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Contents lists available at ScienceDirect
Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi
Volume 189, Issue 3, March 2015 CONTENTS Announcements Peter Fratzl.
Paper of the Year Award . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nikolaus Grigorieff.
159
Paper of the Year Award . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
161
Vahid Abrishami, Javier Vargas, Xueming Li, Yifan Cheng, Roberto Marabini, Carlos Óscar Sánchez Sorzano, José María Carazo. Alignment of direct detection device micrographs using a robust Optical Flow approach . . . . . . . . . . . . . . . . . .
163
Jan Kosinski, Alexander von Appen, Alessandro Ori, Kai Karius, Christoph W. Müller, Martin Beck. Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
177
Nidhi Sharma, Purushotham Selvakumar, Sumit Bhose, Dilip Kumar Ghosh, Pravindra Kumar, Ashwani Kumar Sharma. Crystal structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
184
ˇ ová, Lukas Marsalek, Tomáš Davidovicˇ, Philipp Slusallek. Progressive Stochastic Reconstruction Technique (PSRT) for Beata Turon cryo electron tomography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
195
Zahra El-Schich, Anna Mölder, Helena Tassidis, Pirkko Härkönen, Maria Falck Miniotis, Anette Gjörloff Wingren. Induction of morphological changes in death-induced cancer cells monitored by holographic microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
207
C.O.S. Sorzano, J. Vargas, J.M. de la Rosa-Trevín, J. Otón, A.L. Álvarez-Cabrera, V. Abrishami, E. Sesmero, R. Marabini, J.M. Carazo. A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy . . . . . . . . . . . . . . . . . . . . . . . . .
213
Lidia Delgado, Gema Martínez, Carmen López-Iglesias, Elena Mercadé. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
220
Regular Articles
Continued
Front Cover: Reconstruction scheme of E. Coli 70S ribosome using the Progressive Stochastic Reconstruction Technique (PSRT). The ribosome is gradually reconstructed by placing samples into the reconstructed area in a stochastic manner. The size of the samples is decreased during the process to obtain fine details and there by high-resolution structure.
For a full and complete Guide for Authors, please go to: http://www.elsevier.com/locate/yjsbi Abstracted/indexed in Biological Abstracts, Chemical Abstracts, Current Contents/Life Sciences, EMBASE, EMBiology, Excerpta Medica, MEDLINE® Research Alert, SCISEARCH, Science Citation Index. Also covered in the citation database Scopus®. Full text available on ScienceDirect®
Vera Bin San Chan, Olev Vinn, Chaoyi Li, Xingwen Lu, Anatoliy B. Kudryavtsev, J. William Schopf, Kaimin Shih, Tong Zhang, Vengatesen Thiyagarajan. Evidence of compositional and ultrastructural shifts during the development of calcareous tubes in the biofouling tubeworm, Hydroides elegans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
230
M. Bangera, R. Panigrahi, S.R. Sagurthi, H.S. Savithri, M.R.N. Murthy. Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
238
Andrew D. Hirsh, N.C. Perkins.
DNA buckling in bacteriophage cavities as a mechanism to aid virus assembly . . . . . . . . . . . . . . . . . . . . . .
251
Rong Chen, Jianxun Qi, Hongyu Yuan, Yanan Wu, Wei Hu, Chun Xia. Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
259
Admir Masic, James C. Weaver.
269
Large area sub-micron chemical imaging of magnesium in sea urchin teeth . . . . . . . . . . . . . . . . . . . . . . . .
Structure Report Yangshin Park, Inchul Shin, Sangkee Rhee.
Crystal structure of the effector protein HopA1 from Pseudomonas syringae . . . . . . . . . . . .
276
Robert Langlois, Joachim Frank. Corrigendum to ‘‘A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM’’ [J. Struct. Biol. 175 (2011) 348–352] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
281
Corrigendum
Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi
Volume 189, Issue 3, March 2015 CONTENTS Announcements Peter Fratzl.
Paper of the Year Award . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nikolaus Grigorieff.
159
Paper of the Year Award . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
161
Vahid Abrishami, Javier Vargas, Xueming Li, Yifan Cheng, Roberto Marabini, Carlos Óscar Sánchez Sorzano, José María Carazo. Alignment of direct detection device micrographs using a robust Optical Flow approach . . . . . . . . . . . . . . . . . .
163
Jan Kosinski, Alexander von Appen, Alessandro Ori, Kai Karius, Christoph W. Müller, Martin Beck. Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
177
Nidhi Sharma, Purushotham Selvakumar, Sumit Bhose, Dilip Kumar Ghosh, Pravindra Kumar, Ashwani Kumar Sharma. Crystal structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
184
ˇ ová, Lukas Marsalek, Tomáš Davidovicˇ, Philipp Slusallek. Progressive Stochastic Reconstruction Technique (PSRT) for Beata Turon cryo electron tomography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
195
Zahra El-Schich, Anna Mölder, Helena Tassidis, Pirkko Härkönen, Maria Falck Miniotis, Anette Gjörloff Wingren. Induction of morphological changes in death-induced cancer cells monitored by holographic microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
207
C.O.S. Sorzano, J. Vargas, J.M. de la Rosa-Trevín, J. Otón, A.L. Álvarez-Cabrera, V. Abrishami, E. Sesmero, R. Marabini, J.M. Carazo. A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy . . . . . . . . . . . . . . . . . . . . . . . . .
213
Lidia Delgado, Gema Martínez, Carmen López-Iglesias, Elena Mercadé. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
220
Regular Articles
Continued
Front Cover: Reconstruction scheme of E. Coli 70S ribosome using the Progressive Stochastic Reconstruction Technique (PSRT). The ribosome is gradually reconstructed by placing samples into the reconstructed area in a stochastic manner. The size of the samples is decreased during the process to obtain fine details and there by high-resolution structure.
For a full and complete Guide for Authors, please go to: http://www.elsevier.com/locate/yjsbi Abstracted/indexed in Biological Abstracts, Chemical Abstracts, Current Contents/Life Sciences, EMBASE, EMBiology, Excerpta Medica, MEDLINE® Research Alert, SCISEARCH, Science Citation Index. Also covered in the citation database Scopus®. Full text available on ScienceDirect®
Vera Bin San Chan, Olev Vinn, Chaoyi Li, Xingwen Lu, Anatoliy B. Kudryavtsev, J. William Schopf, Kaimin Shih, Tong Zhang, Vengatesen Thiyagarajan. Evidence of compositional and ultrastructural shifts during the development of calcareous tubes in the biofouling tubeworm, Hydroides elegans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
230
M. Bangera, R. Panigrahi, S.R. Sagurthi, H.S. Savithri, M.R.N. Murthy. Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
238
Andrew D. Hirsh, N.C. Perkins.
DNA buckling in bacteriophage cavities as a mechanism to aid virus assembly . . . . . . . . . . . . . . . . . . . . . .
251
Rong Chen, Jianxun Qi, Hongyu Yuan, Yanan Wu, Wei Hu, Chun Xia. Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
259
Admir Masic, James C. Weaver.
269
Large area sub-micron chemical imaging of magnesium in sea urchin teeth . . . . . . . . . . . . . . . . . . . . . . . .
Structure Report Yangshin Park, Inchul Shin, Sangkee Rhee.
Crystal structure of the effector protein HopA1 from Pseudomonas syringae . . . . . . . . . . . .
276
Robert Langlois, Joachim Frank. Corrigendum to ‘‘A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM’’ [J. Struct. Biol. 175 (2011) 348–352] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
281
Corrigendum