Nature Biotechnology Contents: Volume 29 pp 1055 - 1150

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TALENs® are next generation genome customization tools to knock-out genes or introduce modifications in any gene, at any position, in any genome. Recommend to your library Web feed Available online only Subscribe Advertisement $3 million available now for innovative research funding -Development of therapeutics that target specific B cell lineages involved in MS pathology -Identification of surrogate or endogenous ligands for Orphan G Protein-Coupled Receptors (GPCRs) expressed exclusively or primarily in the central nervous system (CNS) that relate to the pathology of MS Submit Proposals TODAY: www.fastforward.org   Advertisement BioPharma Dealmakers Science, strategy & innovation Recent content exclusively made freely available to you from Nature Biotechnology, Nature Reviews Drug Discovery and Nature Medicine Produced with support from TVG Sign up to receive this new bi-weekly newsletter today.   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Miami 2012 Winter Symposium: Nanotechnology in Biomedicine February 26-29, 2012 • Miami, FL, USA The 45th Miami Winter Symposium will bring together leaders in the field to discuss breakthroughs in new nanomaterials and the challenges in translating these materials into products for the clinic and laboratory. For more information and to register, visit: www.nature.com/natureconferences/miami/ Abstract Submission Deadline EXTENDED to November 30, 2011   In This Issue Top In this issue ppvii - viii doi:10.1038/nbt.2068 Full Text | PDF Editorial Top Tilting toward secrecy p1055 doi:10.1038/nbt.2075 A European high court ruling on the patentability of inventions related to human embryonic stem cells could promote secrecy and reduce access to data and cell lines. Full Text | PDF News Top European court bans embryonic stem cell patents pp1057 - 1059 Nuala Moran doi:10.1038/nbt1211-1057 Full Text | PDF Conflicts of interest go online p1058 Gunjan Sinha doi:10.1038/nbt1211-1058 Full Text | PDF Shutdown by auction p1060 Brian Orelli doi:10.1038/nbt1211-1060a Full Text | PDF GlaxoSmithKline malaria vaccine phase 3 trial heralded pp1060 - 1062 Simon Franz doi:10.1038/nbt1211-1060b Full Text | PDF Interest groups jostle to influence PDUFA V p1062 Jeffrey L Fox doi:10.1038/nbt1211-1062 Full Text | PDF Cold-tolerant trees win p1063 Emily Walt doi:10.1038/nbt1211-1063b Full Text | PDF Industry continues dabbling with open innovation models pp1063 - 1065 Cormac Sheridan doi:10.1038/nbt1211-1063a Full Text | PDF Around the world in a month p1065 doi:10.1038/nbt1211-1065 Full Text | PDF Jackson's $1.1 billion makeover p1066 Jennifer Rohn doi:10.1038/nbt1211-1066a Full Text | PDF Near-record drug approvals p1066 Jeffrey L. Fox doi:10.1038/nbt1211-1066b Full Text | PDF New startup models emerge as investor landscape shifts pp1066 - 1067 Brady Huggett doi:10.1038/nbt1211-1066c Full Text | PDF Newsmaker: Zafgen p1068 Jennifer Rohn doi:10.1038/nbt1211-1068 Zafgen hopes that small-molecule targeting of methionine aminopeptidase 2 (MetAP2), an enzyme originally associated with tumor angiogenesis, will lead to a new anti-obesity drug. Full Text | PDF Bioentrepreneur Top Shape shifting pp1069 - 1071 Bob Baltera doi:10.1038/bioe.2011.10 Correspondence Top Generation of the potent anti-malarial drug artemisinin in tobacco pp1072 - 1074 Moran Farhi, Elena Marhevka, Julius Ben-Ari, Anna Algamas-Dimantov, Zhuobin Liang, Vardit Zeevi, Orit Edelbaum, Ben Spitzer-Rimon, Hagai Abeliovich, Betty Schwartz, Tzvi Tzfira and Alexander Vainstein doi:10.1038/nbt.2054 Full Text | PDF Relative potential of biosynthetic pathways for biofuels and bio-based products pp1074 - 1078 Deepak Dugar and Gregory Stephanopoulos doi:10.1038/nbt.2055 Full Text | PDF Re-evaluating PARP1 inhibitor in cancer pp1078 - 1079 Alexei Tulin doi:10.1038/nbt.2058 Full Text | PDF Access to human embryonic stem cell lines pp1079 - 1081 Aaron D Levine doi:10.1038/nbt.2029 Full Text | PDF Sarbanes-Oxley overburdens biotech companies pp1081 - 1082 Mark Kessel doi:10.1038/nbt.2059 Full Text | PDF Features Top What's fueling the biotech engine[mdash]2010 to 2011 pp1083 - 1089 Saurabh Aggarwal doi:10.1038/nbt.2060 In the past year, biologics sector sales grew by single digits, driven by monoclonal antibodies and insulin products. New product launches are showing mixed results and are facing rising challenges from changes to reimbursement policies. Full Text | PDF Patents Agricultural microbial resources: private property or global commons? pp1091 - 1093 David Kothamasi, Matthew Spurlock and E Toby Kiers doi:10.1038/nbt.2056 Agricultural microbes have become an attractive target for patenting, but the lack of a consistent global patent regime and increasingly heated debates over microbial ownership rights are barriers to the development of this resource. Full Text | PDF Recent patent applications related to agricultural microbes p1094 doi:10.1038/nbt.2066 Full Text | PDF News and Views Top Dissecting cancer heterogeneity pp1095 - 1096 David Dornan and Jeff Settleman doi:10.1038/nbt.2063 Transcriptional profiling of single cells in colon tumors may enable prediction of patient outcomes. Full Text | PDF See also: Research by Dalerba et al. Genomic rearrangement in three dimensions pp1096 - 1098 PJ Hastings and Susan M Rosenberg doi:10.1038/nbt.2064 Two studies illuminate why genome rearrangements in cancer cells occur where they do. Full Text | PDF See also: Computational Biology by De & Michor | Computational Biology by Fudenberg et al. The new landscape of protein ubiquitination pp1098 - 1100 Guoqiang Xu and Samie R Jaffrey doi:10.1038/nbt.2061 Proteome-wide identification of ubiquitination events reveals their functional classes and identifies substrates for ubiquitin ligases. Full Text | PDF Research Highlights Top Two antibodies for the price of one | Multigenome analysis of variation | Ribosomes reveal proteome complexity | Sifting proteins for proteomics | New role for VEGF Computational Biology Top Analysis DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes pp1103 - 1108 Subhajyoti De and Franziska Michor doi:10.1038/nbt.2030 Copy-number changes in cancer genomes may be caused by errors during the replication of colocalized DNA regions. De and Michor provide genome-wide evidence for this model by integrating data on DNA replication timing, the three-dimensional organization of the genome and copy-number alterations in cancer. Abstract | Full Text | PDF See also: News and Views by Hastings & Rosenberg High order chromatin architecture shapes the landscape of chromosomal alterations in cancer pp1109 - 1113 Geoff Fudenberg, Gad Getz, Matthew Meyerson and Leonid A Mirny doi:10.1038/nbt.2049 Copy-number changes, point mutations and rearrangements are all usually found in cancer genomes, but their relative frequencies are highly variable. Using statistical approaches to model different processes, Fudenberg et al. find that copy number gain and loss is influenced by the three-dimensional organization of the genome in the nucleus. Abstract | Full Text | PDF See also: News and Views by Hastings & Rosenberg Research Top Brief Communications In silico feedback for in vivo regulation of a gene expression circuit pp1114 - 1116 Andreas Milias-Argeitis, Sean Summers, Jacob Stewart-Ornstein, Ignacio Zuleta, David Pincus, Hana El-Samad, Mustafa Khammash and John Lygeros doi:10.1038/nbt.2018 Creating synthetic biological circuits can be maddeningly difficult because of unpredictable stimuli and unknown variability in the system. Milias-Argeitis et al. circumvent these problems by moving control functions outside the cell[mdash]to a computer[mdash]and connecting computer and cell through optogenetics. Abstract | Full Text | PDF Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells pp1117 - 1119 Kitai Kim, Rui Zhao, Akiko Doi, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, Martin J Aryee, M William Lensch, Hu Li, James J Collins, Andrew P Feinberg and George Q Daley doi:10.1038/nbt.2052 Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al. study this question in human cells and document both incomplete erasure of methylation and aberrant de novo methylation during reprogramming. Abstract | Full Text | PDF Article Single-cell dissection of transcriptional heterogeneity in human colon tumors pp1120 - 1127 Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Pradeep S Rajendran, Michael E Rothenberg, Anne A Leyrat, Sopheak Sim, Jennifer Okamoto, Darius M Johnston, Dalong Qian, Maider Zabala, Janet Bueno, Norma F Neff, Jianbin Wang, Andrew A Shelton, Brendan Visser, Shigeo Hisamori, Yohei Shimono, Marc van de Wetering, Hans Clevers, Michael F Clarke and Stephen R Quake doi:10.1038/nbt.2038 Not all cells in a tumor are alike, but our ability to characterize cancer heterogeneity in detail has been limited. Dalerba et al. use high-throughput single-cell expression analysis to define clinically relevant subpopulations in normal and cancerous colon tissue. Abstract | Full Text | PDF See also: News and Views by Dornan & Settleman Letter Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance pp1128 - 1131 Bruce E Tabashnik, Fangneng Huang, Mukti N Ghimire, B Rogers Leonard, Blair D Siegfried, Murugesan Rangasamy, Yajun Yang, Yidong Wu, Linda J Gahan, David G Heckel, Alejandra Bravo and Mario Soberon doi:10.1038/nbt.1988 The benefits of crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are threatened by the emergence of insect resistance. Working with five major crop pests, Tabashnik et al. show that previously described variant Bt toxins kill pests rendered resistant to native Bt toxins by multiple mechanisms. First paragraph | Full Text | PDF Resources Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage pp1132 - 1144 Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil, Nissim Benvenisty, Dalit Ben-Yosef, Juan-Carlos Biancotti, Alexis Bosman, Romulo Martin Brena, Daniel Brison, Gunilla Caisander, Maria V Camarasa, Jieming Chen, Eric Chiao, Young Min Choi, Andre B H Choo, Daniel Collins, Alan Colman, Jeremy M Crook, George Q Daley, Anne Dalton, Paul A De Sousa, Chris Denning, Janet Downie, Petr Dvorak, Karen D Montgomery, Anis Feki, Angela Ford, Victoria Fox, Ana M Fraga, Tzvia Frumkin, Lin Ge, Paul J Gokhale, Tamar Golan-Lev, Hamid Gourabi, Michal Gropp, Lu Guangxiu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Johan Hyllner, Maneesha S Inamdar, Astrid Kresentia Irwanto, Tetsuya Ishii, Marisa Jaconi, Ying Jin, Susan Kimber, Sergey Kiselev, Barbara B Knowles, Oded Kopper, Valeri Kukharenko, Anver Kuliev, Maria A Lagarkova, Peter W Laird, Majlinda Lako, Andrew L Laslett, Neta Lavon, Dong Ryul Lee, Jeoung Eun Lee, Chunliang Li, Linda S Lim, Tenneille E Ludwig, Yu Ma, Edna Maltby, Ileana Mateizel, Yoav Mayshar, Maria Mileikovsky, Stephen L Minger, Takamichi Miyazaki, Shin Yong Moon, Harry Moore, Christine Mummery, Andras Nagy, Norio Nakatsuji, Kavita Narwani, Steve K W Oh, Sun Kyung Oh, Cia Olson, Timo Otonkoski, Fei Pan, In-Hyun Park, Steve Pells, Martin F Pera, Lygia V Pereira, Ouyang Qi, Grace Selva Raj, Benjamin Reubinoff, Alan Robins, Paul Robson, Janet Rossant, Ghasem H Salekdeh, Thomas C Schulz, Karen Sermon, Jameelah Sheik Mohamed, Hui Shen, Eric Sherrer, Kuldip Sidhu, Shirani Sivarajah, Heli Skottman, Claudia Spits, Glyn N Stacey, Raimund Strehl, Nick Strelchenko, Hirofumi Suemori, Bowen Sun, Riitta Suuronen, Kazutoshi Takahashi, Timo Tuuri, Parvathy Venu, Yuri Verlinsky, Dorien Ward-van Oostwaard, Daniel J Weisenberger, Yue Wu, Shinya Yamanaka, Lorraine Young, Qi Zhou and The International Stem Cell Initiative:  Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil, Nissim Benvenisty, Dalit Ben-Yosef, Juan-Carlos Biancotti, Alexis Bosman, Romulo Martin Brena, Daniel Brison, Gunilla Caisander, Maria V Camarasa, Jieming Chen, Eric Chiao, Young Min Choi, Andre B H Choo, Daniel Collins, Alan Colman, Jeremy M Crook, George Q Daley, Anne Dalton, Paul A De Sousa, Chris Denning, Janet Downie, Petr Dvorak, Karen D Montgomery, Anis Feki, Angela Ford, Victoria Fox, Ana M Fraga, Tzvia Frumkin, Lin Ge, Paul J Gokhale, Tamar Golan-Lev, Hamid Gourabi, Michal Gropp, Lu Guangxiu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Johan Hyllner, Maneesha S Inamdar, Astrid Kresentia Irwanto, Tetsuya Ishii, Marisa Jaconi, Ying Jin, Susan Kimber, Sergey Kiselev, Barbara B Knowles, Oded Kopper, Valeri Kukharenko, Anver Kuliev, Maria A Lagarkova, Peter W Laird, Majlinda Lako, Andrew L Laslett, Neta Lavon, Dong Ryul Lee, Jeoung Eun Lee, Chunliang Li, Linda S Lim, Tenneille E Ludwig, Yu Ma, Edna Maltby, Ileana Mateizel, Yoav Mayshar, Maria Mileikovsky, Stephen L Minger, Takamichi Miyazaki, Shin Yong Moon, Harry Moore, Christine Mummery, Andras Nagy, Norio Nakatsuji, Kavita Narwani, Steve K W Oh, Sun Kyung Oh, Cia Olson, Timo Otonkoski, Fei Pan, In-Hyun Park, Steve Pells, Martin F Pera, Lygia V Pereira, Ouyang Qi, Grace Selva Raj, Benjamin Reubinoff, Alan Robins, Paul Robson, Janet Rossant, Ghasem H Salekdeh, Thomas C Schulz, Karen Sermon, Jameelah Sheik Mohamed, Hui Shen, Eric Sherrer, Kuldip Sidhu, Shirani Sivarajah, Heli Skottman, Claudia Spits, Glyn N Stacey, Raimund Strehl, Nick Strelchenko, Hirofumi Suemori, Bowen Sun, Riitta Suuronen, Kazutoshi Takahashi, Timo Tuuri, Parvathy Venu, Yuri Verlinsky, Dorien Ward-van Oostwaard, Daniel J Weisenberger, Yue Wu, Shinya Yamanaka, Lorraine Young and Qi Zhou doi:10.1038/nbt.2051 The International Stem Cell Initiative compares 125 ethnically diverse human embryonic stem cell lines at early and late passage. Data on karotype, single-nucleotide polymorphisms and methylation shed light on how the cells adapt to long-term culture. Abstract | Full Text | PDF Careers and Recruitment Top The challenges of modern interdisciplinary medical research pp1145 - 1148 Philipp von Roth, Benedict J Canny, Hans-Dieter Volk, J Alison Noble, Charles G Prober, Carsten Perka and Georg N Duda doi:10.1038/nbt.2062 The increasing complexity of medical science poses significant challenges to medical education, leading to a growing gap between medical researchers and treating practitioners. Full Text | PDF People People p1150 doi:10.1038/nbt.2067 Full Text | PDF Top Advertisement Nature Reviews Cancer POSTER - Proteasome inhibition and cancer therapy Author: Q. Ping Dou This poster highlights recent achievements and progress in targeting the ubiquitin-proteasome degradation pathway for cancer therapy. 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