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1. L'Accordo dell'Uruguay Round: una prima valutazione dei suoi effetti sull'UE e sui PSV

Author: C. MASTROPASQUA and V. ROLLI
Subjects: Uruguay round, GATT, trade, agriculture, intellectual property, Finance, HG1-9999, Economic theory. Demography, HB1-3840
Abstract: On December 15th of last year, seven years after its start, the Uruguay Round negotiations for the reform of the General Agreement on Tariffs and Trade came to a conclusion. This paper aims to provide a qualitative assessment of the results achieved in the fields of agriculture, market access, trade rules and intellectual property protection, leaving out services, given the limited results of liberalisation achieved in this area. In this limited context, the focus is on the European Union and developing countries. The authors describe the details of the agreement by sector before analysing the effects on the EU and developing countries. The effects of intellectual property protection both industrial countries and developing countries is then assessed. JEL Codes: F13
Published: 2013
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2. Quantifying the δ15N trophic offset in a cold-water scleractinian coral (CWC): implications for the CWC diet and coral δ15N as a marine N cycle proxy

Author: J. L. Mottram, A. M. Gothmann, M. G. Prokopenko, A. Cordova, V. Rollinson, K. Dobkowski, and J. Granger
Subjects: Ecology, QH540-549.5, Life, QH501-531, Geology, QE1-996.5
Abstract: The nitrogen (N) isotope composition (δ15N) of cold-water corals is a promising proxy for reconstructing past ocean N cycling, as a strong correlation was found between the δ15N of the organic nitrogen preserved in coral skeletons and the δ15N of particulate organic matter exported from the surface ocean. However, a large offset of 8 ‰–9 ‰ between the δ15N recorded by the coral and that of exported particulate organic matter remains unexplained. The 8 ‰–9 ‰ offset may signal a higher trophic level of coral dietary sources, an unusually large trophic isotope effect or a biosynthetic δ15N offset between the coral's soft tissue and skeletal organic matter, or some combinations of these factors. To understand the origin of the offset and further validate the proxy, we investigated the trophic ecology of the asymbiotic scleractinian cold-water coral Balanophyllia elegans, both in a laboratory setting and in its natural habitat. A long-term incubation experiment of B. elegans fed on an isotopically controlled diet yielded a canonical trophic isotope effect of 3.0 ± 0.1 ‰ between coral soft tissue and the Artemia prey. The trophic isotope effect was not detectably influenced by sustained food limitation. A long N turnover of coral soft tissue, expressed as an e-folding time, of 291 ± 15 d in the well-fed incubations indicates that coral skeleton δ15N is not likely to track subannual (e.g., seasonal) variability in diet δ15N. Specimens of B. elegans from the subtidal zone near San Juan Channel (WA, USA) revealed a modest difference of 1.2 ± 0.6 ‰ between soft tissue and skeletal δ15N. The δ15N of the coral soft tissue was 12.0 ± 0.6 ‰, which was ∼6 ‰ higher than that of suspended organic material that was comprised dominantly of phytoplankton – suggesting that phytoplankton is not the primary component of B. elegans' diet. An analysis of size-fractionated net tow material suggests that B. elegans fed predominantly on a size class of zooplankton ≥500 µm, implicating a two-level trophic transfer between phytoplankton material and coral tissue. These results point to a feeding strategy that may result in an influence of the regional food web structure on the cold-water coral δ15N. This factor should be taken into consideration when applying the proxy to paleo-oceanographic studies of ocean N cycling.
Published: 2024
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3. PARP-2, A Novel Mammalian DNA Damage-dependent Poly(ADP-ribose) Polymerase

Author: Valérie Schreiber, Jean-Christophe Amé, Patrice Decker, V. Rolli, Gilbert de Murcia, Thomas Höger, Josiane Ménissier-de Murcia, Sylviane Muller, Françoise Apiou, Claude Niedergang, Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), Immuno-Rhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), Physiopathologie, cibles et thérapies de la polyarthrite rhumatoïde (Li2P), Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-UFR Santé, Médecine et Biologie Humaine-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunologie et chimie thérapeutiques (ICT), Cancéropôle du Grand Est-Centre National de la Recherche Scientifique (CNRS), Cancérogenèse et mutagenèse moléculaire et structurale (CMMS), Centre National de la Recherche Scientifique (CNRS), Biotechnologie et signalisation cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, and Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR Santé, Médecine et Biologie Humaine-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)
Subjects: DNA damage, Poly ADP ribose polymerase, Molecular Sequence Data, Biology, Biochemistry, Mice, 03 medical and health sciences, 0302 clinical medicine, Complementary DNA, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Lymphocytes, RNA, Messenger, Cloning, Molecular, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, Poly(ADP-ribose) glycohydrolase, In Situ Hybridization, Fluorescence, ComputingMilieux_MISCELLANEOUS, Polymerase, 030304 developmental biology, Chromosomes, Human, Pair 14, 0303 health sciences, PARG, Chromosome Mapping, Nuclear Proteins, 3T3 Cells, Cell Biology, Base excision repair, Molecular biology, Recombinant Proteins, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], DNA-Binding Proteins, Enzyme Activation, 030220 oncology & carcinogenesis, biology.protein, Poly(ADP-ribose) Polymerases, Poly [ADP-Ribose] Polymerase 2, Sequence Alignment, DNA Damage
Abstract: Poly(ADP-ribosylation) is a post-translational modification of nuclear proteins in response to DNA damage that activates the base excision repair machinery. Poly(ADP-ribose) polymerase which we will now call PARP-1, has been the only known enzyme of this type for over 30 years. Here, we describe a cDNA encoding a 62-kDa protein that shares considerable homology with the catalytic domain of PARP-1 and also contains a basic DNA-binding domain. We propose to call this enzyme poly(ADP-ribose) polymerase 2 (PARP-2). The PARP-2 gene maps to chromosome 14C1 and 14q11.2 in mouse and human, respectively. Purified recombinant mouse PARP-2 is a damaged DNA-binding protein in vitro and catalyzes the formation of poly(ADP-ribose) polymers in a DNA-dependent manner. PARP-2 displays automodification properties similar to PARP-1. The protein is localized in the nucleus in vivo and may account for the residual poly(ADP-ribose) synthesis observed in PARP-1-deficient cells, treated with alkylating agents or hydrogen peroxide.
Published: 1999

4. Photoaffinity labelling of human poly(ADP-ribose) polymerase catalytic domain

Author: J Reinbolt, A. Ruf, J Ménissier-de Murcia, G. de Murcia, Frédéric Simonin, V. Rolli, Georg E. Schulz, H Kim, Myron K. Jacobson, University of Kentucky, Biotechnologie et signalisation cellulaire (BSC), and Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Light, DNA Mutational Analysis, Peptide, MESH: Amino Acid Sequence, Biochemistry, MESH: Recombinant Proteins, MESH: DNA Mutational Analysis, MESH: Peptide Fragments, Peptide sequence, Polymerase, chemistry.chemical_classification, biology, Chemistry, Tryptophan, MESH: NAD, Affinity Labels, Recombinant Proteins, MESH: Mutagenesis, Site-Directed, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Poly(ADP-ribose) Polymerases, Sequence Analysis, MESH: Photochemistry, MESH: Models, Molecular, Research Article, Azides, Photochemistry, Stereochemistry, Poly ADP ribose polymerase, Molecular Sequence Data, MESH: Sequence Analysis, Labelling, Humans, MESH: Lysine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Binding site, Molecular Biology, MESH: Tryptophan, MESH: Affinity Labels, MESH: Humans, MESH: Molecular Sequence Data, Binding Sites, Lysine, MESH: Poly(ADP-ribose) Polymerases, Mutagenesis, Cell Biology, NAD, MESH: Azides, MESH: Light, Peptide Fragments, MESH: Binding Sites, Mutagenesis, Site-Directed, biology.protein, NAD+ kinase
Abstract: Photoaffinity labelling of the human poly(ADP-ribose) polymerase (PARP) catalytic domain (40 kDa) with the NAD+ photoaffinity analogue 2-azido-[α-32P]NAD+ has been used to identify NAD+-binding residues. In the presence of UV, photoinsertion of the analogue was observed with a stoichiometry of 0.73 mol of 2-azido-[α-32P]NAD+ per mol of catalytic domain. Competition experiments indicated that 3-aminobenzamide strongly protected the insertion site. Residues binding the adenine ring of NAD+ were identified by trypsin digestion and boronate affinity chromatography in combination with reverse-phase HPLC. Two major NAD+-binding residues, Trp1014 of peptide Thr1011–Trp1014 and Lys893 of peptide Ile879 –Lys893, were identified. The site-directed mutagenesis of these two residues revealed that Lys893, but not Trp1014, is critical for activity. The close positioning of Lys893 near the adenine ring of NAD+ has been confirmed by the recently solved crystallographic structure of the chicken PARP catalytic domain [Ruf, Ménissier-de Murcia, de Murcia and Schulz (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 7481–7485].
Published: 1997

5. Poly(ADP-ribose) polymerase: Structure-function relationship

Author: M. Masson, V. Rolli, F. Dantzer, C. Trucco, V. Schreiber, S. Fribourg, M. Molinete, A. Ruf, E. Alves Miranda, C. Niedergang, D. Hunting, B. Gowans, G.E. Schulz, J.Ménissier de Murcia, and G. de Murcia
Subjects: DNA Repair, DNA repair, DNA damage, Poly ADP ribose polymerase, Crystallography, X-Ray, Transfection, Biochemistry, Catalysis, Structure-Activity Relationship, Protein structure, Animals, Humans, Structure–activity relationship, Glyceraldehyde 3-phosphate dehydrogenase, Polymerase, chemistry.chemical_classification, biology, Genome, Human, General Medicine, Recombinant Proteins, Protein Structure, Tertiary, DNA-Binding Proteins, Enzyme, chemistry, biology.protein, Poly(ADP-ribose) Polymerases, Crystallization, Chickens, DNA Damage, HeLa Cells
Abstract: Dissection of the human poly(ADP-ribose) polymerase (PARP) molecule in terms of its structure-function relationship has proved to be an essential step towards understanding the biological role of poly(ADP-ribosylation) as a cellular response to DNA damage in eukaryotes. Current approaches aimed at elucidating the implication of this multifunctional enzyme in the maintenance of the genomic integrity will be presented.
Published: 1995

6. The ATLAS Inner Detector commissioning and calibration

Author: The ATLAS Collaboration Aad, G. Abbott, B. Abdallah, J. Abdelalim, A.A. Abdesselam, A. Abdinov, O. Abi, B. Abolins, M. Abramowicz, H. Abreu, H. Acharya, B.S. Adams, D.L. Addy, T.N. Adelman, J. Adorisio, C. Adragna, P. Adye, T. Aefsky, S. Aguilar-Saavedra, J.A. Aharrouche, M. Ahlen, S.P. Ahles, F. Ahmad, A. Ahsan, M. Aielli, G. Akdogan, T. Åkesson, T.P.A. Akimoto, G. Akimov, A.V. Aktas, A. Alam, M.S. Alam, M.A. Albrand, S. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexander, G. Alexandre, G. Alexopoulos, T. Alhroob, M. Aliev, M. Alimonti, G. Alison, J. Aliyev, M. Allport, P.P. Allwood-Spiers, S.E. Almond, J. Aloisio, A. Alon, R. Alonso, A. Alviggi, M.G. Amako, K. Amelung, C. Amorim, A. Amorós, G. Amram, N. Anastopoulos, C. Andeen, T. Anders, C.F. Anderson, K.J. Andreazza, A. Andrei, V. Anduaga, X.S. Angerami, A. Anghinolfi, F. Anjos, N. Annovi, A. Antonaki, A. Antonelli, M. Antonelli, S. Antos, J. Antunovic, B. Anulli, F. Aoun, S. Arabidze, G. Aracena, I. Arai, Y. Arce, A.T.H. Archambault, J.P. Arfaoui, S. Arguin, J.-F. Argyropoulos, T. Arik, M. Armbruster, A.J. Arnaez, O. Arnault, C. Artamonov, A. Arutinov, D. Asai, M. Asai, S. Asfandiyarov, R. Ask, S. Åsman, B. Asner, D. Asquith, L. Assamagan, K. Astvatsatourov, A. Atoian, G. Auerbach, B. Augsten, K. Aurousseau, M. Austin, N. Avolio, G. Avramidou, R. Ay, C. Azuelos, G. Azuma, Y. Baak, M.A. Bach, A.M. Bachacou, H. Bachas, K. Backes, M. Badescu, E. Bagnaia, P. Bai, Y. Bain, T. Baines, J.T. Baker, O.K. Baker, M.D. Baker, S. Dos Pedrosa, F.B.S. Banas, E. Banerjee, P. Banerjee, S. Banfi, D. Bangert, A. Bansal, V. Baranov, S.P. Barashkou, A. Barber, T. Barberio, E.L. Barberis, D. Barbero, M. Bardin, D.Y. Barillari, T. Barisonzi, M. Barklow, T. Barlow, N. Barnett, B.M. Barnett, R.M. Baroncelli, A. Barr, A.J. Barreiro, F. Guimarães da Costa, J.B. Barrillon, P. Bartoldus, R. Bartsch, D. Bates, R.L. Batkova, L. Batley, J.R. Battaglia, A. Battistin, M. Bauer, F. Bawa, H.S. Bazalova, M. Beare, B. Beau, T. Beauchemin, P.H. Beccherle, R. Bechtle, P. Beck, G.A. Beck, H.P. Beckingham, M. Becks, K.H. Beddall, A.J. Beddall, A. Bednyakov, V.A. Bee, C. Begel, M. Harpaz, S.B. Behera, P.K. Beimforde, M. Belanger-Champagne, C. Bell, P.J. Bell, W.H. Bella, G. Bellagamba, L. Bellina, F. Bellomo, M. Belloni, A. Belotskiy, K. Beltramello, O. Ami, S.B. Benary, O. Benchekroun, D. Bendel, M. Benedict, B.H. Benekos, N. Benhammou, Y. Benjamin, D.P. Benoit, M. Bensinger, J.R. Benslama, K. Bentvelsen, S. Beretta, M. Berge, D. Kuutmann, E.B. Berger, N. Berghaus, F. Berglund, E. Beringer, J. Bernabéu, J. Bernat, P. Bernhard, R. Bernius, C. Berry, T. Bertin, A. Besana, M.I. Besson, N. Bethke, S. Bianchi, R.M. Bianco, M. Biebel, O. Biesiada, J. Biglietti, M. Bilokon, H. Bindi, M. Bingul, A. Bini, C. Biscarat, C. Bitenc, U. Black, K.M. Blair, R.E. Blanchard, J.-B. Blanchot, G. Blocker, C. Blondel, A. Blum, W. Blumenschein, U. Bobbink, G.J. Bocci, A. Boehler, M. Boek, J. Boelaert, N. Böser, S. Bogaerts, J.A. Bogouch, A. Bohm, C. Bohm, J. Boisvert, V. Bold, T. Boldea, V. Bondarenko, V.G. Bondioli, M. Boonekamp, M. Bordoni, S. Borer, C. Borisov, A. Borissov, G. Borjanovic, I. Borroni, S. Bos, K. Boscherini, D. Bosman, M. Boterenbrood, H. Bouchami, J. Boudreau, J. Bouhova-Thacker, E.V. Boulahouache, C. Bourdarios, C. Boveia, A. Boyd, J. Boyko, I.R. Bozovic-Jelisavcic, I. Bracinik, J. Braem, A. Branchini, P. Brandt, A. Brandt, G. Brandt, O. Bratzler, U. Brau, B. Brau, J.E. Braun, H.M. Brelier, B. Bremer, J. Brenner, R. Bressler, S. Britton, D. Brochu, F.M. Brock, I. Brock, R. Brodet, E. Bromberg, C. Brooijmans, G. Brooks, W.K. Brown, G. Bruckman de Renstrom, P.A. Bruncko, D. Bruneliere, R. Brunet, S. Bruni, A. Bruni, G. Bruschi, M. Bucci, F. Buchanan, J. Buchholz, P. Buckley, A.G. Budagov, I.A. Budick, B. Büscher, V. Bugge, L. Bulekov, O. Bunse, M. Buran, T. Burckhart, H. Burdin, S. Burgess, T. Burke, S. Busato, E. Bussey, P. Buszello, C.P. Butin, F. Butler, B. Butler, J.M. Buttar, C.M. Butterworth, J.M. Byatt, T. Caballero, J. Cabrera Urbán, S. Caforio, D. Cakir, O. Calafiura, P. Calderini, G. Calfayan, P. Calkins, R. Caloba, L.P. Calvet, D. Camarri, P. Cameron, D. Campana, S. Campanelli, M. Canale, V. Canelli, F. Canepa, A. Cantero, J. Capasso, L. Garrido, M.D.M.C. Caprini, I. Caprini, M. Capua, M. Caputo, R. Caramarcu, C. Cardarelli, R. Carli, T. Carlino, G. Carminati, L. Caron, B. Caron, S. Montoya, G.D.C. Montero, S.C. Carter, A.A. Carter, J.R. Carvalho, J. Casadei, D. Casado, M.P. Cascella, M. Castaneda Hernandez, A.M. Castaneda-Miranda, E. Gimenez, V.C. Castro, N.F. Cataldi, G. Catinaccio, A. Catmore, J.R. Cattai, A. Cattani, G. Caughron, S. Cavalleri, P. Cavalli, D. Cavalli-Sforza, M. Cavasinni, V. Ceradini, F. Cerqueira, A.S. Cerri, A. Cerrito, L. Cerutti, F. Cetin, S.A. Chafaq, A. Chakraborty, D. Chan, K. Chapman, J.D. Chapman, J.W. Chareyre, E. Charlton, D.G. Chavda, V. Cheatham, S. Chekanov, S. Chekulaev, S.V. Chelkov, G.A. Chen, H. Chen, S. Chen, X. Cheplakov, A. Chepurnov, V.F. Cherkaoui El Moursli, R. Tcherniatine, V. Chesneanu, D. Cheu, E. Cheung, S.L. Chevalier, L. Chevallier, F. Chiefari, G. Chikovani, L. Childers, J.T. Chilingarov, A. Chiodini, G. Chizhov, V. Choudalakis, G. Chouridou, S. Christidi, I.A. Christov, A. Chromek-Burckhart, D. Chu, M.L. Chudoba, J. Ciapetti, G. Ciftci, A.K. Ciftci, R. Cinca, D. Cindro, V. Ciobotaru, M.D. Ciocca, C. Ciocio, A. Cirilli, M. Clark, A. Clark, P.J. Cleland, W. Clemens, J.C. Clement, B. Clement, C. Coadou, Y. Cobal, M. Coccaro, A. Cochran, J. Coggeshall, J. Cogneras, E. Colijn, A.P. Collard, C. Collins, N.J. Collins-Tooth, C. Collot, J. Colon, G. Conde Muiño, P. Coniavitis, E. Conidi, M.C. Consonni, M. Constantinescu, S. Conta, C. Conventi, F. Cooke, M. Cooper, B.D. Cooper-Sarkar, A.M. Cooper-Smith, N.J. Copic, K. Cornelissen, T. Corradi, M. Corriveau, F. Corso-Radu, A. Cortes-Gonzalez, A. Cortiana, G. Costa, G. Costa, M.J. Costanzo, D. Costin, T. Côté, D. Torres, R.C. Courneyea, L. Cowan, G. Cowden, C. Cox, B.E. Cranmer, K. Cranshaw, J. Cristinziani, M. Crosetti, G. Crupi, R. Crépé-Renaudin, S. Almenar, C.C. Donszelmann, T.C. Curatolo, M. Curtis, C.J. Cwetanski, P. Czyczula, Z. D'Auria, S. D'Onofrio, M. D'Orazio, A. Da Via, C. Dabrowski, W. Dai, T. Dallapiccola, C. Dallison, S.J. Daly, C.H. Dam, M. Danielsson, H.O. Dannheim, D. Dao, V. Darbo, G. Darlea, G.L. Davey, W. Davidek, T. Davidson, N. Davidson, R. Davies, M. Davison, A.R. Dawson, I. Daya, R.K. De, K. de Asmundis, R. De Castro, S. De Faria Salgado, P.E.C. De Cecco, S. de Graat, J. De Groot, N. de Jong, P. De Mora, L. De Branco, M.O. De Pedis, D. De Salvo, A. De Sanctis, U. De Santo, A. De Vivie De Regie, J.B. Dean, S. Dedovich, D.V. Degenhardt, J. Dehchar, M. Del Papa, C. Del Peso, J. Del Prete, T. Dell'Acqua, A. Dell'Asta, L. Della Pietra, M. della Volpe, D. Delmastro, M. Delsart, P.A. Deluca, C. Demers, S. Demichev, M. Demirkoz, B. Deng, J. Deng, W. Denisov, S.P. Derkaoui, J.E. Derue, F. Dervan, P. Desch, K. Deviveiros, P.O. Dewhurst, A. DeWilde, B. Dhaliwal, S. Dhullipudi, R. Di Ciaccio, A. Di Ciaccio, L. Di Girolamo, A. Di Girolamo, B. Di Luise, S. Di Mattia, A. Di Nardo, R. Di Simone, A. Di Sipio, R. Diaz, M.A. Diblen, F. Diehl, E.B. Dietrich, J. Dietzsch, T.A. Diglio, S. Yagci, K.D. Dingfelder, J. Dionisi, C. Dita, P. Dita, S. Dittus, F. Djama, F. Djilkibaev, R. Djobava, T. do Vale, M.A.B. Do Wemans, A.V. Doan, T.K.O. Dobos, D. Dobson, E. Dobson, M. Doglioni, C. Doherty, T. Dolejsi, J. Dolenc, I. Dolezal, Z. Dolgoshein, B.A. Dohmae, T. Donega, M. Donini, J. Dopke, J. Doria, A. Dos Anjos, A. Dotti, A. Dova, M.T. Doxiadis, A. Doyle, A.T. Drasal, Z. Dris, M. Dubbert, J. Duchovni, E. Duckeck, G. Dudarev, A. Dudziak, F. Dührssen, M. Duflot, L. Dufour, M.-A. Dunford, M. Yildiz, H.D. Duxfield, R. Dwuznik, M. Düren, M. Ebenstein, W.L. Ebke, J. Eckweiler, S. Edmonds, K. Edwards, C.A. Egorov, K. Ehrenfeld, W. Ehrich, T. Eifert, T. Eigen, G. Einsweiler, K. Eisenhandler, E. Ekelof, T. El Kacimi, M. Ellert, M. Elles, S. Ellinghaus, F. Ellis, K. Ellis, N. Elmsheuser, J. Elsing, M. Emeliyanov, D. Engelmann, R. Engl, A. Epp, B. Eppig, A. Erdmann, J. Ereditato, A. Eriksson, D. Ermoline, I. Ernst, J. Ernst, M. Ernwein, J. Errede, D. Errede, S. Ertel, E. Escalier, M. Escobar, C. Curull, X.E. Esposito, B. Etienvre, A.I. Etzion, E. Evans, H. Fabbri, L. Fabre, C. Facius, K. Fakhrutdinov, R.M. Falciano, S. Fang, Y. Fanti, M. Farbin, A. Farilla, A. Farley, J. Farooque, T. Farrington, S.M. Farthouat, P. Fassnacht, P. Fassouliotis, D. Fatholahzadeh, B. Fayard, L. Fayette, F. Febbraro, R. Federic, P. Fedin, O.L. Fedorko, W. Feligioni, L. Felzmann, C.U. Feng, C. Feng, E.J. Fenyuk, A.B. Ferencei, J. Ferland, J. Fernandes, B. Fernando, W. Ferrag, S. Ferrando, J. Ferrara, V. Ferrari, A. Ferrari, P. Ferrari, R. Ferrer, A. Ferrer, M.L. Ferrere, D. Ferretti, C. Fiascaris, M. Fiedler, F. Filipčič, A. Filippas, A. Filthaut, F. Fincke-Keeler, M. Fiolhais, M.C.N. Fiorini, L. Firan, A. Fischer, G. Fisher, M.J. Flechl, M. Fleck, I. Fleckner, J. Fleischmann, P. Fleischmann, S. Flick, T. Castillo, L.R.F. Flowerdew, M.J. Martin, T.F. Formica, A. Forti, A. Fortin, D. Fournier, D. Fowler, A.J. Fowler, K. Fox, H. Francavilla, P. Franchino, S. Francis, D. Franklin, M. Franz, S. Fraternali, M. Fratina, S. Freestone, J. French, S.T. Froeschl, R. Froidevaux, D. Frost, J.A. Fukunaga, C. Torregrosa, E.F. Fuster, J. Gabaldon, C. Gabizon, O. Gadfort, T. Gadomski, S. Gagliardi, G. Gagnon, P. Galea, C. Gallas, E.J. Gallo, V. Gallop, B.J. Gallus, P. Galyaev, E. Gan, K.K. Gao, Y.S. Gaponenko, A. Garcia-Sciveres, M. García, C. Navarro, J.E.G. Gardner, R.W. Garelli, N. Garitaonandia, H. Garonne, V. Gatti, C. Gaudio, G. Gautard, V. Gauzzi, P. Gavrilenko, I.L. Gay, C. Gaycken, G. Gazis, E.N. Ge, P. Gee, C.N.P. Geich-Gimbel, C. Gellerstedt, K. Gemme, C. Genest, M.H. Gentile, S. Georgatos, F. George, S. Gershon, A. Ghazlane, H. Ghodbane, N. Giacobbe, B. Giagu, S. Giakoumopoulou, V. 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Triplett, N. Trischuk, W. Trivedi, A. Trocmé, B. Troncon, C. Trzupek, A. Tsarouchas, C. Tseng, J.C.-L. Tsiakiris, M. Tsiareshka, P.V. Tsionou, D. Tsipolitis, G. Tsiskaridze, V. Tskhadadze, E.G. Tsukerman, I.I. Tsulaia, V. Tsung, J.-W. Tsuno, S. Tsybychev, D. Tuggle, J.M. Turecek, D. Cakir, I.T. Turlay, E. Tuts, P.M. Twomey, M.S. Tylmad, M. Tyndel, M. Uchida, K. Ueda, I. Ueno, R. Ugland, M. Uhlenbrock, M. Uhrmacher, M. Ukegawa, F. Unal, G. Undrus, A. Unel, G. Unno, Y. Urbaniec, D. Urkovsky, E. Urquijo, P. Urrejola, P. Usai, G. Uslenghi, M. Vacavant, L. Vacek, V. Vachon, B. Vahsen, S. Valente, P. Valentinetti, S. Valkar, S. Gallego, E.V. Vallecorsa, S. Ferrer, J.A.V. van Berg, R. van der Graaf, H. van der Kraaij, E. van der Poel, E. van der Ster, D. van Eldik, N. van Gemmeren, P. van Kesteren, Z. van Vulpen, I. Vandelli, W. Vaniachine, A. Vankov, P. Vannucci, F. Vari, R. Varnes, E.W. Varouchas, D. Vartapetian, A. Varvell, K.E. Vasilyeva, L. Vassilakopoulos, V.I. Vazeille, F. 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Subjects: Physics::Instrumentation and Detectors
Abstract: The ATLAS Inner Detector is a composite tracking system consisting of silicon pixels, silicon strips and straw tubes in a 2 T magnetic field. Its installation was completed in August 2008 and the detector took part in data-taking with single LHC beams and cosmic rays. The initial detector operation, hardware commissioning and in-situ calibrations are described. Tracking performance has been measured with 7. 6 million cosmic-ray events, collected using a tracking trigger and reconstructed with modular pattern-recognition and fitting software. The intrinsic hit efficiency and tracking trigger efficiencies are close to 100%. Lorentz angle measurements for both electrons and holes, specific energy-loss calibration and transition radiation turn-on measurements have been performed. Different alignment techniques have been used to reconstruct the detector geometry. After the initial alignment, a transverse impact parameter resolution of 22. 1±0. 9 μm and a relative momentum resolution σp/p=(4. 83±0. 16)×10-4 GeV-1×pT have been measured for high momentum tracks. © 2010 CERN for the benefit of the ATLAS collaboration.
Published: 2010

7. Commissioning of the ATLAS Muon Spectrometer with cosmic rays

Author: The ATLAS Collaboration Aad, G. Abbott, B. Abdallah, J. Abdelalim, A.A. Abdesselam, A. Abdinov, O. Abi, B. Abolins, M. Abramowicz, H. Abreu, H. Acharya, B.S. Adams, D.L. Addy, T.N. Adelman, J. Adorisio, C. Adragna, P. Adye, T. Aefsky, S. Aguilar-Saavedra, J.A. Aharrouche, M. Ahlen, S.P. Ahles, F. Ahmad, A. Ahmed, H. Ahsan, M. Aielli, G. Akdogan, T. Åkesson, T.P.A. Akimoto, G. Akimov, A.V. Aktas, A. Alam, M.S. Alam, M.A. Albrand, S. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexander, G. Alexandre, G. Alexopoulos, T. Alhroob, M. Aliev, M. Alimonti, G. Alison, J. Aliyev, M. Allport, P.P. Allwood-Spiers, S.E. Almond, J. Aloisio, A. Alon, R. Alonso, A. Alviggi, M.G. Amako, K. Amelung, C. Amorim, A. Amorós, G. Amram, N. Anastopoulos, C. Andeen, T. Anders, C.F. Anderson, K.J. Andreazza, A. Andrei, V. Anduaga, X.S. Angerami, A. Anghinolfi, F. Anjos, N. Annovi, A. Antonaki, A. Antonelli, M. Antonelli, S. Antos, J. Antunovic, B. Anulli, F. Aoun, S. Arabidze, G. Aracena, I. Arai, Y. Arce, A.T.H. Archambault, J.P. Arfaoui, S. Arguin, J.-F. Argyropoulos, T. Arik, M. Armbruster, A.J. Arnaez, O. Arnault, C. Artamonov, A. Arutinov, D. Asai, M. Asai, S. Asfandiyarov, R. Ask, S. Åsman, B. Asner, D. Asquith, L. Assamagan, K. Astbury, A. Astvatsatourov, A. Atoian, G. Auerbach, B. Augsten, K. Aurousseau, M. Austin, N. Avolio, G. Avramidou, R. Axen, D. Ay, C. Azuelos, G. Azuma, Y. Baak, M.A. Bach, A.M. Bachacou, H. Bachas, K. Backes, M. Badescu, E. Bagnaia, P. Bai, Y. Bain, T. Baines, J.T. Baker, O.K. Baker, M.D. Baker, S. Dos Santos Pedrosa, F.B. Banas, E. Banerjee, P. Banerjee, S. Banfi, D. Bangert, A. Bansal, V. Baranov, S.P. Baranov, S. Barashkou, A. Barber, T. Barberio, E.L. Barberis, D. Barbero, M. Bardin, D.Y. Barillari, T. Barisonzi, M. Barklow, T. Barlow, N. Barnett, B.M. Barnett, R.M. Baroncelli, A. Barr, A.J. Barreiro, F. Barreiro Guimarães da Costa, J. Barrillon, P. Bartoldus, R. Bartsch, D. Bates, R.L. Batkova, L. Batley, J.R. Battaglia, A. Battistin, M. Bauer, F. Bawa, H.S. Bazalova, M. Beare, B. Beau, T. Beauchemin, P.H. Beccherle, R. Becerici, N. Bechtle, P. Beck, G.A. Beck, H.P. Beckingham, M. Becks, K.H. Beddall, A.J. Beddall, A. Bednyakov, V.A. Bee, C. Begel, M. Harpaz, S.B. Behera, P.K. Beimforde, M. Belanger-Champagne, C. Bell, P.J. Bell, W.H. Bella, G. Bellagamba, L. Bellina, F. Bellomo, M. Belloni, A. Belotskiy, K. Beltramello, O. Ben Ami, S. Benary, O. Benchekroun, D. Bendel, M. Benedict, B.H. Benekos, N. Benhammou, Y. Benincasa, G.P. Benjamin, D.P. Benoit, M. Bensinger, J.R. Benslama, K. Bentvelsen, S. Beretta, M. Berge, D. Bergeaas Kuutmann, E. Berger, N. Berghaus, F. Berglund, E. Beringer, J. Bernat, P. Bernhard, R. Bernius, C. Berry, T. Bertin, A. Besana, M.I. Besson, N. Bethke, S. Bianchi, R.M. Bianco, M. Biebel, O. Biesiada, J. Biglietti, M. Bilokon, H. Bindi, M. Binet, S. Bingul, A. Bini, C. Biscarat, C. Bitenc, U. Black, K.M. Blair, R.E. Blanchard, J.-B. Blanchot, G. Blocker, C. Blondel, A. Blum, W. Blumenschein, U. 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Subjects: Physics::Instrumentation and Detectors, Physics::Accelerator Physics, High Energy Physics::Experiment, Nuclear Experiment
Abstract: The ATLAS detector at the Large Hadron Collider has collected several hundred million cosmic ray events during 2008 and 2009. These data were used to commission the Muon Spectrometer and to study the performance of the trigger and tracking chambers, their alignment, the detector control system, the data acquisition and the analysis programs. We present the performance in the relevant parameters that determine the quality of the muon measurement. We discuss the single element efficiency, resolution and noise rates, the calibration method of the detector response and of the alignment system, the track reconstruction efficiency and the momentum measurement. The results show that the detector is close to the design performance and that the Muon Spectrometer is ready to detect muons produced in high energy proton-proton collisions. © 2010 CERN for the benefit of the ATLAS collaboration.
Published: 2010

8. The ATLAS Simulation Infrastructure

Author: The ATLAS Collaboration Aad, G. Abbott, B. Abdallah, J. Abdelalim, A.A. Abdesselam, A. Abdinov, O. Abi, B. Abolins, M. Abramowicz, H. Abreu, H. Acharya, B.S. Adams, D.L. Addy, T.N. Adelman, J. Adorisio, C. Adragna, P. Adye, T. Aefsky, S. Aguilar-Saavedra, J.A. Aharrouche, M. Ahlen, S.P. Ahles, F. Ahmad, A. Ahmed, H. Ahsan, M. Aielli, G. Akdogan, T. Åkesson, T.P.A. Akimoto, G. Akimov, A.V. Aktas, A. Alam, M.S. Alam, M.A. Albrand, S. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexander, G. Alexandre, G. Alexopoulos, T. Alhroob, M. Aliev, M. Alimonti, G. Alison, J. Aliyev, M. Allport, P.P. Allwood-Spiers, S.E. Almond, J. Aloisio, A. Alon, R. Alonso, A. Alviggi, M.G. Amako, K. Amelung, C. Amorim, A. Amorós, G. Amram, N. Anastopoulos, C. Andeen, T. Anders, C.F. Anderson, K.J. Andreazza, A. Andrei, V. Anduaga, X.S. Angerami, A. Anghinolfi, F. Anjos, N. Annovi, A. Antonaki, A. Antonelli, M. Antonelli, S. Antos, J. Antunovic, B. Anulli, F. Aoun, S. Arabidze, G. Aracena, I. Arai, Y. Arce, A.T.H. Archambault, J.P. Arfaoui, S. Arguin, J.-F. Argyropoulos, T. Arik, M. Armbruster, A.J. Arnaez, O. Arnault, C. Artamonov, A. Arutinov, D. Asai, M. Asai, S. Asfandiyarov, R. Ask, S. Åsman, B. Asner, D. Asquith, L. Assamagan, K. Astbury, A. Astvatsatourov, A. Atoian, G. Auerbach, B. Augsten, K. Aurousseau, M. Austin, N. Avolio, G. Avramidou, R. Axen, D. Ay, C. Azuelos, G. Azuma, Y. Baak, M.A. Bach, A.M. Bachacou, H. Bachas, K. Backes, M. Badescu, E. Bagnaia, P. Bai, Y. Bain, T. Baines, J.T. Baker, O.K. Baker, M.D. Baker, S. Dos Santos Pedrosa, F.B. Banas, E. Banerjee, P. Banerjee, S. Banfi, D. Bangert, A. Bansal, V. Baranov, S.P. Baranov, S. Barashkou, A. Barber, T. Barberio, E.L. Barberis, D. Barbero, M. Bardin, D.Y. Barillari, T. Barisonzi, M. Barklow, T. Barlow, N. Barnett, B.M. Barnett, R.M. Baroncelli, A. Barr, A.J. Barreiro, F. Guimarães da Costa, J.B. Barrillon, P. Bartoldus, R. Bartsch, D. Bates, R.L. Batkova, L. Batley, J.R. Battaglia, A. Battistin, M. Bauer, F. Bawa, H.S. Bazalova, M. Beare, B. Beau, T. Beauchemin, P.H. Beccherle, R. Becerici, N. Bechtle, P. Beck, G.A. Beck, H.P. Beckingham, M. Becks, K.H. Beddall, A.J. Beddall, A. Bednyakov, V.A. Bee, C. Begel, M. Behar Harpaz, S. Behera, P.K. Beimforde, M. Belanger-Champagne, C. Bell, P.J. Bell, W.H. Bella, G. Bellagamba, L. Bellina, F. Bellomo, M. Belloni, A. Belotskiy, K. Beltramello, O. Ben Ami, S. Benary, O. Benchekroun, D. Bendel, M. Benedict, B.H. Benekos, N. Benhammou, Y. Benincasa, G.P. Benjamin, D.P. Benoit, M. Bensinger, J.R. Benslama, K. Bentvelsen, S. Beretta, M. Berge, D. Kuutmann, E.B. Berger, N. Berghaus, F. Berglund, E. Beringer, J. Bernat, P. Bernhard, R. Bernius, C. Berry, T. Bertin, A. Besana, M.I. Besson, N. Bethke, S. Bianchi, R.M. Bianco, M. Biebel, O. Biesiada, J. Biglietti, M. Bilokon, H. Bindi, M. Binet, S. Bingul, A. Bini, C. Biscarat, C. Bitenc, U. Black, K.M. Blair, R.E. Blanchard, J.-B. Blanchot, G. Blocker, C. Blondel, A. Blum, W. Blumenschein, U. Bobbink, G.J. Bocci, A. Boehler, M. Boek, J. Boelaert, N. Böser, S. Bogaerts, J.A. Bogouch, A. Bohm, C. Bohm, J. Boisvert, V. Bold, T. Boldea, V. Bondarenko, V.G. Bondioli, M. Boonekamp, M. Bordoni, S. Borer, C. Borisov, A. Borissov, G. Borjanovic, I. Borroni, S. Bos, K. Boscherini, D. Bosman, M. Boterenbrood, H. Bouchami, J. Boudreau, J. Bouhova-Thacker, E.V. Boulahouache, C. Bourdarios, C. Boveia, A. Boyd, J. Boyko, I.R. Bozovic-Jelisavcic, I. Bracinik, J. Braem, A. Branchini, P. Brandenburg, G.W. Brandt, A. Brandt, G. Brandt, O. Bratzler, U. Brau, B. Brau, J.E. Braun, H.M. Brelier, B. Bremer, J. Brenner, R. Bressler, S. Britton, D. Brochu, F.M. Brock, I. Brock, R. Brodet, E. Bromberg, C. Brooijmans, G. Brooks, W.K. Brown, G. Bruckman de Renstrom, P.A. Bruncko, D. Bruneliere, R. Brunet, S. Bruni, A. Bruni, G. Bruschi, M. Bucci, F. Buchanan, J. Buchholz, P. Buckley, A.G. Budagov, I.A. Budick, B. Büscher, V. Bugge, L. Bulekov, O. Bunse, M. Buran, T. Burckhart, H. Burdin, S. Burgess, T. Burke, S. Busato, E. Bussey, P. Buszello, C.P. Butin, F. Butler, B. Butler, J.M. Buttar, C.M. Butterworth, J.M. Byatt, T. Caballero, J. Urbán, S.C. Caforio, D. Cakir, O. Calafiura, P. Calderini, G. Calfayan, P. Calkins, R. Caloba, L.P. Calvet, D. Camarri, P. Cameron, D. Campana, S. Campanelli, M. Canale, V. Canelli, F. Canepa, A. Cantero, J. Capasso, L. Garrido, M.D.M.C. Caprini, I. Caprini, M. Capua, M. Caputo, R. Caramarcu, C. Cardarelli, R. Carli, T. Carlino, G. Carminati, L. Caron, B. Caron, S. Montoya, G.D.C. Montero, S.C. Carter, A.A. Carter, J.R. Carvalho, J. Casadei, D. Casado, M.P. Cascella, M. Castaneda Hernandez, A.M. Castaneda-Miranda, E. Gimenez, V.C. Castro, N.F. Cataldi, G. Catinaccio, A. Catmore, J.R. Cattai, A. Cattani, G. Caughron, S. Cauz, D. Cavalleri, P. Cavalli, D. Cavalli-Sforza, M. Cavasinni, V. Ceradini, F. Cerqueira, A.S. Cerri, A. Cerrito, L. Cerutti, F. Cetin, S.A. Chafaq, A. Chakraborty, D. Chan, K. Chapman, J.D. Chapman, J.W. Chareyre, E. Charlton, D.G. Chavda, V. Cheatham, S. Chekanov, S. Chekulaev, S.V. Chelkov, G.A. Chen, H. Chen, S. Chen, X. Cheplakov, A. Chepurnov, V.F. Cherkaoui El Moursli, R. Tcherniatine, V. Chesneanu, D. Cheu, E. Cheung, S.L. Chevalier, L. Chevallier, F. Chiarella, V. Chiefari, G. Chikovani, L. Childers, J.T. Chilingarov, A. Chiodini, G. Chizhov, V. Choudalakis, G. Chouridou, S. Christidi, I.A. Christov, A. Chromek-Burckhart, D. Chu, M.L. Chudoba, J. Ciapetti, G. Ciftci, A.K. Ciftci, R. Cinca, D. Cindro, V. Ciobotaru, M.D. Ciocca, C. Ciocio, A. Cirilli, M. Citterio, M. Clark, A. Clark, P.J. Cleland, W. Clemens, J.C. Clement, B. Clement, C. Coadou, Y. Cobal, M. Coccaro, A. Cochran, J. Coggeshall, J. Cogneras, E. Colijn, A.P. Collard, C. Collins, N.J. Collins-Tooth, C. Collot, J. Colon, G. Conde Muiño, P. Coniavitis, E. Consonni, M. Constantinescu, S. Conta, C. Conventi, F. Cooke, M. Cooper, B.D. Cooper-Sarkar, A.M. Cooper-Smith, N.J. Copic, K. Cornelissen, T. Corradi, M. Corriveau, F. Corso-Radu, A. Cortes-Gonzalez, A. Cortiana, G. Costa, G. Costa, M.J. Costanzo, D. Costin, T. Côté, D. Torres, R.C. Courneyea, L. Cowan, G. Cowden, C. Cox, B.E. Cranmer, K. Cranshaw, J. Cristinziani, M. Crosetti, G. Crupi, R. Crépé-Renaudin, S. Almenar, C.C. Donszelmann, T.C. Curatolo, M. Curtis, C.J. Cwetanski, P. Czyczula, Z. D'Auria, S. D'Onofrio, M. D'Orazio, A. da Via, C. Dabrowski, W. Dai, T. Dallapiccola, C. Dallison, S.J. Daly, C.H. Dam, M. Danielsson, H.O. Dannheim, D. Dao, V. Darbo, G. Darlea, G.L. Davey, W. Davidek, T. Davidson, N. Davidson, R. Davies, M. Davison, A.R. Dawson, I. Daya, R.K. De, K. de Asmundis, R. de Castro, S. De Faria Salgado, P.E.C. De Cecco, S. de Graat, J. De Groot, N. de Jong, P. De Mora, L. De Branco, M.O. De Pedis, D. De Salvo, A. de Sanctis, U. de Santo, A. de Vivie de Regie, J.B. de Zorzi, G. Dean, S. Dedovich, D.V. Degenhardt, J. Dehchar, M. Del Papa, C. Del Peso, J. Del Prete, T. Dell'Acqua, A. Dell'Asta, L. Della Pietra, M. della Volpe, D. Delmastro, M. Delsart, P.A. Deluca, C. Demers, S. Demichev, M. Demirkoz, B. Deng, J. Deng, W. Denisov, S.P. Derkaoui, J.E. Derue, F. Dervan, P. Desch, K. Deviveiros, P.O. Dewhurst, A. DeWilde, B. Dhaliwal, S. Dhullipudi, R. Di Ciaccio, A. Di Ciaccio, L. Di Domenico, A. Di Girolamo, A. Di Girolamo, B. Di Luise, S. Di Mattia, A. Di Nardo, R. Di Simone, A. Di Sipio, R. Diaz, M.A. Diblen, F. Diehl, E.B. Dietrich, J. Dietzsch, T.A. Diglio, S. Yagci, K.D. Dingfelder, J. Dionisi, C. Dita, P. Dita, S. Dittus, F. Djama, F. Djilkibaev, R. Djobava, T. do Vale, M.A.B. Do Wemans, A.V. Doan, T.K.O. Dobos, D. Dobson, E. Dobson, M. Doglioni, C. Doherty, T. Dolejsi, J. Dolenc, I. Dolezal, Z. Dolgoshein, B.A. Dohmae, T. Donega, M. Donini, J. Dopke, J. Doria, A. Dos Anjos, A. Dotti, A. Dova, M.T. Doxiadis, A. Doyle, A.T. Drasal, Z. Dris, M. Dubbert, J. Duchovni, E. Duckeck, G. Dudarev, A. Dudziak, F. Dührssen, M. Duflot, L. Dufour, M.-A. Dunford, M. Duran Yildiz, H. Dushkin, A. Duxfield, R. Dwuznik, M. Düren, M. Ebenstein, W.L. Ebke, J. Eckweiler, S. Edmonds, K. Edwards, C.A. Egorov, K. Ehrenfeld, W. Ehrich, T. Eifert, T. Eigen, G. Einsweiler, K. Eisenhandler, E. Ekelof, T. El Kacimi, M. Ellert, M. Elles, S. Ellinghaus, F. Ellis, K. Ellis, N. Elmsheuser, J. Elsing, M. Emeliyanov, D. Engelmann, R. Engl, A. Epp, B. Eppig, A. Erdmann, J. Ereditato, A. Eriksson, D. Ermoline, I. Ernst, J. Ernst, M. Ernwein, J. Errede, D. Errede, S. Ertel, E. Escalier, M. Escobar, C. Curull, X.E. Esposito, B. Etienvre, A.I. Etzion, E. Evans, H. Fabbri, L. Fabre, C. Facius, K. Fakhrutdinov, R.M. Falciano, S. Fang, Y. Fanti, M. Farbin, A. Farilla, A. Farley, J. Farooque, T. Farrington, S.M. Farthouat, P. Fassnacht, P. Fassouliotis, D. Fatholahzadeh, B. Fayard, L. Fayette, F. Febbraro, R. Federic, P. Fedin, O.L. Fedorko, W. Feligioni, L. Felzmann, C.U. Feng, C. Feng, E.J. Fenyuk, A.B. Ferencei, J. Ferland, J. Fernandes, B. Fernando, W. Ferrag, S. Ferrando, J. Ferrara, V. Ferrari, A. Ferrari, P. Ferrari, R. Ferrer, A. Ferrer, M.L. Ferrere, D. Ferretti, C. Fiascaris, M. Fiedler, F. Filipčič, A. Filippas, A. Filthaut, F. Fincke-Keeler, M. Fiolhais, M.C.N. Fiorini, L. Firan, A. Fischer, G. Fisher, M.J. Flechl, M. Fleck, I. Fleckner, J. Fleischmann, P. Fleischmann, S. Flick, T. Castillo, L.R.F. Flowerdew, M.J. Martin, T.F. Formica, A. Forti, A. Fortin, D. Fournier, D. Fowler, A.J. Fowler, K. Fox, H. Francavilla, P. Franchino, S. Francis, D. Franklin, M. Franz, S. Fraternali, M. Fratina, S. Freestone, J. French, S.T. Froeschl, R. Froidevaux, D. Frost, J.A. Fukunaga, C. Torregrosa, E.F. Fuster, J. Gabaldon, C. Gabizon, O. Gadfort, T. Gadomski, S. Gagliardi, G. Gagnon, P. Galea, C. Gallas, E.J. Gallas, M.V. Gallo, V. Gallop, B.J. Gallus, P. Galyaev, E. Gan, K.K. Gao, Y.S. Gaponenko, A. Garcia-Sciveres, M. García, C. Navarro, J.E.G. Gardner, R.W. Garelli, N. Garitaonandia, H. Garonne, V. Gatti, C. Gaudio, G. Gautard, V. Gauzzi, P. Gavrilenko, I.L. Gay, C. Gaycken, G. Gazis, E.N. Ge, P. Gee, C.N.P. Geich-Gimbel, C. Gellerstedt, K. Gemme, C. Genest, M.H. Gentile, S. Georgatos, F. George, S. Gershon, A. Ghazlane, H. Ghodbane, N. Giacobbe, B. Giagu, S. Giakoumopoulou, V. Giangiobbe, V. Gianotti, F. Gibbard, B. Gibson, A. Gibson, S.M. Gilbert, L.M. Gilchriese, M. Gilewsky, V. Gingrich, D.M. Ginzburg, J. Giokaris, N. Giordani, M.P. Giordano, R. Giorgi, F.M. Giovannini, P. Giraud, P.F. Girtler, P. Giugni, D. Giusti, P. Gjelsten, B.K. Gladilin, L.K. Glasman, C. Glazov, A. Glitza, K.W. Glonti, G.L. Godfrey, J. Godlewski, J. Goebel, M. Göpfert, T. Goeringer, C. Gössling, C. Göttfert, T. Goggi, V. Goldfarb, S. Goldin, D. Golling, T. Gomes, A. Gomez Fajardo, L.S. Gonçalo, R. Gonella, L. Gong, C. González de la Hoz, S. Silva, M.L.G. Gonzalez-Sevilla, S. Goodson, J.J. Goossens, L. Gordon, H.A. Gorelov, I. Gorfine, G. Gorini, B. Gorini, E. Gorišek, A. Gornicki, E. Gosdzik, B. Gosselink, M. Gostkin, M.I. Eschrich, I.G. Gouighri, M. Goujdami, D. Goulette, M.P. Goussiou, A.G. Goy, C. Grabowska-Bold, I. Grafström, P. Grahn, K.-J. Grancagnolo, S. Grassi, V. Gratchev, V. Grau, N. Gray, H.M. Gray, J.A. Graziani, E. Green, B. Greenshaw, T. Greenwood, Z.D. Gregor, I.M. Grenier, P. Griesmayer, E. Griffiths, J. Grigalashvili, N. Grillo, A.A. Grimm, K. Grinstein, S. Grishkevich, Y.V. Groh, M. Groll, M. Gross, E. Grosse-Knetter, J. Groth-Jensen, J. Grybel, K. Guicheney, C. Guida, A. Guillemin, T. Guler, H. Gunther, J. Guo, B. Gupta, A. Gusakov, Y. Gutierrez, A. Gutierrez, P. Guttman, N. Gutzwiller, O. Guyot, C. Gwenlan, C. Gwilliam, C.B. Haas, A. Haas, S. Haber, C. Hadavand, H.K. Hadley, D.R. Haefner, P. Härtel, R. Hajduk, Z. Hakobyan, H. Haller, J. Hamacher, K. Hamilton, A. Hamilton, S. Han, L. Hanagaki, K. Hance, M. Handel, C. Hanke, P. Hansen, J.R. Hansen, J.B. Hansen, J.D. Hansen, P.H. Hansl-Kozanecka, T. Hansson, P. Hara, K. Hare, G.A. Harenberg, T. Harrington, R.D. Harris, O.M. Harrison, K. Hartert, J. Hartjes, F. Harvey, A. Hasegawa, S. Hasegawa, Y. Hashemi, K. Hassani, S. Haug, S. Hauschild, M. Hauser, R. Havranek, M. Hawkes, C.M. Hawkings, R.J. Hayakawa, T. Hayward, H.S. Haywood, S.J. Head, S.J. Hedberg, V. Heelan, L. Heim, S. Heinemann, B. Heisterkamp, S. Helary, L. Heller, M. Hellman, S. Helsens, C. Hemperek, T. Henderson, R.C.W. Henke, M. Henrichs, A. Henriques Correia, A.M. Henrot-Versille, S. Hensel, C. Henß, T. Jiménez, Y.H. Hershenhorn, A.D. Herten, G. Hertenberger, R. Hervas, L. Hessey, N.P. Higón-Rodriguez, E. Hill, J.C. Hiller, K.H. Hillert, S. Hillier, S.J. Hinchliffe, I. Hines, E. Hirose, M. Hirsch, F. Hirschbuehl, D. Hobbs, J. Hod, N. Hodgkinson, M.C. Hodgson, P. Hoecker, A. Hoeferkamp, M.R. Hoffman, J. Hoffmann, D. Hohlfeld, M. Holy, T. Holzbauer, J.L. Homma, Y. Horazdovsky, T. Hori, T. Horn, C. Horner, S. Horvat, S. Hostachy, J.-Y. Hou, S. Hoummada, A. Howe, T. Hrivnac, J. Hryn'ova, T. Hsu, P.J. Hsu, S.-C. Huang, G.S. Hubacek, Z. Hubaut, F. Huegging, F. Hughes, E.W. Hughes, G. Hurwitz, M. Husemann, U. Huseynov, N. Huston, J. Huth, J. Iacobucci, G. Iakovidis, G. Ibragimov, I. Iconomidou-Fayard, L. Idarraga, J. Iengo, P. Igonkina, O. Ikegami, Y. Ikeno, M. Ilchenko, Y. Iliadis, D. Ince, T. Ioannou, P. Iodice, M. Irles Quiles, A. Ishikawa, A. Ishino, M. Ishmukhametov, R. Isobe, T. Issakov, V. Issever, C. Istin, S. Itoh, Y. Ivashin, A.V. Iwanski, W. Iwasaki, H. Izen, J.M. Izzo, V. Jackson, B. Jackson, J.N. Jackson, P. Jaekel, M.R. Jain, V. Jakobs, K. Jakobsen, S. Jakubek, J. Jana, D.K. Jansen, E. Jantsch, A. Janus, M. Jared, R.C. Jarlskog, G. Jeanty, L. Plante, I.J. Jenni, P. Jez, P. Jézéquel, S. Ji, W. Jia, J. Jiang, Y. Belenguer, M.J. Jin, S. Jinnouchi, O. Joffe, D. Johansen, M. Johansson, K.E. Johansson, P. Johnert, S. Johns, K.A. Jon-And, K. Jones, G. Jones, R.W.L. Jones, T.J. Jorge, P.M. Joseph, J. Juranek, V. Jussel, P. Kabachenko, V.V. Kaci, M. Kaczmarska, A. Kado, M. Kagan, H. Kagan, M. Kaiser, S. Kajomovitz, E. Kalinin, S. Kalinovskaya, L.V. Kalinowski, A. Kama, S. Kanaya, N. Kaneda, M. Kantserov, V.A. Kanzaki, J. Kaplan, B. Kapliy, A. Kaplon, J. Kar, D. Karagounis, M. Unel, M.K. Kartvelishvili, V. Karyukhin, A.N. Kashif, L. Kasmi, A. Kass, R.D. Kastanas, A. Kastoryano, M. Kataoka, M. Kataoka, Y. Katsoufis, E. Katzy, J. Kaushik, V. Kawagoe, K. Kawamoto, T. Kawamura, G. Kayl, M.S. Kayumov, F. Kazanin, V.A. Kazarinov, M.Y. Keates, J.R. Keeler, R. Keener, P.T. Kehoe, R. Keil, M. Kekelidze, G.D. Kelly, M. Kenyon, M. Kepka, O. Kerschen, N. Kerševan, B.P. Kersten, S. Kessoku, K. Khakzad, M. Khalil-zada, F. Khandanyan, H. Khanov, A. Kharchenko, D. Khodinov, A. Khomich, A. Khoriauli, G. Khovanskiy, N. Khovanskiy, V. Khramov, E. Khubua, J. Kim, H. Kim, M.S. Kim, P.C. Kim, S.H. Kind, O. Kind, P. King, B.T. Kirk, J. Kirsch, G.P. Kirsch, L.E. Kiryunin, A.E. Kisielewska, D. Kittelmann, T. Kiyamura, H. Kladiva, E. Klein, M. Klein, U. Kleinknecht, K. Klemetti, M. Klier, A. Klimentov, A. Klingenberg, R. Klinkby, E.B. Klioutchnikova, T. Klok, P.F. Klous, S. Kluge, E.-E. Kluge, T. Kluit, P. Klute, M. Kluth, S. Knecht, N.S. Kneringer, E. Ko, B.R. Kobayashi, T. Kobel, M. Koblitz, B. Kocian, M. Kocnar, A. Kodys, P. Köneke, K. König, A.C. Koenig, S. Köpke, L. Koetsveld, F. Koevesarki, P. Koffas, T. Koffeman, E. Kohn, F. Kohout, Z. Kohriki, T. Kolanoski, H. Kolesnikov, V. Koletsou, I. Koll, J. Kollar, D. Kolos, S. Kolya, S.D. Komar, A.A. Komaragiri, J.R. Kondo, T. Kono, T. Konoplich, R. Konovalov, S.P. Konstantinidis, N. Koperny, S. Korcyl, K. Kordas, K. Korn, A. Korolkov, I. Korolkova, E.V. Korotkov, V.A. Kortner, O. Kostka, P. Kostyukhin, V.V. Kotov, S. Kotov, V.M. Kotov, K.Y. Kourkoumelis, C. Koutsman, A. Kowalewski, R. Kowalski, H. Kowalski, T.Z. Kozanecki, W. Kozhin, A.S. Kral, V. Kramarenko, V.A. Kramberger, G. Krasny, M.W. Krasznahorkay, A. Kreisel, A. Krejci, F. Kretzschmar, J. Krieger, N. Krieger, P. Kroeninger, K. Kroha, H. Kroll, J. Kroseberg, J. Krstic, J. Kruchonak, U. Krüger, H. Krumshteyn, Z.V. Kubota, T. Kuehn, S. Kugel, A. Kuhl, T. Kuhn, D. 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Valladolid Gallego, E. Vallecorsa, S. Ferrer, J.A.V. Van Berg, R. van der Graaf, H. van der Kraaij, E. van der Poel, E. van der Ster, D. van Eldik, N. van Gemmeren, P. van Kesteren, Z. van Vulpen, I. Vandelli, W. Vaniachine, A. Vankov, P. Vannucci, F. Vari, R. Varnes, E.W. Varouchas, D. Vartapetian, A. Varvell, K.E. Vasilyeva, L. Vassilakopoulos, V.I. Vazeille, F. Vellidis, C. Veloso, F. Veneziano, S. Ventura, A. Ventura, D. Venturi, M. Venturi, N. Vercesi, V. Verducci, M. Verkerke, W. Vermeulen, J.C. Vetterli, M.C. Vichou, I. Vickey, T. Viehhauser, G.H.A. Villa, M. Villani, E.G. Perez, M.V. Vilucchi, E. Vincter, M.G. Vinek, E. Vinogradov, V.B. Viret, S. Virzi, J. Vitale, A. Vitells, O. Vivarelli, I. Vaque, F.V. Vlachos, S. Vlasak, M. Vlasov, N. Vogel, A. Vokac, P. Volpi, M. von der Schmitt, H. von Loeben, J. von Radziewski, H. von Toerne, E. Vorobel, V. Vorwerk, V. Vos, M. Voss, R. Voss, T.T. Vossebeld, J.H. Vranjes, N. Milosavljevic, M.V. Vrba, V. Vreeswijk, M. Anh, T.V. 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Wu, X. Wulf, E. Wynne, B.M. Xaplanteris, L. Xella, S. Xie, S. Xu, D. Xu, N. Yamada, M. Yamamoto, A. Yamamoto, K. Yamamoto, S. Yamamura, T. Yamaoka, J. Yamazaki, T. Yamazaki, Y. Yan, Z. Yang, H. Yang, U.K. Yang, Z. Yao, W.-M. Yao, Y. Yasu, Y. Ye, J. Ye, S. Yilmaz, M. Yoosoofmiya, R. Yorita, K. Yoshida, R. Young, C. Youssef, S.P. Yu, D. Yu, J. Yuan, L. Yurkewicz, A. Zaidan, R. Zaitsev, A.M. Zajacova, Z. Zambrano, V. Zanello, L. Zaytsev, A. Zeitnitz, C. Zeller, M. Zemla, A. Zendler, C. Zenin, O. Zenis, T. Zenonos, Z. Zenz, S. Zerwas, D. della Porta, G.Z. Zhan, Z. Zhang, H. Zhang, J. Zhang, Q. Zhang, X. Zhao, L. Zhao, T. Zhao, Z. Zhemchugov, A. Zhong, J. Zhou, B. Zhou, N. Zhou, Y. Zhu, C.G. Zhu, H. Zhu, Y. Zhuang, X. Zhuravlov, V. Zimmermann, R. Zimmermann, S. Zimmermann, S. Ziolkowski, M. Živković, L. Zobernig, G. Zoccoli, A. zur Nedden, M. Zutshi, V.
Subjects: Physics::Instrumentation and Detectors, High Energy Physics::Experiment
Abstract: The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes. © 2010 CERN for the benefit of the ATLAS collaboration.
Published: 2010

9. The ATLAS Collaboration

Author: Aad, G. Abbott, B. Abdallah, J. Abdelalim, A.A. Abdesselam, A. Abdinov, O. Abi, B. Abolins, M. Abramowicz, H. Acerbi, E. Acharya, B.S. Adams, D.L. Addy, T.N. Adelman, J. Adorisio, C. Adragna, P. Adye, T. Aefsky, S. Aguilar-Saavedra, J.A. Aharrouche, M. Ahlen, S.P. Ahles, F. Ahmad, A. Ahmed, H. Ahsan, M. Aielli, G. Akdogan, T. Åkesson, T.P.A. Akimoto, G. Akimov, A.V. Alam, M.S. Alam, M.A. Albert, J. Albrand, S. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexander, G. Alexandre, G. Alexopoulos, T. Alhroob, M. Aliev, M. Alimonti, G. Alison, J. Aliyev, M. Allport, P.P. Allwood-Spiers, S.E. Aloisio, A. Alon, R. Alonso, A. Alviggi, M.G. Amako, K. Amelung, C. Ammosov, V.V. Amorim, A. Amorós, G. Amram, N. Anastopoulos, C. Anders, C.F. Anderson, K.J. Andreazza, A. Andrei, V. Anduaga, X.S. Angerami, A. Anghinolfi, F. Anjos, N. Antonaki, A. Antonelli, M. Antonelli, S. Antunovic, B. Anulli, F. Arabidze, G. Aracena, I. Arai, Y. Arce, A.T.H. Archambault, J.P. Arfaoui, S. Arguin, J.-F. Argyropoulos, T. Arik, M. Armbruster, A.J. Arnaez, O. Arnault, C. Artamonov, A. Arutinov, D. Asai, M. Asai, S. Asfandiyarov, R. Ask, S. Åsman, B. Asner, D. Asquith, L. Assamagan, K. Astbury, A. Astvatsatourov, A. Atoian, G. Auerbach, B. Auge, E. Augsten, K. Aurousseau, M. Austin, N. Avolio, G. Avramidou, R. Axen, D. Ay, C. Azuelos, G. Azuma, Y. Baak, M.A. Bacci, C. Bach, A. Bachacou, H. Bachas, K. Backes, M. Badescu, E. Bagnaia, P. Bai, Y. Bailey, D.C. Bain, T. Baines, J.T. Baker, O.K. Baker, M.D. Baltasar Dos Santos Pedrosa, F. Banas, E. Banerjee, P. Banerjee, S. Banfi, D. Bangert, A. Bansal, V. Baranov, S.P. Baranov, S. Barashkou, A. Barber, T. Barberio, E.L. Barberis, D. Barbero, M. Bardin, D.Y. Barillari, T. Barisonzi, M. Barklow, T. Barlow, N. Barnett, B.M. Barnett, R.M. Baroncelli, A. Barr, A.J. Barreiro, F. Barreiro Guimarães da Costa, J. Barrillon, P. Barros, N. Bartoldus, R. Bartsch, D. Bastos, J. Bates, R.L. Bathe, S. Batley, J.R. Battaglia, A. Battistin, M. Bauer, F. 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Ebenstein, W.L. Ebke, J. Eckert, S. Eckweiler, S. Edmonds, K. Edwards, C.A. Eerola, P. Egorov, K. Ehrenfeld, W. Ehrich, T. Eifert, T. Eigen, G. Einsweiler, K. Eisenhandler, E. Ekelof, T. El Kacimi, M. Ellert, M. Elles, S. Ellis, K. Ellis, N. Elmsheuser, J. Elsing, M. Ely, R. Emeliyanov, D. Engelmann, R. Engl, A. Epp, B. Eppig, A. Epshteyn, V.S. Ereditato, A. Eriksson, D. Ermoline, I. Ernst, J. Ernst, M. Ernwein, J. Errede, D. Errede, S. Ertel, E. Escalier, M. Escobar, C. Espinal Curull, X. Esposito, B. Etienvre, A.I. Etzion, E. Evans, H. Fabbri, L. Facius, K. Fakhrutdinov, R.M. Falciano, S. Falou, A.C. Fang, Y. Fanti, M. Farbin, A. Farilla, A. Farley, J. Farooque, T. Farrington, S.M. Farthouat, P. Fassnacht, P. Fassouliotis, D. Fatholahzadeh, B. Fayard, L. Fayette, F. Febbraro, R. Federic, P. Fedin, O.L. Fedorko, I. Feligioni, L. Felzmann, C.U. Feng, C. Feng, E.J. Fenyuk, A.B. Ferencei, J. Ferland, J. Fernando, W. Ferrag, S. Ferrando, J. Ferrari, A. Ferrari, P. Ferrari, R. Ferrer, A. 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Rodriguez, D. Rodriguez, Y. Roe, S. Røhne, O. Rojo, V. Rolli, S. Romaniouk, A. Romanov, V.M. Romeo, G. Romero Maltrana, D. Roos, L. Ros, E. Rosati, M. Rosati, S. Rosenbaum, G.A. Rosenberg, E.I. Rosselet, L. Rossi, L.P. Rotaru, M. Rothberg, J. Rottländer, I. Rousseau, D. Royon, C.R. Rozanov, A. Rozen, Y. Ruckert, B. Ruckstuhl, N. Rud, V.I. Rudolph, G. Rühr, F. Ruggieri, F. Ruiz-Martinez, A. Rumyantsev, L. Rusakovich, N.A. Rutherfoord, J.P. Ruwiedel, C. Ruzicka, P. Ryabov, Y.F. Ryan, P. Rybin, A.M. Rybkin, G. Rzaeva, S. Saavedra, A.F. Sadrozinski, H.F.-W. Sadykov, R. Sakamoto, H. Salamanna, G. Salamon, A. Saleem, M. Salihagic, D. Salnikov, A. Salt, J. Salvachua Ferrando, B.M. Salvatore, D. Salvatore, F. Salvucci, A. Salzburger, A. Sampsonidis, D. Samset, B.H. Sandaker, H. Sander, H.G. Sandhoff, M. Sandstroem, R. Sandvoss, S. Sankey, D.P.C. Sanny, B. Sansoni, A. Santamarina Rios, C. Santoni, C. Santonico, R. Santos, D. Santos, J. Saraiva, J.G. Sarangi, T. Saremi, S. Sarkisyan-Grinbaum, E. Sarri, F. Sasaki, O. Sasao, N. Satsounkevitch, I. Sauvage, G. Savard, P. Savine, A.Y. Savinov, V. Sawyer, L. Saxon, D.H. Says, L.P. Sbarra, C. Sbrizzi, A. Scannicchio, D.A. Schaarschmidt, J. Schacht, P. Schäfer, U. Schaetzel, S. Schaffer, A.C. Schaile, D. Schamberger, R.D. Schamov, A.G. Schegelsky, V.A. Schernau, M. Scherzer, M.I. Schiavi, C. Schieck, J. Schioppa, M. Schlenker, S. Schmid, P. Schmitt, C. Schmitz, M. Schott, M. Schouten, D. Schovancova, J. Schram, M. Schreiner, A. Schroeder, C. Schroer, N. Schroers, M. Schultes, J. Schultz-Coulon, H.-C. Schumacher, J. Schumacher, M. Schumm, B.A. Schune, Ph. Schwanenberger, C. Schwartzman, A. Schwemling, Ph. Schwienhorst, R. Schwierz, R. Schwindling, J. Scott, W.G. Searcy, J. Sedykh, E. Segura, E. Seidel, S.C. Seiden, A. Seifert, F. Seixas, J.M. Sekhniaidze, G. Seliverstov, D.M. Sellden, B. Semprini-Cesari, N. Serfon, C. Serin, L. Seuster, R. Severini, H. Sevior, M.E. Sfyrla, A. Shan, L.Y. Shank, J.T. Shao, Q.T. Shapiro, M. Shatalov, P.B. Shaw, K. Sherman, D. Sherwood, P. Shibata, A. Shimojima, M. Shin, T. Shmeleva, A. Shochet, M.J. Shupe, M.A. Sicho, P. Sidoti, A. Siegrist, J. Sijacki, Dj. Silbert, O. Silva, J. Silverstein, D. Silverstein, S.B. Simak, V. Simic, Lj. Simion, S. Simmons, B. Simonyan, M. Sinervo, P. Sinev, N.B. Sipica, V. Siragusa, G. Sisakyan, A.N. Sivoklokov, S.Yu. Sjoelin, J. Sjursen, T.B. Skubic, P. Slater, M. Slavicek, T. Sliwa, K. Sloper, J. Sluka, T. Smakhtin, V. Smirnov, S.Yu. Smirnov, Y. Smirnova, L.N. Smirnova, O. Smith, B.C. Smith, D. Smith, K.M. Smizanska, M. Smolek, K. Snesarev, A.A. Snow, S.W. Snow, J. Snuverink, J. Snyder, S. Soares, M. Sobie, R. Sodomka, J. Soffer, A. Solans, C.A. Solar, M. Solfaroli Camillocci, E. Solodkov, A.A. Solovyanov, O.V. Soluk, R. Sondericker, J. Sopko, V. Sopko, B. Sosebee, M. Sosnovtsev, V.V. Soukharev, A. Spagnolo, S. Spanò, F. Spencer, E. Spighi, R. Spigo, G. Spila, F. Spiwoks, R. Spousta, M. Spreitzer, T. Spurlock, B. St. Denis, R.D. Stahl, T. Stamen, R. Stancu, S.N. Stanecka, E. Stanek, R.W. Stanescu, C. Stapnes, S. Starchenko, E.A. Stark, J. Staroba, P. Stastny, J. Staude, A. Stavina, P. Steinbach, P. Steinberg, P. Stekl, I. Stelzer, B. Stelzer, H.J. Stenzel, H. Stevenson, K. Stewart, G. Stockton, M.C. Stoicea, G. Stonjek, S. Strachota, P. Stradling, A. Straessner, A. Strandberg, J. Strandberg, S. Strandlie, A. Strauss, M. Strizenec, P. Ströhmer, R. Strom, D.M. Stroynowski, R. Stugu, B. Soh, D.A. Su, D. Suchkov, S.I. Sugaya, Y. Sugimoto, T. Suhr, C. Sulin, V.V. Sultansoy, S. Sun, X. Sundermann, J.E. Suruliz, K. Sushkov, S. Susinno, G. Sutton, M.R. Suzuki, T. Suzuki, Y. Sykora, I. Sykora, T. Szymocha, T. Sánchez, J. Ta, D. Taffard, A. Tafirout, R. Taga, A. Takahashi, Y. Takai, H. Takashima, R. Takeda, H. Takeshita, T. Talby, M. Talyshev, A. Tamsett, M.C. Tanaka, J. Tanaka, R. Tanaka, S. Tanaka, S. Tapprogge, S. Tardif, D. Tarem, S. Tarrade, F. Tartarelli, G.F. Tas, P. Tasevsky, M. Tassi, E. Taylor, C. Taylor, F.E. Taylor, G.N. Taylor, R.P. Taylor, W. Teixeira-Dias, P. Ten Kate, H. Teng, P.K. Terada, S. Terashi, K. Terron, J. Terwort, M. Testa, M. Teuscher, R.J. Tevlin, C.M. Thananuwong, R. Thioye, M. Thoma, S. Thomas, J.P. Thomas, T.L. Thompson, E.N. Thompson, P.D. Thompson, P.D. Thompson, R.J. Thompson, A.S. Thomson, E. Thun, R.P. Tic, T. Tikhomirov, V.O. Tikhonov, Y.A. Tipton, P. Tique Aires Viegas, F.J. Tisserant, S. Toczek, B. Todorov, T. Todorova-Nova, S. Tojo, J. Tokár, S. Tokushuku, K. Tomasek, L. Tomasek, M. Tomasz, F. Tomoto, M. Tompkins, D. Tompkins, L. Toms, K. Tonoyan, A. Topfel, C. Topilin, N.D. Torrence, E. Torró Pastor, E. Toth, J. Touchard, F. Tovey, D.R. Tovey, S.N. Trefzger, T. Tremblet, L. Tricoli, A. Trigger, I.M. Trincaz-Duvoid, S. Tripiana, M.F. Triplett, N. Trischuk, W. Trivedi, A. Trocmé, B. Troncon, C. Trzupek, A. Tsarouchas, C. Tseng, J.C.-L. Tsiakiris, M. Tsiareshka, P.V. Tsipolitis, G. Tsiskaridze, V. Tskhadadze, E.G. Tsukerman, I.I. Tsulaia, V. Tsuno, S. Turecek, D. Turk Cakir, I. Turlay, E. Tuts, P.M. Twomey, M.S. Tylmad, M. Tyndel, M. Tzanakos, G. Uchida, K. Ueda, I. Uhrmacher, M. Ukegawa, F. Unal, G. Underwood, D.G. Undrus, A. Unel, G. Unno, Y. Urbaniec, D. Urkovsky, E. Urquijo, P. Urrejola, P. Usai, G. Vacavant, L. Vacek, V. Vachon, B. Vahsen, S. Valenta, J. Valente, P. Valentinetti, S. Valkar, S. Vallecorsa, S. Valls Ferrer, J.A. van der Graaf, H. van der Kraaij, E. van der Poel, E. Van Der Ster, D. van Eldik, N. van Gemmeren, P. van Kesteren, Z. van Vulpen, I. VanBerg, R. Vandelli, W. Vaniachine, A. Vankov, P. Vannucci, F. Vari, R. Varnes, E.W. Varouchas, D. Vartapetian, A. Varvell, K.E. Vassilakopoulos, V.I. Vassilieva, L. Vazeille, F. Veillet, J.J. Vellidis, C. Veloso, F. Veneziano, S. Ventura, A. Ventura, D. Venturi, M. Venturi, N. Vercesi, V. Verducci, M. Verkerke, W. Vermeulen, J.C. Vetterli, M.C. Vichou, I. Vickey, T. Viehhauser, G.H.A. Villa, M. Villani, E.G. Villaplana Perez, M. Villate, J. Vilucchi, E. Vincter, M.G. Vinogradov, V.B. Viret, S. Virzi, J. Vitale, A. Vitells, O.V. Vivarelli, I. Vives Vaques, F. Vlachos, S. Vlasak, M. Vlasov, N. Vokac, P. Volpi, M. von der Schmitt, H. von Loeben, J. von Radziewski, H. von Toerne, E. Vorobel, V. Vorobiev, A.P. Vorwerk, V. Vos, M. Voss, R. Voss, T.T. Vossebeld, J.H. Vranjes, N. Vranjes Milosavljevic, M. Vrba, V. Vreeswijk, M. Vu Anh, T. Vudragovic, D. Vuillermet, R. Vukotic, I. Wagner, P. Wahlen, H. Walbersloh, J. Walder, J. Walker, R. Walkowiak, W. Wall, R. Wang, C. Wang, J. Wang, S.M. Ward, C.P. Warsinsky, M. Watkins, P.M. Watson, A.T. Watts, G. Watts, S. Waugh, A.T. Waugh, B.M. Webel, M. Weber, J. Weber, M.D. Weber, M. Weber, M.S. Weber, P. Weidberg, A.R. Weingarten, J. Weiser, C. Wellenstein, H. Wells, P.S. Wemans, A. Wen, M. Wenaus, T. Wendler, S. Wengler, T. Wenig, S. Wermes, N. Werner, M. Werner, P. Werthenbach, U. Wessels, M. Whalen, K. Wheeler-Ellis, S.J. White, A. White, M.J. White, S. Whiteson, D. Whittington, D. Wicek, F. Wicke, D. Wickens, F.J. Wiedenmann, W. Wielers, M. Wienemann, P. Wiglesworth, C. Wildauer, A. Wildt, M.A. Wilkens, H.G. Williams, E. Williams, H.H. Willocq, S. Wilson, J.A. Wilson, M.G. Wilson, A. Wingerter-Seez, I. Winklmeier, F. Wittgen, M. Wolter, M.W. Wolters, H. Wosiek, B.K. Wotschack, J. Woudstra, M.J. Wraight, K. Wright, C. Wright, D. Wrona, B. Wu, S.L. Wu, X. Wulf, E. Xella, S. Xie, S. Xu, N. Yamada, M. Yamamoto, A. Yamamoto, S. Yamamura, T. Yamanaka, K. Yamaoka, J. Yamazaki, T. Yamazaki, Y. Yan, Z. Yang, H. Yang, U.K. Yang, Z. Yao, W.-M. Yao, Y. Yasu, Y. Ye, J. Ye, S. Yilmaz, M. Yoosoofmiya, R. Yorita, K. Yoshida, R. Young, C. Youssef, S.P. Yu, D. Yu, J. Yuan, J. Yuan, L. Yurkewicz, A. Zaidan, R. Zaitsev, A.M. Zajacova, Z. Zambrano, V. Zanello, L. Zarzhitsky, P. Zaytsev, A. Zeitnitz, C. Zeller, M. Zema, P.F. Zemla, A. Zendler, C. Zenis, T. Zenonos, Z. Zenz, S. Zerwas, D. Zevi della Porta, G. Zhan, Z. Zhang, H. Zhang, J. Zhang, Q. Zhang, X. Zhao, L. Zhao, T. Zhao, Z. Zhemchugov, A. Zhong, J. Zhou, B. Zhou, N. Zhou, Y. Zhu, C.G. Zhu, H. Zhu, Y. Zhuang, X. Zhuravlov, V. Zimmermann, R. Zimmermann, S. Ziolkowski, M. Zitoun, R. Živković, L. Zobernig, G. Zoccoli, A. zur Nedden, M.
Published: 2009

10. A dual approach in the study of poly (ADP-ribose) polymerase: in vitro random mutagenesis and generation of deficient mice

Author: C, Trucco, V, Rolli, F J, Oliver, E, Flatter, M, Masson, F, Dantzer, C, Niedergang, B, Dutrillaux, J, Ménissier-de Murcia, and G, de Murcia
Subjects: Mice, Knockout, Models, Molecular, Models, Genetic, Body Weight, Age Factors, Apoptosis, Catalysis, Mice, Mutagenesis, Escherichia coli, Animals, Humans, Poly(ADP-ribose) Polymerases, Sister Chromatid Exchange
Abstract: A dual approach to the study of poly (ADP-ribose)polymerase (PARP) in terms of its structure and function has been developed in our laboratory. Random mutagenesis of the DNA binding domain and catalytic domain of the human PARP, has allowed us to identify residues that are crucial for its enzymatic activity. In parallel PARP knock-out mice were generated by inactivation of both alleles by gene targeting. We showed that: (i) they are exquisitely sensitive to gamma-irradiation, (ii) they died rapidly from acute radiation toxicity to the small intestine, (iii) they displayed a high genomic instability to gamma-irradiation and MNU injection and, (iv) bone marrow cells rapidly underwent apoptosis following MNU treatment, demonstrating that PARP is a survival factor playing an essential and positive role during DNA damage recovery and survival.
Published: 1999

11. Involvement of poly(ADP-ribose) polymerase in base excision repair

Author: Guadalupe De La Rubia, Gilbert de Murcia, Javier Oliver, V. Rolli, F. Dantzer, Josiane Ménissier-de Murcia, Eric Flatter, Valérie Schreiber, Claude Niedergang, and Carlotta Trucco
Subjects: Mice, Knockout, DNA Repair, DNA damage, DNA repair, Poly ADP ribose polymerase, General Medicine, Base excision repair, Biology, DNA repair protein XRCC4, Biochemistry, Molecular biology, Mice, DNA glycosylase, Mutation, Animals, Humans, Poly(ADP-ribose) Polymerases, Replication protein A, Nucleotide excision repair, DNA Damage, HeLa Cells
Abstract: Poly(ADP-ribose) polymerase (PARP) is a zinc-finger DNA binding protein that detects and signals DNA strand breaks generated directly or indirectly by genotoxic agents. In response to these lesions, the immediate poly(ADP-ribosylation) of nuclear proteins converts DNA interruptions into intracellular signals that activate DNA repair or cell death programs. To elucidate the biological function of PARP in vivo, the mouse PARP gene was inactivated by homologous recombination to generate mice lacking a functional PARP gene. PARP knockout mice and the derived mouse embryonic fibroblasts (MEFs) were acutely sensitive to monofunctional alkylating agents and gamma-irradiation demonstrating that PARP is involved in recovery from DNA damage that triggers the base excision repair (BER) process. To address the issue of the role of PARP in BER, the ability of PARP-deficient mammalian cell extracts to repair a single abasic site present on a circular duplex plasmid molecule was tested in a standard in vitro repair assay. The results clearly demonstrate, for the first time, the involvement of PARP in the DNA synthesis step of the base excision repair process.
Published: 1999

12. Importance of poly(ADP-ribose) polymerase and its cleavage in apoptosis. Lesson from an uncleavable mutant

Author: F J, Oliver, G, de la Rubia, V, Rolli, M C, Ruiz-Ruiz, G, de Murcia, and J M, Murcia
Subjects: Cell Nucleus, Alkylating Agents, Cytoplasm, Mice, Hydrolysis, Mutagenesis, Site-Directed, Animals, Apoptosis, fas Receptor, Poly(ADP-ribose) Polymerases, Cell Line, Transformed
Abstract: We have studied the apoptotic response of poly(ADP-ribose) polymerase (PARP)-/- cells to different inducers and the consequences of the expression of an uncleavable mutant of PARP on the apoptotic process. The absence of PARP drastically increases the sensitivity of primary bone marrow PARP-/- cells to apoptosis induced by an alkylating agent but not by a topoisomerase I inhibitor CPT-11 or by interleukin-3 removal. cDNA of wild type or of an uncleavable PARP mutant (D214A-PARP) has been introduced into PARP-/- fibroblasts, which were exposed to anti-CD95 or an alkylating agent to induce apoptosis. The expression of D214A-PARP results in a significant delay of cell death upon CD95 stimulation. Morphological analysis shows a retarded cell shrinkage and nuclear condensation. Upon treatment with an alkylating agent, expression of wild-type PARP cDNA into PARP-deficient mouse embryonic fibroblasts results in the restoration of the cell viability, and the D214A-PARP mutant had no further effect on cell recovery. In conclusion, PARP-/- cells are extremely sensitive to apoptosis induced by triggers (like alkylating agents), which activates the base excision repair pathway of DNA, and the cleavage of PARP during apoptosis facilitates cellular disassembly and ensures the completion and irreversibility of the process.
Published: 1998

13. The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis

Author: G. de Murcia, A. Ruf, V. Rolli, and Georg E. Schulz
Subjects: Models, Molecular, Niacinamide, Stereochemistry, Poly ADP ribose polymerase, Poly(ADP-ribose) Polymerase Inhibitors, Crystallography, X-Ray, Structure-Activity Relationship, Structural Biology, Transferase, Animals, Humans, Binding site, Enzyme Inhibitors, Molecular Biology, Polymerase, chemistry.chemical_classification, Adenosine Diphosphate Ribose, Binding Sites, biology, NAD, Acceptor, Peptide Fragments, Enzyme, chemistry, Biochemistry, Mutagenesis, ADP-ribosylation, biology.protein, NAD+ kinase, Poly(ADP-ribose) Polymerases, Chickens
Abstract: The binding site for the acceptor substrate poly(ADP-ribose) in the elongation reaction of the ADP-ribosyl transferase poly(ADP-ribose) polymerase (PARP) was detected by cocrystallizing the enzyme with an NAD+ analogue. The site was confirmed by mutagenesis studies. In conjunction with the binding site of the donor NAD+, the bound acceptor reveals the geometry of the elongation reaction. It shows in particular that the strictly conserved glutamate residue of all ADP-ribosylating enzymes (Glu988 of PARP) facilitates the reaction by polarizing both, donor and acceptor. Moreover, the binding properties of the acceptor site suggest a mechanism for the branching reaction, that also explains the dual specificity of this transferase for elongation and branching, which is unique among polymer-forming enzymes.
Published: 1998

14. Poly(ADP-Ribose) Polymerase Is Required for Maintenance of Genomic Integrity During Base Excision Repair

Author: F. Dantzer, G. De Murcia, Claude Niedergang, F. J. Oliver, J. Ménissier-De Murcia, V. Rolli, and C. Trucco
Subjects: chemistry.chemical_compound, PARG, biology, chemistry, Poly ADP ribose polymerase, Topoisomerase, biology.protein, DNA replication, Base excision repair, Molecular biology, Polymerase, DNA, Chromatin
Abstract: In eukaryotes, DNA strand breaks introduced either directly by ionizing radiations or indirectly following enzymatic incision of a DNA-base lesion trigger immediately the synthesis of poly(ADP-ribose) by the enzyme poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30). At a site of breakage, PARP catalyzes the transfer of the ADP-ribose moiety from its substrate, NAD+, to a limited number of protein acceptors (heteromodification) involved in chromatin architecture (histones H1, H2B, lamin B) or in DNA metabolism (topoisomerases, DNA replication factors) including PARP itself (automodification) (for reviews see Althaus and Richter 1987; Lautier et al. 1993; Oei et al. 1997). These modified proteins, mainly DNA-binding proteins, carrying chains of negatively charged ADP-ribose polymers, lose their affinity for DNA and consequently are inactivated. The short half-life of the polymer is attributed to the high activity of poly(ADP-ribose) glycohydrolase (PARG) which cleaves the ribose-ribose bond (Alvarez-Gonzalez and Althaus 1989; Lin et al. 1997). Poly(ADP-ribosylation) is therefore an immediate and transient posttranslational modification of nuclear proteins induced by DNA strand breaks (Fig. 1A).
Published: 1998

15. A pleiotropic recurrent dominant ITPR3 variant causes a complex multisystemic disease.

Author: Molitor A, Lederle A, Radosavljevic M, Sapuru V, Zavorka Thomas ME, Yang J, Shirin M, Collin-Bund V, Jerabkova-Roda K, Miao Z, Bernard A, Rolli V, Grenot P, Castro CN, Rosenzwajg M, Lewis EG, Person R, Esperón-Moldes US, Kaare M, Nokelainen PT, Batzir NA, Hoffer GZ, Paul N, Stemmelen T, Naegely L, Hanauer A, Bibi-Triki S, Grün S, Jung S, Busnelli I, Tripolszki K, Al-Ali R, Ordonez N, Bauer P, Song E, Zajo K, Partida-Sanchez S, Robledo-Avila F, Kumanovics A, Louzoun Y, Hirschler A, Pichot A, Toker O, Mejía CAM, Parvaneh N, Knapp E, Hersh JH, Kenney H, Delmonte OM, Notarangelo LD, Goetz JG, Kahwash SB, Carapito C, Bajwa RPS, Thomas C, Ehl S, Isidor B, Carapito R, Abraham RS, Hite RK, Marcus N, Bertoli-Avella A, and Bahram S
Subjects: Humans, Male, Female, Calcium metabolism, Child, Mutation, Jurkat Cells, Child, Preschool, Genes, Dominant, Pedigree, Phenotype, Inositol 1,4,5-Trisphosphate Receptors genetics, Inositol 1,4,5-Trisphosphate Receptors metabolism
Abstract: Inositol 1,4,5-trisphosphate (IP3) receptor type 1 ( ITPR1 ), 2 ( ITPR2 ), and 3 ( ITPR3 ) encode the IP3 receptor (IP3R), a key player in intracellular calcium release. In four unrelated patients, we report that an identical ITPR3 de novo variant-NM_002224.3:c.7570C>T, p.Arg2524Cys-causes, through a dominant-negative effect, a complex multisystemic disorder with immunodeficiency. This leads to defective calcium homeostasis, mitochondrial malfunction, CD4 + lymphopenia, a quasi-absence of naïve CD4 + and CD8 + cells, an increase in memory cells, and a distinct TCR repertoire. The calcium defect was recapitulated in Jurkat knock-in. Site-directed mutagenesis displayed the exquisite sensitivity of Arg 2524 to any amino acid change. Despite the fact that all patients had severe immunodeficiency, they also displayed variable multisystemic involvements, including ectodermal dysplasia, Charcot-Marie-Tooth disease, short stature, and bone marrow failure. In conclusion, unlike previously reported ITPR1-3 deficiencies leading to narrow, mainly neurological phenotypes, a recurrent dominant ITPR3 variant leads to a multisystemic disease, defining a unique role for IP3R3 in the tetrameric IP3R complex.
Published: 2024
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16. Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.

Author: Carapito R, Li R, Helms J, Carapito C, Gujja S, Rolli V, Guimaraes R, Malagon-Lopez J, Spinnhirny P, Lederle A, Mohseninia R, Hirschler A, Muller L, Bastard P, Gervais A, Zhang Q, Danion F, Ruch Y, Schenck M, Collange O, Chamaraux-Tran TN, Molitor A, Pichot A, Bernard A, Tahar O, Bibi-Triki S, Wu H, Paul N, Mayeur S, Larnicol A, Laumond G, Frappier J, Schmidt S, Hanauer A, Macquin C, Stemmelen T, Simons M, Mariette X, Hermine O, Fafi-Kremer S, Goichot B, Drenou B, Kuteifan K, Pottecher J, Mertes PM, Kailasan S, Aman MJ, Pin E, Nilsson P, Thomas A, Viari A, Sanlaville D, Schneider F, Sibilia J, Tharaux PL, Casanova JL, Hansmann Y, Lidar D, Radosavljevic M, Gulcher JR, Meziani F, Moog C, Chittenden TW, and Bahram S
Subjects: ADAM Proteins, Artificial Intelligence, Humans, Intensive Care Units, Membrane Proteins, Respiration, Artificial, SARS-CoV-2, COVID-19
Abstract: The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 “critical” (in the intensive care unit under mechanical ventilation) and 25 “non-critical” (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9 . This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.
Published: 2022
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17. NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.

Author: Castro CN, Rosenzwajg M, Carapito R, Shahrooei M, Konantz M, Khan A, Miao Z, Groß M, Tranchant T, Radosavljevic M, Paul N, Stemmelen T, Pitoiset F, Hirschler A, Nespola B, Molitor A, Rolli V, Pichot A, Faletti LE, Rinaldi B, Friant S, Mednikov M, Karauzum H, Aman MJ, Carapito C, Lengerke C, Ziaee V, Eyaid W, Ehl S, Alroqi F, Parvaneh N, and Bahram S
Subjects: Actins metabolism, Animals, Cell Degranulation, Cell Proliferation, Child, Cytotoxicity, Immunologic, Family, Female, Homozygote, Humans, Immunologic Deficiency Syndromes immunology, Immunological Synapses metabolism, Infant, Inflammation immunology, Inflammation pathology, Lymphocyte Activation immunology, Lymphoproliferative Disorders immunology, Male, Membrane Proteins chemistry, Membrane Proteins deficiency, Membrane Proteins genetics, Mutation genetics, Pedigree, Phenotype, Syndrome, Zebrafish, Immunologic Deficiency Syndromes complications, Inflammation complications, Lymphoproliferative Disorders complications, Membrane Proteins metabolism
Abstract: The Nck-associated protein 1-like (NCKAP1L) gene, alternatively called hematopoietic protein 1 (HEM-1), encodes a hematopoietic lineage-specific regulator of the actin cytoskeleton. Nckap1l-deficient mice have anomalies in lymphocyte development, phagocytosis, and neutrophil migration. Here we report, for the first time, NCKAP1L deficiency cases in humans. In two unrelated patients of Middle Eastern origin, recessive mutations in NCKAP1L abolishing protein expression led to immunodeficiency, lymphoproliferation, and hyperinflammation with features of hemophagocytic lymphohistiocytosis. Immunophenotyping showed an inverted CD4/CD8 ratio with a major shift of both CD4+ and CD8+ cells toward memory compartments, in line with combined RNA-seq/proteomics analyses revealing a T cell exhaustion signature. Consistent with the core function of NCKAP1L in the reorganization of the actin cytoskeleton, patients' T cells displayed impaired early activation, immune synapse morphology, and leading edge formation. Moreover, knockdown of nckap1l in zebrafish led to defects in neutrophil migration. Hence, NCKAP1L mutations lead to broad immune dysregulation in humans, which could be classified within actinopathies., Competing Interests: Disclosures: The authors declare no competing interests exist., (© 2020 Castro et al.)
Published: 2020
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18. Compatibility at amino acid position 98 of MICB reduces the incidence of graft-versus-host disease in conjunction with the CMV status.

Author: Carapito R, Aouadi I, Pichot A, Spinnhirny P, Morlon A, Kotova I, Macquin C, Rolli V, Cesbron A, Gagne K, Oudshoorn M, van der Holt B, Labalette M, Spierings E, Picard C, Loiseau P, Tamouza R, Toubert A, Parissiadis A, Dubois V, Paillard C, Maumy-Bertrand M, Bertrand F, von dem Borne PA, Kuball JHE, Michallet M, Lioure B, Peffault de Latour R, Blaise D, Cornelissen JJ, Yakoub-Agha I, Claas F, Moreau P, Charron D, Mohty M, Morishima Y, Socié G, and Bahram S
Subjects: Amino Acids, Humans, Incidence, Retrospective Studies, Cytomegalovirus Infections epidemiology, Cytomegalovirus Infections prevention & control, Graft vs Host Disease etiology, Graft vs Host Disease prevention & control, Hematopoietic Stem Cell Transplantation adverse effects
Abstract: Graft-versus-host disease (GVHD) and cytomegalovirus (CMV)-related complications are leading causes of mortality after unrelated-donor hematopoietic cell transplantation (UD-HCT). The non-conventional MHC class I gene MICB, alike MICA, encodes a stress-induced polymorphic NKG2D ligand. However, unlike MICA, MICB interacts with the CMV-encoded UL16, which sequestrates MICB intracellularly, leading to immune evasion. Here, we retrospectively analyzed the impact of mismatches in MICB amino acid position 98 (MICB98), a key polymorphic residue involved in UL16 binding, in 943 UD-HCT pairs who were allele-matched at HLA-A, -B, -C, -DRB1, -DQB1 and MICA loci. HLA-DP typing was further available. MICB98 mismatches were significantly associated with an increased incidence of acute (grade II-IV: HR, 1.20; 95% CI, 1.15 to 1.24; P < 0.001; grade III-IV: HR, 2.28; 95% CI, 1.56 to 3.34; P < 0.001) and chronic GVHD (HR, 1.21; 95% CI, 1.10 to 1.33; P < 0.001). MICB98 matching significantly reduced the effect of CMV status on overall mortality from a hazard ratio of 1.77 to 1.16. MICB98 mismatches showed a GVHD-independent association with a higher incidence of CMV infection/reactivation (HR, 1.84; 95% CI, 1.34 to 2.51; P < 0.001). Hence selecting a MICB98-matched donor significantly reduces the GVHD incidence and lowers the impact of CMV status on overall survival.
Published: 2020
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19. Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency.

Author: Carapito R, Carapito C, Morlon A, Paul N, Vaca Jacome AS, Alsaleh G, Rolli V, Tahar O, Aouadi I, Rompais M, Delalande F, Pichot A, Georgel P, Messer L, Sibilia J, Cianferani S, Van Dorsselaer A, and Bahram S
Subjects: Adult, Exome, Female, Gene Expression Profiling methods, Humans, Middle Aged, Mutation, Missense, Phenotype, Polymorphism, Single Nucleotide, Proteomics methods, Genes, Modifier, Mevalonate Kinase Deficiency genetics, STAT1 Transcription Factor genetics
Abstract: Objectives: The objective of the present study was to explain why two siblings carrying both the same homozygous pathogenic mutation for the autoinflammatory disease hyper IgD syndrome, show opposite phenotypes, that is, the first being asymptomatic, the second presenting all classical characteristics of the disease., Methods: Where single omics (mainly exome) analysis fails to identify culprit genes/mutations in human complex diseases, multiomics analyses may provide solutions, although this has been seldom used in a clinical setting. Here we combine exome, transcriptome and proteome analyses to decipher at a molecular level, the phenotypic differences between the two siblings., Results: This multiomics approach led to the identification of a single gene -STAT1 -which harboured a rare missense variant and showed a significant overexpression of both mRNA and protein in the symptomatic versus the asymptomatic sister. This variant was shown to be of gain of function nature, involved in an increased activation of the Janus kinase/signal transducer and activator of transcription signalling (JAK/STAT) pathway, known to play a critical role in inflammatory diseases and for which specific biotherapies presently exist. Pathway analyses based on information from differentially expressed transcripts and proteins confirmed the central role of STAT1 in the proposed regulatory network leading to an increased inflammatory phenotype in the symptomatic sibling., Conclusions: This study demonstrates the power of a multiomics approach to uncover potential clinically actionable targets for a personalised therapy. In more general terms, we provide a proteogenomics analysis pipeline that takes advantage of subject-specific genomic and transcriptomic information to improve protein identification and hence advance individualised medicine., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2018. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
Published: 2018
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20. Zinc-Alpha-2-Glycoprotein in Inflammatory Bowel Disease.

Author: Rolli V, Macquin C, Kokten T, Hablot J, Ndiaye NC, Netter P, Bahram S, Jouzeau JY, Peyrin-Biroulet L, Georgel P, and Moulin D
Subjects: Animals, Case-Control Studies, Disease Models, Animal, Humans, Mice, Mice, Knockout, Seminal Plasma Proteins genetics, Zn-Alpha-2-Glycoprotein, Colitis, Ulcerative blood, Seminal Plasma Proteins blood
Published: 2018
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21. Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features.

Author: Carapito R, Konantz M, Paillard C, Miao Z, Pichot A, Leduc MS, Yang Y, Bergstrom KL, Mahoney DH, Shardy DL, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller JS, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho CS, Amati-Bonneau P, Procaccio V, Mosca-Boidron AL, Marle N, Osmani N, Lefebvre O, Goetz JG, Unal S, Akarsu NA, Radosavljevic M, Chenard MP, Rialland F, Grain A, Béné MC, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming MD, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, and Bahram S
Subjects: Animals, Child, Congenital Bone Marrow Failure Syndromes, DNA Mutational Analysis, Female, Genetic Association Studies, Humans, Infant, Male, Models, Molecular, Neutropenia genetics, Pancreas, Exocrine metabolism, Phenotype, Protein Domains, Shwachman-Diamond Syndrome, Signal Recognition Particle chemistry, Zebrafish, Bone Marrow Diseases genetics, Exocrine Pancreatic Insufficiency genetics, Lipomatosis genetics, Neutropenia congenital, Signal Recognition Particle genetics
Abstract: Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.
Published: 2017
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22. Zinc-α2-Glycoprotein Exerts Antifibrotic Effects in Kidney and Heart.

Author: Sörensen-Zender I, Bhayana S, Susnik N, Rolli V, Batkai S, Baisantry A, Bahram S, Sen P, Teng B, Lindner R, Schiffer M, Thum T, Melk A, Haller H, and Schmitt R
Subjects: Adipokines, Animals, Aorta pathology, Carrier Proteins metabolism, Cell Differentiation, Epithelium pathology, Fibroblasts metabolism, Fibrosis pathology, Gene Deletion, Glycoproteins metabolism, HEK293 Cells, Humans, Kidney pathology, Kidney Diseases metabolism, Kidney Failure, Chronic metabolism, Male, Mice, Myocardium pathology, Phosphorylation, Protein Biosynthesis, Rats, Recombinant Proteins chemistry, Signal Transduction, Transforming Growth Factor beta metabolism, Ureteral Obstruction pathology, Zn-Alpha-2-Glycoprotein, Kidney metabolism, Kidney Failure, Chronic genetics, Myocardium metabolism, Seminal Plasma Proteins metabolism
Abstract: Zinc-α2-glycoprotein (AZGP1) is a secreted protein synthesized by epithelial cells and adipocytes that has roles in lipid metabolism, cell cycling, and cancer progression. Our previous findings in AKI indicated a new role for AZGP1 in the regulation of fibrosis, which is a unifying feature of CKD. Using two models of chronic kidney injury, we now show that mice with genetic AZGP1 deletion develop significantly more kidney fibrosis. This destructive phenotype was rescued by injection of recombinant AZGP1. Exposure of AZGP1-deficient mice to cardiac stress by thoracic aortic constriction revealed that antifibrotic effects were not restricted to the kidney but were cardioprotective. In vitro, recombinant AZGP1 inhibited kidney epithelial dedifferentiation and antagonized fibroblast activation by negatively regulating TGF-β signaling. Patient sera with high levels of AZGP1 similarly attenuated TGF-β signaling in fibroblasts. Taken together, these findings indicate a novel role for AZGP1 as a negative regulator of fibrosis progression, suggesting that recombinant AZGP1 may have translational effect for treating fibrotic disease., (Copyright © 2015 by the American Society of Nephrology.)
Published: 2015
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23. Activated factor X cleaves factor VIII at arginine 562, limiting its cofactor efficiency.

Author: Plantier JL, Rolli V, Ducasse C, Dargaud Y, Enjolras N, Boukerche H, and Négrier C
Subjects: Animals, Arginine, CHO Cells, Cricetinae, Cricetulus, Factor IXa metabolism, Factor VIII chemistry, Factor VIII genetics, Humans, Kinetics, Mutation, Phospholipids metabolism, Protein Structure, Tertiary, Recombinant Proteins metabolism, Substrate Specificity, Transfection, von Willebrand Factor metabolism, Factor VIII metabolism, Factor Xa metabolism, Protein Processing, Post-Translational
Abstract: Background: Factor VIII (FVIII) and its activated form (FVIIIa) are subject to proteolysis that dampens their cofactor function. Among the proteases that attack FVIII (activated factor X (FXa), activated protein C (APC) and plasmin), only APC cleaves within the FVIII A2 domain at R562 to fully abolish FVIII activity., Objectives: We investigated the possible involvement of the FXa cleavage at R562 within the A2 domain in the process of FVIII inactivation., Methods: An antibody (GMA012/R8B12) that recognizes the carboxy-terminus extremity of the A2 domain (A2C) was used to evaluate FXa action. A molecule mutated at R562 was also generated to assess the functional role of this particular residue., Results and Conclusions: The appearance of the A2C domain as a function of time evidenced the identical cleavage within the A2 domain of FVIII and FVIIIa by FXa. This cleavage required phospholipids and occurred within minutes. In contrast, the isolated A2 domain was not cleaved by FXa. Von Willebrand factor and activated FIX inhibited the cleavage in a dose-dependent manner. Mutation R562K increased both the FVIII specific activity and the generation of FXa due to an increase in FVIII catalytic efficiency. Moreover, A2C fragment could not be identified from FVIII-R562K cleavage. In summary, this study defines a new mechanism for A2 domain-mediated FVIII degradation by FXa and implicates the bisecting of the A2 domain at R562.
Published: 2010
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24. Lipolysis is altered in MHC class I zinc-alpha(2)-glycoprotein deficient mice.

Author: Rolli V, Radosavljevic M, Astier V, Macquin C, Castan-Laurell I, Visentin V, Guigné C, Carpéné C, Valet P, Gilfillan S, and Bahram S
Subjects: Adipocytes metabolism, Adrenergic beta-3 Receptor Agonists, Alleles, Animals, Base Sequence, CHO Cells, Cricetinae, Cricetulus, DNA genetics, Dietary Fats administration & dosage, Gene Expression, Gene Targeting, HeLa Cells, Histocompatibility Antigens Class I genetics, Humans, In Vitro Techniques, Liver immunology, Liver metabolism, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, RNA, Messenger genetics, RNA, Messenger metabolism, Receptors, Adrenergic, beta-3 metabolism, Recombinant Proteins genetics, Recombinant Proteins metabolism, Seminal Plasma Proteins genetics, Tissue Distribution, Transfection, Weight Gain, Zn-Alpha-2-Glycoprotein, Histocompatibility Antigens Class I metabolism, Lipolysis physiology, Seminal Plasma Proteins metabolism
Abstract: Non-conventional major histocompatibility complex class I molecules are involved in a variety of physiological functions, most at the periphery of the immune system per se. Zinc-alpha(2)-glycoprotein (ZAG), the sole soluble member of this superfamily has been implicated in cachexia, a poorly understood yet life-threatening, severe wasting syndrome. To further ascertain the role of ZAG in lipid metabolism and perhaps the immune system, we inactivated both ZAG alleles by gene targeting in mice. Subjecting these ZAG deficient animals to standard or lipid rich food regimens led to increased body weight in comparison to identically treated wild-type mice. This phenotype appeared to correlate with a significant decrease in adipocytic lipolysis that could not be rescued by several pharmacological agents including beta(3)-adrenoreceptor agonists. Furthermore, in contrast to previously reported data, ZAG was found to be ubiquitously and constitutively expressed, with an especially high level in the mouse liver. No overt immunological phenotype was identified in these animals.
Published: 2007
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25. B-domain deleted factor VIII is aggregated and degraded through proteasomal and lysosomal pathways.

Author: Plantier JL, Guillet B, Ducasse C, Enjolras N, Rodriguez MH, Rolli V, and Négrier C
Subjects: Animals, Antigens, CD biosynthesis, CHO Cells, Centrifugation, Density Gradient, Cricetinae, Detergents pharmacology, Factor VIII chemistry, Furin chemistry, Glycosylation, Immunoblotting, Immunoprecipitation, Leupeptins chemistry, Lysosomal Membrane Proteins, Microscopy, Confocal, Microscopy, Fluorescence, Neuraminidase metabolism, Octoxynol pharmacology, Peptide Fragments chemistry, Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase metabolism, Protein Structure, Tertiary, Sucrose pharmacology, Transfection, Tunicamycin pharmacology, Factor VIII physiology, Lysosomes metabolism, Peptide Fragments physiology, Proteasome Endopeptidase Complex metabolism
Abstract: Factor VIII (FVIII) processing within mammalian cells is demonstrated to be much less efficient than proteins of similar size. The deletion of the B-domain from FVIII improves the level of production, due partly to the increase in mRNA synthesis. We aimed to characterise the cellular fate and the intracellular processing of the FVIII molecule devoid of B-domain. A B-domain deleted factor VIII (BDD-FVIII) possessing a furin consensus cleavage site in the connecting segment between the heavy and the light chain, was produced in CHO cell line. In such cells, FVIII was retained as two single chain products from which a majority was aggregated. The two species were located in Triton X-100 soluble (for 60-80%) and insoluble fractions (for 20-40%). The incubation of the expressing cells with tunicamycin (5 mug/ml) and the treatment of the intracellular species with a mixture of Neuraminidase and N-glycosidase-F revealed that both intracellular species were N-glycosylated. Furin over-expression neither diminished the intracellular FVIII contents nor improved its extracellular production. Intracellular FVIII was degraded through both lysosomal and proteasomal pathways as evidenced by inhibitor treatments (e.g. NH(4)Cl, leupeptin, clasto-Lactacystin beta-lactone and MG-132), pulse-chase analysis and confocal observations. This study demonstrates that a BDD-FVIII expressed in CHO cells is inefficiently processed consecutively to intracellular aggregation, proteasomal degradation, and routage to lysosomes.
Published: 2005
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26. Amplification of B cell antigen receptor signaling by a Syk/ITAM positive feedback loop.

Author: Rolli V, Gallwitz M, Wossning T, Flemming A, Schamel WW, Zürn C, and Reth M
Subjects: Animals, Binding Sites, Blotting, Western, Cell Line, Drosophila, Glutathione Transferase metabolism, Hydrogen Peroxide pharmacology, Intracellular Signaling Peptides and Proteins, Models, Biological, Models, Genetic, Mutagenesis, Site-Directed, Oxidation-Reduction, Phosphorylation, Plasmids metabolism, Protein Binding, Protein Structure, Tertiary, Syk Kinase, Transfection, Tyrosine metabolism, src-Family Kinases metabolism, Enzyme Precursors metabolism, Protein-Tyrosine Kinases metabolism, Receptors, Antigen, B-Cell metabolism, Signal Transduction
Abstract: We have established a protocol allowing transient and inducible coexpression of many foreign genes in Drosophila S2 Schneider cells. With this powerful approach of reverse genetics, we studied the interaction of the protein tyrosine kinases Syk and Lyn with the B cell antigen receptor (BCR). We find that Lyn phosphorylates only the first tyrosine whereas Syk phosphorylates both tyrosines of the BCR immunoreceptor tyrosine-based activation motif (ITAM). Furthermore, we show that Syk is a positive allosteric enzyme, which is strongly activated by the binding to the phosphorylated ITAM tyrosines, thus initiating a positive feedback loop at the receptor. The BCR-dependent Syk activation and signal amplification is efficiently counterbalanced by protein tyrosine phosphatases, the activity of which is regulated by H(2)O(2) and the redox equilibrium inside the cell.
Published: 2002
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27. PARP-2, A novel mammalian DNA damage-dependent poly(ADP-ribose) polymerase.

Author: Amé JC, Rolli V, Schreiber V, Niedergang C, Apiou F, Decker P, Muller S, Höger T, Ménissier-de Murcia J, and de Murcia G
Subjects: 3T3 Cells, Amino Acid Sequence, Animals, Chromosome Mapping, Chromosomes, Human, Pair 14 genetics, Cloning, Molecular, DNA-Binding Proteins chemistry, DNA-Binding Proteins genetics, Enzyme Activation genetics, Humans, In Situ Hybridization, Fluorescence, Lymphocytes enzymology, Mice, Molecular Sequence Data, Nuclear Proteins genetics, Nuclear Proteins metabolism, Poly(ADP-ribose) Polymerases chemistry, RNA, Messenger metabolism, Recombinant Proteins genetics, Sequence Alignment, DNA Damage genetics, Poly(ADP-ribose) Polymerases genetics
Abstract: Poly(ADP-ribosylation) is a post-translational modification of nuclear proteins in response to DNA damage that activates the base excision repair machinery. Poly(ADP-ribose) polymerase which we will now call PARP-1, has been the only known enzyme of this type for over 30 years. Here, we describe a cDNA encoding a 62-kDa protein that shares considerable homology with the catalytic domain of PARP-1 and also contains a basic DNA-binding domain. We propose to call this enzyme poly(ADP-ribose) polymerase 2 (PARP-2). The PARP-2 gene maps to chromosome 14C1 and 14q11.2 in mouse and human, respectively. Purified recombinant mouse PARP-2 is a damaged DNA-binding protein in vitro and catalyzes the formation of poly(ADP-ribose) polymers in a DNA-dependent manner. PARP-2 displays automodification properties similar to PARP-1. The protein is localized in the nucleus in vivo and may account for the residual poly(ADP-ribose) synthesis observed in PARP-1-deficient cells, treated with alkylating agents or hydrogen peroxide.
Published: 1999
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28. A dual approach in the study of poly (ADP-ribose) polymerase: in vitro random mutagenesis and generation of deficient mice.

Author: Trucco C, Rolli V, Oliver FJ, Flatter E, Masson M, Dantzer F, Niedergang C, Dutrillaux B, Ménissier-de Murcia J, and de Murcia G
Subjects: Age Factors, Animals, Apoptosis, Body Weight, Catalysis, Escherichia coli genetics, Humans, Mice, Models, Genetic, Models, Molecular, Sister Chromatid Exchange, Mice, Knockout, Mutagenesis, Poly(ADP-ribose) Polymerases genetics
Abstract: A dual approach to the study of poly (ADP-ribose)polymerase (PARP) in terms of its structure and function has been developed in our laboratory. Random mutagenesis of the DNA binding domain and catalytic domain of the human PARP, has allowed us to identify residues that are crucial for its enzymatic activity. In parallel PARP knock-out mice were generated by inactivation of both alleles by gene targeting. We showed that: (i) they are exquisitely sensitive to gamma-irradiation, (ii) they died rapidly from acute radiation toxicity to the small intestine, (iii) they displayed a high genomic instability to gamma-irradiation and MNU injection and, (iv) bone marrow cells rapidly underwent apoptosis following MNU treatment, demonstrating that PARP is a survival factor playing an essential and positive role during DNA damage recovery and survival.
Published: 1999

29. Involvement of poly(ADP-ribose) polymerase in base excision repair.

Author: Dantzer F, Schreiber V, Niedergang C, Trucco C, Flatter E, De La Rubia G, Oliver J, Rolli V, Ménissier-de Murcia J, and de Murcia G
Subjects: Animals, DNA Damage, HeLa Cells, Humans, Mice, Mice, Knockout, Mutation, Poly(ADP-ribose) Polymerases genetics, DNA Repair, Poly(ADP-ribose) Polymerases metabolism
Abstract: Poly(ADP-ribose) polymerase (PARP) is a zinc-finger DNA binding protein that detects and signals DNA strand breaks generated directly or indirectly by genotoxic agents. In response to these lesions, the immediate poly(ADP-ribosylation) of nuclear proteins converts DNA interruptions into intracellular signals that activate DNA repair or cell death programs. To elucidate the biological function of PARP in vivo, the mouse PARP gene was inactivated by homologous recombination to generate mice lacking a functional PARP gene. PARP knockout mice and the derived mouse embryonic fibroblasts (MEFs) were acutely sensitive to monofunctional alkylating agents and gamma-irradiation demonstrating that PARP is involved in recovery from DNA damage that triggers the base excision repair (BER) process. To address the issue of the role of PARP in BER, the ability of PARP-deficient mammalian cell extracts to repair a single abasic site present on a circular duplex plasmid molecule was tested in a standard in vitro repair assay. The results clearly demonstrate, for the first time, the involvement of PARP in the DNA synthesis step of the base excision repair process.
Published: 1999
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30. Importance of poly(ADP-ribose) polymerase and its cleavage in apoptosis. Lesson from an uncleavable mutant.

Author: Oliver FJ, de la Rubia G, Rolli V, Ruiz-Ruiz MC, de Murcia G, and Murcia JM
Subjects: Alkylating Agents pharmacology, Animals, Cell Line, Transformed, Cell Nucleus enzymology, Cell Nucleus metabolism, Cytoplasm enzymology, Cytoplasm metabolism, Hydrolysis, Mice, Mutagenesis, Site-Directed, Poly(ADP-ribose) Polymerases genetics, fas Receptor metabolism, Apoptosis drug effects, Poly(ADP-ribose) Polymerases metabolism
Abstract: We have studied the apoptotic response of poly(ADP-ribose) polymerase (PARP)-/- cells to different inducers and the consequences of the expression of an uncleavable mutant of PARP on the apoptotic process. The absence of PARP drastically increases the sensitivity of primary bone marrow PARP-/- cells to apoptosis induced by an alkylating agent but not by a topoisomerase I inhibitor CPT-11 or by interleukin-3 removal. cDNA of wild type or of an uncleavable PARP mutant (D214A-PARP) has been introduced into PARP-/- fibroblasts, which were exposed to anti-CD95 or an alkylating agent to induce apoptosis. The expression of D214A-PARP results in a significant delay of cell death upon CD95 stimulation. Morphological analysis shows a retarded cell shrinkage and nuclear condensation. Upon treatment with an alkylating agent, expression of wild-type PARP cDNA into PARP-deficient mouse embryonic fibroblasts results in the restoration of the cell viability, and the D214A-PARP mutant had no further effect on cell recovery. In conclusion, PARP-/- cells are extremely sensitive to apoptosis induced by triggers (like alkylating agents), which activates the base excision repair pathway of DNA, and the cleavage of PARP during apoptosis facilitates cellular disassembly and ensures the completion and irreversibility of the process.
Published: 1998
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31. The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis.

Author: Ruf A, Rolli V, de Murcia G, and Schulz GE
Subjects: Adenosine Diphosphate Ribose metabolism, Animals, Binding Sites, Chickens, Crystallography, X-Ray, Enzyme Inhibitors, Humans, Models, Molecular, Mutagenesis, NAD chemistry, NAD metabolism, Niacinamide analogs & derivatives, Peptide Fragments chemistry, Poly(ADP-ribose) Polymerase Inhibitors, Poly(ADP-ribose) Polymerases genetics, Structure-Activity Relationship, NAD analogs & derivatives, Poly(ADP-ribose) Polymerases chemistry, Poly(ADP-ribose) Polymerases metabolism
Abstract: The binding site for the acceptor substrate poly(ADP-ribose) in the elongation reaction of the ADP-ribosyl transferase poly(ADP-ribose) polymerase (PARP) was detected by cocrystallizing the enzyme with an NAD+ analogue. The site was confirmed by mutagenesis studies. In conjunction with the binding site of the donor NAD+, the bound acceptor reveals the geometry of the elongation reaction. It shows in particular that the strictly conserved glutamate residue of all ADP-ribosylating enzymes (Glu988 of PARP) facilitates the reaction by polarizing both, donor and acceptor. Moreover, the binding properties of the acceptor site suggest a mechanism for the branching reaction, that also explains the dual specificity of this transferase for elongation and branching, which is unique among polymer-forming enzymes., (Copyright 1998 Academic Press Limited.)
Published: 1998
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32. Random mutagenesis of the poly(ADP-ribose) polymerase catalytic domain reveals amino acids involved in polymer branching.

Author: Rolli V, O'Farrell M, Ménissier-de Murcia J, and de Murcia G
Subjects: Amino Acid Sequence, Catalysis, Humans, Molecular Sequence Data, Mutagenesis, Site-Directed, Polymerase Chain Reaction, Structure-Activity Relationship, Amino Acids chemistry, Amino Acids genetics, Poly(ADP-ribose) Polymerases chemistry, Poly(ADP-ribose) Polymerases genetics, Polymers chemistry, Protein Structure, Tertiary
Abstract: Poly(ADP-ribose) polymerase (PARP) is a multifunctional nuclear zinc finger protein which participates in the immediate response of mammalian cells exposed to DNA damaging agents. Given the complexity of the poly(ADP-ribosylation) reaction, we developed a large-scale screening procedure in Escherichia coli to identify randomly amino acids involved in the various aspects of this mechanism. Random mutations were generated by the polymerase chain reaction in a cDNA sequence covering most of the catalytic domain. Out of 26 individual mutations that diversely inactivated the full-length PARP, 22 were found at conserved positions in the primary structure, and 24 were located in the core domain formed by two beta-sheets containing the active site. Most of the PARP mutants were altered in poly(ADP-ribose) elongation and/or branching. The spatial proximity of some residues involved in chain elongation (E988) and branching (Y986) suggests a proximity or a superposition of these two catalytic sites. Other residues affected in branching were located at the surface of the molecule (R847, E923, G972), indicating that protein-protein contacts are necessary for optimal polymer branching. This screening procedure provides a simple and efficient method to explore further the structure-function relationship of the enzyme.
Published: 1997
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33. Photoaffinity labelling of human poly(ADP-ribose) polymerase catalytic domain.

Author: Kim H, Jacobson MK, Rolli V, Ménissier-de Murcia J, Reinbolt J, Simonin F, Ruf A, Schulz G, and de Murcia G
Subjects: Amino Acid Sequence, Binding Sites, DNA Mutational Analysis, Humans, Light, Lysine genetics, Lysine metabolism, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, NAD metabolism, Peptide Fragments chemistry, Photochemistry, Poly(ADP-ribose) Polymerases genetics, Recombinant Proteins metabolism, Sequence Analysis, Tryptophan genetics, Tryptophan metabolism, Affinity Labels metabolism, Azides metabolism, NAD analogs & derivatives, Poly(ADP-ribose) Polymerases metabolism
Abstract: Photoaffinity labelling of the human poly(ADP-ribose) polymerase (PARP) catalytic domain (40 kDa) with the NAD+ photoaffinity analogue 2-azido-[alpha-32P]NAD+ has been used to identify NAD+-binding residues. In the presence of UV, photo-insertion of the analogue was observed with a stoichiometry of 0.73 mol of 2-azido-[alpha-32P]NAD+ per mol of catalytic domain. Competition experiments indicated that 3-aminobenzamide strongly protected the insertion site. Residues binding the adenine ring of NAD+ were identified by trypsin digestion and boronate affinity chromatography in combination with reverse-phase HPLC. Two major NAD+-binding residues, Trp1014 of peptide Thr1011-Trp1014 and Lys893 of peptide Ile979-Lys893, were identified. The site-directed mutagenesis of these two residues revealed that Lys893, but not Trp1014, is critical for activity. The close positioning of Lys893 near the adenine ring of NAD+ has been confirmed by the recently solved crystallographic structure of the chicken PARP catalytic domain [Ruf, Menissier-de Murcia, de Murcia and Schulz (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 7481-7485].
Published: 1997
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34. Poly(ADP-ribose) polymerase: structure-function relationship.

Author: Masson M, Rolli V, Dantzer F, Trucco C, Schreiber V, Fribourg S, Molinete M, Ruf A, Miranda EA, and Niedergang C
Subjects: Animals, Catalysis, Chickens, Crystallization, Crystallography, X-Ray, DNA Damage, DNA-Binding Proteins chemistry, DNA-Binding Proteins physiology, Genome, Human, HeLa Cells, Humans, Protein Structure, Tertiary, Recombinant Proteins chemistry, Structure-Activity Relationship, Transfection, DNA Repair, Poly(ADP-ribose) Polymerases chemistry, Poly(ADP-ribose) Polymerases physiology
Abstract: Dissection of the human poly(ADP-ribose) polymerase (PARP) molecule in terms of its structure-function relationship has proved to be an essential step towards understanding the biological role of poly(ADP-ribosylation) as a cellular response to DNA damage in eukaryotes. Current approaches aimed at elucidating the implication of this multifunctional enzyme in the maintenance of the genomic integrity will be presented.
Published: 1995
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34 results on '"V. Rolli"'

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5. Poly(ADP-ribose) polymerase: Structure-function relationship

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13. The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis

14. Poly(ADP-Ribose) Polymerase Is Required for Maintenance of Genomic Integrity During Base Excision Repair

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27. PARP-2, A novel mammalian DNA damage-dependent poly(ADP-ribose) polymerase.

28. A dual approach in the study of poly (ADP-ribose) polymerase: in vitro random mutagenesis and generation of deficient mice.

29. Involvement of poly(ADP-ribose) polymerase in base excision repair.

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34. Poly(ADP-ribose) polymerase: structure-function relationship.

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34 results on '"V. Rolli"'

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