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TABLE OF CONTENTS
| March 2012 Volume 30, Issue 3 |  | | |  |  In This Issue
Focus
Editorials
News
Bioentrepreneur
Correspondence
Features
News and Views
Research Highlights
Computational Biology
 Research
Careers and Recruitment
| | | | | |
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doi:10.1038/nbt.2166
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| | Focus | Top | Plant Technologies
Sixteen years after the commercialization of crops produced by traditional transgenic technology, a raft of new approaches are opening new opportunities in plant biotechnology. This focus issue of Nature Biotechnology highlights these technologies and their impact on plant breeding and their impact on regulatory oversight.
Table of Contents
| | Editorials | Top | | | | Agnostic about agriculture p197
doi:10.1038/nbt.2168
Averting a global food crisis will require the deconstruction of several hurdles to the deployment of new strategies in plant breeding.
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| | | | Another nail in the biosimilar coffin? p198
doi:10.1038/nbt.2169
The US Food and Drug Administration (FDA) has raised the bar very high for those who seek to make a business out of biosimilars.
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| | News | Top | | | | Companies in rapid pursuit of Btk immunokinase pp199 - 200
Cormac Sheridan
doi:10.1038/nbt0312-199
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| | | | One patent for Europe p200
Gunjan Sinha
doi:10.1038/nbt0312-200
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| | | | Diabetes once-weekly drug p201
Gunjan Sinha
doi:10.1038/nbt0312-201b
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| | | | Cystic fibrosis drug Vertex's latest triumph pp201 - 202
Heidi Ledford
doi:10.1038/nbt0312-201a
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| | | | Check a patent at WIPO p202
Michael Francisco
doi:10.1038/nbt0312-202a
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| | | | RNAi patent win p202
Jennifer Rohn
doi:10.1038/nbt0312-202b
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| | | | Hedgehog hopes lifted by approval... and stung by failure p203
Malorye Allison
doi:10.1038/nbt0312-203
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| | | | NCATS launches p204
Jeffrey L Fox
doi:10.1038/nbt0312-204a
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| | | | BASF moves GM crop research to US p204
Lucas Laursen
doi:10.1038/nbt0312-204b
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| | | | HIV neutralizing antibodies reignite interest in vaccine pp204 - 205
Emily Waltz
doi:10.1038/nbt0312-204c
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| | | | Around the world in a month p205
doi:10.1038/nbt0312-205
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| | | | Mission Therapeutics p206
Ken Garber
doi:10.1038/nbt0312-206
Synthetic lethality pioneers spin out an oncology company targeting DNA repair through interruption of ubiquitin pathways.
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| | | | | Data Page | | | | Existing agbiotech traits continue global march p207
Andrew Marshall
doi:10.1038/nbt.2154
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| | | | | Opinion | | | | Confronting the Gordian knot pp208 - 209
L Val Giddings, Ingo Potrykus, Klaus Ammann and Nina V Fedoroff
doi:10.1038/nbt.2145
Galvanizing plant science in Europe will depend on an overhaul of the tangle of indefensible regulations themselves, not on the advent of new plant breeding technologies that may escape existing rules.
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| | | | | News Features | | | | Agbiotech 2.0 pp211 - 214
Daniel Gruskin
doi:10.1038/nbt.2144
As parts of the developing world embrace biotech, the focus is shifting from food production to fuels, industrial chemicals and even drugs. Daniel Grushkin investigates.
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| | | | Tiptoeing around transgenics pp215 - 217
Emily Waltz
doi:10.1038/nbt.2143
New techniques for manipulating plant genomes are yielding plants touted as nontransgenic. Will that relieve regulatory burden? Emily Waltz investigates.
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Learn more here. |  | | Bioentrepreneur | Top | | | | Know before you go pp219 - 220
Mark Kessel
doi:10.1038/nbt.2115
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| | Correspondence | Top | | | | The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome pp221 - 223
Young-Ki Paik, Seul-Ki Jeong, Gilbert S Omenn, Mathias Uhlen, Samir Hanash, Sang Yun Cho, Hyoung-Joo Lee, Keun Na, Eun-Young Choi, Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Yong Cheng, Rui Chen, Gyorgy Marko-Varga, Eric W Deutsch, Hoguen Kim, Ja-Young Kwon, Ruedi Aebersold, Amos Bairoch, Allen D Taylor, Kwang Youl Kim, Eun-Young Lee, Denis Hochstrasser, Pierre Legrain and William S. Hancock
doi:10.1038/nbt.2152
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| | | | BLUEPRINT to decode the epigenetic signature written in blood pp224 - 226
David Adams, Lucia Altucci, Stylianos E Antonarakis, Juan Ballesteros, Stephan Beck, Adrian Bird, Christoph Bock, Bernhard Boehm, Elias Campo, Andrea Caricasole, Fredrik Dahl, Emmanouil T Dermitzakis, Tariq Enver, Manel Esteller, Xavier Estivill, Anne Ferguson-Smith, Jude Fitzgibbon, Paul Flicek, Claudia Giehl, Thomas Graf, Frank Grosveld, Roderic Guigo, Ivo Gut, Kristian Helin, Jonas Jarvius, Ralf Kuppers, Hans Lehrach, Thomas Lengauer, Ake Lernmark, David Leslie, Markus Loeffler, Elizabeth Macintyre, Antonello Mai, Joost HA Martens, Saverio Minucci, Willem H Ouwehand, Pier Giuseppe Pelicci, Helene Pendeville, Bo Porse, Vardhman Rakyan, Wolf Reik, Martin Schrappe, Dirk Schubeler, Martin Seifert, Reiner Siebert, David Simmons, Nicole Soranzo, Salvatore Spicuglia, Michael Stratton, Hendrik G Stunnenberg, Amos Tanay, David Torrents, Alfonso Valencia, Edo Vellenga, Martin Vingron, Jorn Walter and Spike Willcocks
doi:10.1038/nbt.2153
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| | | | Detecting and annotating genetic variations using the HugeSeq pipeline pp226 - 229
Hugo Y K Lam, Cuiping Pan, Michael J Clark, Phil Lacroute, Rui Chen, Rajini Haraksingh, Maeve O'Huallachain, Mark B Gerstein, Jeffrey M Kidd, Carlos D Bustamante and Michael Snyder
doi:10.1038/nbt.2134
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| | | | Update on the first cloned goats pp229 - 230
Stephen Blash, Michael Schofield, Yann Echelard and William Gavin
doi:10.1038/nbt.2140
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| | Features | Top | | | | Deployment of new biotechnologies in plant breeding pp231 - 239
Maria Lusser, Claudia Parisi, Damien Plan and Emilio Rodriguez-Cerezo
doi:10.1038/nbt.2142
The first crops obtained through new plant breeding techniques are close to commercialization. Regulatory issues will determine the adoption of the techniques by breeders.
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| | | | | Patents | | | | Debunking the myth that whole-genome sequencing infringes thousands of gene patents pp240 - 244
Christopher M Holman
doi:10.1038/nbt.2146
The fear that human gene patents pose a threat to whole-genome sequencing is based largely on widely held misconceptions.
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| | | | Recent patent applications in single-molecule technologies p245
Julien Muzard
doi:10.1038/nbt.2148
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Download the brochure |  | | | News and Views | Top | | | | | | Research Highlights | Top | | | | ES cell therapy in two patients with eye disease | Turning seaweed into biofuel | Engineering control in biofilms | Resveratrol mechanism revealed | Reprogramming illuminates Alzheimer's
| Computational Biology | Top | | | | | Analysis | | | | Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome pp253 - 260
Zhiyu Peng, Yanbing Cheng, Bertrand Chin-Ming Tan, Lin Kang, Zhijian Tian, Yuankun Zhu, Wenwei Zhang, Yu Liang, Xueda Hu, Xuemei Tan, Jing Guo, Zirui Dong, Yan Liang, Li Bao and Jun Wang
doi:10.1038/nbt.2122
Sites where RNA editing occurs can be found using RNA-Seq, but false positives confound the data analysis. Peng et al. describe algorithms for accurately calling editing events, and apply them to identify ~22,600 events, mostly A[rarr]G changes, in a human transcriptome.
Abstract | Full Text | PDF
See also: News and Views by Pachter
| | Research | Top | | | | | Brief Communications | | | | Functional beta-cell maturation is marked by an increased glucose threshold and by expression of urocortin 3 pp261 - 264
Barak Blum, Sinissa Hrvatin, Christian Schuetz, Claire Bonal, Alireza Rezania and Douglas A Melton
doi:10.1038/nbt.2141
Cultured human pluripotent stem cells can be differentiated to immature pancreatic beta cells, but no one has yet succeeded in maturing these cells in vitro. Blum et al. define markers of beta-cell maturation that can be used to screen conditions for generating fully functional beta cells.
First paragraph | Full Text | PDF
| | | | | Articles | | | | Massively parallel functional dissection of mammalian enhancers in vivo pp265 - 270
Rupali P Patwardhan, Joseph B Hiatt, Daniela M Witten, Mee J Kim, Robin P Smith, Dalit May, Choli Lee, Jennifer M Andrie, Su-In Lee, Gregory M Cooper, Nadav Ahituv, Len A Pennacchio and Jay Shendure
doi:10.1038/nbt.2136
Two groups describe approaches for synthesizing and assaying the function of thousands of variants of mammalian DNA regulatory elements. Melnikov et al. use their results to engineer short optimized regulatory elements in human cells, whereas Patwardhan et al. study enhancers hundreds of bases long in mice.
Abstract | Full Text | PDF
| | | | Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay pp271 - 277
Alexandre Melnikov, Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov, Soheil Feizi, Andreas Gnirke, Curtis G Callan Jr, Justin B Kinney, Manolis Kellis, Eric S Lander and Tarjei S Mikkelsen
doi:10.1038/nbt.2137
An improved understanding of enhancers in mammalian genomes could facilitate the design of new regulatory elements. Melnikov et al. synthesize thousands of ~90 nt enhancer variants, assay their activity in human cells and use the data to rationally optimize synthetic enhancers.
Abstract | Full Text | PDF
| | | | | Letter | | | | Tracking the progression of the human inner cell mass during embryonic stem cell derivation pp278 - 282
Thomas O'Leary, Bjorn Heindryckx, Sylvie Lierman, David van Bruggen, Jelle J Goeman, Mado Vandewoestyne, Dieter Deforce, Susana M Chuva de Sousa Lopes and Petra De Sutter
doi:10.1038/nbt.2135
The events that lead from plated human blastocysts to embryonic stem cells are poorly understood. Close analysis reveals a transient intermediate state with a distinct molecular profile.
First paragraph | Full Text | PDF
See also: News and Views by Pribluda & Hanna
| | | | | Resources | | | | Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors pp283 - 288
Elisabet Wahlberg, Tobias Karlberg, Ekaterina Kouznetsova, Natalia Markova, Antonio Macchiarulo, Ann-Gerd Thorsell, Ewa Pol, Asa Frostell, Torun Ekblad, Delal Oncu, Bjorn Kull, Graeme Michael Robertson, Roberto Pellicciari, Herwig Schuler and Johan Weigelt
doi:10.1038/nbt.2121
PARP inhibitors have recently entered phase 3 clinical trials as cancer therapeutics, but the specificity of many of these compounds is unknown. Wahlberg et al. used biochemical approaches to show that most PARP inhibitors target multiple PARP family members.
Abstract | Full Text | PDF
See also: News and Views by Jones
| | Careers and Recruitment | Top | | | | Pay increases for executives at private life sciences companies hit a 12-year low pp289 - 291
Bruce Rychlik
doi:10.1038/nbt.2155
In 2011, year-over-year executive cash compensation increased just 1.6%, well below the historical 5% annual rise, according to a nationwide survey.
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| | | | | People | | | | People p292
doi:10.1038/nbt.2159
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