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Research at the interface between chemistry and the -omic sciences and systems biology.
Contents list for Molecular BioSystems, issue 6, 2013
Cover
Front cover
Mol. BioSyst., 2013, 9, 1047
DOI: 10.1039/C3MB90014B
Inside front cover
Mol. BioSyst., 2013, 9, 1048
DOI: 10.1039/C3MB90015K
Front/Back Matter
Contents list
Mol. BioSyst., 2013, 9, 1049
DOI: 10.1039/C3MB90017G
Editorial
Digital and analogical reality in proteomics investigation
Andrea Urbani, Massimo Castagnola, Mauro Fasano, Luca Bini, Alessandra Modesti, Anna Maria Timperio and Paola Roncada,
Mol. BioSyst., 2013, 9, 1062
DOI: 10.1039/c3mb90013d
Opinion
Genotype–phenotype relationships in light of a modular protein interaction landscape
Matthias Gstaiger and Ruedi Aebersold,
Mol. BioSyst., 2013, 9, 1064
DOI: 10.1039/c3mb25583b
Review Articles
Essential genes in Bacillus subtilis: a re-evaluation after ten years
Fabian M. Commichau, Nico Pietack and Jörg Stülke,
Mol. BioSyst., 2013, 9, 1068
DOI: 10.1039/c3mb25595f
Application of proteomics technology in adipocyte biology
Johan Renes and Edwin Mariman,
Mol. BioSyst., 2013, 9, 1076
DOI: 10.1039/c3mb25596d
Some remarks on predicting multi-label attributes in molecular biosystems
Kuo-Chen Chou,
Mol. BioSyst., 2013, 9, 1092
DOI: 10.1039/c3mb25555g
Method
Detection of high molecular weight proteins by MALDI imaging mass spectrometry
Veronica Mainini, Giorgio Bovo, Clizia Chinello, Erica Gianazza, Marco Grasso, Giorgio Cattoretti and Fulvio Magni,
Mol. BioSyst., 2013, 9, 1101
DOI: 10.1039/c2mb25296a
Papers
Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary open angle glaucoma naďve to therapy
Damiana Pieragostino, Luca Agnifili, Vincenzo Fasanella, Simona D'Aguanno, Rodolfo Mastropasqua, Carmine Di Ilio, Paolo Sacchetta, Andrea Urbani and Piero Del Boccio,
Mol. BioSyst., 2013, 9, 1108
DOI: 10.1039/c3mb25463a
Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells
Domenico Ciavardelli, Melania D'Orazio, Luisa Pieroni, Ada Consalvo, Claudia Rossi, Paolo Sacchetta, Carmine Di Ilio, Andrea Battistoni and Andrea Urbani,
Mol. BioSyst., 2013, 9, 1117
DOI: 10.1039/c3mb25594h
Comparative proteome profiling of breast tumor cell lines by gel electrophoresis and mass spectrometry reveals an epithelial mesenchymal transition associated protein signature
Daniele Vergara, Pasquale Simeone, Piero del Boccio, Claudia Toto, Damiana Pieragostino, Andrea Tinelli, Raffaele Acierno, Saverio Alberti, Michel Salzet, Gianluigi Giannelli, Paolo Sacchetta and Michele Maffia,
Mol. BioSyst., 2013, 9, 1127
DOI: 10.1039/c2mb25401h
Urinary exosomes and diabetic nephropathy: a proteomic approach
F. Raimondo, S. Corbetta, L. Morosi, C. Chinello, E. Gianazza, G. Castoldi, C. Di Gioia, C. Bombardi, A. Stella, C. Battaglia, C. Bianchi, F. Magni and M. Pitto,
Mol. BioSyst., 2013, 9, 1139
DOI: 10.1039/c2mb25396h
Effect of IR laser on myoblasts: a proteomic study
Monica Monici, Francesca Cialdai, Francesco Ranaldi, Paolo Paoli, Francesca Boscaro, Gloriano Moneti and Anna Caselli,
Mol. BioSyst., 2013, 9, 1147
DOI: 10.1039/c2mb25398d
Alteration of proteomic profiles in PBMC isolated from patients with Fabry disease: preliminary findings
Diego Cigna, Claudia D'Anna, Carmela Zizzo, Daniele Francofonte, Iacopo Sorrentino, Paolo Colomba, Giuseppe Albeggiani, Alessandro Armini, Laura Bianchi, Luca Bini and Giovanni Duro,
Mol. BioSyst., 2013, 9, 1162
DOI: 10.1039/c3mb25402j
Crosstalk between salicylic acid and jasmonate in Arabidopsis investigated by an integrated proteomic and transcriptomic approach
Silvia Proietti, Laura Bertini, Anna Maria Timperio, Lello Zolla, Carlo Caporale and Carla Caruso,
Mol. BioSyst., 2013, 9, 1169
DOI: 10.1039/c3mb25569g
Unravelling the bull fertility proteome
Alessio Soggiu, Cristian Piras, Hany Ahmed Hussein, Michele De Canio, Alessandro Gaviraghi, Andrea Galli, Andrea Urbani, Luigi Bonizzi and Paola Roncada,
Mol. BioSyst., 2013, 9, 1188
DOI: 10.1039/c3mb25494a
Red blood cell metabolism under prolonged anaerobic storage
Angelo D'Alessandro, Federica Gevi and Lello Zolla,
Mol. BioSyst., 2013, 9, 1196
DOI: 10.1039/c3mb25575a
Postnatal cardiomyocyte growth and mitochondrial reorganization cause multiple changes in the proteome of human cardiomyocytes
Jaakko L. O. Pohjoismäki, Marcus Krüger, Natalie Al-Furoukh, Anssi Lagerstedt, Pekka J. Karhunen and Thomas Braun,
Mol. BioSyst., 2013, 9, 1210
DOI: 10.1039/c3mb25556e
Differential protein profiling of renal cell carcinoma urinary exosomes
F. Raimondo, L. Morosi, S. Corbetta, C. Chinello, P. Brambilla, P. Della Mina, A. Villa, G. Albo, C. Battaglia, S. Bosari, F. Magni and M. Pitto,
Mol. BioSyst., 2013, 9, 1220
DOI: 10.1039/c3mb25582d
Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins
Elisa Dell'Aglio, Cécile Giustini, Daniel Salvi, Sabine Brugičre, Faustine Delpierre, Lucas Moyet, Mathieu Baudet, Daphné Seigneurin-Berny, Michel Matringe, Myriam Ferro, Norbert Rolland and Gilles Curien,
Mol. BioSyst., 2013, 9, 1234
DOI: 10.1039/c3mb00004d
Integrative quantitation enables a comprehensive proteome comparison of two Mycoplasma pneumoniae genetic perturbations
Eva Borrŕs, Guadalupe Espadas, Francesco M. Mancuso, Tobias Maier, Cristina Chiva and Eduard Sabidó,
Mol. BioSyst., 2013, 9, 1249
DOI: 10.1039/c3mb25581f
Proteomic analysis of temperature stress-responsive proteins in Arabidopsis thaliana rosette leaves
Mariapina Rocco, Simona Arena, Giovanni Renzone, Gabriella Stefania Scippa, Tonia Lomaglio, Francesca Verrillo, Andrea Scaloni and Mauro Marra,
Mol. BioSyst., 2013, 9, 1257
DOI: 10.1039/c3mb70137a
Review Articles
Network-based drug repositioning
Zikai Wu, Yong Wang and Luonan Chen,
Mol. BioSyst., 2013, 9, 1268
DOI: 10.1039/c3mb25382a
Communications
A controllable gene expression system in liposomes that includes a positive feedback loop
Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta and Tetsuya Yomo,
Mol. BioSyst., 2013, 9, 1282
DOI: 10.1039/c3mb70032a
Identification and characterization of the actinomycin G gene cluster in Streptomyces iakyrus
Xiaoling Wang, Jioji Tabudravu, Mostafa Ezzat Rateb, Krystal Joan Annand, Zhiwei Qin, Marcel Jaspars, Zixin Deng, Yi Yu and Hai Deng,
Mol. BioSyst., 2013, 9, 1286
DOI: 10.1039/c3mb70081j
Papers
JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology
Mary Ann Blätke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred Schaper and Wolfgang Marwan,
Mol. BioSyst., 2013, 9, 1290
DOI: 10.1039/c3mb25593j
Homology modeling of dihydrofolate reductase from T. gondii bonded to antagonists: molecular docking and molecular dynamics simulations
Débora Pacheco Homem, Rogério Flores Jr. , Priscilla Tosqui, Thiago de Castro Rozada, Ernani Abicht Basso, Arquimedes Gasparotto Junior and Flavio Augusto Vicente Seixas,
Mol. BioSyst., 2013, 9, 1308
DOI: 10.1039/c3mb25530a
Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)
Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Li, Jie Shen, Philip W. Lee and Yun Tang,
Mol. BioSyst., 2013, 9, 1316
DOI: 10.1039/c3mb25309k
A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation
Marcel Mischnik, Desislava Boyanova, Katharina Hubertus, Jörg Geiger, Nicole Philippi, Marcus Dittrich, Gaby Wangorsch, Jens Timmer and Thomas Dandekar,
Mol. BioSyst., 2013, 9, 1326
DOI: 10.1039/c3mb25597b
Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins
Moitrayee Bhattacharyya, Kallol Gupta, Konkallu Hanumae Gowd and Padmanabhan Balaram,
Mol. BioSyst., 2013, 9, 1340
DOI: 10.1039/c3mb25534d
Large-scale investigation of oxygen response mutants in Saccharomyces cerevisiae
Bahram Samanfar, Katayoun Omidi, Mohsen Hooshyar, Ben Laliberte, MD Alamgir, Andrew J. Seal, Eman Ahmed-Muhsin, Duber Frey Viteri, Kamaleldin Said, Firoozeh Chalabian, Ardeshir Golshani, Gabriel Wainer, Daniel Burnside, Kristina Shostak, Magdalena Bugno, William G. Willmore, Myron L. Smith and Ashkan Golshani,
Mol. BioSyst., 2013, 9, 1351
DOI: 10.1039/c3mb25516f
Topological patterns in microRNA–gene regulatory network: studies in colorectal and breast cancer
Debarka Sengupta and Sanghamitra Bandyopadhyay,
Mol. BioSyst., 2013, 9, 1360
DOI: 10.1039/c3mb25518b
Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry
Shao-Min Huang, Fengguo Xu, Siew Hong Lam, Zhiyuan Gong and Choon Nam Ong,
Mol. BioSyst., 2013, 9, 1372
DOI: 10.1039/c3mb25450j
A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels
Ning Yin, Jianfeng Pei and Luhua Lai,
Mol. BioSyst., 2013, 9, 1381
DOI: 10.1039/c3mb25471b
Secretome analysis of Glioblastoma cell line - HNGC-2
Manoj Kumar Gupta, Ravindra Varma Polisetty, Kalidoss Ramamoorthy, Shivani Tiwary, Navjot Kaur, Megha S. Uppin, Anjali Shiras and Ravi Sirdeshmukh,
Mol. BioSyst., 2013, 9, 1390
DOI: 10.1039/c3mb25383j
Solution conformational features and interfacial properties of an intrinsically disordered peptide coupled to alkyl chains: a new class of peptide amphiphiles
Antonella Accardo, Marilisa Leone, Diego Tesauro, Rosa Aufiero, Anaďs Bénarouche, Jean-François Cavalier, Sonia Longhi, Frederic Carriere and Filomena Rossi,
Mol. BioSyst., 2013, 9, 1401
DOI: 10.1039/c3mb25507g
Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; a human metabolomic profile approach
Úrsula Catalán, Miguel-Ángel Rodríguez, Maria-Rosa Ras, Alba Maciá, Roger Mallol, Maria Vinaixa, Sara Fernández-Castillejo, Rosa-Maria Valls, Anna Pedret, Julian L Griffin, Reza Salek, Xavier Correig, Ma José Motilva and Rosa Solŕ,
Mol. BioSyst., 2013, 9, 1411
DOI: 10.1039/c3mb25554a
Metabolomic investigation of Arthus reaction in a rat model using proton nuclear magnetic resonance (1H NMR) spectroscopy and rapid resolution liquid chromatography (RRLC)
Xiaoli Zhang, Jianmin Shen, Bei Cao, Luan Xu, Tong Zhao, Xiaoyan Liu and Haixia Zhang,
Mol. BioSyst., 2013, 9, 1423
DOI: 10.1039/c3mb25412g
Delay-managed tradeoff in the molecular dynamics of the segmentation clock
Henglin Song, Zhanjiang Yuan and Tianshou Zhou,
Mol. BioSyst., 2013, 9, 1436
DOI: 10.1039/c3mb70046a
Computationally identifying virulence factors based on KEGG pathways
Weiren Cui, Lei Chen, Tao Huang, Qian Gao, Min Jiang, Ning Zhang, Lulu Zheng, Kaiyan Feng, Yudong Cai and Hongwei Wang,
Mol. BioSyst., 2013, 9, 1447
DOI: 10.1039/c3mb70024k
The pleiotropic effect of WD-40 domain containing proteins on cellular differentiation and production of secondary metabolites in Streptomyces coelicolor
Ale
Ulrych, Jana Goldová, Miroslav Pet
í
ek, Oldich Benada, Olga Kofro
ová, Petra Rampírová, Kateina Petíková and Pavel Branny,
Mol. BioSyst., 2013, 9, 1453
DOI: 10.1039/c3mb25542e
Molecular dynamic simulations of the tubulin–human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol
Manivel Panneerselvam, Kannan Muthu, Muthukumaran Jayaraman, Upasana Sridharan, Pranitha Jenardhanan and Krishna Ramadas,
Mol. BioSyst., 2013, 9, 1470
DOI: 10.1039/c3mb25427e
Gossypol induces apoptosis in ovarian cancer cells through oxidative stress
Jia Wang, Lixu Jin, Xiaoyu Li, Haiyun Deng, Yuling Chen, Qingquan Lian, Renshan Ge and Haiteng Deng,
Mol. BioSyst., 2013, 9, 1489
DOI: 10.1039/c3mb25461e
A proteomics approach to study the molecular basis of enhanced salt tolerance in barley (Hordeum vulgare L.) conferred by the root mutualistic fungus Piriformospora indica
Mehdi Alikhani, Behnam Khatabi, Mozhgan Sepehri, Mojtaba Khayam Nekouei, Mohsen Mardi and Ghasem Hosseini Salekdeh,
Mol. BioSyst., 2013, 9, 1498
DOI: 10.1039/c3mb70069k
Discovery of Rho-kinase inhibitors by docking-based virtual screening
Mingyun Shen, Huidong Yu, Youyong Li, Pixu Li, Peichen Pan, Shunye Zhou, Liling Zhang, Shang Li, Simon Ming-Yuen Lee and Tingjun Hou,
Mol. BioSyst., 2013, 9, 1511
DOI: 10.1039/c3mb00016h
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes
Young-Mo Kim, Brian J. Schmidt, Afshan S. Kidwai, Marcus B. Jones, Brooke L. Deatherage Kaiser, Heather M. Brewer, Hugh D. Mitchell, Bernhard O. Palsson, Jason E. McDermott, Fred Heffron, Richard D. Smith, Scott N. Peterson, Charles Ansong, Daniel R. Hyduke, Thomas O. Metz and Joshua N. Adkins,
Mol. BioSyst., 2013, 9, 1522
DOI: 10.1039/c3mb25598k
Selective binding of 2
-F-c-di-GMP to Ct-E88 and Cb-E43, new class I riboswitches from Clostridium tetani and Clostridium botulinum respectively
Yiling Luo, Jie Zhou, Jingxin Wang, T. Kwaku Dayie and Herman O. Sintim,
Mol. BioSyst., 2013, 9, 1535
DOI: 10.1039/c3mb25560c
Cover
Back cover
Mol. BioSyst., 2013, 9, 1541
DOI: 10.1039/C3MB90016A
