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Suzanne M, Steller H
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Shaping organisms with apoptosis
CELL DEATH AND DIFFERENTIATION 2013 MAY; 20(5):669-675
Programmed cell death is an important process during development that serves to remove superfluous cells and tissues, such as larval organs during metamorphosis, supernumerary cells during nervous system development, muscle patterning and cardiac morphogenesis. Different kinds of cell death have been observed and were originally classified based on distinct morphological features: (1) type I programmed cell death (PCD) or apoptosis is recognized by cell rounding, DNA fragmentation, externalization of phosphatidyl serine, caspase activation and the absence of inflammatory reaction, (2) type II PCD or autophagy is characterized by the presence of large vacuoles and the fact that cells can recover until very late in the process and (3) necrosis is associated with an uncontrolled release of the intracellular content after cell swelling and rupture of the membrane, which commonly induces an inflammatory response. In this review, we will focus exclusively on developmental cell !
Tanaka H, Akagi K, Oneyama C, Tanaka M, Sasaki Y, Kanou T, Lee YH, Yokogawa D, Dobenecker MW, Nakagawa A, Okada M, Ikegami T
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Identification of a New Interaction Mode between the Src Homology 2 Domain of C-terminal Src Kinase (Csk) and Csk-binding Protein/Phosphoprotein Associated with Glycosphingolipid Microdomains
JOURNAL OF BIOLOGICAL CHEMISTRY 2013 MAY 24; 288(21):15240-15254
Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp bindin!
Barros T, Guenther J, Kelch B, Anaya J, Prabhakar A, O'Donnell M, Kuriyan J, Lamers MH
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A structural role for the PHP domain in E. coli DNA polymerase III
BMC STRUCTURAL BIOLOGY 2013 MAY 14; 13(?):? Article 8
Background: In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Results: Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 angstrom resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. Conclusions: While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional nonenzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.
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Klein B, Lellouch J, Marinov A, Mccartin J, Rios AAO, Ryckbosch D, Strobbe N, Thyssen F, Tytgat M, Verwilligen P, Walsh S, Yazgan E, Zaganidis N, Basegmez S, Bruno G, Castello R, Ceard L, Delaere C, du Pree T, Favart D, Forthomme L, Giammanco A, Hollar J, Lemaitre V, Liao J, Militaru C, Nuttens C, Pagano D, Pin A, Piotrzkowski K, Schul N, Garcia JMV, Beliy N, Caebergs T, Daubie E, Hammad GH, Alves GA, Martins MC, Damiao DD, Martins T, Pol ME, Souza MHG, Alda WL, Carvalho W, Custodio A, Da Costa EM, Martins CD, De Souza SF, Figueiredo DM, Mundim L, Nogima H, Oguri V, Da Silva WLP, Santoro A, Jorge LS, Sznajder A, Anjos TS, Bernardes CA, Dias FA, Tomei TRFP, Gregores EM, Lagana C, Marinho F, Mercadante PC, Novaes SF, Padula SS, Genchev V, Iaydjiev P, Piperov S, Rodozov M, Stoykova S, Sultanov G, Tcholakov V, Trayanov R, Vutova M, Dimitrov A, Hadjiiska R, Kozhuharov V, Litov L, Pavlov B, Petkov P, Bian JG, Chen GM, Chen HS, Jiang CH, Liang D, Liang S, Meng X, Tao J, Wang J, Wang X, Wang 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Duchardt D, Erdmann M, Fischer R, Gueth A, Hebbeker T, Heidemann C, Hoepfner K, Klingebiel D, Kreuzer P, Merschmeyer M, Meyer A, Olschewski M, Papacz P, Pieta H, Reithler H, Schmitz SA, Sonnenschein L, Steggemann J, Teyssier D, Weber M, Bontenackels M, Cherepanov V, Erdogan Y, Fltigge G, Geenen H, Geisler M, Ahmad WH, Hoehle F, Kargoll B, Kress T, Kuessel Y, Lingemann J, Nowack A, Per-Challa L, Pooth O, Sauerland P, Stahl A, Martin MA, Behr J, Behrenhoff W, Behrens U, Bergholz M, Bethani A, Borras K, Burgmeier A, Cakir A, Calligaris L, Campbell A, Castro E, Costanza F, Dammann D, Pardos CD, Eckerlin G, Eckstein D, Flucke G, Geiser A, Glushkov I, Gunnellini P, Habib S, Hauk J, Hellwig G, Jung H, Kasemann M, Katsas P, Kleinwort C, Kluge H, Knutsson A, Kraemer M, Kruecker D, Kuznetsova E, Lange W, Lohmann W, Lutz B, Mankel R, Marfin I, Marienfeld M, Melzer-Pellmann IA, Meyer AB, Mnich J, Mussgiller A, Naumann-Emme S, Novgorodova O, Olzem J, Perrey H, Petrukhin A, Pitzl D, Raspereza A, Cipriano PMR, Riedl C, Ron E, Rosin M, Salfeld-Nebgen J, Schmidt R, Schoerner-Sadenius T, Sen N, Spiridonov A, Stein M, Walsh R, Wissing C, Blobel V, Draeger J, Enderle H, Erfle J, Gebbert U, Goerner M, Gosselink M, Hermanns T, Hoeing RS, Kaschube K, Kaussen G, Kirschenmann H, Klanner R, Lange J, Mura B, Nowak F, Peiffer T, Pietsch N, Rathjens D, Sander C, Schettler H, Schleper P, Schlieckau E, Schmidt A, Schroder M, Schum T, Seidel M, Sola VS, Stadie H, Steinbruck G, Thomsen J, Vanelderen L, Barth C, Berger J, Boser C, Chwalek T, De Boer W, Descroix A, Dier-lamm A, Feindt M, Guthoff M, Hackstein C, Hartmann F, Hauth T, Heinrich M, Held H, Hoffmann KH, Husemann U, Katkov I, Komaragiri JR, Pardo PL, Martschei D, Mueller S, Muller T, Niegel M, Nurnberg A, Oberst O, Oehler A, Ott J, Quast G, Rabbertz K, Ratnikov F, Ratnikova N, Rocker S, Schilling FP, Schott G, Simonis HJ, Stober FM, Troendle D, Ulrich R, Wagner-Kuhr J, Wayand S, Weiler T, Zeise M, Daskalakis G, Geralis T, Kesisoglou S, Kyriakis A, Loukas D, Manolakos I, Markou A, Markou C, Mavrommatis C, Ntomari E, Gouskos L, Mertzimekis TJ, Panagiotou A, Saoulidou N, Evangelou I, Foudas C, Kokkas P, Manthos N, Papadopoulos I, Patras V, Bencze G, Hajdu C, Hidas P, Horvath D, Sikler F, Veszpremi V, Vesztergombi G, Beni N, Czellar S, Molnar J, Palinkas J, Szillasi Z, Karancsi J, Raics P, Trocsanyi ZL, Ujvari B, Beri SB, Bhatnagar V, Dhingra N, Gupta R, Kaur M, Mehta MZ, Nishu N, Saini LK, Sharma A, Singh JB, Kumar A, Kumar A, Ahuja S, Bhardwaj A, Choudhary BC, Malhotra S, Naimuddin M, Ranjan K, Sharma V, Shivpuri RK, Banerjee S, Bhattacharya S, Dutta S, Comber B, Jain S, Jain S, Khurana R, Sarkar S, Sharan M, Abdulsalam A, Choudhury RK, Dutta D, Kailas S, Kumar V, Mehta P, Mohanty AK, Pant LM, Shukla P, Aziz T, Ganguly S, Guchait M, Maity M, Majumder G, Mazumdar K, Mo-hanty GB, Panda B, Sudhakar K, Wickramage N, Banerjee S, Dugad S, Arfaei H, Bakhshiansohi H, Etesami SM, Fahim A, Hashemi M, Hesari H, Ja-fari A, Khakzad 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Guio F, Di Matteo L, Fiorendi S, Gennai S, Ghezzi A, Malvezzi S, Manzoni RA, Martelli A, Massironi A, Menasce D, Moroni L, Paganoni M, Pedrini D, Ragazzi S, Redaelli N, Sala S, de Fatis TT, Buontempo S, Montoya CAC, Cavallo N, De Cosa A, Dogangun O, Fabozzi F, Iorio AOM, Lista L, Meola S, Merola M, Paolucci P, Azzi P, Bacchetta N, Bisello D, Branca A, Carlin R, Checchia P, Dorigo T, Dosselli U, Gasparini F, Gasparini U, Gozzelino A, Kanishchev K, Lacaprara S, Lazzizzera I, Margoni M, Meneguzzo AT, Pazzini J, Pozzobon N, Ronchese P, Simonetto F, Torassaa E, Tosi M, Vanini S, Zotto P, Zumerle G, Gabusi M, Ratti SP, Riccardi C, Torre P, Vitulo P, Biasini M, Bilei GM, Fano L, Lariccia P, Mantovani G, Menichelli M, Nappi A, Romeo F, Saha A, Santocchia A, Spiezia A, Taroni S, Azzurri P, Bagliesi G, Bernardini J, Boccali T, Broccolo G, Castaldi R, D'Agnolo RT, Dell'Orso R, Fiori F, Foa L, Giassi A, Kraan A, Ligabue F, Lomtadze T, Martini L, Messineo A, Palla F, Rizzi A, Serban AT, Spagnolo P, Squillacioti P, Tenchini R, Tonelli G, Venturi A, Verdini PC, Barone L, Cavallari F, Del Re D, Diemoz M, Fanelli C, Grassi M, Longo E, Meridiani P, Micheli F, Nourbakhsh S, Organtini G, Paramatti R, Rahatlou S, Sigamani M, Soffi L, Amapane N, Arcidiacono R, Argiro S, Arneodo M, Biino C, Cartiglia N, Costa M, Demaria N, Mariotti C, Maselli S, Migliore E, Monaco V, Musich M, Obertino MM, Pastrone N, Pelliccioni M, Potenza A, Romero A, Ruspa M, Sacchi R, Solano A, Staiano A, Pereira AV, Belforte S, Candelise V, Casarsa M, Cossutti F, Della Ricca G, Gobbo B, Marone M, Montanino D, Penzo A, Schizzi A, Heo SC, Kim TY, Nam SK, Chang S, Kim DH, Kim GN, Kong DJ, Park H, Ro SR, Son DC, Son T, Kim JY, Kim ZJ, Song S, Choi S, Gyun D, Hong B, Jo M, Kim H, Kim TJ, Lee KS, Moon DH, Park SK, Choi M, Kim JH, Park C, Park IC, Park S, Ryu G, Cho Y, Choi Y, Choi YK, Goh J, Kim MS, Kwon E, Lee B, Lee J, Lee S, Seo H, Yu I, Bilinskas MJ, Grigelionis I, Janulis M, Juodagalvis A, Castilla-Valdez H, De la Cruz-Burelo E, Heredia-de La Cruz I, Lopez-Fernandez R, Villalba RM, Martinez-Ortega J, Sanchez-Hernandez A, Villasenor-Cendejas LM, Moreno SC, Valencia FV, Ibarguen HAS, Linares EC, Pineda AM, Reyes-Santos MA, Krofcheck D, Bell AJ, Butler PH, Doesburg R, Reucroft S, Silverwood H, Ahmad M, Ansari MH, Asghar MI, Hoorani HR, Khalid S, Khan WA, Khurshid T, Qazi S, Shah MA, Shoaib M, Bialkowska H, Boimska B, Frueboes T, Gokieli R, Gorski M, Kazana M, Nawrocki K, Romanowska-Rybinska K, Szleper M, Wrochna G, Zalewski P, Brona G, Bunkowski K, Cwiok M, Dominik W, Doroba K, Kalinowski A, Konecki M, Krolikowski J, Almeida N, Bargassa P, David A, Faccioli P, Parracho PCF, Gallinaro M, Seixas J, Varela J, Vischia P, Belotelov I, Bunin P, Gavrilenko M, Golutvin I, Gorbunov I, Kamenev A, Karjavin V, Kozlov G, Laney A, Malakhov A, Moisenz P, Palichik V, Perelygin V, Shmatov S, Smirnov V, Volodko A, Zarubin A, Evstyukhin S, Golovtsov V, Ivanov Y, Kim V, Levchenko P, Murzin V, Oreshkin V, Smirnov I, 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Garcia-Abia P, Lopez OG, Lopez SG, Hernandez JM, Josa MI, Merino G, Pelayo JP, Olmeda AQ, Redondo I, Romero L, Santaolalla J, Soares MS, Willmott C, Albajar C, Codispoti G, de Troconiz JF, Brun H, Cuevas J, Menendez JF, Folgueras S, Caballero IG, Iglesias LL, Gomez JP, Cifuentes JAB, Cabrillo IJ, Calderon A, Chuang SH, Campderros JD, Felcini M, Fernandez M, Gomez G, Sanchez JG, Graziano A, Jorda C, Virto AL, Marco J, Marco R, Rivero CM, Matorras F, Sanchez FJM, Rodrigo T, Rodriguez-Marrero AY, Ruiz-Jimeno A, Scodellaro L, Vila I, Cortabitarte RV, Abbaneo D, Auffray E, Auzinger G, Bachtis M, Baillon P, Ball AH, Barney D, Benitez JF, Bernet C, Bianchi G, Bloch P, Bocci A, Bonato A, Botta C, Breuker H, Camporesi T, Cerminara G, Christiansen T, Perez JAC, D'Enterria D, Dabrowski A, De Roeck A, Di Guida S, Dobson M, Dupont-Sagorin N, Elliott-Peisert A, Frisch B, Funk W, Georgiou G, Giffels M, Gigi D, Gill K, Giordano D, Girone M, Giunta M, Glege F, Garrido RGR, Govoni P, Gowdy S, Guida R, 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Sakharov A, Anderson M, Belknap DA, Borrello L, Carlsmith D, Cepeda M, Dasu S, Friis E, Gray L, Grogg KS, Grothe M, Hall-Wilton R, Herndon M, Herve A, Klabbers P, Klukas J, Lanaro A, Lazaridis C, Leonard J, Loveless R, Mohapatra A, Ojalvo I, Palmonari F, Pierro GA, Ross I, Savin A, Smith WH, Swanson J
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Measurement of the t(t)over-bar production cross section in the all-jet final state in pp collisions at root s=7 TeV
JOURNAL OF HIGH ENERGY PHYSICS 2013 MAY; ?(5):?
A measurement is presented of the t (t) over bar production cross section (sigma(t (t) over bar)) in proton-proton collisions at a centre-of-mass energy of 7 TeV, in the all-jet final state that contains at least six jets, two of which are tagged as originating from b quarks. The data correspond to an integrated luminosity of 3.54 fb(-1), collected with the CMS detector at the LHC. The cross section is determined through an unbinned maximum likelihood fit of background and t (t) over bar signal to the reconstructed mass spectrum of t (t) over bar candidates in the data, in which events are subjected to a kinematic fit assuming a t (t) over bar -> W(+)bW(-)(b) over bar -> 6 jets hypothesis. The measurement yields sigma(t (t) over bar) = 139 +/- 10 (stat.) +/- 26 (syst.) +/- 3 (lum.) pb, a result consistent with those obtained in other t (t) over bar decay channels, as well as with predictions of the standard model.
Wu J, Anczukow O, Krainer AR, Zhang MQ, Zhang CL
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OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
NUCLEIC ACIDS RESEARCH 2013 MAY; 41(10):5149-5163
A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (similar to 14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with publish!
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A, Ojalvo I, Palmonari F, Pierro GA, Ross I, Savin A, Smith WH, Swanson J
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Search for long-lived particles in events with photons and missing energy in proton-proton collisions at root s=7 TeV
PHYSICS LETTERS B 2013 MAY 24; 722(4-5):273-294
Results are presented from a search for long-lived neutralinos decaying into a photon and an invisible particle, a signature associated with gauge-mediated supersymmetry breaking in supersymmetric models. The analysis is based on a 4.9 fb(-1) sample of proton-proton collisions at root s = 7 TeV, collected with the CMS detector at the LHC. The missing transverse energy and the time of arrival of the photon at the electromagnetic calorimeter are used to search for an excess of events over the expected background. No significant excess is observed, and lower limits at the 95% confidence level are obtained on the mass of the lightest neutralino, m > 220 GeV (for c tau < 500 mm), as well as on the proper decay length of the lightest neutralino, c tau > 6000 mm (for m < 150 GeV). (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
Steenrod SC, Phillips MH, Goldberg ME
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The lateral intraparietal area codes the location of saccade targets and not the dimension of the saccades that will be made to acquire them
JOURNAL OF NEUROPHYSIOLOGY 2013 MAY; 109(10):2596-2605
Activity in the lateral intraparietal area (LIP) represents a priority map that can be used to direct attention and guide eye movements. However, it is not known whether this activity represents the location of saccade targets or the actual eye movement made to acquire them. We recorded single neurons from rhesus macaques (Macaca mulatta) while they performed memory-guided delayed saccades to characterize the response profiles of LIP cells. We then separated the saccade target from the saccade end point by saccadic adaptation, a method that induces a change in the gain of the oculomotor system. We plotted LIP activity for all three epochs of the memory-guided delayed-response task (visual, delay period, and presaccadic responses) as a function of target location and saccade end point. We found that under saccadic adaptation the response profile for all three epochs was unchanged as a function of target location. We conclude that neurons in LIP reliably represent the locat!
Kosten TR, Domingo CB, Hamon SC, Nielsen DA
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DBH gene as predictor of response in a cocaine vaccine clinical trial
NEUROSCIENCE LETTERS 2013 APR 29; 541(?):29-33
We examined a pharmacogenetic association of the dopamine beta-hydroxylase (DBH) gene with a response to an anti-cocaine vaccine that was tested in a recent clinical trial. This gene is associated with cocaine-induced paranoia, which has a slower onset than the euphoria from cocaine. The vaccine reduced euphoria by slowing the entry of cocaine into the brain, but it may not reduce aversive symptoms like paranoia. A 16-week Phase IIb randomized double-blind placebo-controlled trial of 114 cocaine and opioid dependent subjects who received five vaccinations over the first 12 weeks was examined. We genotyped 71 subjects for the rs1611115 (-1021C>T) variant of the DBH gene and compared vaccine to placebo subjects on cocaine-free urines. Using repeated measures analysis of variance, corrected for population structure, vaccine pharmacotherapy reduced cocaine positive urines significantly based on DBH genotype. Patients with the low D beta H level genotype dropped from 77% to 51!
Cho-Park PF, Steller H
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Proteasome Regulation by ADP-Ribosylation
CELL 2013 APR 25; 153(3):614-627
Protein degradation by the ubiquitin-proteasome system is central to cell homeostasis and survival. Defects in this process are associated with diseases such as cancer and neurodegenerative disorders. The 26S proteasome is a large protease complex that degrades ubiquitinated proteins. Here, we show that ADP-ribosylation promotes 26S proteasome activity in both Drosophila and human cells. We identify the ADP-ribosyltransferase tankyrase (TNKS) and the 19S assembly chaperones dp27 and dS5b as direct binding partners of the proteasome regulator PI31. TNKS-mediated ADP-ribosylation of PI31 drastically reduces its affinity for 20S proteasome alpha subunits to relieve 20S repression by PI31. Additionally, PI31 modification increases binding to and sequestration of dp27 and dS5b from 19S regulatory particles, promoting 26S assembly. Inhibition of TNKS by either RNAi or a small-molecule inhibitor, XAV939, blocks this process to reduce 26S assembly. These results unravel a mechani!
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Search for new physics in final states with a lepton and missing transverse energy in pp collisions at the LHC
PHYSICAL REVIEW D 2013 APR 8; 87(7):? Article 072005
This Letter describes the search for an enhanced production rate of events with a charged lepton and a neutrino in high-energy pp collisions at the LHC. The analysis uses data collected with the CMS detector, with an integrated luminosity of 5.0 fb(-1) at root s = 7 TeV, and a further 3.7 fb(-1) at root s = 8 TeV. No evidence is found for an excess. The results are interpreted in terms of limits on a heavy charged gauge boson (W') in the sequential standard model, a split universal extra dimension model, and contact interactions in the helicity-nonconserving model. For the last, values of the binding energy below 10.5 (8.8) TeV in the electron (muon) channel are excluded at a 95% confidence level. Interpreting the l(nu) final state in terms of a heavy W' with standard model couplings, masses below 2.90 TeV are excluded. DOI: 10.1103/PhysRevD.87.072005