Browsing by Author "Zhang, Chi"

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    ItemOpen Access
    26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3
    (2017-08-18) Newton, Adam J H; Seidenstein, Alexandra H; McDougal, Robert A; Pérez-Cervera, Alberto; Huguet, Gemma; M-Seara, Tere; Haimerl, Caroline; Angulo-Garcia, David; Torcini, Alessandro; Cossart, Rosa; Malvache, Arnaud; Skiker, Kaoutar; Maouene, Mounir; Ragognetti, Gianmarco; Lorusso, Letizia; Viggiano, Andrea; Marcelli, Angelo; Senatore, Rosa; Parziale, Antonio; Stramaglia, S.; Pellicoro, M.; Angelini, L.; Amico, E.; Aerts, H.; Cortés, J.; Laureys, S.; Marinazzo, D.; Stramaglia, S.; Bassez, I.; Faes, L.; Almgren, Hannes; Razi, Adeel; Van de Steen, Frederik; Krebs, Ruth; Aerts, Hannelore; Kanari, Lida; Dlotko, Pawel; Scolamiero, Martina; Levi, Ran; Shillcock, Julian; de Kock, Christiaan P; Hess, Kathryn; Markram, Henry; Ly, Cheng; Marsat, Gary; Gillespie, Tom; Sandström, Malin; Abrams, Mathew; Grethe, Jeffrey S; Martone, Maryann; De Gernier, Robin; Solinas, Sergio; Rössert, Christian; Haelterman, Marc; Massar, Serge; Pasquale, Valentina; Pastore, Vito P; Martinoia, Sergio; Massobrio, Paolo; Capone, Cristiano; Tort-Colet, Núria; Sanchez-Vives, Maria V; Mattia, Maurizio; Almasi, Ali; Cloherty, Shaun L; Grayden, David B; Wong, Yan T; Ibbotson, Michael R; Meffin, Hamish; Prince, Luke Y; Tsaneva-Atanasova, Krasimira; Mellor, Jack R; Mazzoni, Alberto; Rosa, Manuela; Carpaneto, Jacopo; Romito, Luigi M; Priori, Alberto; Micera, Silvestro; Migliore, Rosanna; Lupascu, Carmen A; Franchina, Francesco; Bologna, Luca L; Romani, Armando; Saray, Sára; Van Geit, Werner; Káli, Szabolcs; Thomson, Alex; Mercer, Audrey; Lange, Sigrun; Falck, Joanne; Muller, Eilif; Schürmann, Felix; Todorov, Dmitrii; Capps, Robert; Barnett, William; Molkov, Yaroslav; Devalle, Federico; Pazó, Diego; Montbrió, Ernest; Mochol, Gabriela; Azab, Habiba; Hayden, Benjamin Y; Moreno-Bote, Rubén; Balasubramani, Pragathi P; Chakravarthy, Srinivasa V; Muddapu, Vignayanandam R; Gheorghiu, Medorian D; Mimica, Bartul; Withlock, Jonathan; Mureșan, Raul C; Zick, Jennifer L; Schultz, Kelsey; Blackman, Rachael K; Chafee, Matthew V; Netoff, Theoden I; Roberts, Nicholas; Nagaraj, Vivek; Lamperski, Andrew; Netoff, Theoden I; Grado, Logan L; Johnson, Matthew D; Darrow, David P; Lonardoni, Davide; Amin, Hayder; Di Marco, Stefano; Maccione, Alessandro; Berdondini, Luca; Nieus, Thierry; Stimberg, Marcel; Goodman, Dan F M; Nowotny, Thomas; Koren, Veronika; Dragoi, Valentin; Obermayer, Klaus; Castro, Samy; Fernandez, Mariano; El-Deredy, Wael; Xu, Kesheng; Maidana, Jean P; Orio, Patricio; Chen, Weiliang; Hepburn, Iain; Casalegno, Francesco; Devresse, Adrien; Ovcharenko, Aleksandr; Pereira, Fernando; Delalondre, Fabien; De Schutter, Erik; Bratby, Peter; Gallimore, Andrew R; Klingbeil, Guido; Zamora, Criseida; Zang, Yunliang; Crotty, Patrick; Palmerduca, Eric; Antonietti, Alberto; Casellato, Claudia; Erö, Csaba; D’Angelo, Egidio; Gewaltig, Marc-Oliver; Pedrocchi, Alessandra; Bytschok, Ilja; Dold, Dominik; Schemmel, Johannes; Meier, Karlheinz; Petrovici, Mihai A; Shen, Hui-An; Surace, Simone C; Pfister, Jean-Pascal; Lefebvre, Baptiste; Marre, Olivier; Yger, Pierre; Papoutsi, Athanasia; Park, Jiyoung; Ash, Ryan; Smirnakis, Stelios; Poirazi, Panayiota; Felix, Richard A; Dimitrov, Alexander G; Portfors, Christine; Daun, Silvia; Toth, Tibor I; Jędrzejewska-Szmek, Joanna; Kabbani, Nadine; Blackwel, Kim T; Moezzi, Bahar; Schaworonkow, Natalie; Plogmacher, Lukas; Goldsworthy, Mitchell R; Hordacre, Brenton; McDonnell, Mark D; Iannella, Nicolangelo; Ridding, Michael C; Triesch, Jochen; Maex, Reinoud; Safaryan, Karen; Steuber, Volker; Tang, Rongxiang; Tang, Yi-Yuan; Verveyko, Darya V; Brazhe, Alexey R; Verisokin, Andrey Y; Postnov, Dmitry E; Günay, Cengiz; Panuccio, Gabriella; Giugliano, Michele; Prinz, Astrid A; Varona, Pablo; Rabinovich, Mikhail I; Denham, Jack; Ranner, Thomas; Cohen, Netta; Reva, Maria; Rebola, Nelson; Kirizs, Tekla; Nusser, Zoltan; DiGregorio, David; Mavritsaki, Eirini; Rentzelas, Panos; Ukani, Nikul H; Tomkins, Adam; Yeh, Chung-Heng; Bruning, Wesley; Fenichel, Allison L; Zhou, Yiyin; Huang, Yu-Chi; Florescu, Dorian; Ortiz, Carlos L; Richmond, Paul; Lo, Chung-Chuan; Coca, Daniel; Chiang, Ann-Shyn; Lazar, Aurel A; Moezzi, Bahar; Creaser, Jennifer L; Lin, Congping; Ashwin, Peter; Brown, Jonathan T; Ridler, Thomas; Levenstein, Daniel; Watson, Brendon O; Buzsáki, György; Rinzel, John; Curtu, Rodica; Nguyen, Anh; Assadzadeh, Sahand; Robinson, Peter A; Sanz-Leon, Paula; Forlim, Caroline G; de Almeida, Lírio O B; Pinto, Reynaldo D; Rodríguez, Francisco B; Lareo, Ángel; Forlim, Caroline G; Rodríguez, Francisco B; Montero, Aaron; Mosqueiro, Thiago; Huerta, Ramon; Rodriguez, Francisco B; Changoluisa, Vinicio; Rodriguez, Francisco B; Cordeiro, Vinícius L; Ceballos, César C; Kamiji, Nilton L; Roque, Antonio C; Lytton, William W; Knox, Andrew; Rosenthal, Joshua J C; Daun, Silvia; Popovych, Svitlana; Liu, Liqing; Wang, Bin A; Tóth, Tibor I; Grefkes, Christian; Fink, Gereon R; Rosjat, Nils; Perez-Trujillo, Abraham; Espinal, Andres; Sotelo-Figueroa, Marco A; Cruz-Aceves, Ivan; Rostro-Gonzalez, Horacio; Zapotocky, Martin; Hoskovcová, Martina; Kopecká, Jana; Ulmanová, Olga; Růžička, Evžen; Gärtner, Matthias; Duvarci, Sevil; Roeper, Jochen; Schneider, Gaby; Albert, Stefan; Schmack, Katharina; Remme, Michiel; Schreiber, Susanne; Migliore, Michele; Lupascu, Carmen A; Bologna, Luca L; Antonel, Stefano M; Courcol, Jean-Denis; Schürmann, Felix; Çelikok, Sami U; Navarro-López, Eva M; Şengör, Neslihan S; Elibol, Rahmi; Sengor, Neslihan S; Özdemir, Mustafa Y; Li, Tianyi; Arleo, Angelo; Sheynikhovich, Denis; Nakamura, Akihiro; Shimono, Masanori; Song, Youngjo; Park, Sol; Choi, Ilhwan; Jeong, Jaeseung; Shin, Hee-sup; Sadeh, Sadra; Gleeson, Padraig; Angus Silver, R.; Chatzikalymniou, Alexandra P; Skinner, Frances K; Sanchez-Rodriguez, Lazaro M; Sotero, Roberto C; Hertäg, Loreen; Mackwood, Owen; Sprekeler, Henning; Puhlmann, Steffen; Weber, Simon N; Higgins, David; Naumann, Laura B; Weber, Simon N; Iyer, Ramakrisnan; Mihalas, Stefan; Ticcinelli, Valentina; Stankovski, Tomislav; McClintock, Peter V E; Stefanovska, Aneta; Janjić, Predrag; Solev, Dimitar; Seifert, Gerald; Kocarev, Ljupčo; Steinhäuser, Christian; Salmasi, Mehrdad; Glasauer, Stefan; Stemmler, Martin; Zhang, Danke; Zhang, Chi; Stepanyants, Armen; Goncharenko, Julia; Kros, Lieke; Davey, Neil; de Zeeuw, Chris; Hoebeek, Freek; Sinha, Ankur; Adams, Roderick; Schmuker, Michael; Psarrou, Maria; Schilstra, Maria; Torben-Nielsen, Benjamin; Metzner, Christoph; Schweikard, Achim; Mäki-Marttunen, Tuomo; Zurowski, Bartosz; Marinazzo, Daniele; Faes, Luca; Stramaglia, Sebastiano; Jordan, Henry O C; Stringer, Simon M; Gajewska-Dendek, Elżbieta; Suffczyński, Piotr; Tam, Nicoladie; Zouridakis, George; Pollonini, Luca; Tang, Yi-Yuan; Asl, Mojtaba M; Valizadeh, Alireza; Tass, Peter A; Nold, Andreas; Fan, Wei; Konrad, Sara; Endle, Heiko; Vogt, Johannes; Tchumatchenko, Tatjana; Herpich, Juliane; Tetzlaff, Christian; Luboeinski, Jannik; Nachstedt, Timo; Ciba, Manuel; Bahmer, Andreas; Thielemann, Christiane; Kuebler, Eric S; Tauskela, Joseph S; Thivierge, Jean-Philippe; Bakker, Rembrandt; García-Amado, María; Evangelio, Marian; Clascá, Francisco; Tiesinga, Paul; Buckley, Christopher L; Toyoizumi, Taro; Dubreuil, Alexis M; Monasson, Rémi; Treves, Alessandro; Spalla, Davide; Rosay, Sophie; Kleberg, Florence I; Wong, Willy; de Oliveira Floriano, Bruno; Matsuo, Toshihiko; Uchida, Tetsuya; Dibenedetto, Domenica; Uludağ, Kâmil; Goodarzinick, Abdorreza; Schmidt, Maximilian; Hilgetag, Claus C; Diesmann, Markus; van Albada, Sacha J; Fauth, Michael; van Rossum, Mark; Reyes-Sánchez, Manuel; Amaducci, Rodrigo; Muñiz, Carlos; Varona, Pablo; Elices, Irene; Arroyo, David; Levi, Rafael; Cohen, Ben; Chow, Carson; Vattikuti, Shashaank; Bertolotti, Elena; Burioni, Raffaella; di Volo, Matteo; Vezzani, Alessandro; Menzat, Bayar; Vogels, Tim P; Wagatsuma, Nobuhiko; Saha, Susmita; Kapoor, Reena; Kerr, Robert; Wagner, John; del Molino, Luis C G; Yang, Guangyu R; Mejias, Jorge F; Wang, Xiao-Jing; Song, Hanbing; Goodliffe, Joseph; Luebke, Jennifer; Weaver, Christina M; Thomas, John; Sinha, Nishant; Shaju, Nikhita; Maszczyk, Tomasz; Jin, Jing; Cash, Sydney S; Dauwels, Justin; Brandon Westover, M.; Karimian, Maryam; Moerel, Michelle; De Weerd, Peter; Burwick, Thomas; Westra, Ronald L; Abeysuriya, Romesh; Hadida, Jonathan; Sotiropoulos, Stamatios; Jbabdi, Saad; Woolrich, Mark; Bensmail, Chama; Wrobel, Borys; Zhou, Xiaolong; Ji, Zilong; Liu, Xiao; Xia, Yan; Wu, Si; Wang, Xiao; Zhang, Mingsha; Wu, Si; Ofer, Netanel; Shefi, Orit; Yaari, Gur; Carnevale, Ted; Majumdar, Amit; Sivagnanam, Subhashini; Yoshimoto, Kenneth; Smirnova, Elena Y; Amakhin, Dmitry V; Malkin, Sergey L; Zaitsev, Aleksey V; Chizhov, Anton V; Zaleshina, Margarita; Zaleshin, Alexander; Barranca, Victor J; Zhu, George; Skilling, Quinton M; Maruyama, Daniel; Ognjanovski, Nicolette; Aton, Sara J; Zochowski, Michal; Wu, Jiaxing; Aton, Sara; Rich, Scott; Booth, Victoria; Budak, Maral; Dura-Bernal, Salvador; Neymotin, Samuel A; Suter, Benjamin A; Shepherd, Gordon M G; Felton, Melvin A; Yu, Alfred B; Boothe, David L; Oie, Kelvin S; Franaszczuk, Piotr J; Shuvaev, Sergey A; Başerdem, Batuhan; Zador, Anthony; Koulakov, Alexei A; López-Madrona, Víctor J; Pereda, Ernesto; Mirasso, Claudio R; Canals, Santiago; Masoli, Stefano; Rongala, Udaya B; Mazzoni, Alberto; Spanne, Anton; Jorntell, Henrik; Oddo, Calogero M; Vartanov, Alexander V; Neklyudova, Anastasia K; Kozlovskiy, Stanislav A; Kiselnikov, Andrey A; Marakshina, Julia A; Teleńczuk, Maria; Teleńczuk, Bartosz; Destexhe, Alain; Kuokkanen, Paula T; Kraemer, Anna; McColgan, Thomas; Carr, Catherine E; Kempter, Richard
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    ItemOpen Access
    Identification and characterization of RNA target sequences of plant RNA-binding proteins
    (2016) Zhang, Chi; Muench, Douglas; Hansen, David; Samuel, Marcus; McGhee, James; von Arnim, Albrecht
    Eukaryotic cells express a variety of RNA-binding proteins that have important roles in post-transcriptional control of gene expression, including RNA maturation, transport, stability/decay and translation. Here, in vitro RNA target selection was used in an effort to identify the consensus RNA target sequences for members of two groups of plant RNA-binding proteins: the PUF family of RNA-binding proteins, and two peroxisomal matrix proteins that have previously been shown to bind to RNA. Plant genomes encode large families of PUF proteins and these show variability in their predicted Puf repeat number, organization, and amino acid sequence. RNA target identification using in vitro selection identified high confidence data for four Arabidopsis PUF (APUM) proteins. Three of these proteins bound to classical PUF RNA target sequences. However one, the nucleolar targeted APUM23, bound to a novel PUF RNA binding sequence. The APUM23 binding sequence is ten nucleotides in length, containing a centrally located UUGA core element, and a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, as all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5’ end and lack specificity for cytosine. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. The RNA in vitro selection results for the peroxisomal matrix proteins malate dehydrogenase (pMDH) and multifunctional protein (pMFP) demonstrated that pMDH (but not pMFP) possesses sequence-specific RNA binding activity. pMDH bound with high affinity to two RNA consensus sequences, one that consisted of a triple-repeat of a four nucleotide sequence, and the other sequence was a nine-nucleotide palindrome. This research provides insight into the novelty of plant RNA-binding proteins and their target RNA sequences, and sheds light on the role of these two classes of proteins in post-transcriptional control of gene expression. It reveals that APUM23 could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs. This work also builds upon existing evidence for authentic RNA binding activities for some metabolic enzymes.
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    ItemOpen Access
    In-situ Variable Temperature Ellipsometry of Nafion Thin Films
    (2016) Zhang, Chi; Karan, Kunal
    ABSTRACT This work presents the study of thermal behaviour in thin Nafion films. The experiments have been carried out with variable angle spectroscopic ellipsometry (VASE), atomic force microscopy (AFM), and goniometer. The results from this investigation focused on thin films between 10 and 700 nm thick on different substrates. The thermal behaviour of thin films was studied by analyzing the thermal expansion coefficients (α) and glass transition temperature (Tg). Moreover, the influence of different substrates on the thin films’ thermal behaviour was investigated. It was found that Nafion thin films did not show clear glass transition behaviour between 25 and 200°C. The α values of thin films showed clear deviation from that of Nafion membrane. Moreover, the thin films on hydrophilic substrates (Au and Pt). showed decrease in α compared to membrane, while intermediate substrates (SiO2, graphene) showed increase. There is a strong correlation between water contact angle and α values.