.; Tecchio, M.; Teng, P. K.; Thom, J.; Thomson, E.; Thukral, V.; Toback, D.; Tokar, S.; Tollefson, K.; Tomura, T.; Tonelli, D.; Torre, S.; Torretta, D.; Totaro, P.; Trovato, M.; Ukegawa, F.; Uozumi, S.; Vázquez, F.; Velev, G.; Vellidis, C.; Vernieri, C.; Vidal, M.; Vilar, R.; Vizán, J.; Vogel, M.; Volpi, G.; Wagner, P.; Wallny, R.; Wang, S. M.; Waters, D.; Wester, W. C.; Whiteson, D.; Wicklund, A. B.; Wilbur, S.; Williams, H. H.; Wilson, J. S.; Wilson, P.; Winer, B. L.; Wittich, P.; Wolbers, S.; Wolfe, H.; Wright, T.; Wu, X.; Wu, Z.; Yamamoto, K.; Yamato, D.; Yang, T.; Yang, U. K.; Yang, Y. C.; Yao, W.-M.; Yeh, G. P.; Yi, K.; Yoh, J.; Yorita, K.; Yoshida, T.; Yu, G. B.; Yu, I.; Zanetti, A. M.; Zeng, Y.; Zhou, C.; Zucchelli, S.; CDF Collaboration

2016-06-01

We measure the forward-backward asymmetry of the production of top-quark and antiquark pairs in proton-antiproton collisions at center-of-mass energy √{s }=1.96 TeV using the full data set collected by the Collider Detector at Fermilab (CDF) in Tevatron Run II corresponding to an integrated luminosity of 9.1 fb-1 . The asymmetry is characterized by the rapidity difference between top quarks and antiquarks (Δ y ) and measured in the final state with two charged leptons (electrons and muons). The inclusive asymmetry, corrected to the entire phase space at parton level, is measured to be AFBt t ¯=0.12 ±0.13 , consistent with the expectations from the standard model (SM) and previous CDF results in the final state with a single charged lepton. The combination of the CDF measurements of the inclusive AFBt t ¯ in both final states yields AFBt t ¯=0.160 ±0.045 , which is consistent with the SM predictions. We also measure the differential asymmetry as a function of Δ y . A linear fit to AFBt t ¯(|Δ y |), assuming zero asymmetry at Δ y =0 , yields a slope of α =0.14 ±0.15 , consistent with the SM prediction and the previous CDF determination in the final state with a single charged lepton. The combined slope of AFBt t ¯(|Δ y |) in the two final states is α =0.227 ±0.057 , which is 2.0 σ larger than the SM prediction.

Wnt-mediated down-regulation of Sp1 target genes by a transcriptional repressor Sp5

Czech Academy of Sciences Publication Activity Database

Fujimura, Naoko; Vacík, Tomáš; Machoň, Ondřej; Vlček, Čestmír; Scalabrin, S.; Speth, M.; Diep, D.; Krauss, S.; Kozmik, Zbyněk

2007-01-01

Roč. 282, č. 2 (2007), s. 1225-1237 ISSN 0021-9258 Institutional research plan: CEZ:AV0Z50520514 Keywords : Wnt -mediated signaling * Sp5 transcription factor * Sp1 target genes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.581, year: 2007

Gene transfection mediated by polyethyleneimine-polyethylene glycol nanocarrier prevents cisplatin-induced spiral ganglion cell damage

Directory of Open Access Journals (Sweden)

Guan-gui Chen

2015-01-01

Full Text Available Polyethyleneimine-polyethylene glycol (PEI-PEG, a novel nanocarrier, has been used for transfection and gene therapy in a variety of cells. In our previous study, we successfully carried out PEI-PEG-mediated gene transfer in spiral ganglion cells. It remains unclear whether PEI-PEG could be used for gene therapy with X-linked inhibitor of apoptosis protein (XIAP in the inner ear. In the present study, we performed PEI-PEG-mediated XIAP gene transfection in the cochlea of Sprague-Dawley rats, via scala tympani fenestration, before daily cisplatin injections. Auditory brainstem reflex tests demonstrated the protective effects of XIAP gene therapy on auditory function. Immunohistochemical staining revealed XIAP protein expression in the cytoplasm of cells in the spiral ganglion, the organ of Corti and the stria vascularis. Reverse transcription-PCR detected high levels of XIAP mRNA expression in the cochlea. The present findings suggest that PEI-PEG nanocarrier-mediated XIAP gene transfection results in XIAP expression in the cochlea, prevents damage to cochlear spiral ganglion cells, and protects hearing.

Investigating Gene Function in Cereal Rust Fungi by Plant-Mediated Virus-Induced Gene Silencing.

Science.gov (United States)

Panwar, Vinay; Bakkeren, Guus

2017-01-01

Cereal rust fungi are destructive pathogens, threatening grain production worldwide. Targeted breeding for resistance utilizing host resistance genes has been effective. However, breakdown of resistance occurs frequently and continued efforts are needed to understand how these fungi overcome resistance and to expand the range of available resistance genes. Whole genome sequencing, transcriptomic and proteomic studies followed by genome-wide computational and comparative analyses have identified large repertoire of genes in rust fungi among which are candidates predicted to code for pathogenicity and virulence factors. Some of these genes represent defence triggering avirulence effectors. However, functions of most genes still needs to be assessed to understand the biology of these obligate biotrophic pathogens. Since genetic manipulations such as gene deletion and genetic transformation are not yet feasible in rust fungi, performing functional gene studies is challenging. Recently, Host-induced gene silencing (HIGS) has emerged as a useful tool to characterize gene function in rust fungi while infecting and growing in host plants. We utilized Barley stripe mosaic virus-mediated virus induced gene silencing (BSMV-VIGS) to induce HIGS of candidate rust fungal genes in the wheat host to determine their role in plant-fungal interactions. Here, we describe the methods for using BSMV-VIGS in wheat for functional genomics study in cereal rust fungi.

Test of long scintillating counter prototypes for CDF-II

International Nuclear Information System (INIS)

Budagov, Yu.; Chirikov-Zorin, I.; Pukhov, O.; Incagli, M.; Leone, S.; Menzione, A.; Pauletta, G.; Tokar, S.

2000-01-01

New type long (up to 3 m) scintillating counter prototypes, developed for CDF-II, have been tested. The shift-spectrum fiber ribbons were used for light collection, and modern ultra compact photomultipliers R5600 were used for light detection. The efficiency for m.i.p. was excellent for all prototypes. The light yield from the far end of the counters was found to be more than 20 photoelectrons

Rapidity gaps between jets at D0 and CDF

International Nuclear Information System (INIS)

Bertram, I.

1995-08-01

Results are presented from analyses of particle multiplicity distributions between high transverse energy jets produced at the Fermilab Tevatron p bar p collider at √s = 1.8 Tev. D0 and CDF examine the particle multiplicity distribution between the two highest transverse energy jets. Both experiments observe a significant excess of events at low tagged particle multiplicity which is consistent with a strongly interacting color-singlet exchange process

Measurements of the top-quark decay width and mass at CDF using the template method.

Energy Technology Data Exchange (ETDEWEB)

Tang, Jian [Univ. of Chicago, IL (United States)

2012-05-10

Measurements of the top quark decay width and mass are presented using the tt events produced in p p collisions at Fermilab's Tevatron collider and collected by the CDF II detector. A data sample corresponding to 4.3 fb^-1 of integrated luminosity is used for the top quark width measurement. Two estimators, the reconstructed top quark mass and the mass of hadronically decaying W boson that comes from the top-quark decay are reconstructed for each event and compared with templates of different input top quark widths and deviations from nominal CDF jet energy scale (ΔJES) to perform a simultaneous fit for both parameters. ΔJES is used for the in situ calibration of the jet energy scale at CDF. By applying a Feldman-Cousins limit-setting approach, we establish an upper limit at 95% confidence level (CL) of Γtop < 7.6 GeV and a two-sided 68% CL interval of (0.3 GeV, 4.4) GeV assuming a top quark mass of 172.5 GeV/c², which are consistent with the standard model prediction. The measurement of the top quark mass uses a data sample of tt events in 5.7 fb^-1 of integrated luminosity collected by the same detector. Candidate events in the top quark mass measurement are required to have large missing transverse energy, no identified charged leptons, and four, five, or six jets with at least one jet tagged as coming from a b quark. This analysis considers events from the semileptonic tt decay channel, including events that contain tau leptons. The measurement is based on a multidimensional template method, in a similar way to the top quark width measurement, and the top quark mass is measured to be Mtop = 172.32 ± 2.37 ± 0.98 GeV/c² .

Agrobacterium mediated transient gene silencing (AMTS in Stevia rebaudiana: insights into steviol glycoside biosynthesis pathway.

Directory of Open Access Journals (Sweden)

Praveen Guleria

Full Text Available Steviol glycoside biosynthesis pathway has emerged as bifurcation from ent-kaurenoic acid, substrate of methyl erythritol phosphate pathway that also leads to gibberellin biosynthesis. However, the genetic regulation of steviol glycoside biosynthesis has not been studied. So, in present study RNA interference (RNAi based Agrobacterium mediated transient gene silencing (AMTS approach was followed. SrKA13H and three SrUGTs (SrUGT85C2, SrUGT74G1 and SrUGT76G1 genes encoding ent-kaurenoic acid-13 hydroxylase and three UDP glycosyltransferases of steviol glycoside biosynthesis pathway were silenced in Stevia rebaudiana to understand its molecular mechanism and association with gibberellins.RNAi mediated AMTS of SrKA13H and three SrUGTs has significantly reduced the expression of targeted endogenous genes as well as total steviol glycoside accumulation. While gibberellins (GA3 content was significantly enhanced on AMTS of SrUGT85C2 and SrKA13H. Silencing of SrKA13H and SrUGT85C2 was found to block the metabolite flux of steviol glycoside pathway and shifted it towards GA3 biosynthesis. Further, molecular docking of three SrUGT proteins has documented highest affinity of SrUGT76G1 for the substrates of alternate pathways synthesizing steviol glycosides. This could be a plausible reason for maximum reduction in steviol glycoside content on silencing of SrUGT76G1 than other genes.SrKA13H and SrUGT85C2 were identified as regulatory genes influencing carbon flux between steviol glycoside and gibberellin biosynthesis. This study has also documented the existence of alternate steviol glycoside biosynthesis route.

Operation of the CDF Silicon Vertex Detector with colliding beams at Fermilab

International Nuclear Information System (INIS)

Bedeschi, F.; Bolognesi, V.; Dell'Agnello, S.; Galeotti, S.; Grieco, G.; Mariotti, M.; Menzione, A.; Punzi, G.; Raffaelli, F.; Ristori, L.; Tartarelli, F.; Turini, N.; Wenzel, H.; Zetti, F.; Bailey, M.W.; Garfinkel, A.F.; Kruse, M.C.; Shaw, N.M.; Carithers, W.C.; Ely, R.; Haber, C.; Holland, S.; Kleinfelder, S.; Merrick, T.; Schneider, O.; Wester, W.; Wong, M.; Yao, W.; Carter, H.; Flaugher, B.; Nelson, C.; Segler, S.; Shaw, T.; Tkaczyk, S.; Turner, K.; Wesson, T.R.; Barnett, B.; Boswell, C.; Skarha, J.; Snider, F.D.; Spies, A.; Tseng, J.; Vejcik, S.; Amidei, D.; Derwent, P.F.; Song, T.Y.; Dunn, A.; Gold, M.; Matthews, J.; Bacchetta, N.; Azzi, P.; Bisello, D.; Busetto, G.; Castro, A.; Loreti, M.; Pescara, L.; Tipton, P.; Watts, G.

1992-10-01

In this paper we briefly describe the main features of the CDF Silicon Vertex Detector (SVX) and discuss its performance during actual colliding beam operation at the Fermilab Tevatron. Details on S/N ratio, alignment, resolution and efficiency are given

Adaptor protein complex 2-mediated, clathrin-dependent endocytosis, and related gene activities, are a prominent feature during maturation stage amelogenesis.

Science.gov (United States)

Lacruz, Rodrigo S; Brookes, Steven J; Wen, Xin; Jimenez, Jaime M; Vikman, Susanna; Hu, Ping; White, Shane N; Lyngstadaas, S Petter; Okamoto, Curtis T; Smith, Charles E; Paine, Michael L

2013-03-01

Molecular events defining enamel matrix removal during amelogenesis are poorly understood. Early reports have suggested that adaptor proteins (AP) participate in ameloblast-mediated endocytosis. Enamel formation involves the secretory and maturation stages, with an increase in resorptive function during the latter. Here, using real-time PCR, we show that the expression of clathrin and adaptor protein subunits are upregulated in maturation stage rodent enamel organ cells. AP complex 2 (AP-2) is the most upregulated of the four distinct adaptor protein complexes. Immunolocalization confirms the presence of AP-2 and clathrin in ameloblasts, with strongest reactivity at the apical pole. These data suggest that the resorptive functions of enamel cells involve AP-2 mediated, clathrin-dependent endocytosis, thus implying the likelihood of specific membrane-bound receptor(s) of enamel matrix protein debris. The mRNA expression of other endocytosis-related gene products is also upregulated during maturation including: lysosomal-associated membrane protein 1 (Lamp1); cluster of differentiation 63 and 68 (Cd63 and Cd68); ATPase, H(+) transporting, lysosomal V0 subunit D2 (Atp6v0d2); ATPase, H(+) transporting, lysosomal V1 subunit B2 (Atp6v1b2); chloride channel, voltage-sensitive 7 (Clcn7); and cathepsin K (Ctsk). Immunohistologic data confirms the expression of a number of these proteins in maturation stage ameloblasts. The enamel of Cd63-null mice was also examined. Despite increased mRNA and protein expression in the enamel organ during maturation, the enamel of Cd63-null mice appeared normal. This may suggest inherent functional redundancies between Cd63 and related gene products, such as Lamp1 and Cd68. Ameloblast-like LS8 cells treated with the enamel matrix protein complex Emdogain showed upregulation of AP-2 and clathrin subunits, further supporting the existence of a membrane-bound receptor-regulated pathway for the endocytosis of enamel matrix proteins. These data

Search for Electroweak Single-Top Quark Production with the CDF II Experiment

Energy Technology Data Exchange (ETDEWEB)

Buehler, Matthias; /Karlsruhe U., EKP

2006-08-01

The CDF II experiment and the Tevatron proton-antiproton collider are parts of the Fermi National Laboratories (Fermilab). The Fermilab is located in the vicinity of Chicago, USA. Today, the Tevatron is the only collider which is able to produce the heaviest known elementary particle, the top quark. The top quark was discovered at the Tevatron by the CDF and the D0 collaborations in 1995 [1]. So far, all the top quarks found are produced via the strong interaction as top-antitop pairs. The Standard Model of elementary particle physics also predicts single-top quark production via the electroweak interaction. This production mode has not yet been observed. The CDF and the D0 collaborations have set upper limits on the cross section for that process in Run I [2, 3] and improved those results in Run II [4, 5]. Single-top quark production is one of the major interests in Run II of the Tevatron as it offers several ways to test the Standard Model and to search for potential physics beyond the Standard Model. The measurement of the cross section of singly produced top quarks via the electroweak interaction offers the possibility to determine the Cabbibo-Kobayashi-Maskawa (CKM) matrix element V{sub tb} directly. The CKM matrix defines the transformation from the eigenstates of the electroweak interactions to the mass eigenstates of the quarks. V{sub tb} gives the strength of the coupling at the Wtb vertex. The single-top quark is produced at this vertex and therefore the cross section of the single-top quark production is directly proportional to |V{sub tb}|{sup 2}. In the Standard Model, three generations of quarks and the unitarity of the CKM matrix are predicted. This leads to V{sub tb} {approx} 1. Up to now, there is no possibility to measure V{sub tb} without using the assumption that there are a certain number of quark generations. Since the measurement of the cross section of single-top quark production is independent of this assumption it could verify another

Imaging Herpes Simplex Virus Type 1 Amplicon Vector–Mediated Gene Expression in Human Glioma Spheroids

Directory of Open Access Journals (Sweden)

Christine Kaestle

2011-05-01

Full Text Available Vectors derived from herpes simplex virus type 1 (HSV-1 have great potential for transducing therapeutic genes into the central nervous system; however, inefficient distribution of vector particles in vivo may limit their therapeutic potential in patients with gliomas. This study was performed to investigate the extent of HSV-1 amplicon vector–mediated gene expression in a three-dimensional glioma model of multicellular spheroids by imaging highly infectious HSV-1 virions expressing green fluorescent protein (HSV-GFP. After infection or microscopy-guided vector injection of glioma spheroids at various spheroid sizes, injection pressures and injection times, the extent of HSV-1 vector–mediated gene expression was investigated via laser scanning microscopy. Infection of spheroids with HSV-GFP demonstrated a maximal depth of vector-mediated GFP expression at 70 to 80 μm. A > 80% transduction efficiency was reached only in small spheroids with a diameter of 90%. The results demonstrated that vector-mediated gene expression in glioma spheroids was strongly dependent on the mode of vector application—injection pressure and injection time being the most important parameters. The assessment of these vector application parameters in tissue models will contribute to the development of safe and efficient gene therapy protocols for clinical application.

RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe

International Nuclear Information System (INIS)

Smialowska, Agata; Djupedal, Ingela; Wang, Jingwen; Kylsten, Per; Swoboda, Peter; Ekwall, Karl

2014-01-01

Highlights: • Protein coding genes accumulate anti-sense sRNAs in fission yeast S. pombe. • RNAi represses protein-coding genes in S. pombe. • RNAi-mediated gene repression is post-transcriptional. - Abstract: RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe

New shower maximum trigger for electrons and photons at CDF

International Nuclear Information System (INIS)

Amidei, D.; Burkett, K.; Gerdes, D.; Miao, C.; Wolinski, D.

1994-01-01

For the 1994 Tevatron collider run, CDF has upgraded the electron and photo trigger hardware to make use of shower position and size information from the central shower maximum detector. For electrons, the upgrade has resulted in a 50% reduction in backgrounds while retaining approximately 90% of the signal. The new trigger also eliminates the background to photon triggers from single-phototube spikes

New shower maximum trigger for electrons and photons at CDF

International Nuclear Information System (INIS)

Gerdes, D.

1994-08-01

For the 1994 Tevatron collider run, CDF has upgraded the electron and photon trigger hardware to make use of shower position and size information from the central shower maximum detector. For electrons, the upgrade has resulted in a 50% reduction in backgrounds while retaining approximately 90% of the signal. The new trigger also eliminates the background to photon triggers from single-phototube discharge

Silencing the SpMPK1, SpMPK2, and SpMPK3 Genes in Tomato Reduces Abscisic Acid—Mediated Drought Tolerance

Directory of Open Access Journals (Sweden)

Yan Liang

2013-11-01

Full Text Available Drought is a major threat to agriculture production worldwide. Mitogen-activated protein kinases (MAPKs play a pivotal role in sensing and converting stress signals into appropriate responses so that plants can adapt and survive. To examine the function of MAPKs in the drought tolerance of tomato plants, we silenced the SpMPK1, SpMPK2, and SpMPK3 genes in wild-type plants using the virus-induced gene silencing (VIGS method. The results indicate that silencing the individual genes or co-silencing SpMPK1, SpMPK2, and SpMPK3 reduced the drought tolerance of tomato plants by varying degrees. Co-silencing SpMPK1 and SpMPK2 impaired abscisic acid (ABA-induced and hydrogen peroxide (H2O2-induced stomatal closure and enhanced ABA-induced H2O2 production. Similar results were observed when silencing SpMPK3 alone, but not when SpMPK1 and SpMPK2 were individually silenced. These data suggest that the functions of SpMPK1 and SpMPK2 are redundant, and they overlap with that of SpMPK3 in drought stress signaling pathways. In addition, we found that SpMPK3 may regulate H2O2 levels by mediating the expression of CAT1. Hence, SpMPK1, SpMPK2, and SpMPK3 may play crucial roles in enhancing tomato plants’ drought tolerance by influencing stomatal activity and H2O2 production via the ABA-H2O2 pathway.

Resveratrol inhibits LXRα-dependent hepatic lipogenesis through novel antioxidant Sestrin2 gene induction

Energy Technology Data Exchange (ETDEWEB)

Jin, So Hee; Yang, Ji Hye; Shin, Bo Yeon; Seo, Kyuhwa; Shin, Sang Mi [College of Pharmacy, Chosun University, Gwangju 501-759 (Korea, Republic of); Cho, Il Je, E-mail: skek023@dhu.ac.kr [MRC-GHF, College of Korean Medicine, Daegu Haany University, Gyeongsan, Gyeongsangbukdo 712-715 (Korea, Republic of); Ki, Sung Hwan, E-mail: shki@chosun.ac.kr [College of Pharmacy, Chosun University, Gwangju 501-759 (Korea, Republic of)

2013-08-15

Liver X receptor-α (LXRα), a member of the nuclear receptor superfamily of ligand-activated transcription factors, regulates de novo fatty acid synthesis that leads to stimulate hepatic steatosis. Although, resveratrol has beneficial effects on metabolic disease, it is not known whether resveratrol affects LXRα-dependent lipogenic gene expression. This study investigated the effect of resveratrol in LXRα-mediated lipogenesis and the underlying molecular mechanism. Resveratrol inhibited the ability of LXRα to activate sterol regulatory element binding protein-1c (SREBP-1c) and thereby inhibited target gene expression in hepatocytes. Moreover, resveratrol decreased LXRα–RXRα DNA binding activity and LXRE-luciferase transactivation. Resveratrol is known to activate Sirtuin 1 (Sirt1) and AMP-activated protein kinase (AMPK), although its precise mechanism of action remains controversial. We found that the ability of resveratrol to repress T0901317-induced SREBP-1c expression was not dependent on AMPK and Sirt1. It is well established that hepatic steatosis is associated with antioxidant and redox signaling. Our data showing that expression of Sestrin2 (Sesn2), which is a novel antioxidant gene, was significantly down-regulated in the livers of high-fat diet-fed mice. Moreover, resveratrol up-regulated Sesn2 expression, but not Sesn1 and Sesn3. Sesn2 overexpression repressed LXRα-activated SREBP-1c expression and LXRE-luciferase activity. Finally, Sesn2 knockdown using siRNA abolished the effect of resveratrol in LXRα-induced FAS luciferase gene transactivation. We conclude that resveratrol affects Sesn2 gene induction and contributes to the inhibition of LXRα-mediated hepatic lipogenesis. - Highlights: • We investigated the effect of resveratrol in LXRα-mediated lipogenesis. • Resveratrol attenuated the ability of the LXRα-mediated lipogenic gene expression. • Resveratrol’s effects on T090-induced lipogenesis is not dependent on Sirt1 or AMPK. �

Resveratrol inhibits LXRα-dependent hepatic lipogenesis through novel antioxidant Sestrin2 gene induction

International Nuclear Information System (INIS)

Jin, So Hee; Yang, Ji Hye; Shin, Bo Yeon; Seo, Kyuhwa; Shin, Sang Mi; Cho, Il Je; Ki, Sung Hwan

2013-01-01

Liver X receptor-α (LXRα), a member of the nuclear receptor superfamily of ligand-activated transcription factors, regulates de novo fatty acid synthesis that leads to stimulate hepatic steatosis. Although, resveratrol has beneficial effects on metabolic disease, it is not known whether resveratrol affects LXRα-dependent lipogenic gene expression. This study investigated the effect of resveratrol in LXRα-mediated lipogenesis and the underlying molecular mechanism. Resveratrol inhibited the ability of LXRα to activate sterol regulatory element binding protein-1c (SREBP-1c) and thereby inhibited target gene expression in hepatocytes. Moreover, resveratrol decreased LXRα–RXRα DNA binding activity and LXRE-luciferase transactivation. Resveratrol is known to activate Sirtuin 1 (Sirt1) and AMP-activated protein kinase (AMPK), although its precise mechanism of action remains controversial. We found that the ability of resveratrol to repress T0901317-induced SREBP-1c expression was not dependent on AMPK and Sirt1. It is well established that hepatic steatosis is associated with antioxidant and redox signaling. Our data showing that expression of Sestrin2 (Sesn2), which is a novel antioxidant gene, was significantly down-regulated in the livers of high-fat diet-fed mice. Moreover, resveratrol up-regulated Sesn2 expression, but not Sesn1 and Sesn3. Sesn2 overexpression repressed LXRα-activated SREBP-1c expression and LXRE-luciferase activity. Finally, Sesn2 knockdown using siRNA abolished the effect of resveratrol in LXRα-induced FAS luciferase gene transactivation. We conclude that resveratrol affects Sesn2 gene induction and contributes to the inhibition of LXRα-mediated hepatic lipogenesis. - Highlights: • We investigated the effect of resveratrol in LXRα-mediated lipogenesis. • Resveratrol attenuated the ability of the LXRα-mediated lipogenic gene expression. • Resveratrol’s effects on T090-induced lipogenesis is not dependent on Sirt1 or AMPK. �

The ULT1 and ULT2 trxG genes play overlapping roles in Arabidopsis development and gene regulation.

Science.gov (United States)

Monfared, Mona M; Carles, Cristel C; Rossignol, Pascale; Pires, Helena R; Fletcher, Jennifer C

2013-09-01

The epigenetic regulation of gene expression is critical for ensuring the proper deployment and stability of defined genome transcription programs at specific developmental stages. The cellular memory of stable gene expression states during animal and plant development is mediated by the opposing activities of Polycomb group (PcG) factors and trithorax group (trxG) factors. Yet, despite their importance, only a few trxG factors have been characterized in plants and their roles in regulating plant development are poorly defined. In this work, we report that the closely related Arabidopsis trxG genes ULTRAPETALA1 (ULT1) and ULT2 have overlapping functions in regulating shoot and floral stem cell accumulation, with ULT1 playing a major role but ULT2 also making a minor contribution. The two genes also have a novel, redundant activity in establishing the apical–basal polarity axis of the gynoecium, indicating that they function in differentiating tissues. Like ULT1 proteins, ULT2 proteins have a dual nuclear and cytoplasmic localization, and the two proteins physically associate in planta. Finally, we demonstrate that ULT1 and ULT2 have very similar overexpression phenotypes and regulate a common set of key development target genes, including floral MADS-box genes and class I KNOX genes. Our results reveal that chromatin remodeling mediated by the ULT1 and ULT2 proteins is necessary to control the development of meristems and reproductive organs. They also suggest that, like their animal counterparts, plant trxG proteins may function in multi-protein complexes to up-regulate the expression of key stage- and tissue-specific developmental regulatory genes.

Pollen-Mediated Movement of Herbicide Resistance Genes in Lolium rigidum.

Directory of Open Access Journals (Sweden)

Iñigo Loureiro

Full Text Available The transfer of herbicide resistance genes by pollen is a major concern in cross-pollinated species such as annual ryegrass (Lolium rigidum. A two-year study was conducted in the greenhouse, under favorable conditions for pollination, to generate information on potential maximum cross-pollination. This maximum cross-pollination rate was 56.1%. A three-year field trial was also conducted to study the cross-pollination rates in terms of distance and orientation to an herbicide-resistant pollen source. Under field conditions, cross-pollination rates varied from 5.5% to 11.6% in plants adjacent to the pollen source and decreased with increasing distances (1.5 to 8.9% at 15 m distance and up to 4.1% at 25 m in the downwind direction. Environmental conditions influenced the cross-pollination both under greenhouse and field conditions. Data were fit to an exponential decay model to predict gene flow at increasing distances. This model predicted an average gene flow of 7.1% when the pollen donor and recipient plants were at 0 m distance from each other. Pollen-mediated gene flow declined by 50% at 16.7 m from the pollen source, yet under downwind conditions gene flow of 5.2% was predicted at 25 m, the farthest distance studied. Knowledge of cross-pollination rates will be useful for assessing the spread of herbicide resistance genes in L. rigidum and in developing appropriate strategies for its mitigation.

J/ψ production and beauty physics at CDF

International Nuclear Information System (INIS)

Smith, D.A.

1991-01-01

The Fermilab proton-antiproton collider makes about 50 beauty mesons per second, giving a unique opportunity to test the higher order QCD calculations that have recently been completed. CDF, the Collider Detector at Fermilab, finished its first large-scale data run in June 1989, recording 4.7 pb -1 using a variety of triggers. As of this workshop, only half of the data have been fully reconstructed, and the beauty analysis is at an early stage. Therefore this paper shows only work-in-progress on the analysis methods. The authors estimate the B cross section to be consistent with theoretical predictions. CDF is an azimuthally symmetric detector with good solid angle coverage, consisting of high-granularity hadron calorimeters and shower counters, high-resolution tracking in an 1.4-T axial magnetic field, a vertex time projection chamber, and muon tracking. This paper shows the geometry of the muon chambers. Sets of muon chambers lie behind five interaction lengths of calorimetry, over the angle 56 degrees < θ < 124 degrees from the beam. They have four layers of δφ ∼ 1 degree cells, using charge division to measure the longitudinal track coordinate and drift time for the transverse coordinate. A level-1 trigger rejects low transverse momentum tracks by testing the drift-time difference between alternate layers of the chambers, which amounts to a cut on the bending of the track in the magnetic field

Top quark pair production and top quark properties at CDF

Energy Technology Data Exchange (ETDEWEB)

Moon, Chang-Seong [INFN, Pisa

2016-06-02

We present the most recent measurements of top quark pairs production and top quark properties in proton-antiproton collisions with center-of-mass energy of 1.96 TeV using CDF II detector at the Tevatron. The combination of top pair production cross section measurements and the direct measurement of top quark width are reported. The test of Standard Model predictions for top quark decaying into $b$-quarks, performed by measuring the ratio $R$ between the top quark branching fraction to $b$-quark and the branching fraction to any type of down quark is shown. The extraction of the CKM matrix element $|V_{tb}|$ from the ratio $R$ is discussed. We also present the latest measurements on the forward-backward asymmetry ($A_{FB}$) in top anti-top quark production. With the full CDF Run II data set, the measurements are performed in top anti-top decaying to final states that contain one or two charged leptons (electrons or muons). In addition, we combine the results of the leptonic forward-backward asymmetry in $t\\bar t$ system between the two final states. All the results show deviations from the next-to-leading order (NLO) standard model (SM) calculation.

Cadmium-mediated disruption of cortisol biosynthesis involves suppression of corticosteroidogenic genes in rainbow trout

International Nuclear Information System (INIS)

Sandhu, Navdeep; Vijayan, Mathilakath M.

2011-01-01

Cadmium is widely distributed in the aquatic environment and is toxic to fish even at sublethal concentrations. This metal is an endocrine disruptor, and one well established role in teleosts is the suppression of adrenocorticotrophic hormone (ACTH)-stimulated cortisol biosynthesis by the interrenal tissue. However the mechanism(s) leading to this steroid suppression is poorly understood. We tested the hypothesis that cadmium targets genes encoding proteins critical for corticosteroid biosynthesis, including melanocortin 2 receptor (MC2R), steroidogenic acute regulatory protein (StAR) and cytochrome P450 side chain cleavage enzyme (P450scc), in rainbow trout (Oncorhynchus mykiss). To test this, head kidney slices (containing the interrenal tissues) were incubated in vitro with cadmium chloride (0, 10, 100 and 1000 nM) for 4 h either in the presence or absence of ACTH (0.5 IU/mL). In the unstimulated head kidney slices, cadmium exposure did not affect basal cortisol secretion and the mRNA levels of MC2R and P450scc, while StAR gene expression was significantly reduced. Cadmium exposure significantly suppressed ACTH-stimulated cortisol production in a dose-related fashion. This cadmium-mediated suppression in corticosteroidogenesis corresponded with a significant reduction in MC2R, StAR and P450scc mRNA levels in trout head kidney slices. The inhibition of ACTH-stimulated cortisol production and suppression of genes involved in corticosteroidogenesis by cadmium were completely abolished in the presence of 8-Bromo-cAMP (a cAMP analog). Overall, cadmium disrupts the expression of genes critical for corticosteroid biosynthesis in rainbow trout head kidney slices. However, the rescue of cortisol production as well as StAR and P450scc gene expressions by cAMP analog suggests that cadmium impact occurs upstream of cAMP production. We propose that MC2R signaling, the primary step in ACTH-induced cortocosteroidogenesis, is a key target for cadmium-mediated disruption of

Cadmium-mediated disruption of cortisol biosynthesis involves suppression of corticosteroidogenic genes in rainbow trout

Energy Technology Data Exchange (ETDEWEB)

Sandhu, Navdeep [Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Vijayan, Mathilakath M., E-mail: mvijayan@uwaterloo.ca [Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada)

2011-05-15

Cadmium is widely distributed in the aquatic environment and is toxic to fish even at sublethal concentrations. This metal is an endocrine disruptor, and one well established role in teleosts is the suppression of adrenocorticotrophic hormone (ACTH)-stimulated cortisol biosynthesis by the interrenal tissue. However the mechanism(s) leading to this steroid suppression is poorly understood. We tested the hypothesis that cadmium targets genes encoding proteins critical for corticosteroid biosynthesis, including melanocortin 2 receptor (MC2R), steroidogenic acute regulatory protein (StAR) and cytochrome P450 side chain cleavage enzyme (P450scc), in rainbow trout (Oncorhynchus mykiss). To test this, head kidney slices (containing the interrenal tissues) were incubated in vitro with cadmium chloride (0, 10, 100 and 1000 nM) for 4 h either in the presence or absence of ACTH (0.5 IU/mL). In the unstimulated head kidney slices, cadmium exposure did not affect basal cortisol secretion and the mRNA levels of MC2R and P450scc, while StAR gene expression was significantly reduced. Cadmium exposure significantly suppressed ACTH-stimulated cortisol production in a dose-related fashion. This cadmium-mediated suppression in corticosteroidogenesis corresponded with a significant reduction in MC2R, StAR and P450scc mRNA levels in trout head kidney slices. The inhibition of ACTH-stimulated cortisol production and suppression of genes involved in corticosteroidogenesis by cadmium were completely abolished in the presence of 8-Bromo-cAMP (a cAMP analog). Overall, cadmium disrupts the expression of genes critical for corticosteroid biosynthesis in rainbow trout head kidney slices. However, the rescue of cortisol production as well as StAR and P450scc gene expressions by cAMP analog suggests that cadmium impact occurs upstream of cAMP production. We propose that MC2R signaling, the primary step in ACTH-induced cortocosteroidogenesis, is a key target for cadmium-mediated disruption of

Modelling Energy Loss Mechanisms and a Determination of the Electron Energy Scale for the CDF Run II W Mass Measurement

Energy Technology Data Exchange (ETDEWEB)

Riddick, Thomas [Univ. College London, Bloomsbury (United Kingdom)

2012-06-15

The calibration of the calorimeter energy scale is vital to measuring the mass of the W boson at CDF Run II. For the second measurement of the W boson mass at CDF Run II, two independent simulations were developed. This thesis presents a detailed description of the modification and validation of Bremsstrahlung and pair production modelling in one of these simulations, UCL Fast Simulation, comparing to both geant4 and real data where appropriate. The total systematic uncertainty on the measurement of the W boson mass in the W → ev_e channel from residual inaccuracies in Bremsstrahlung modelling is estimated as 6.2 ±3.2 MeV/c² and the total systematic uncertainty from residual inaccuracies in pair production modelling is estimated as 2.8± 2.7 MeV=c². Two independent methods are used to calibrate the calorimeter energy scale in UCL Fast Simulation; the results of these two methods are compared to produce a measurement of the Z boson mass as a cross-check on the accuracy of the simulation.

Observation of Electroweak Single Top-Quark Production with the CDF II Experiment

International Nuclear Information System (INIS)

Lueck, Jan

2009-01-01

presents a neural network search for combined as well as separate s- and t-channel single top-quark production with the CDF II experiment at the Tevatron using 3.2 fb -1 of collision data. It is the twelfth thesis dealing with single top-quark production performed within the CDF Collaboration, whereas three have been done in Run I and eight in Run II

Observation of Electroweak Single Top-Quark Production with the CDF II Experiment

Energy Technology Data Exchange (ETDEWEB)

Lueck, Jan [Karlsruhe Inst. of Technology (Germany)

2009-07-24

significance. This thesis presents a neural network search for combined as well as separate s- and t-channel single top-quark production with the CDF II experiment at the Tevatron using 3.2 fb^-1 of collision data. It is the twelfth thesis dealing with single top-quark production performed within the CDF Collaboration, whereas three have been done in Run I and eight in Run II.

Agrobacterium Mediated Transient Gene Silencing (AMTS) in Stevia rebaudiana: Insights into Steviol Glycoside Biosynthesis Pathway

Science.gov (United States)

Guleria, Praveen; Yadav, Sudesh Kumar

2013-01-01

Background Steviol glycoside biosynthesis pathway has emerged as bifurcation from ent-kaurenoic acid, substrate of methyl erythritol phosphate pathway that also leads to gibberellin biosynthesis. However, the genetic regulation of steviol glycoside biosynthesis has not been studied. So, in present study RNA interference (RNAi) based Agrobacterium mediated transient gene silencing (AMTS) approach was followed. SrKA13H and three SrUGTs (SrUGT85C2, SrUGT74G1 and SrUGT76G1) genes encoding ent-kaurenoic acid-13 hydroxylase and three UDP glycosyltransferases of steviol glycoside biosynthesis pathway were silenced in Stevia rebaudiana to understand its molecular mechanism and association with gibberellins. Methodology/Principal Findings RNAi mediated AMTS of SrKA13H and three SrUGTs has significantly reduced the expression of targeted endogenous genes as well as total steviol glycoside accumulation. While gibberellins (GA3) content was significantly enhanced on AMTS of SrUGT85C2 and SrKA13H. Silencing of SrKA13H and SrUGT85C2 was found to block the metabolite flux of steviol glycoside pathway and shifted it towards GA3 biosynthesis. Further, molecular docking of three SrUGT proteins has documented highest affinity of SrUGT76G1 for the substrates of alternate pathways synthesizing steviol glycosides. This could be a plausible reason for maximum reduction in steviol glycoside content on silencing of SrUGT76G1 than other genes. Conclusions SrKA13H and SrUGT85C2 were identified as regulatory genes influencing carbon flux between steviol glycoside and gibberellin biosynthesis. This study has also documented the existence of alternate steviol glycoside biosynthesis route. PMID:24023961

Evaluating the role of CRM1-mediated export for adenovirus gene expression

International Nuclear Information System (INIS)

Carter, Christoph C.; Izadpanah, Reza; Bridge, Eileen

2003-01-01

A complex of the Adenovirus (Ad) early region 1b 55-kDa (E1b-55kDa) and early region 4 ORF6 34-kDa (E4-34kDa) proteins promotes viral late gene expression. E1b-55kDa and E4-34kDa have leucine-rich nuclear export signals (NESs) similar to that of HIV Rev. It was proposed that E1b-55kDa and/or E4-34kDa might promote the export of Ad late mRNA via their Rev-like NESs, and the transport receptor CRM1. We treated infected cells with the cytotoxin leptomycin B to inhibit CRM1-mediated export; treatment initially delays the onset of late gene expression, but this activity completely recovers as the late phase progresses. We find that the E1b-55kDa NES is not required to promote late gene expression. Previous results showed that E4-34kDa-mediated late gene expression does not require an intact NES (J. Virol. 74 (2000), 6684-6688). Our results indicate that these Ad regulatory proteins promote late gene expression without intact NESs or active CRM1

Search for non-standard model signatures in the WZ/ZZ final state at CDF Run II

International Nuclear Information System (INIS)

Norman, Matthew

2009-01-01

This thesis discusses a search for non-Standard Model physics in heavy diboson production in the dilepton-dijet final state, using 1.9 fb -1 of data from the CDF Run II detector. New limits are set on the anomalous coupling parameters for ZZ and WZ production based on limiting the production cross-section at high (cflx s). Additionally limits are set on the direct decay of new physics to ZZ andWZ diboson pairs. The nature and parameters of the CDF Run II detector are discussed, as are the influences that it has on the methods of our analysis.

Search for non-standard model signatures in the WZ/ZZ final state at CDF run II

Energy Technology Data Exchange (ETDEWEB)

Norman, Matthew [Univ. of California, San Diego, CA (United States)

2009-01-01

This thesis discusses a search for non-Standard Model physics in heavy diboson production in the dilepton-dijet final state, using 1.9 fb ^-1 of data from the CDF Run II detector. New limits are set on the anomalous coupling parameters for ZZ and WZ production based on limiting the production cross-section at high š. Additionally limits are set on the direct decay of new physics to ZZ andWZ diboson pairs. The nature and parameters of the CDF Run II detector are discussed, as are the influences that it has on the methods of our analysis.

Nrf2 mediates redox adaptations to exercise

Directory of Open Access Journals (Sweden)

Aaron J. Done

2016-12-01

Full Text Available The primary aim of this review is to summarize the current literature on the effects of acute exercise and regular exercise on nuclear factor erythroid 2-related factor 2 (Nrf2 activity and downstream targets of Nrf2 signaling. Nrf2 (encoded in humans by the NFE2L2 gene is the master regulator of antioxidant defenses, a transcription factor that regulates expression of more than 200 cytoprotective genes. Increasing evidence indicates that Nrf2 signaling plays a key role in how oxidative stress mediates the beneficial effects of exercise. Episodic increases in oxidative stress induced through bouts of acute exercise stimulate Nrf2 activation and when applied repeatedly, as with regular exercise, leads to upregulation of endogenous antioxidant defenses and overall greater ability to counteract the damaging effects of oxidative stress. The evidence of Nrf2 activation in response to exercise across variety of tissues may be an important mechanism of how exercise exerts its well-known systemic effects that are not limited to skeletal muscle and myocardium. Additionally there are emerging data that results from animal studies translate to humans.

The CDF silicon vertex detector SVX and its upgrades

International Nuclear Information System (INIS)

Seidel, S.; Univ. of New Mexico, Albuquerque, NM

1994-11-01

The three generations of CDF silicon vertex detectors, SVX, SVX', and SVX II, are described. SVX, which operated during Tevatron run Ia, achieved 10.6 μm resolution in r - φ. SVX' is a radiation-hard device for run Ib with a similar but improved mechanical design and improved signal/noise. SVX II, which will be installed for run II, will track in three dimensions with radiation tolerance and electronics appropriate to a Main Injector environment

LncRNA H19 and Target Gene-mediated Cleft Palate Induced by TCDD.

Science.gov (United States)

Gao, Li Yun; Zhang, Feng Quan; Zhao, Wei Hui; Han, Guang Liang; Wang, Xiao; Li, Qiang; Gao, Shan Shan; Wu, Wei Dong

2017-09-01

This study investigated the role of long non-coding RNAs (lncRNAs) in the development of the palatal tissues. Cleft palates in mice were induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression levels of long non-coding RNA H19 (lncRNA H19) and insulin-like growth factor 2 (IGF2) gene were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The rate of occurrence of cleft palate was found to be 100% by TCDD exposure, and TCDD could cause short upper limb, cerebral fissure, webbed neck, and short neck. The expression levels of lncRNA H19 and IGF2 gene specifically showed embryo age-related differences on E13, E14, and E15 in the palatal tissues. The expression levels of lncRNA H19 and IGF2 gene showed an inverse relationship on E13, E14, and E15. These findings demonstrated that lncRNA H19 and IGF2 can mediate the development of mouse cleft palate. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Disruption of prefoldin-2 protein synthesis in root-knot nematodes via host-mediated gene silencing efficiently reduces nematode numbers and thus protects plants.

Science.gov (United States)

Ajjappala, Hemavathi; Chung, Ha Young; Sim, Joon-Soo; Choi, Inchan; Hahn, Bum-Soo

2015-03-01

The aim of this study is to demonstrate the feasibility of down-regulating endogeneous prefoldin-2 root-knot nematode transcripts by expressing dsRNA with sequence identity to the nematode gene in tobacco roots under the influence of strong Arabidopsis ubiquitin (UBQ1) promoter. Root-knot nematodes (RKNs) are sedentary endoparasites infecting a wide range of plant species. They parasitise the root system, thereby disrupting water and nutrient uptake and causing major reductions in crop yields. The most reliable means of controlling RKNs is via the use of soil fumigants such as methyl bromide. With the emergence of RNA interference (RNAi) technology, which permits host-mediated nematode gene silencing, a new strategy to control plant pathogens has become available. In the present study, we investigated host-induced RNAi gene silencing of prefoldin-2 in transgenic Nicotiana benthamiana. Reductions in prefoldin-2 mRNA transcript levels were observed when nematodes were soaked in a dsRNA solution in vitro. Furthermore, nematode reproduction was suppressed in RNAi transgenic lines, as evident by reductions in the numbers of root knots (by 34-60 % in independent RNAi lines) and egg masses (by 33-58 %). Endogenous expression of prefoldin-2, analysed via real-time polymerase chain reaction and Western blotting, revealed that the gene was strongly expressed in the pre-parasitic J2 stage. Our observations demonstrate the relevance and potential importance of targeting the prefoldin gene during the nematode life cycle. The work also suggests that further improvements in silencing efficiency in economically important crops can be accomplished using RNAi directed against plant-parasitic nematodes.

MicroRNA-Mediated Gene Silencing in Plant Defense and Viral Counter-Defense

Directory of Open Access Journals (Sweden)

Sheng-Rui Liu

2017-09-01

Full Text Available MicroRNAs (miRNAs are non-coding RNAs of approximately 20–24 nucleotides in length that serve as central regulators of eukaryotic gene expression by targeting mRNAs for cleavage or translational repression. In plants, miRNAs are associated with numerous regulatory pathways in growth and development processes, and defensive responses in plant–pathogen interactions. Recently, significant progress has been made in understanding miRNA-mediated gene silencing and how viruses counter this defense mechanism. Here, we summarize the current knowledge and recent advances in understanding the roles of miRNAs involved in the plant defense against viruses and viral counter-defense. We also document the application of miRNAs in plant antiviral defense. This review discusses the current understanding of the mechanisms of miRNA-mediated gene silencing and provides insights on the never-ending arms race between plants and viruses.

Search for a $Z(4430)^{\\pm} \\to \\psi(2S)\\pi^{\\pm}$ resonance in hadron collisions at CDF II

Energy Technology Data Exchange (ETDEWEB)

Rubbo, Francesco [Univ. of Turin, Torino (Italy)

2010-01-01

The work described in this thesis is the first search for a Z^-(4430) resonance in hadron collisions and has been conceived, carried out and concluded entirely by the author. An ad-hoc analysis framework has been developed based on reconstruction code already consolidated in other analysis, adapted and modified for the purpose of this work. The progress of the work has been periodically presented in internal meetings of the CDF B-physics group and documented in internal notes.

Efficacy of In Vivo Electroporation-Mediated IL-10 Gene Delivery on Survival of Skin Flaps.

Science.gov (United States)

Seyed Jafari, S Morteza; Shafighi, Maziar; Beltraminelli, Helmut; Weber, Benedikt; Schmid, Ralph A; Geiser, Thomas; Gazdhar, Amiq; Hunger, Robert E

2018-04-01

Despite advances in understanding the underlying mechanisms of flap necrosis and improvement in surgical techniques, skin flap necrosis after reconstructive surgery remains a crucial issue. We investigated the efficacy of electroporation-mediated IL-10 gene transfer to random skin flap with an aim to accelerate wound healing and improve skin flap survival. Nine male Wistar rats (300-330 g) were divided in two groups (a) control group (n = 5), only surgery no gene transfer, and (b) experimental group, received electroporation-mediated IL-10 gene transfer 24 h before the surgery as prophylaxis (n = 4). Random skin flap (McFarlane) was performed in both groups. Planimetry, Laser Doppler imaging, and immunohistochemistry were used to evaluate the effect of IL-10 gene transfer between study groups at day 7. Electroporation-mediated IL-10 gene transfer decreased percentage of flap necrosis (p value = 0.0159) and increased cutaneous perfusion compared to the control group (p value = 0.0159). In addition, Spearman's rank correlation showed a significant negative correlation between percentage of flap necrosis and Laser Index (p value = 0.0083, r -0.83, respectively). Furthermore, significantly higher mean CD31 + vessel density was detected in the experimental group compared to the control group (p value = 0.0159). Additionally, semi-quantitative image analysis showed lower inflammatory cell count in experimental group compared to control group (p value = 0.0317). In vivo electroporation-mediated IL-10 gene transfer reduced necrosis, enhanced survival and vascularity in the ischemic skin flap.

CNPY2 inhibits MYLIP-mediated AR protein degradation in prostate cancer cells.

Science.gov (United States)

Ito, Saya; Ueno, Akihisa; Ueda, Takashi; Nakagawa, Hideo; Taniguchi, Hidefumi; Kayukawa, Naruhiro; Fujihara-Iwata, Atsuko; Hongo, Fumiya; Okihara, Koji; Ukimura, Osamu

2018-04-03

The androgen receptor (AR) is a ligand-dependent transcription factor that promotes prostate cancer (PC) cell growth through control of target gene expression. This report suggests that Canopy FGF signaling regulator 2 (CNPY2) controls AR protein levels in PC cells. We found that AR was ubiquitinated by an E3 ubiquitin ligase, myosin regulatory light chain interacting protein (MYLIP) and then degraded through the ubiquitin-proteasome pathway. CNPY2 decreased the ubiquitination activity of MYLIP by inhibition of interaction between MYLIP and UBE2D1, an E2 ubiquitin ligase. CNPY2 up-regulated gene expression of AR target genes such as KLK3 gene which encodes the prostate specific antigen (PSA) and promoted cell growth of PC cells. The cell growth inhibition by CNPY2 knockdown was rescued by AR overexpression. Furthermore, positive correlation of expression levels between CNPY2 and AR/AR target genes was observed in tissue samples from human prostate cancer patients. Together, these results suggested that CNPY2 promoted cell growth of PC cells by inhibition of AR protein degradation through MYLIP-mediated AR ubiquitination.

ABCF2, an Nrf2 target gene, contributes to cisplatin resistance in ovarian cancer cells.

Science.gov (United States)

Bao, Lingjie; Wu, Jianfa; Dodson, Matthew; Rojo de la Vega, Elisa Montserrat; Ning, Yan; Zhang, Zhenbo; Yao, Ming; Zhang, Donna D; Xu, Congjian; Yi, Xiaofang

2017-06-01

Previously, we have demonstrated that NRF2 plays a key role in mediating cisplatin resistance in ovarian cancer. To further explore the mechanism underlying NRF2-dependent cisplatin resistance, we stably overexpressed or knocked down NRF2 in parental and cisplatin-resistant human ovarian cancer cells, respectively. These two pairs of stable cell lines were then subjected to microarray analysis, where we identified 18 putative NRF2 target genes. Among these genes, ABCF2, a cytosolic member of the ABC superfamily of transporters, has previously been reported to contribute to chemoresistance in clear cell ovarian cancer. A detailed analysis on ABCF2 revealed a functional antioxidant response element (ARE) in its promoter region, establishing ABCF2 as an NRF2 target gene. Next, we investigated the contribution of ABCF2 in NRF2-mediated cisplatin resistance using our stable ovarian cancer cell lines. The NRF2-overexpressing cell line, containing high levels of ABCF2, was more resistant to cisplatin-induced apoptosis compared to its control cell line; whereas the NRF2 knockdown cell line with low levels of ABCF2, was more sensitive to cisplatin treatment than its control cell line. Furthermore, transient overexpression of ABCF2 in the parental cells decreased apoptosis and increased cell viability following cisplatin treatment. Conversely, knockdown of ABCF2 using specific siRNA notably increased apoptosis and decreased cell viability in cisplatin-resistant cells treated with cisplatin. This data indicate that the novel NRF2 target gene, ABCF2, plays a critical role in cisplatin resistance in ovarian cancer, and that targeting ABCF2 may be a new strategy to improve chemotherapeutic efficiency. © 2017 Wiley Periodicals, Inc.

Investigation of tt in the full hadronic final state at CDF with a neural network approach

CERN Document Server

Sidoti, A; Busetto, G; Castro, A; Dusini, S; Lazzizzera, I; Wyss, J

2001-01-01

In this work we present the results of a neural network (NN) approach to the measurement of the tt production cross-section and top mass in the all-hadronic channel, analyzing data collected at the Collider Detector at Fermilab (CDF) experiment. We have used a hardware implementation of a feedforward neural network, TOTEM, the product of a collaboration of INFN (Istituto Nazionale Fisica Nucleare)-IRST (Istituto per la Ricerca Scientifica e Tecnologica)-University of Trento, Italy. Particular attention has been paid to the evaluation of the systematics specifically related to the NN approach. The results are consistent with those obtained at CDF by conventional data selection techniques. (38 refs).

RNAi-mediated silencing of MAP kinase signalling genes (Fmk1, Hog1, and Pbs2) in Fusarium oxysporum reduces pathogenesis on tomato plants.

Science.gov (United States)

Pareek, Manish; Rajam, Manchikatla Venkat

2017-09-01

Fusarium oxysporum is a soil-borne plant fungal pathogen, and causes colossal losses in several crop plants including tomato. Effective control measures include the use of harmful fungicides and resistant cultivars, but these methods have shown limited success. Conventional methods to validate fungal pathogenic genes are labour intensive. Therefore, an alternative strategy is required to efficiently characterize unknown pathogenic genes. RNA interference (RNAi) has emerged as a potential tool to functionally characterize novel fungal pathogenic genes and also to control fungal diseases. Here, we report an efficient method to produce stable RNAi transformants of F. oxysporum using Agrobacterium-mediated transformation (AMT). We have transformed F. oxysporum spores using RNAi constructs of Fmk1, Hog1, and Pbs2 MAP kinase signalling genes. Fmk1 RNAi fungal transformants showed loss of surface hydrophobicity, reduced invasive growth on tomato fruits and hypo-virulence on tomato seedlings. Hog1 and Pbs2 RNAi transformants showed altered conidial size, and reduced invasive growth and pathogenesis. These results showed that AMT using RNAi constructs is an effective approach for dissecting the role of genes involved in pathogenesis in F. oxysporum and this could be extended for other fungal systems. The obtained knowledge can be easily translated for developing fungal resistant crops by RNAi. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Structural variations in the H-2 genes of AKR lymphomas.

NARCIS (Netherlands)

K. Hui; L. Minamide; N. Prandoni; H. Festenstein; F.G. Grosveld (Frank)

1986-01-01

textabstractK36.16 is an AKR H-2k thymoma which expresses an aberrant H-2Dd-like allospecificity, does not have a detectable amount of the H-2Kk syngeneic antigen and grows very easily in syngeneic mice. By DNA-mediated gene transfer experiments, we were able to obtain transformed clones which do

Control and data acquisition electronics for the CDF Silicon Vertex Detector

Energy Technology Data Exchange (ETDEWEB)

Turner, K.J.; Nelson, C.A.; Shaw, T.M.; Wesson, T.R.

1991-11-01

A control and data acquisition system has been designed for the CDF Silicon Vertex Detector (SVX) at Fermilab. The system controls the operation of the SVX Rev D integrated circuit (SVX IC) that is used to instrument a 46,000 microstrip silicon detector. The system consists of a Fastbus Sequencer, a Crate Controller and Digitizer modules. 11 refs., 6 figs., 3 tabs.

Control and data acquisition electronics for the CDF Silicon Vertex Detector

International Nuclear Information System (INIS)

Turner, K.J.; Nelson, C.A.; Shaw, T.M.; Wesson, T.R.

1991-11-01

A control and data acquisition system has been designed for the CDF Silicon Vertex Detector (SVX) at Fermilab. The system controls the operation of the SVX Rev D integrated circuit (SVX IC) that is used to instrument a 46,000 microstrip silicon detector. The system consists of a Fastbus Sequencer, a Crate Controller and Digitizer modules. 11 refs., 6 figs., 3 tabs

Control and data acquisition electronics for the CDF silicon vertex detector

International Nuclear Information System (INIS)

urner, K.J.; Nelson, C.A.; Shaw, T.M.; Wesson, T.R.

1992-01-01

This paper reports on a control and data acquisition system that has been designed for the CDF Silicon Vertex Detector (SVX) at Fermilab. The system controls the operation of the SVX Rev D integrated circuit (SVX IC) that is used to instrument a 46,000 microstrip silicon detector. The system consists of a Fastbus Sequencer, a Crate Controller and Digitizer modules

Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury.

Directory of Open Access Journals (Sweden)

Lin Cheng

Full Text Available Epigenetic predisposition is thought to critically contribute to adult-onset disorders, such as retinal neurodegeneration. The histone methyltransferase, enhancer of zeste homolog 2 (Ezh2, is transiently expressed in the perinatal retina, particularly enriched in retinal ganglion cells (RGCs. We previously showed that embryonic deletion of Ezh2 from retinal progenitors led to progressive photoreceptor degeneration throughout life, demonstrating a role for embryonic predisposition of Ezh2-mediated repressive mark in maintaining the survival and function of photoreceptors in the adult. Enrichment of Ezh2 in RGCs leads to the question if Ezh2 also mediates gene expression and function in postnatal RGCs, and if its deficiency changes RGC susceptibility to cell death under injury or disease in the adult. To test this, we generated mice carrying targeted deletion of Ezh2 from RGC progenitors driven by Math5-Cre (mKO. mKO mice showed no detectable defect in RGC development, survival, or cell homeostasis as determined by physiological analysis, live imaging, histology, and immunohistochemistry. Moreover, RGCs of Ezh2 deficient mice revealed similar susceptibility against glaucomatous and acute optic nerve trauma-induced neurodegeneration compared to littermate floxed or wild-type control mice. In agreement with the above findings, analysis of RNA sequencing of RGCs purified from Ezh2 deficient mice revealed few gene changes that were related to RGC development, survival and function. These results, together with our previous report, support a cell lineage-specific mechanism of Ezh2-mediated gene repression, especially those critically involved in cellular function and homeostasis.

Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E).

Science.gov (United States)

Parker, Jennifer K; Havird, Justin C; De La Fuente, Leonardo

2012-03-01

Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.

Diet-induced obesity mediated by the JNK/DIO2 signal transduction pathway

Science.gov (United States)

Vernia, Santiago; Cavanagh-Kyros, Julie; Barrett, Tamera; Jung, Dae Young; Kim, Jason K.; Davis, Roger J.

2013-01-01

The cJun N-terminal kinase (JNK) signaling pathway is a key mediator of metabolic stress responses caused by consuming a high-fat diet, including the development of obesity. To test the role of JNK, we examined diet-induced obesity in mice with targeted ablation of Jnk genes in the anterior pituitary gland. These mice exhibited an increase in the pituitary expression of thyroid-stimulating hormone (TSH), an increase in the blood concentration of thyroid hormone (T4), increased energy expenditure, and markedly reduced obesity compared with control mice. The increased amount of pituitary TSH was caused by reduced expression of type 2 iodothyronine deiodinase (Dio2), a gene that is required for T4-mediated negative feedback regulation of TSH expression. These data establish a molecular mechanism that accounts for the regulation of energy expenditure and the development of obesity by the JNK signaling pathway. PMID:24186979

Dual effects of adenovirus-mediated thrombopoietin gene transfer on hepatic oval cell proliferation and platelet counts

International Nuclear Information System (INIS)

Ichiba, Miho; Shimomura, Takashi; Murai, Rie; Hashiguchi, Koichi; Saeki, Toshiya; Yoshida, Yoko; Kanbe, Takamasa; Tanabe, Naotada; Tsuchiya, Hiroyuki; Miura, Norimasa; Tajima, Fumihito; Kurimasa, Akihiro; Hamada, Hirofumi; Shiota, Goshi

2005-01-01

Thrombopoietin (TPO) is the growth factor for megakaryocytes and platelets, however, it also acts as a potent regulator of stem cell proliferation. To examine the significance of TPO expression in proliferation of hepatic oval cells, the effect of adenovirus-mediated TPO gene transfer into livers of the Solt-Farber model, which mimics the condition where liver regeneration is impaired, was examined. Hepatic TPO mRNA peaked its expression at 2 days after gene transduction and then gradually decreased. The peripheral platelet number began to increase at 4 days (P < 0.05) and reached its plateau at 9 days (P < 0.01). Oval cells expressed c-Mpl, a receptor for TPO as well as immature hematopoietic and hepatocytic surface markers such as CD34 and AFP. The proliferating cell nuclear antigen-positive oval cells in rats into which adenovirus-TPO gene was transferred at 7 and 9 days were significantly greater than those in adenovirus-LacZ gene transferred (P < 0.05, each), and the total numbers of oval cells in the adenovirus-TPO gene transferred at 9 and 13 days were also significantly greater than those in adenovirus-LacZ gene transferred (P < 0.05, each). Expression of SCF protein was increased at 4, 7, and 9 days by TPO gene administration and that of c-Kit was increased at 4 and 7 days. These data suggest that adenovirus-mediated TPO gene transfer stimulated oval cell proliferation in liver as well as increasing peripheral platelet counts, emphasizing the significance of the TPO/c-Mpl system in proliferation of hepatic oval cells

Early induction of NRF2 antioxidant pathway by RHBDF2 mediates rapid cutaneous wound healing.

Science.gov (United States)

Hosur, Vishnu; Burzenski, Lisa M; Stearns, Timothy M; Farley, Michelle L; Sundberg, John P; Wiles, Michael V; Shultz, Leonard D

2017-04-01

Rhomboid family protein RHBDF2, an upstream regulator of the epidermal growth factor (EGF) receptor signaling, has been implicated in cutaneous wound healing. However, the underlying molecular mechanisms are still emerging. In humans, a gain-of-function mutation in the RHBDF2 gene accelerates cutaneous wound healing in an EGFR-dependent manner. Likewise, a gain-of-function mutation in the mouse Rhbdf2 gene (Rhbdf2 cub/cub ) shows a regenerative phenotype (rapid ear-hole closure) resulting from constitutive activation of the EGFR pathway. Because the RHBDF2-regulated EGFR pathway is relevant to cutaneous wound healing in humans, we used Rhbdf2 cub/cub mice to investigate the biological networks and pathways leading to accelerated ear-hole closure, with the goal of identifying therapeutic targets potentially effective in promoting wound healing in humans. Comparative transcriptome analysis of ear pinna tissue from Rhbdf2 cub/cub and Rhbdf2 +/+ mice at 0h, 15min, 2h, and 24h post-wounding revealed an early induction of the nuclear factor E2-related factor 2 (NRF2)-mediated anti-oxidative pathway (0h and 15min), followed by the integrin-receptor aggregation pathway (2h) as early-stage events immediately and shortly after wounding in Rhbdf2 cub/cub mice. Additionally, we observed genes enriched for the Fc fragment of the IgG receptor IIIa (FCGR3A)-mediated phagocytosis pathway 24h post-wounding. Although cutaneous wound repair in healthy individuals is generally non-problematic, it can be severely impaired due to aging, diabetes, and chronic inflammation. This study suggests that activation of the NRF2-antioxidant pathway by rhomboid protein RHBDF2 might be beneficial in treating chronic non-healing wounds. Copyright © 2017 Elsevier Inc. All rights reserved.

Evaluation on the effectiveness of 2-deoxyglucose-6-phosphate phosphatase (DOGR1) gene as a selectable marker for oil palm (Elaeis guineensis Jacq.) embryogenic calli transformation mediated by Agrobacterium tumefaciens

Science.gov (United States)

Izawati, Abang Masli Dayang; Masani, Mat Yunus Abdul; Ismanizan, Ismail; Parveez, Ghulam Kadir Ahmad

2015-01-01

DOGR1, which encodes 2-deoxyglucose-6-phosphate phosphatase, has been used as a selectable marker gene to produce transgenic plants. In this study, a transformation vector, pBIDOG, which contains the DOGR1 gene, was transformed into oil palm embryogenic calli (EC) mediated by Agrobacterium tumefaciens strain LBA4404. Transformed EC were exposed to 400 mg l-1 2-deoxyglucose (2-DOG) as the selection agent. 2-DOG resistant tissues were regenerated into whole plantlets on various regeneration media containing the same concentration of 2-DOG. The plantlets were later transferred into soil and grown in a biosafety screenhouse. PCR and subsequently Southern blot analyses were carried out to confirm the integration of the transgene in the plantlets. A transformation efficiency of about 1.0% was obtained using DOGR1 gene into the genome of oil palm. This result demonstrates the potential of using combination of DOGR1 gene and 2-DOG for regenerating transgenic oil palm. PMID:26442041

Activation of transcription factor AP-2 mediates UVA radiation- and singlet oxygen-induced expression of the human intercellular adhesion molecule 1 gene

International Nuclear Information System (INIS)

Grether-Beck, S.; Olaizola-Horn, S.; Schmitt, H.; Grewe, M.

1996-01-01

UVA radiation is the major component of the UV solar spectrum that reaches the earth, and the therapeutic application of UVA radiation is increasing in medicine. Analysis of the cellular effects of UVA radiation has revealed that exposure of human cells to UVA radiation at physiological doses leads to increased gene expression and that this UVA response is primarily mediated through the generation of singlet oxygen. In this study, the mechanisms by which UVA radiation induces transcriptional activation of the human intercellular adhesion molecule 1 (ICAM-1) were examined. UVA radiation was capable of inducing activation of the human ICAM-1 promoter and increasing OCAM-1 mRNA and protein expression. These UVA radiation effects were inhibited by singlet oxygen quenchers, augmented by enhancement of singlet oxygen life-time, and mimicked in unirradiated cells by a singlet oxygen-generating system. UVA radiation as well as singlet oxygen-induced ICAM-1 promoter activation required activation of the transcription factor AP-2. Accordingly, both stimuli activated AP-2, and deletion of the putative AP-2-binding site abrogated ICAM-1 promoter activation in this system. This study identified the AP-2 site as the UVA radiation- and singlet oxygen-responsive element of the human ICAM-1 gene. The capacity of UVA radiation and/or singlet oxygen to induce human gene expression through activation of AP-2 indicates a previously unrecognized role of this transcription factor in the mammalian stress response. 38 refs., 3 figs., 3 tabs

Complementation of a threonine dehydratase-deficient Nicotiana plumbaginifolia mutant after Agrobacterium tumefaciens-mediated transfer of the Saccharomyces cerevisiae ILV1 gene.

OpenAIRE

Colau, D; Negrutiu, I; Van Montagu, M; Hernalsteens, J P

1987-01-01

The Saccharomyces cerevisiae ILV1 gene, encoding threonine dehydratase (EC 4.2.1.16) was fused to the transferred DNA nopaline synthase promoter and the 3' noncoding region of the octopine synthase gene. It was introduced, by Agrobacterium tumefaciens-mediated gene transfer, into an isoleucine-requiring Nicotiana plumbaginifolia auxotroph deficient in threonine dehydratase. Functional complementation by the ILV1 gene product was demonstrated by the selection of several transformed lines on a ...

Thermo-Regulation of Genes Mediating Motility and Plant Interactions in Pseudomonas syringae

Science.gov (United States)

Hockett, Kevin L.; Burch, Adrien Y.; Lindow, Steven E.

2013-01-01

Pseudomonas syringae is an important phyllosphere colonist that utilizes flagellum-mediated motility both as a means to explore leaf surfaces, as well as to invade into leaf interiors, where it survives as a pathogen. We found that multiple forms of flagellum-mediated motility are thermo-suppressed, including swarming and swimming motility. Suppression of swarming motility occurs between 28° and 30°C, which coincides with the optimal growth temperature of P. syringae. Both fliC (encoding flagellin) and syfA (encoding a non-ribosomal peptide synthetase involved in syringafactin biosynthesis) were suppressed with increasing temperature. RNA-seq revealed 1440 genes of the P. syringae genome are temperature sensitive in expression. Genes involved in polysaccharide synthesis and regulation, phage and IS elements, type VI secretion, chemosensing and chemotaxis, translation, flagellar synthesis and motility, and phytotoxin synthesis and transport were generally repressed at 30°C, while genes involved in transcriptional regulation, quaternary ammonium compound metabolism and transport, chaperone/heat shock proteins, and hypothetical genes were generally induced at 30°C. Deletion of flgM, a key regulator in the transition from class III to class IV gene expression, led to elevated and constitutive expression of fliC regardless of temperature, but did not affect thermo-regulation of syfA. This work highlights the importance of temperature in the biology of P. syringae, as many genes encoding traits important for plant-microbe interactions were thermo-regulated. PMID:23527276

A neural jet charge tagger for the measurement of the B/s0 anti-B/s0 oscillation frequency at CDF

International Nuclear Information System (INIS)

Lecci, Claudia; Karlsruhe U., EKP

2005-01-01

A Jet Charge Tagger algorithm for b-flavour tagging for the measurement of Δm s at CDF has been presented. The tagger is based on a b-track probability variable and a b-jet probability variable, both obtained by combining the information available in b(bar b) events with a Neural Network. The tagging power measured on data is 0.917 ± 0.031% e+SVT sample; 0.938 ± 0.029% μ+SVT sample which is ∼30% larger than the cut based Jet Charge Tagger employed for the B s 0 mixing analysis presented by CDF at the Winter Conferences 2005. The improved power of the tagger is due to the selection of the b-jet with a Neural Network variable, which uses correlated jet variables in an optimal way. The development of the track and jet probability has profited from studies performed on simulated events, which allowed to understand better the features of b(bar b) events. For the first time in the CDF B group a Monte Carlo sample comprising flavour creation and additional b(bar b) production processes has been examined and compared to Run II data. It has been demonstrated that a Monte Carlo sample with only flavour creation b(bar b) production processes is not sufficient to describe b(bar b) data collected at CDF. The sample with additional processes introduced in this thesis is thus essential for tagging studies. Although the event description is satisfactory, the flavour information in the Monte Carlo sample differs with respect to data. This difference needs to be clarified by further studies. In addition, the track and the jet probabilities are the first official tools based on Neural Networks for B-Physics at CDF. They have proven that the simulation is understood to such an advanced level that Neural Networks can be employed. Further work is going on in this direction: a Soft Electron and a Soft Muon Tagger based on Neural Networks are under development as of now. Several possible tagger setups have been studied and the Jet Charge Tagger reached a high level of optimization

Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri.

Science.gov (United States)

Gao, Chunxu; Major, Angela; Rendon, David; Lugo, Monica; Jackson, Vanessa; Shi, Zhongcheng; Mori-Akiyama, Yuko; Versalovic, James

2015-12-15

Probiotics and commensal intestinal microbes suppress mammalian cytokine production and intestinal inflammation in various experimental model systems. Limited information exists regarding potential mechanisms of probiotic-mediated immunomodulation in vivo. In this report, we demonstrate that specific probiotic strains of Lactobacillus reuteri suppress intestinal inflammation in a trinitrobenzene sulfonic acid (TNBS)-induced mouse colitis model. Only strains that possess the hdc gene cluster, including the histidine decarboxylase and histidine-histamine antiporter genes, can suppress colitis and mucosal cytokine (interleukin-6 [IL-6] and IL-1β in the colon) gene expression. Suppression of acute colitis in mice was documented by diminished weight loss, colonic injury, serum amyloid A (SAA) protein concentrations, and reduced uptake of [(18)F]fluorodeoxyglucose ([(18)F]FDG) in the colon by positron emission tomography (PET). The ability of probiotic L. reuteri to suppress colitis depends on the presence of a bacterial histidine decarboxylase gene(s) in the intestinal microbiome, consumption of a histidine-containing diet, and signaling via the histamine H2 receptor (H2R). Collectively, luminal conversion of l-histidine to histamine by hdc(+) L. reuteri activates H2R, and H2R signaling results in suppression of acute inflammation within the mouse colon. Probiotics are microorganisms that when administered in adequate amounts confer beneficial effects on the host. Supplementation with probiotic strains was shown to suppress intestinal inflammation in patients with inflammatory bowel disease and in rodent colitis models. However, the mechanisms of probiosis are not clear. Our current studies suggest that supplementation with hdc(+) L. reuteri, which can convert l-histidine to histamine in the gut, resulted in suppression of colonic inflammation. These findings link luminal conversion of dietary components (amino acid metabolism) by gut microbes and probiotic-mediated

Plant-Mediated Changes in Soil N-Cycling Genes during Revegetation of Copper Mine Tailings

Directory of Open Access Journals (Sweden)

Yang Li

2017-11-01

Full Text Available Nitrogen limitation represents a major bottleneck during the revegetation of mine tailings. However, controls over key nitrogen-cycling genes in rhizospheric soils under differential vegetation management remain poorly understood. The abundance and transcriptional activity of nitrogen-cycling genes and the enzymatic activity of nitrogen transformation are mediated differentially during revegetation of mine tailings by Imperata cylindrica and Chrysopogon zizanioides plants. Results showed that the highest total organic carbon (TOC, total nitrogen (TN, and NH4+-N contents were found in the rhizosphere of I. cylindrica. The nifH gene abundances differed between I. cylindrica and C. zizanioides, and were higher in I. cylindrica which demonstrated by 3.39-fold higher mRNA transcript abundance of the nifH gene and a 2.15-fold higher nitrogen fixation rate in the rhizosphere. In addition, C. zizanioides exhibited a 4.94-fold higher transcript abundance of the archaeal amoA gene and the highest nitrification rate (1.706 ± 0.293 μg N-NO2- g−1 h−1 in the rhizosphere. In conclusion, I. cylindrica and C. zizanioides stimulated the abundances and activities of nifH gene and archaeal amoA gene, respectively. In addition, I. cylindrica appears to be capable of enhancing nitrogen fixation and exhibited accelerated nitrogen accumulation, which may be particularly useful for the rehabilitation of mine tailings.

The CDF top search in the multijet decay mode

International Nuclear Information System (INIS)

Denby, B.

1994-01-01

A status report on the CDF top search in the multijet channel is given. After topological cuts and the requirement of a secondary vertex in the silicon microvertex detector, about 120 events remain (21.4 pb -1 ), in which the signal to background ratio (for a nominal top mass of 160 GeV) is estimated to be 1/10. With further improvements it should be possible to improve this ratio to 1/1 while retaining good efficiency for top, which will make the multijet channel an important cross check for the leptonic modes

Measurement of correlated b quark cross sections at CDF

International Nuclear Information System (INIS)

Gerdes, D.

1994-09-01

Using data collected during the 1992--93 collider run at Fermilab, CDF has made measurements of correlated b quark cross section where one b is detected from a muon from semileptonic decay and the second b is detected with secondary vertex techniques. We report on measurements of the cross section as a function of the momentum of the second b and as a function of the azimuthal separation of the two b quarks, for transverse momentum of the initial b quark greater than 15 GeV. Results are compared to QCD predictions

Inclusive jet cross sections and jet shapes at CDF

International Nuclear Information System (INIS)

Wainer, N.

1991-09-01

The inclusive jet cross section and jet shapes at √s = 1.8 TeV have been measured by CDF at the Fermilab Tevatron Collider. results are compared to recent next-to-leading order QCD calculations, which predict variation of the cross section with cone size, as well as variation of the jet shape with energy. A lower limit on the parameter Λ c , which characterize a contact interaction associated with quark sub-structure is determined to be 1400 GeV at the 95% confidence level. 3 refs., 4 figs

PLGA Nanoparticles for Ultrasound-Mediated Gene Delivery to Solid Tumors

Directory of Open Access Journals (Sweden)

Marxa Figueiredo

2012-01-01

Full Text Available This paper focuses on novel approaches in the field of nanotechnology-based carriers utilizing ultrasound stimuli as a means to spatially target gene delivery in vivo, using nanoparticles made with either poly(lactic-co-glycolic acid (PLGA or other polymers. We specifically discuss the potential for gene delivery by particles that are echogenic (amenable to destruction by ultrasound composed either of polymers (PLGA, polystyrene or other contrast agent materials (Optison, SonoVue microbubbles. The use of ultrasound is an efficient tool to further enhance gene delivery by PLGA or other echogenic particles in vivo. Echogenic PLGA nanoparticles are an attractive strategy for ultrasound-mediated gene delivery since this polymer is currently approved by the US Food and Drug Administration for drug delivery and diagnostics in cancer, cardiovascular disease, and also other applications such as vaccines and tissue engineering. This paper will review recent successes and the potential of applying PLGA nanoparticles for gene delivery, which include (a echogenic PLGA used with ultrasound to enhance local gene delivery in tumors or muscle and (b PLGA nanoparticles currently under development, which could benefit in the future from ultrasound-enhanced tumor targeted gene delivery.

Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish

Science.gov (United States)

Wang, Haifang; Du, Jiulin; Yan, Jun

2013-01-01

In the study of circadian rhythms, it has been a puzzle how a limited number of circadian clock genes can control diverse aspects of physiology. Here we investigate circadian gene expression genome-wide using larval zebrafish as a model system. We made use of a spatial gene expression atlas to investigate the expression of circadian genes in various tissues and cell types. Comparison of genome-wide circadian gene expression data between zebrafish and mouse revealed a nearly anti-phase relationship and allowed us to detect novel evolutionarily conserved circadian genes in vertebrates. We identified three groups of zebrafish genes with distinct responses to light entrainment: fast light-induced genes, slow light-induced genes, and dark-induced genes. Our computational analysis of the circadian gene regulatory network revealed several transcription factors (TFs) involved in diverse aspects of circadian physiology through transcriptional cascade. Of these, microphthalmia-associated transcription factor a (mitfa), a dark-induced TF, mediates a circadian rhythm of melanin synthesis, which may be involved in zebrafish's adaptation to daily light cycling. Our study describes a systematic method to discover previously unidentified TFs involved in circadian physiology in complex organisms. PMID:23468616

CRISPR/Cas9-loxP-Mediated Gene Editing as a Novel Site-Specific Genetic Manipulation Tool.

Science.gov (United States)

Yang, Fayu; Liu, Changbao; Chen, Ding; Tu, Mengjun; Xie, Haihua; Sun, Huihui; Ge, Xianglian; Tang, Lianchao; Li, Jin; Zheng, Jiayong; Song, Zongming; Qu, Jia; Gu, Feng

2017-06-16

Cre-loxP, as one of the site-specific genetic manipulation tools, offers a method to study the spatial and temporal regulation of gene expression/inactivation in order to decipher gene function. CRISPR/Cas9-mediated targeted genome engineering technologies are sparking a new revolution in biological research. Whether the traditional site-specific genetic manipulation tool and CRISPR/Cas9 could be combined to create a novel genetic tool for highly specific gene editing is not clear. Here, we successfully generated a CRISPR/Cas9-loxP system to perform gene editing in human cells, providing the proof of principle that these two technologies can be used together for the first time. We also showed that distinct non-homologous end-joining (NHEJ) patterns from CRISPR/Cas9-mediated gene editing of the targeting sequence locates at the level of plasmids (episomal) and chromosomes. Specially, the CRISPR/Cas9-mediated NHEJ pattern in the nuclear genome favors deletions (64%-68% at the human AAVS1 locus versus 4%-28% plasmid DNA). CRISPR/Cas9-loxP, a novel site-specific genetic manipulation tool, offers a platform for the dissection of gene function and molecular insights into DNA-repair pathways. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Experience with parallel optical link for the CDF silicon detector

International Nuclear Information System (INIS)

Hou, S.

2003-01-01

The Dense Optical Interface Module (DOIM) is a byte-wide optical link developed for the Run II upgrade of the CDF silicon tracking system [1]. The module consists of a transmitter with a laser-diode array for conversion of digitized detector signals to light outputs, a 22 m optical fiber ribbon cable for light transmission, and a receiver converting the light pulses back to electrical signals. We report on the design feature, characteristics, and radiation tolerance

Status of the Tevatron CDF and D0 experiments

International Nuclear Information System (INIS)

Rolli, Simona

2010-01-01

The status of the Tevatron Collider is reviewed and highlights of the rich physics program carried out by the CDF and D0 experiments are presented. The Tevatron Collider has been performing remarkably well in the past few years and it is continuing to deliver record luminosity. The machine collides proton and anti-proton beams at an energy in the center of mass of 1.96 TeV, with average peak luminosity of 300E30 cm -2 s -1 . The total delivered luminosity is slightly above 9 fb -1 . The CDF and D0 experiments have been collecting data with an average efficiency of 90%, while the experiments have enjoyed an annual doubling of the integrated luminosity delivered and recorded. This has led to an avalanche of new results from areas as diverse as QCD, top, searches for new physics and the area of electroweak symmetry breaking with particular focus on direct searches for the Higgs boson. The physics reach of the Tevatron is built on a mountain of measurements that confirm the ability of the Tevatron collaborations to use their detectors to discover new particles. Each measurement is of itself a significant result. Measurements begin with the largest cross section processes, those of B physics, but move on to processes with small branching ratios and backgrounds that are hard to distinguish from the signal. The measurement of Bs oscillations demonstrates the performance of the silicon tracking and vertexing. Discovery of single top production, WZ production, and evidence for the ZZ production in both leptonic and now hadronic modes provide the final base camp from which the Higgs summit is in sight. Processes such as single top and ZZ act as important messengers heralding the impending arrival of the Higgs. This journey through lower and lower cross section processes represents our approach to provide convincing evidence of these processes, first as discovery then as measurements that constrain the Standard Model.

Ovarian cancer targeted adenoviral-mediated mda-7/IL-24 gene therapy

NARCIS (Netherlands)

Mahasreshti, PJ; Kataram, M; Wu, HJ; Yalavarthy, LP; Carey, D; Dent, P; Chada, S; Alvarez, RD; Haisma, HJ; Fisher, PB; Curiel, DT

Objective. We have previously shown that adenoviral-mediated melanoma differentiation-associated gene-7 (Ad.mda-7) therapy induces apoptosis in ovarian cancer cells. However, the apoptosis induction was low and directly correlated with infectivity of Ad.mda-7. The objective of this study was to

Pollen-mediated gene flow in flax (Linum usitatissimum L.): can genetically engineered and organic flax coexist?

Science.gov (United States)

Jhala, A J; Bhatt, H; Topinka, K; Hall, L M

2011-04-01

Coexistence allows growers and consumers the choice of producing or purchasing conventional or organic crops with known standards for adventitious presence of genetically engineered (GE) seed. Flax (Linum usitatissimum L.) is multipurpose oilseed crop in which product diversity and utility could be enhanced for industrial, nutraceutical and pharmaceutical markets through genetic engineering. If GE flax were released commercially, pollen-mediated gene flow will determine in part whether GE flax could coexist without compromising other markets. As a part of pre-commercialization risk assessment, we quantified pollen-mediated gene flow between two cultivars of flax. Field experiments were conducted at four locations during 2006 and 2007 in western Canada using a concentric donor (20 × 20 m) receptor (120 × 120 m) design. Gene flow was detected through the xenia effect of dominant alleles of high α-linolenic acid (ALA; 18:3(cisΔ9,12,15)) to the low ALA trait. Seeds were harvested from the pollen recipient plots up to a distance of 50 m in eight directions from the pollen donor. High ALA seeds were identified using a thiobarbituric acid test and served as a marker for gene flow. Binomial distribution and power analysis were used to predict the minimum number of seeds statistically required to detect the frequency of gene flow at specific α (confidence interval) and power (1-β) values. As a result of the low frequency of gene flow, approximately 4 million seeds were screened to derive accurate quantification. Frequency of gene flow was highest near the source: averaging 0.0185 at 0.1 m but declined rapidly with distance, 0.0013 and 0.00003 at 3 and 35 m, respectively. Gene flow was reduced to 50% (O₅₀) and 90% (O₉₀) between 0.85 to 2.64 m, and 5.68 to 17.56 m, respectively. No gene flow was detected at any site or year > 35 m distance from the pollen source, suggesting that frequency of gene flow was ≤ 0.00003 (P = 0.95). Although it is not possible to

Investigation of tt-bar in the full hadronic final state at CDF with a neural network approach

International Nuclear Information System (INIS)

Sidoti, A.; Azzi, P.; Busetto, G.; Castro, A.; Dusini, S.; Lazzizzera, I.; Wyss, J.L.

2001-01-01

In this work we present the results of a neural network (NN) approach to the measurement of the tt-bar production cross-section and top mass in the all-hadronic channel, analyzing data collected at the Collider Detector at Fermilab (CDF) experiment. We have used a hardware implementation of a feed forward neural network, TOTEM, the product of a collaboration of INFN (Istituto Nazionale Fisica Nucleare) - IRST (Istituto per la Ricerca Scientifica e Tecnologica) - University of Trento, Italy. Particular attention has been paid to the evaluation of the systematics specifically related to the NN approach. The results are consistent with those obtained at CDF by conventional data selection techniques

Measurement of the top-quark mass with dilepton events selected using neuroevolution at CDF.

Science.gov (United States)

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Copic, K; Cordelli, M; Cortiana, G; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kusakabe, Y; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, E; Lee, S W; Leone, S; Lewis, J D; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lu, R-S; Lucchesi, D; Lueck, J; Luci, C; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlok, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shalhout, S Z; Shears, T; Shekhar, R; Shepard, P F; Sherman, D; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Tu, Y; Turini, N; Ukegawa, F; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner-Kuhr, J; Wagner, W; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Whiteson, S; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zheng, Y; Zucchelli, S

2009-04-17

We report a measurement of the top-quark mass M_{t} in the dilepton decay channel tt[over ] --> bl;{'+} nu_{l};{'}b[over ]l;{-}nu[over ]_{l}. Events are selected with a neural network which has been directly optimized for statistical precision in top-quark mass using neuroevolution, a technique modeled on biological evolution. The top-quark mass is extracted from per-event probability densities that are formed by the convolution of leading order matrix elements and detector resolution functions. The joint probability is the product of the probability densities from 344 candidate events in 2.0 fb;{-1} of pp[over ] collisions collected with the CDF II detector, yielding a measurement of M_{t} = 171.2 +/- 2.7(stat) +/- 2.9(syst) GeV / c;{2}.

Measurement of the Top-Quark Mass with Dilepton Events Selected Using Neuroevolution at CDF

International Nuclear Information System (INIS)

Aaltonen, T.; Maki, T.; Mehtala, P.; Orava, R.; Osterberg, K.; Saarikko, H.; Remortel, N. van; Adelman, J.; Brubaker, E.; Fedorko, W. T.; Grosso-Pilcher, C.; Kim, Y. K.; Krop, D.; Kwang, S.; Paramonov, A. A.; Schmidt, M. A.; Shiraishi, S.; Shochet, M.; Wolfe, C.; Yang, U. K.

2009-01-01

We report a measurement of the top-quark mass M t in the dilepton decay channel tt→bl '+ ν l ' bl - ν l . Events are selected with a neural network which has been directly optimized for statistical precision in top-quark mass using neuroevolution, a technique modeled on biological evolution. The top-quark mass is extracted from per-event probability densities that are formed by the convolution of leading order matrix elements and detector resolution functions. The joint probability is the product of the probability densities from 344 candidate events in 2.0 fb -1 of pp collisions collected with the CDF II detector, yielding a measurement of M t =171.2±2.7(stat)±2.9(syst) GeV/c 2

Search for high-mass diphoton states and limits on Randall-Sundrum gravitons at CDF.

Science.gov (United States)

Aaltonen, T; Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carrillo, S; Carlsmith, D; Carosi, R; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Cilijak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; DaRonco, S; Datta, M; D'Auria, S; Davies, T; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Dörr, C; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraan, A C; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moon, C S; Moore, R; Morello, M; Fernandez, P Movilla; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuno, S; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vazquez, F; Velev, G; Vellidis, C; Veramendi, G; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-10-26

We have performed a search for new particles which decay to two photons using 1.2 fb(-1) of integrated luminosity from pp[over] collisions at square root s = 1.96 TeV collected using the CDF II detector at the Fermilab Tevatron. We find the diphoton mass spectrum to be in agreement with the standard model expectation, and set limits on the cross section times branching ratio for the Randall-Sundrum graviton, as a function of diphoton mass. We subsequently derive lower limits for the graviton mass of 230 GeV/c(2) and 850 GeV/c(2), at the 95% confidence level, for coupling parameters (k/M[over](Pl)) of 0.01 and 0.1, respectively.

The tumor suppressor Rb and its related Rbl2 genes are regulated by Utx histone demethylase

Energy Technology Data Exchange (ETDEWEB)

Terashima, Minoru; Ishimura, Akihiko; Yoshida, Masakazu [Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa (Japan); Suzuki, Yutaka; Sugano, Sumio [Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Chiba (Japan); Suzuki, Takeshi, E-mail: suzuki-t@staff.kanazawa-u.ac.jp [Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa (Japan)

2010-08-20

Research highlights: {yields} Utx increases expression of Rb and Rbl2 genes through its demethylase activity. {yields} Utx changes histone H3 methylation on the Rb and Rbl2 promoters. {yields} Utx induces decreased cell proliferation of mammalian primary cells. -- Abstract: Utx is a candidate tumor suppressor gene that encodes histone H3 lysine 27 (H3K27) demethylase. In this study, we found that ectopic expression of Utx enhanced the expression of retinoblastoma tumor suppressor gene Rb and its related gene Rbl2. This activation was dependent on the demethylase activity of Utx, and was suggested to contribute to the decreased cell proliferation induced by Utx. A chromatin immunoprecipitation assay showed that over-expressed Utx was associated with the promoter regions of Rb and Rbl2 resulting in the removal of repressive H3K27 tri-methylation and the increase in active H3K4 tri-methylation. Furthermore, siRNA-mediated knockdown of Utx revealed the recruitment of endogenous Utx protein on the promoters of Rb and Rbl2 genes. These results indicate that Rb and Rbl2 are downstream target genes of Utx and may play important roles in Utx-mediated cell growth control.

Effects of aerobic exercise training on ACE and ADRB2 gene expression, plasma angiotensin II level, and flow-mediated dilation: a study on obese postmenopausal women with prehypertension.

Science.gov (United States)

Azadpour, Noushin; Tartibian, Bakhtyar; Koşar, Şükran Nazan

2017-03-01

The purpose of this study is to determine the effect of 10 weeks of moderate-intensity aerobic exercise training (MIET) on blood pressure (BP), angiotensin-converting enzyme (ACE) and β2-adrenergic receptor (ADRB2) gene expression in leukocytes, plasma angiotensin II (Ang II), and flow-mediated dilation (FMD) in obese postmenopausal women (PMW) with prehypertension. Twenty-four obese prehypertensive PMW (aged 50-70 y; body mass index ≥30 kg/m) randomly assigned to control (n = 12) and exercise (n = 12) groups. Exercise group performed MIET (25-40 min/d, 3 d/wk at 50%-70% of heart rate reserve) for 10 weeks. Control group maintained their normal daily physical activity level. Body composition, VO2max, BP, ACE and ADRB2 gene expression, plasma Ang II, and FMD were measured before and after the training program. After MIET, systolic and diastolic BPs decreased by 4.6% and 2.4%, respectively (P ACE gene expressions (P ACE (r values range 0.68-0.86) (P ACE and ADRB2 gene expression, decreases Ang II plasma levels, and improves endothelial function in obese PMW, and these alterations are associated with reduction in BP.

CRISPR/Cas9 nuclease-mediated gene knock-in in bovine-induced pluripotent cells.

Science.gov (United States)

Heo, Young Tae; Quan, Xiaoyuan; Xu, Yong Nan; Baek, Soonbong; Choi, Hwan; Kim, Nam-Hyung; Kim, Jongpil

2015-02-01

Efficient and precise genetic engineering in livestock such as cattle holds great promise in agriculture and biomedicine. However, techniques that generate pluripotent stem cells, as well as reliable tools for gene targeting in livestock, are still inefficient, and thus not routinely used. Here, we report highly efficient gene targeting in the bovine genome using bovine pluripotent cells and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 nuclease. First, we generate induced pluripotent stem cells (iPSCs) from bovine somatic fibroblasts by the ectopic expression of yamanaka factors and GSK3β and MEK inhibitor (2i) treatment. We observed that these bovine iPSCs are highly similar to naïve pluripotent stem cells with regard to gene expression and developmental potential in teratomas. Moreover, CRISPR/Cas9 nuclease, which was specific for the bovine NANOG locus, showed highly efficient editing of the bovine genome in bovine iPSCs and embryos. To conclude, CRISPR/Cas9 nuclease-mediated homologous recombination targeting in bovine pluripotent cells is an efficient gene editing method that can be used to generate transgenic livestock in the future.

Top quark mass measurement in non-tagged lepton + jets events at CDF

International Nuclear Information System (INIS)

Bellettini, G.; Budagov, Yu.; Chlachidze, G.; Velev, G.

2005-01-01

We report on the first CDF-II measurement of the top quark mass in non-tagged sample of lepton + 4 jet events from p anti p collisions at √s=1.96 TeV. The integrated luminosity of the data sample is 193.5 pb -1 . To improve the sample purity a cut at E T >21 GeV was applied on transverse energy of the jets. 39 events were reconstructed as t anti t and fitted as a superposition of top and W + jet events. The signal-constrained fit imposing a signal of 15.5±3.2 events returned a mass M top =179.1± 9.5 10.5 (stat.) ±8.5 (syst.) GeV/c 2 . The unconstrained fit returned M top =177.5± 7.7 9.1 (stat.) ±8.5 (syst.) GeV/c 2

A Search for the Standard Model Higgs Boson in CDF II Data

Energy Technology Data Exchange (ETDEWEB)

Lockwitz, Sarah E. [Yale Univ., New Haven, CT (United States)

2012-01-01

This dissertation presents a search for the standard model Higgs boson in the associated production process p $\\bar{p}$ → ZH → e⁺e^-b$\\bar{b}$. Data amounting to an integrated luminosity of 7.5 fb^-1 at √s = 1.96 TeV collected at the Collider Detector at Fermilab (CDF) at the Tevatron are analyzed. Two objectives are pursued in the methods applied: maximize acceptance, and distinguish the signal from background. The first aim is met by applying a neural-network-based electron identi cation and considering multiple electron triggers in an effort to improve Z acceptance. In an attempt to maximize the Higgs acceptance, three b quark identification schemes are used allowing for varying event conditions. The latter goal is met by employing more multivariate techniques. First, the dijet mass resolution is improved by a neural network. Then, both single variables and boosted decision tree outputs are fed into a segmented final discriminant simultaneously isolating the signal-like events from the Z with additional jets background and the kinematically di erent tt background. Good agreement is seen with the null hypothesis and upper production cross section ( ZH) times branching ratio (BR(H →b $\\bar{b}$)) limits are set for 11 mass hypotheses between 100 and 150 GeV/c² at the 95% confidence level. For a Higgs boson mass of 115 GeV/c², this channel sets an observed (expected) upper limit of 3.9 (5.8) times the standard model value of ZH BR(H → b $\\bar{b}$). The inclusion of this channel within the combined CDF and Tevatron limits is discussed.

New particle searches at CDF

International Nuclear Information System (INIS)

Nodulman, L.J.

1995-09-01

One of the fundamental roles of a general purpose detector exploring, by means of increasing luminosity, higher and higher mass reach, is to search for new particles and exotic phenomena. This is a continuing effort for the CDF collaboration, and will report on several searches using about 20 pb -1 from the 1992/93 run labelled open-quotes run 1aclose quotes and ∼50 of the 90 pb -1 so far from the current open-quotes run 1b.close quotes These are mostly preliminary analyses, typically using a total of 70 pb -1 . Our limits on SUSY using missing E T with jets as well as three leptons are discussed elsewhere; results from the D0 collaboration are similar. I will discuss searches for additional vector bosons Z' and W', second generation scalar leptoquarks, as well as a broad search for objects decaying into jet pairs, including b-tagged jet pairs. I will also describe two events which do not fit in comfortably with either the standard model or a phenomenologically motivated search

Elevated CO2 increases R gene-dependent resistance of Medicago truncatula against the pea aphid by up-regulating a heat shock gene.

Science.gov (United States)

Sun, Yucheng; Guo, Huijuan; Yuan, Erliang; Ge, Feng

2018-03-01

Resistance against pathogens and herbivorous insects in many plant results from the expression of resistance (R) genes. Few reports, however, have considered the effects of elevated CO 2 on R gene-based resistance in plants. The current study determined the responses of two near isogenic Medicago truncatula genotypes (Jester has an R gene and A17 does not) to the pea aphid and elevated CO 2 in open-top chambers in the field. Aphid abundance, mean relative growth rate and feeding efficiency were increased by elevated CO 2 on A17 plants but were reduced on Jester plants. According to proteomic and gene expression data, elevated CO 2 enhanced pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) but decreased the effector-triggered immunity (ETI) in aphid-infested A17 plants. For aphid-infested Jester plants, by contrast, elevated CO 2 enhanced the ETI-related heat shock protein (HSP) 90 and its co-chaperones, the jasmonic acid (JA) signaling pathway, and ubiquitin-mediated proteolysis. In a loss-of-function experiment, silencing of the HSP90 gene in Jester plants impaired the JA signaling pathway and ubiquitin-mediated proteolysis against the aphid under ambient CO 2 , and negated the increased resistance against the aphid under elevated CO 2 . Our results suggest that increases in expression of HSP90 are responsible for the enhanced resistance against the aphid under elevated CO 2 . © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Higgs searches and prospects at CDF

International Nuclear Information System (INIS)

Pavel A Murat

2003-01-01

The Standard model of electroweak interactions (SM) has been extremely successful in describing interactions of elementary particles over the last decades. The Higgs scalar boson is one of the key elements of the SM: Higgs interactions with the other particles generate the particle masses and allow to keep the theory renormalizable at electroweak scale. All the particles predicted by the SM but the Higgs boson have already been observed experimentally and therefore search for the Higgs is one of the most important scientific goals for high energy physics. The current lower limit on the SM Higgs mass M H > 114.4 GeV at 95% CL has been established by LEP experiments. In this paper we review CDF Run I results on Higgs searches including the Higgs bosons predicted by the minimal supersymmetric extention of the Standard Model (MSSM) and discuss the Run II prospects

Claudin-2 knockout by TALEN-mediated gene targeting in MDCK cells: claudin-2 independently determines the leaky property of tight junctions in MDCK cells.

Directory of Open Access Journals (Sweden)

Shinsaku Tokuda

Full Text Available Tight junctions (TJs regulate the movements of substances through the paracellular pathway, and claudins are major determinants of TJ permeability. Claudin-2 forms high conductive cation pores in TJs. The suppression of claudin-2 expression by RNA interference in Madin-Darby canine kidney (MDCK II cells (a low-resistance strain of MDCK cells was shown to induce a three-fold increase in transepithelial electrical resistance (TER, which, however, was still lower than in high-resistance strains of MDCK cells. Because RNA interference-mediated knockdown is not complete and only reduces gene function, we considered the possibility that the remaining claudin-2 expression in the knockdown study caused the lower TER in claudin-2 knockdown cells. Therefore, we investigated the effects of claudin-2 knockout in MDCK II cells by establishing claudin-2 knockout clones using transcription activator-like effector nucleases (TALENs, a recently developed genome editing method for gene knockout. Surprisingly, claudin-2 knockout increased TER by more than 50-fold in MDCK II cells, and TER values in these cells (3000-4000 Ω·cm2 were comparable to those in the high-resistance strains of MDCK cells. Claudin-2 re-expression restored the TER of claudin-2 knockout cells dependent upon claudin-2 protein levels. In addition, we investigated the localization of claudin-1, -2, -3, -4, and -7 at TJs between control MDCK cells and their respective knockout cells using their TALENs. Claudin-2 and -7 were less efficiently localized at TJs between control and their knockout cells. Our results indicate that claudin-2 independently determines the 'leaky' property of TJs in MDCK II cells and suggest the importance of knockout analysis in cultured cells.

2,3,4,7,8-Pentachlorodibenzofuran is far less potent than 2,3,7,8-tetrachlorodibenzo-p-dioxin in disrupting the pituitary–gonad axis of the rat fetus

Energy Technology Data Exchange (ETDEWEB)

Taura, Junki; Takeda, Tomoki; Fujii, Misaki; Hattori, Yukiko; Ishii, Yuji [Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka (Japan); Kuroki, Hiroaki [Daiichi University of Pharmacy, Fukuoka (Japan); Tsukimori, Kiyomi [Department of Obstetrics, Fukuoka Children' s Hospital, Fukuoka (Japan); Uchi, Hiroshi [Research and Clinical Center for Yusho and Dioxin, Kyushu University Hospital, Fukuoka (Japan); Furue, Masutaka [Research and Clinical Center for Yusho and Dioxin, Kyushu University Hospital, Fukuoka (Japan); Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Yamada, Hideyuki, E-mail: hyamada@phar.kyushu-u.ac.jp [Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka (Japan)

2014-11-15

The effect of 2,3,4,7,8-pentachlorodibenzofuran (PnCDF) on the fetal pituitary–gonad axis was compared with that produced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in Wistar rats. Maternal treatment at gestational day (GD) 15 with PnCDF and TCDD reduced the fetal expression at GD20 of pituitary luteinizing hormone (LH) and the testicular proteins necessary for steroidogenesis. The relative potencies of PnCDF ranged from 1/42nd to 1/63rd of the TCDD effect. While PnCDF, at a dose sufficient to cause a reduction in fetal LH, provoked defects in sexual behavior at adulthood, a dose less than the ED{sub 50} failed to produce any abnormality. There was a loss of fetal body weight following in utero exposure to PnCDF, and the effect of PnCDF was also much less than that of TCDD. The disturbance in fetal growth was suggested to be due to a reduction in the level of fetal growth hormone (GH) by dioxins. The disorder caused by PnCDF/TCDD in the fetal pituitary–gonad axis occurred at doses less than those needed to cause wasting syndrome in pubertal rats. The harmful effect of PnCDF relative to TCDD was more pronounced in fetal rats than in pubertal rats. These lines of evidence suggest that: 1) PnCDF as well as TCDD imprints defects in sexual behavior by disrupting the fetal pituitary–gonad axis; 2) these dioxins hinder fetal growth by reducing the expression of fetal GH; and 3) the fetal effects of PnCDF/TCDD are more sensitive than sub-acute toxicity during puberty, and the relative effect of PnCDF varies markedly depending on the indices used. - Highlights: • 2,3,4,7,8-Pentachlorodibenzofuran (PnCDF) lowers gonadal steroidogenesis in fetuses. • PnCDF exerts the above effect through an initial attenuation in gonadotropin level. • PnCDF imprints sexual immaturity by transiently disrupting the pituitary–gonad axis. • PnCDF also disturbs pup growth probably due to a reduction in growth hormone level. • The above effects are far lesser in PnCDF than 2

2,3,4,7,8-Pentachlorodibenzofuran is far less potent than 2,3,7,8-tetrachlorodibenzo-p-dioxin in disrupting the pituitary–gonad axis of the rat fetus

International Nuclear Information System (INIS)

Taura, Junki; Takeda, Tomoki; Fujii, Misaki; Hattori, Yukiko; Ishii, Yuji; Kuroki, Hiroaki; Tsukimori, Kiyomi; Uchi, Hiroshi; Furue, Masutaka; Yamada, Hideyuki

2014-01-01

The effect of 2,3,4,7,8-pentachlorodibenzofuran (PnCDF) on the fetal pituitary–gonad axis was compared with that produced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in Wistar rats. Maternal treatment at gestational day (GD) 15 with PnCDF and TCDD reduced the fetal expression at GD20 of pituitary luteinizing hormone (LH) and the testicular proteins necessary for steroidogenesis. The relative potencies of PnCDF ranged from 1/42nd to 1/63rd of the TCDD effect. While PnCDF, at a dose sufficient to cause a reduction in fetal LH, provoked defects in sexual behavior at adulthood, a dose less than the ED 50 failed to produce any abnormality. There was a loss of fetal body weight following in utero exposure to PnCDF, and the effect of PnCDF was also much less than that of TCDD. The disturbance in fetal growth was suggested to be due to a reduction in the level of fetal growth hormone (GH) by dioxins. The disorder caused by PnCDF/TCDD in the fetal pituitary–gonad axis occurred at doses less than those needed to cause wasting syndrome in pubertal rats. The harmful effect of PnCDF relative to TCDD was more pronounced in fetal rats than in pubertal rats. These lines of evidence suggest that: 1) PnCDF as well as TCDD imprints defects in sexual behavior by disrupting the fetal pituitary–gonad axis; 2) these dioxins hinder fetal growth by reducing the expression of fetal GH; and 3) the fetal effects of PnCDF/TCDD are more sensitive than sub-acute toxicity during puberty, and the relative effect of PnCDF varies markedly depending on the indices used. - Highlights: • 2,3,4,7,8-Pentachlorodibenzofuran (PnCDF) lowers gonadal steroidogenesis in fetuses. • PnCDF exerts the above effect through an initial attenuation in gonadotropin level. • PnCDF imprints sexual immaturity by transiently disrupting the pituitary–gonad axis. • PnCDF also disturbs pup growth probably due to a reduction in growth hormone level. • The above effects are far lesser in PnCDF than 2

AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings

Science.gov (United States)

2014-01-01

Background Transient gene expression via Agrobacterium-mediated DNA transfer offers a simple and fast method to analyze transgene functions. Although Arabidopsis is the most-studied model plant with powerful genetic and genomic resources, achieving highly efficient and consistent transient expression for gene function analysis in Arabidopsis remains challenging. Results We developed a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST (Agrobacterium-mediated enhanced seedling transformation), which achieves versatile analysis of diverse gene functions in intact Arabidopsis seedlings. Using β-glucuronidase (GUS) as a reporter for Agrobacterium-mediated transformation assay, we show that the use of a specific disarmed Agrobacterium strain with vir gene pre-induction resulted in homogenous GUS staining in cotyledons of young Arabidopsis seedlings. Optimization with AB salts in plant culture medium buffered with acidic pH 5.5 during Agrobacterium infection greatly enhanced the transient expression levels, which were significantly higher than with two existing methods. Importantly, the optimized method conferred 100% infected seedlings with highly increased transient expression in shoots and also transformation events in roots of ~70% infected seedlings in both the immune receptor mutant efr-1 and wild-type Col-0 seedlings. Finally, we demonstrated the versatile applicability of the method for examining transcription factor action and circadian reporter-gene regulation as well as protein subcellular localization and protein–protein interactions in physiological contexts. Conclusions AGROBEST is a simple, fast, reliable, and robust transient expression system enabling high transient expression and transformation efficiency in Arabidopsis seedlings. Demonstration of the proof-of-concept experiments elevates the transient expression technology to the level of functional studies in Arabidopsis seedlings in addition to previous

MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3

DEFF Research Database (Denmark)

Hallenborg, P.; Siersbæk, M.; Barrio-Hernandez, I.

2016-01-01

on activation of the STAT family of transcription factors. Their activation was required for the cAMP-mediated induction of target genes. Interestingly, rather than influencing all cAMP-stimulated genes, inhibition of the kinases directly responsible for STAT activation, namely JAKs, or ablation of MDM2, each......The ubiquitin ligase MDM2 is best known for balancing the activity of the tumor suppressor p53. We have previously shown that MDM2 is vital for adipocyte conversion through controlling Cebpd expression in a p53-independent manner. Here, we show that the proadipogenic effect of MDM2 relies...... resulted in abolished induction of a subset of cAMP-stimulated genes, with Cebpd being among the most affected. Moreover, STATs were able to interact with the transcriptional cofactors CRTC2 and CRTC3, hitherto only reported to associate with the cAMP-responsive transcription factor CREB. Last...

Plant–Agrobacterium interaction mediated by ethylene and super-Agrobacterium conferring efficient gene transfer

OpenAIRE

Nonaka, Satoko; Ezura, Hiroshi

2014-01-01

Agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. This ability has been utilized for plant genetic engineering. However, the efficiency is not sufficient for all plant species. Several studies have shown that ethylene decreased the Agrobacterium-mediated transformation frequency. Thus, A. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of Agrobacterium-mediated transformation. Some studies showed that plant growth-pro...

Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development.

Science.gov (United States)

José-Edwards, Diana S; Oda-Ishii, Izumi; Nibu, Yutaka; Di Gregorio, Anna

2013-06-01

T-box genes are potent regulators of mesoderm development in many metazoans. In chordate embryos, the T-box transcription factor Brachyury (Bra) is required for specification and differentiation of the notochord. In some chordates, including the ascidian Ciona, members of the Tbx2 subfamily of T-box genes are also expressed in this tissue; however, their regulatory relationships with Bra and their contributions to the development of the notochord remain uncharacterized. We determined that the notochord expression of Ciona Tbx2/3 (Ci-Tbx2/3) requires Ci-Bra, and identified a Ci-Tbx2/3 notochord CRM that necessitates multiple Ci-Bra binding sites for its activity. Expression of mutant forms of Ci-Tbx2/3 in the developing notochord revealed a role for this transcription factor primarily in convergent extension. Through microarray screens, we uncovered numerous Ci-Tbx2/3 targets, some of which overlap with known Ci-Bra-downstream notochord genes. Among the Ci-Tbx2/3 notochord targets are evolutionarily conserved genes, including caspases, lineage-specific genes, such as Noto4, and newly identified genes, such as MLKL. This work sheds light on a large section of the notochord regulatory circuitry controlled by T-box factors, and reveals new components of the complement of genes required for the proper formation of this structure.

Tests of structure functions using leptons at CDF: The charge asymmetry in W-boson decays

International Nuclear Information System (INIS)

DeBarbaro, P.

1994-08-01

The charge asymmetry of W-bosons produced in p bar p collisions has been measured using 19 039 W → eν and W → μν decays recorded by the CDF detector during the 1992--93 Tevatron collider run. The asymmetry is sensitive to the slope of the proton's d/u quark distribution ratio down to x 2 ∼ M W 2 , where nonperturbative QCD effects are minimal. Of recent parton distribution functions, those of Martin, Roberts and Stirling are favored over those of the CTEQ collaboration. This difference is seen even though both sets agree, at the level of the nuclear shadowing corrections, with the recent NMC measurements of F 2 μn /F 2 μp

Mediator subunit MED1 is a T3-dependent and T3-independent coactivator on the thyrotropin β gene promoter

Energy Technology Data Exchange (ETDEWEB)

Matsui, Keiji; Oda, Kasumi; Mizuta, Shumpei; Ishino, Ruri; Urahama, Norinaga; Hasegawa, Natsumi [Laboratory of Hematology, Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe 654-0142 (Japan); Roeder, Robert G. [Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (United States); Ito, Mitsuhiro, E-mail: itomi@med.kobe-u.ac.jp [Laboratory of Hematology, Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe 654-0142 (Japan); Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (United States); Department of Family and Community Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 654-0142 (Japan); Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 159-8555 (Japan)

2013-10-11

Highlights: •MED1 is a bona fide T3-dependent coactivator on TSHB promoter. •Mice with LxxLL-mutant MED1 have attenuated TSHβ mRNA and thyroid hormone levels. •MED1 activates TSHB promoter T3-dependently in cultured cells. •T3-dependent MED1 action is enhanced when SRC1/SRC2 or HDAC2 is downregulated. •MED1 is also a T3-independent GATA2/Pit1 coactivator on TSHB promoter. -- Abstract: The MED1 subunit of the Mediator transcriptional coregulator complex is a nuclear receptor-specific coactivator. A negative feedback mechanism of thyroid-stimulating hormone (TSH, or thyrotropin) expression in the thyrotroph in the presence of triiodothyronine (T3) is employed by liganded thyroid hormone receptor β (TRβ) on the TSHβ gene promoter, where conventional histone-modifying coactivators act as corepressors. We now provide evidence that MED1 is a ligand-dependent positive cofactor on this promoter. TSHβ gene transcription was attenuated in MED1 mutant mice in which the nuclear receptor-binding ability of MED1 was specifically disrupted. MED1 stimulated GATA2- and Pit1-mediated TSHβ gene promoter activity in a ligand-independent manner in cultured cells. MED1 also stimulated transcription from the TSHβ gene promoter in a T3-dependent manner. The transcription was further enhanced when the T3-dependent corepressors SRC1, SRC2, and HDAC2 were downregulated. Hence, MED1 is a T3-dependent and -independent coactivator on the TSHβ gene promoter.

Search for the Higgs-Boson with the CDF experiment at Tevatron

Energy Technology Data Exchange (ETDEWEB)

Hennecke, Martin [Univ. of Karlsruhe (Germany)

2005-06-10

A search for a low-mass SM Higgs-Boson in the channel WH → lvb$\\bar{b}$ has been performed using neural networks. The data were taken by the CDF experiment at the p-$\\bar{p}$ collider Tevatron from 2000-2003, corresponding to in integrated luminosity of L_int = 162 pb^-1 at a CMS-energy of √s = 1.96 TeV. 95% confidence level upper limits are set on σ × BR, the product of the production cross section times the Branching ratio, as a function of the Higgs boson mass. Cross sections above 8 pb are excluded for six different Higgs masses between 110 GeV/c² and 150 GeV/c². The required integrated luminosities for a 95% C.L. exclusion, 3σ evidence and 5σ discovery are calculated.

Finite-element stress and deflection analysis of CDF yike and end plug

International Nuclear Information System (INIS)

Wands, R.; Grimson, J.; Kephart, R.; Theriot, D.

1982-01-01

A large detector is being designed to study anti pp collisions at center-of-mass energies of up to 2000 GeV as part of the Fermilab Collider Detector Facility (CDF). The central detector of this facility consists of a solenoid, calorimeter yoke, and a variety of particle measurement devices. The yoke will be a large steel structure that will provide the magnetic flux return path as well as support structure for calorimetry and other instrumentation. It must resist both electromagnetic and gravitational loads while exhibiting only small elastic deformations. The instrumented endplugs of the yoke are subjected to large electromagnetic loads. Moreover, due to the presence of wire chambers within these plugs, they must also be particularly stiff. The purpose of this paper is to present the results of a finite element stress and deflection analysis of these structures under various anticipated load conditions. The PATRAN-G finite element modeling program, installed on a CDF-VAX 11/780 and operating from a Ramtek 6212 colorgraphics terminal, was used to generate the analysis models. The actual finite element analysis was performed by the ANSYS general purpose finite element program, installed on the Fermilab Cyber 175's

Ultrasound-Mediated Local Drug and Gene Delivery Using Nanocarriers

Science.gov (United States)

Zhou, Qiu-Lan; Chen, Zhi-Yi; Yang, Feng

2014-01-01

With the development of nanotechnology, nanocarriers have been increasingly used for curative drug/gene delivery. Various nanocarriers are being introduced and assessed, such as polymer nanoparticles, liposomes, and micelles. As a novel theranostic system, nanocarriers hold great promise for ultrasound molecular imaging, targeted drug/gene delivery, and therapy. Nanocarriers, with the properties of smaller particle size, and long circulation time, would be advantageous in diagnostic and therapeutic applications. Nanocarriers can pass through blood capillary walls and cell membrane walls to deliver drugs. The mechanisms of interaction between ultrasound and nanocarriers are not clearly understood, which may be related to cavitation, mechanical effects, thermal effects, and so forth. These effects may induce transient membrane permeabilization (sonoporation) on a single cell level, cell death, and disruption of tissue structure, ensuring noninvasive, targeted, and efficient drug/gene delivery and therapy. The system has been used in various tissues and organs (in vitro or in vivo), including tumor tissues, kidney, cardiac, skeletal muscle, and vascular smooth muscle. In this review, we explore the research progress and application of ultrasound-mediated local drug/gene delivery with nanocarriers. PMID:25202710

Ultrasound-Mediated Local Drug and Gene Delivery Using Nanocarriers

Directory of Open Access Journals (Sweden)

Qiu-Lan Zhou

2014-01-01

Full Text Available With the development of nanotechnology, nanocarriers have been increasingly used for curative drug/gene delivery. Various nanocarriers are being introduced and assessed, such as polymer nanoparticles, liposomes, and micelles. As a novel theranostic system, nanocarriers hold great promise for ultrasound molecular imaging, targeted drug/gene delivery, and therapy. Nanocarriers, with the properties of smaller particle size, and long circulation time, would be advantageous in diagnostic and therapeutic applications. Nanocarriers can pass through blood capillary walls and cell membrane walls to deliver drugs. The mechanisms of interaction between ultrasound and nanocarriers are not clearly understood, which may be related to cavitation, mechanical effects, thermal effects, and so forth. These effects may induce transient membrane permeabilization (sonoporation on a single cell level, cell death, and disruption of tissue structure, ensuring noninvasive, targeted, and efficient drug/gene delivery and therapy. The system has been used in various tissues and organs (in vitro or in vivo, including tumor tissues, kidney, cardiac, skeletal muscle, and vascular smooth muscle. In this review, we explore the research progress and application of ultrasound-mediated local drug/gene delivery with nanocarriers.

E2F1-Mediated Induction of NFYB Attenuates Apoptosis via Joint Regulation of a Pro-Survival Transcriptional Program.

Directory of Open Access Journals (Sweden)

Xiaolei Jiang

Full Text Available The E2F1 transcription factor regulates cell proliferation and apoptosis through the control of a considerable variety of target genes. Previous work has detailed the role of other transcription factors in mediating the specificity of E2F function. Here we identify the NF-YB transcription factor as a novel direct E2F1 target. Genome-wide expression analysis of the effects of NFYB knockdown on E2F1-mediated transcription identified a large group of genes that are co-regulated by E2F1 and NFYB. We also provide evidence that knockdown of NFYB enhances E2F1-induced apoptosis, suggesting a pro-survival function of the NFYB/E2F1 joint transcriptional program. Bioinformatic analysis suggests that deregulation of these NFY-dependent E2F1 target genes might play a role in sarcomagenesis as well as drug resistance.

New measurements from fully reconstructed hadronic final states of the $B^0_2$ meson at CDF II experiment

Energy Technology Data Exchange (ETDEWEB)

Da Ronco, Saverio [Univ. of Padua (Italy)

2006-01-01

This thesis reports the reconstruction and lifetime measurement of B⁺, B$0/atop{d}$ and B$0/atop{s}$ mesons, performed using fully reconstructed hadronic decays collected by a dedicated trigger at CDF II experiment. This dedicated trigger selects significantly displaced tracks from primary vertex of p$\\bar{p}$ collisions generated at Tevatron collider, obtaining, in this way, huge data samples enriched of long-lived particles, and is therefore suitable for reconstruction of B meson in hadronic decay modes. Due to the trigger track impact parameter selections, the proper decay time distributions of the B mesons no longer follow a simply exponential decay law. This complicates the lifetime measurement and requires a correct understanding and treatment of all the involved effects to keep systematic uncertainties under control. This thesis presents a method to extract the lifetime of B mesons in “ct- biased” samples, based on a Monte Carlo approach, to correct for the effects of the trigger and analysis selections. We present the results of this method when applied on fully re- constructed decays of B collected by CDF II in the data taking runs up to August 2004, corresponding to an integrated luminosity of about 360 pb^-1. The lifetimes are extracted using the decay modes B⁺ → $\\bar{D}$⁰π⁺,B$0\\atop{d}$ → D^-π⁺, B$0\\atop{d}$ → D^-π⁺π^-π⁺, B$0\\atop{s}$ → D$-\\atop{s}$π⁺ and B$0\\atop{s}$ → D$-\\atop{s}$ π⁺π^-π⁺(and c.c.) and performing combined mass-lifetime unbinned maximum likelihood fits.

Computing Models of CDF and D0 in Run II

International Nuclear Information System (INIS)

Lammel, S.

1997-05-01

The next collider run of the Fermilab Tevatron, Run II, is scheduled for autumn of 1999. Both experiments, the Collider Detector at Fermilab (CDF) and the D0 experiment are being modified to cope with the higher luminosity and shorter bunchspacing of the Tevatron. New detector components, higher event complexity, and an increased data volume require changes from the data acquisition systems up to the analysis systems. In this paper we present a summary of the computing models of the two experiments for Run II

Computing Models of CDF and D0 in Run II

International Nuclear Information System (INIS)

Lammel, S.

1997-01-01

The next collider run of the Fermilab Tevatron, Run II, is scheduled for autumn of 1999. Both experiments, the Collider Detector at Fermilab (CDF) and the D0 experiment are being modified to cope with the higher luminosity and shorter bunch spacing of the Tevatron. New detector components, higher event complexity, and an increased data volume require changes from the data acquisition systems up to the analysis systems. In this paper we present a summary of the computing models of the two experiments for Run II

Measurement of the W Plus N Inclusive Jets Cross-Section at CDF Run II

Energy Technology Data Exchange (ETDEWEB)

Stentz, Dale James [Northwestern Univ., Evanston, IL (United States)

2012-01-01

In this thesis we present the study of the production of the W boson in association with hadronic jets at the Collider Detector at Fermilab (CDF). Along with the electroweak properties the W boson, we examine jet kinematic variables with the aim of studying predictions of perturbative quantum chromodynamics. We derive several di erential crosssections as a function of the inclusive jet multiplicity and the transverse momenta of each jet. In this analysis, we are using 2.8 fb^-1 of data and consider both the electron and muon lepton nal states for the W boson decay.

Z$^{0}$Z$^{0}$ production cross section measurement in the four lepton decay channel at CDF experiment

Energy Technology Data Exchange (ETDEWEB)

Bauce, Matteo [Padua U.

2009-01-01

This thesis describes the measurement of Z 0 Z 0 production cross section in pp collisions at the CDF (Compact Detector at Fermilab) experiment at Tevatron. The determination of this quantity is important to test Standard Model predictions of Electro-Weak couplings. Moreover the Z$^{0}$Z^{0}$ reconstruction is an important step for the Higgs boson searches in the high mass region. The cross section measurement has been done in the four massive lepton decay channel that has a small branching ratio but it is characterized by a very low background contribution. The search for Z$^{0$Z$^{0}$ $\\rightarrow$ $llll$ ($l=e,\\mu$) has been performed using 4.8 fb$^{-1}$ of data collected by CDF using lepton triggers. The number of expected signal events is 4.68 $\\pm$ 0.78 while the background contributes with 0.041 $\\pm$ 0.033 events. We observe 5 events, that corresponds to a significance of 5.70 $\\sigma$. This is the first observation of a Z$^{0}$Z$^{0}$ signal at CDF. With these events we measure a cross section of 1.56$^{+0.80}_{-0.63}$ (stat.) $\\pm$ 0.25(syst.) pb, in agreement with the Standard Model value 1.4 $\\pm$ 0.1 pb at Next to Leading Order.

Hunting for CDF multi-muon ''ghost'' events at collider and fixed-target experiments

International Nuclear Information System (INIS)

Bornhauser, Nicki; Drees, Manuel

2011-01-01

In 2008 the CDF collaboration discovered a large excess of events containing two or more muons, at least one of which seemed to have been produced outside the beam pipe. We investigate whether similar ''ghost'' events could (and should) have been seen in already completed experiments. The CDF di-muon data can be reproduced by a simple model where a relatively light X particle undergoes 4-body decay. This model predicts a large number of ghost events in Fermilab fixed-target experiments E772, E789 and E866, applying the cuts optimized for analyses of Drell-Yan events. A correct description of events with more than two muons requires a more complicated model, where two X particles are produced from a very broad resonance Y. This model can be tested in fixed-target experiments only if the cut on the angles, or rapidities, of the muons can be relaxed. Either way, the UA1 experiment at the CERN p anti p collider should have observed O(100) ghost events. (orig.)

Measurement of the top quark mass with dilepton events selected using neuroevolution at CDF

International Nuclear Information System (INIS)

Aaltonen, T.; Helsinki Inst. of Phys.; Adelman, J.; Chicago U., EFI; Akimoto, T.; Tsukuba U.; Albrow, M.G.; Fermilab; Alvarez Gonzalez, B.; Cantabria U., Santander; Amerio, S.; Padua U.; Amidei, D.; Michigan U.; Anastassov, A.; Northwestern U.; Annovi, A.; Frascati; Antos, J.; Comenius U.; Apollinari, G.

2008-01-01

We report a measurement of the top quark mass M t in the dilepton decay channel t(bar t) to b(ell)(prime) + ν(prime) # ell# (bar b)(ell) - (bar ν) # ell#. Events are selected with a neural network which has been directly optimized for statistical precision in top quark mass using neuroevolution, a technique modeled on biological evolution. The top quark mass is extracted from per-event probability densities that are formed by the convolution of leading order matrix elements and detector resolution functions. The joint probability is the product of the probability densities from 344 candidate events in 2.0 fb -1 of p(bar p) collisions collected with the CDF II detector, yielding a measurement of M t = 171.2 ± 2.7(stat.) ± 2.9(syst.) GeV/c 2

Analysis of the siRNA-Mediated Gene Silencing Process Targeting Three Homologous Genes Controlling Soybean Seed Oil Quality.

Science.gov (United States)

Lu, Sha; Yin, Xiaoyan; Spollen, William; Zhang, Ning; Xu, Dong; Schoelz, James; Bilyeu, Kristin; Zhang, Zhanyuan J

2015-01-01

In the past decade, RNA silencing has gained significant attention because of its success in genomic scale research and also in the genetic improvement of crop plants. However, little is known about the molecular basis of siRNA processing in association with its target transcript. To reveal this process for improving hpRNA-mediated gene silencing in crop plants, the soybean GmFAD3 gene family was chosen as a test model. We analyzed RNAi mutant soybean lines in which three members of the GmFAD3 gene family were silenced. The silencing levels of FAD3A, FAD3B and FAD3C were correlated with the degrees of sequence homology between the inverted repeat of hpRNA and the GmFAD3 transcripts in the RNAi lines. Strikingly, transgenes in two of the three RNAi lines were heavily methylated, leading to a dramatic reduction of hpRNA-derived siRNAs. Small RNAs corresponding to the loop portion of the hairpin transcript were detected while much lower levels of siRNAs were found outside of the target region. siRNAs generated from the 318-bp inverted repeat were found to be diced much more frequently at stem sequences close to the loop and associated with the inferred cleavage sites on the target transcripts, manifesting "hot spots". The top candidate hpRNA-derived siRNA share certain sequence features with mature miRNA. This is the first comprehensive and detailed study revealing the siRNA-mediated gene silencing mechanism in crop plants using gene family GmFAD3 as a test model.

Observation of single top-quark production with the CDF II experiment

International Nuclear Information System (INIS)

Lueck, J.

2010-01-01

We present the observation of electroweak single top-quark production using up to 3.2 fb -1 of data collected by the CDF experiment. Lepton plus jets candidate events are classified by four parallel analysis techniques: one likelihood discriminant, one matrix-element discriminant, one decision-tree discriminant, and one neural-network discriminant. These outputs are combined with a super discriminant based on a neural-network analysis in order to improve the expected sensitivity. In conjunction with one neural-network discriminant using a complementary dataset of MET plus jets events with a veto on identified leptons we observe a signal consistent with the standard model but inconsistent with the background-only model by 5.0 standard deviations, with a median expected sensitivity in excess of 5.9 standard deviations.

Recent results on top quark physics and B physics at CDF

International Nuclear Information System (INIS)

Kim, S.

1998-01-01

We present the recent results on top quark physics and B physics with the Collider Detector at Fermilab (CDF). These results come from analyses using a full data sample at an integrated luminosity of 109 pb -1 cross section in 1.8-TeV p anti p collisions. We measure the top quark mass to be 175.8±6.5 GeV/c 2 and the t anti t production cross section to be 7.6 +1.8 -1.5 pb. We also present measurements of the lifetimes of B-hadrons and the time- dependent B 0 -anti B 0 mixing which results in the mass difference between heavy and light B 0 d mesons (Δm d ) of 0.464±0.030(stat)±0.026(syst) ps -1

The CDF Central Electromagnetic Calorimeter for Proton - Anti-proton Collision Experiment at Tevatron

Energy Technology Data Exchange (ETDEWEB)

Kamon, Teruki [Univ. of Tsukuba (Japan)

1986-06-01

The CDF central electromagnetic calorimeter modules were calibrated with test beam and cosmic ray muons. It is found that (a) the modules are identical to each other by 1 % on the response map and (b) the uncertaity on the measurement of the energy of showering particle is better than 1.1 % in the 85 % of whole area.

Amplification of TLO Mediator Subunit Genes Facilitate Filamentous Growth in Candida Spp.

Science.gov (United States)

Liu, Zhongle; Moran, Gary P.; Myers, Lawrence C.

2016-01-01

Filamentous growth is a hallmark of C. albicans pathogenicity compared to less-virulent ascomycetes. A multitude of transcription factors regulate filamentous growth in response to specific environmental cues. Our work, however, suggests the evolutionary history of C. albicans that resulted in its filamentous growth plasticity may be tied to a change in the general transcription machinery rather than transcription factors and their specific targets. A key genomic difference between C. albicans and its less-virulent relatives, including its closest relative C. dubliniensis, is the unique expansion of the TLO (TeLOmere-associated) gene family in C. albicans. Individual Tlo proteins are fungal-specific subunits of Mediator, a large multi-subunit eukaryotic transcriptional co-activator complex. This amplification results in a large pool of ‘free,’ non-Mediator associated, Tlo protein present in C. albicans, but not in C. dubliniensis or other ascomycetes with attenuated virulence. We show that engineering a large ‘free’ pool of the C. dubliniensis Tlo2 (CdTlo2) protein in C. dubliniensis, through overexpression, results in a number of filamentation phenotypes typically associated only with C. albicans. The amplitude of these phenotypes is proportional to the amount of overexpressed CdTlo2 protein. Overexpression of other C. dubliniensis and C. albicans Tlo proteins do result in these phenotypes. Tlo proteins and their orthologs contain a Mediator interaction domain, and a potent transcriptional activation domain. Nuclear localization of the CdTlo2 activation domain, facilitated naturally by the Tlo Mediator binding domain or artificially through an appended nuclear localization signal, is sufficient for the CdTlo2 overexpression phenotypes. A C. albicans med3 null mutant causes multiple defects including the inability to localize Tlo proteins to the nucleus and reduced virulence in a murine systemic infection model. Our data supports a model in which the

Amplification of TLO Mediator Subunit Genes Facilitate Filamentous Growth in Candida Spp.

Directory of Open Access Journals (Sweden)

Zhongle Liu

2016-10-01

Full Text Available Filamentous growth is a hallmark of C. albicans pathogenicity compared to less-virulent ascomycetes. A multitude of transcription factors regulate filamentous growth in response to specific environmental cues. Our work, however, suggests the evolutionary history of C. albicans that resulted in its filamentous growth plasticity may be tied to a change in the general transcription machinery rather than transcription factors and their specific targets. A key genomic difference between C. albicans and its less-virulent relatives, including its closest relative C. dubliniensis, is the unique expansion of the TLO (TeLOmere-associated gene family in C. albicans. Individual Tlo proteins are fungal-specific subunits of Mediator, a large multi-subunit eukaryotic transcriptional co-activator complex. This amplification results in a large pool of 'free,' non-Mediator associated, Tlo protein present in C. albicans, but not in C. dubliniensis or other ascomycetes with attenuated virulence. We show that engineering a large 'free' pool of the C. dubliniensis Tlo2 (CdTlo2 protein in C. dubliniensis, through overexpression, results in a number of filamentation phenotypes typically associated only with C. albicans. The amplitude of these phenotypes is proportional to the amount of overexpressed CdTlo2 protein. Overexpression of other C. dubliniensis and C. albicans Tlo proteins do result in these phenotypes. Tlo proteins and their orthologs contain a Mediator interaction domain, and a potent transcriptional activation domain. Nuclear localization of the CdTlo2 activation domain, facilitated naturally by the Tlo Mediator binding domain or artificially through an appended nuclear localization signal, is sufficient for the CdTlo2 overexpression phenotypes. A C. albicans med3 null mutant causes multiple defects including the inability to localize Tlo proteins to the nucleus and reduced virulence in a murine systemic infection model. Our data supports a model in which

Mediator-dependent Nuclear Receptor Functions

Science.gov (United States)

Chen, Wei; Roeder, Robert

2011-01-01

As gene-specific transcription factors, nuclear hormone receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss (i) our current understanding of pathways that nuclear receptors and other interacting cofactors employ to recruit Mediator to target gene enhancers and promoters, including conditional requirements for the strong NR-Mediator interactions mediated by the NR AF2 domain and the MED1 LXXLLL motifs and (ii) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. PMID:21854863

Measurement of the W boson helicity in top-antitop quark events with the CDF II experiment

International Nuclear Information System (INIS)

Chwalek, Thorsten; Karlsruhe U., EKP

2006-01-01

In 1995 the top quark was discovered at the Tevatron proton-antiproton collider at Fermilab by the CDF and D0 collaborations [1, 2]. It is the most massive known elementary particle and its mass is currently measured with a precision of about 1.3% [3, 4]. However, the measurements of several other top quark properties are still statistically limited, so the question remains whether the Standard Model of elementary particle physics successfully predicts these properties. This thesis addresses one interesting aspect of top quark decay, the helicity of the produced W boson. Until the start of the Large Hadron Collider (LHC) at CERN, the Tevatron with a center-of-mass energy of √s = 1.96 TeV is the only collider, where top quarks can be produced. In the Standard Model the top quark decays predominantly into a W boson and a b quark, with a branching ratio close to 100%. The V-A structure of the weak interaction of the Standard Model predicts that the W + bosons from the top quark decay t → W + b are dominantly either longitudinally polarized or left handed, while right handed W bosons are heavily suppressed and even forbidden in the limit of a massless b quark. Under the assumption of a massless b quark, for a top quark mass of 173 GeV/c 2 the Standard Model predicts the fraction F0 of longitudinally polarized W bosons to be 0.7 and 0.3 for the fraction F( ) of left handed W bosons, while the fraction F + of right handed W bosons is predicted to be zero. Since next-to-leading order corrections change these fractions only slightly, a significant deviation from the predicted value for F 0 or a nonzero value for F + could indicate new physics. Left-right symmetric models [5], for example, lead to a significant right handed fraction of W bosons in top decays. Such a right handed component (V+A coupling) would lead to a smaller left handed fraction, while F 0 would remain unchanged. Since the decay rate to longitudinal W bosons depends on the Yukawa coupling of the top

Neuropilin-2 mediated β-catenin signaling and survival in human gastro-intestinal cancer cell lines.

Directory of Open Access Journals (Sweden)

Shaija Samuel

Full Text Available NRP-2 is a high-affinity kinase-deficient receptor for ligands belonging to the class 3 semaphorin and vascular endothelial growth factor families. NRP-2 has been detected on the surface of several types of human cancer cells, but its expression and function in gastrointestinal (GI cancer cells remains to be determined. We sought to determine the function of NRP-2 in mediating downstream signals regulating the growth and survival of human gastrointestinal cancer cells. In human gastric cancer specimens, NRP-2 expression was detected in tumor tissues but not in adjacent normal mucosa. In CNDT 2.5 cells, shRNA mediated knockdown NRP-2 expression led to decreased migration and invasion in vitro (p<0.01. Focused gene-array analysis demonstrated that loss of NRP-2 reduced the expression of a critical metastasis mediator gene, S100A4. Steady-state levels and function of β-catenin, a known regulator of S100A4, were also decreased in the shNRP-2 clones. Furthermore, knockdown of NRP-2 sensitized CNDT 2.5 cells in vitro to 5FU toxicity. This effect was associated with activation of caspases 3 and 7, cleavage of PARP, and downregulation of Bcl-2. In vivo growth of CNDT 2.5 cells in the livers of nude mice was significantly decreased in the shNRP-2 group (p<0.05. Intraperitoneal administration of NRP-2 siRNA-DOPC decreased the tumor burden in mice (p = 0.01. Collectively, our results demonstrate that tumor cell-derived NRP-2 mediates critical survival signaling in gastrointestinal cancer cells.

Agrobacterium-mediated transformation of tomato with the ICE1 transcription factor gene.

Science.gov (United States)

Juan, J X; Yu, X H; Jiang, X M; Gao, Z; Zhang, Y; Li, W; Duan, Y D; Yang, G

2015-01-30

ICE1 genes play a very important role in plants in cold conditions. To improve the cold resistance of tomato, the ICE1 gene of Arabidopsis thaliana was used to construct the plant expression vector p3301-ICE1, and was overexpressed in tomato through Agrobacterium-mediated transformation. Five strains of resistant plants were obtained. PCR and half-quantitative results showed that the ICE1 gene was transferred to tomato; three strains tested positive. After low-temperature stress treatment, praline content and peroxide and catalase activities in the transgenic tomato plants were higher compared with non-transgenic controls, while malondialdehyde content was clearly lower.

Has the substructure of quarks been found by the CDF experiment?

International Nuclear Information System (INIS)

Akama, Keiichi; Terazawa, Hidezumi.

1996-08-01

The significant excess recently found by the CDF Collaboration in the inclusive jet cross section for jet transverse energies E T ≥ 200 GeV over current QCD predictions can be explained either by possible production of excited bosons (excited gluons, weak bosons, Higgs scalars, etc.) or by that of excited quarks. The masses of the excited boson and the excited quark are estimated to be around 1600 GeV and 500 GeV, respectively. (author)

Liver X receptor alpha mediated genistein induction of human dehydroepiandrosterone sulfotransferase (hSULT2A1) in Hep G2 cells

Energy Technology Data Exchange (ETDEWEB)

Chen, Yue; Zhang, Shunfen [Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078 (United States); Zhou, Tianyan [Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100083 (China); Huang, Chaoqun; McLaughlin, Alicia [Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078 (United States); Chen, Guangping, E-mail: guangping.chen@okstate.edu [Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078 (United States)

2013-04-15

Cytosolic sulfotransferases are one of the major families of phase II drug metabolizing enzymes. Sulfotransferase-catalyzed sulfonation regulates hormone activities, metabolizes drugs, detoxifies xenobiotics, and bioactivates carcinogens. Human dehydroepiandrosterone sulfotransferase (hSULT2A1) plays important biological roles by sulfating endogenous hydroxysteroids and exogenous xenobiotics. Genistein, mainly existing in soy food products, is a naturally occurring phytoestrogen with both chemopreventive and chemotherapeutic potential. Our previous studies have shown that genistein significantly induces hSULT2A1 in Hep G2 and Caco-2 cells. In this study, we investigated the roles of liver X receptor (LXRα) in the genistein induction of hSULT2A1. LXRs have been shown to induce expression of mouse Sult2a9 and hSULT2A1 gene. Our results demonstrate that LXRα mediates the genistein induction of hSULT2A1, supported by Western blot analysis results, hSULT2A1 promoter driven luciferase reporter gene assay results, and mRNA interference results. Chromatin immunoprecipitation (ChIP) assay results demonstrate that genistein increase the recruitment of hLXRα binding to the hSULT2A1 promoter. These results suggest that hLXRα plays an important role in the hSULT2A1 gene regulation. The biological functions of phytoestrogens may partially relate to their induction activity toward hydroxysteroid SULT. - Highlights: ► Liver X receptor α mediated genistein induction of hSULT2A1 in Hep G2 cells. ► LXRα and RXRα dimerization further activated this induction. ► Western blot results agreed well with luciferase reporter gene assay results. ► LXRs gene silencing significantly decreased hSULT2A1 expression. ► ChIP analysis suggested that genistein enhances hLXRα binding to the hSULT2A1 promoter.

Recombinant AAV-mediated HSVtk gene transfer with direct intratumoral injections and Tet-On regulation for implanted human breast cancer

International Nuclear Information System (INIS)

Zi-Bo, LI; Zhao-Jun, ZENG; Qian, CHEN; Sai-Qun, LUO; Wei-Xin, HU

2006-01-01

HSVtk/ganciclovir (GCV) gene therapy has been extensively studied in tumors and relies largely on the gene expression of HSVtk. Most studies, however, have failed to demonstrate any significant benefit of a controlled gene expression strategy in cancer treatment. The Tet-On system is commonly used to regulate gene expression following Dox induction. We have evaluated the antitumor effect of HSVtk/ganciclovir gene therapy under Tet-On regulation by means of adeno-associated virus-2 (AAV-2)-mediated HSVtk gene transfer with direct intratumoral injections in mice bearing breast cancer tumors. Recombinant adeno-associated virus-2 (rAAV) was constructed and transduced into MCF-7 cell line. GCV treatment to the rAAV infected MCF-7 cells was performed by MTT assay under the doxycycline (Dox) induction or without Dox induction at a vp (viral particle) number of ≥10 4 /cell. The virus was administered intratumorally to nude mice that had also received GCV intraperitoneally. The antitumor effects were evaluated by measuring tumor regression and histological analysis. We have demonstrated that GCV treatment to the infected MCF-7 cells under the Dox induction was of more inhibited effects than those without Dox induction at ≥10 4 vp/cell. In ex vivo experiments, tumor growth of BALB/C nude mice breast cancer was retarded after rAAV-2/HSVtk/Tet-On was injected into the tumors under the Dox induction. Infiltrating cells were also observed in tumors after Dox induction followed by GCV treatment and cells were profoundly damaged. The expression of HSVtk gene in MCF-7 cells and BALB/C nude mice tumors was up-regulated by Tet-On under Dox induction with reverse transcription-PCR (RT-PCR) analysis. The antitumor effect of rAAV-mediated HSVtk/GCV gene therapy under the Dox induction with direct intratumoral injections may be a useful treatment for breast cancer and other solid tumors

Personal extrapolation of CDF test beam use to the SSC

International Nuclear Information System (INIS)

Nodulman, L.

1986-01-01

The author's personal experience in test beam usage at CDF is used to predict SSC needs at the point of turn-on. It is concluded that the test beam demand will reflect the scale of effort involved in SSC detectors rather than the total number of them. Provision for later expansion is recommended. It is also recommended that the test beam facilities, as well as detector electronics, should reflect the available dynamic range; particularly, a single high energy beam derived from the SSC could be shared by several groups

Personal extrapolation of CDF test beam use to the SSC

Energy Technology Data Exchange (ETDEWEB)

Nodulman, L.

1986-06-23

The author's personal experience in test beam usage at CDF is used to predict SSC needs at the point of turn-on. It is concluded that the test beam demand will reflect the scale of effort involved in SSC detectors rather than the total number of them. Provision for later expansion is recommended. It is also recommended that the test beam facilities, as well as detector electronics, should reflect the available dynamic range; particularly, a single high energy beam derived from the SSC could be shared by several groups. (LEW)