Nature Biotechnology Contents: Volume 30 pp 469 - 566

Advertisement Watch Webinar: The Role of Adenine Methylation in Determining the Pathogenicity of a Bacteria Learn how Eric Schadt, Mt. Sinai Medical Center, identified a deadly strain of E. coli and further characterized it using the base modification detection capabilities of the PacBio® RS. Dr. Schadt shares how SMRT® technology improved the genome assembly of the bacteria in order to properly classify it and then explores the methylome and its effects on the biochemical function of the outbreak strain. TABLE OF CONTENTS June 2012 Volume 30, Issue 6 In This Issue Editorial News Bioentrepreneur Opinion and Comment Features News and Views Research Highlights Computational Biology Research Errata Corrigenda Careers and Recruitment Advertisement Genome editing with pico precision and mega flexibility GeneArt® Precision TALs provide DNA-binding proteins for more precise targeting and genome editing. Target any locus in the genome. Choose your effectors and Gateway® technology–compatible vector. Your clone will typically be delivered within 3 weeks after submitting your order. Learn more Japanese table of contents Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Relay Technology Management Real time business intelligence and data visualization for the Life Science Industry Trend monitoring and comparative asset analysis Click here for more information or to arrange a trial.   In This Issue Top In this issue   ppvii - viii doi:10.1038/nbt.2274 Editorial Top Discontent with consent   p469 doi:10.1038/nbt.2270 A new type of patient consent promises to galvanize how personal genomic and medical data are shared in open research environments. News Top Proof of concept for next-generation nanoparticle drugs in humans   pp471 - 473 Cormac Sheridan doi:10.1038/nbt0612-471 First plant-made biologic approved   p472 Jeffrey L Fox doi:10.1038/nbt0612-472 Pharma bankrolls academic institutes   p474 Gunjan Sinha doi:10.1038/nbt0612-474a Agency defies advice and rejects gene therapy for third time   p474 Nuala Moran doi:10.1038/nbt0612-474b Anti-IL-17 mAbs herald new options in psoriasis   pp475 - 477 Ken Garber doi:10.1038/nbt0612-475 Claims expose fatal events   p476 Malorye Allison doi:10.1038/nbt0612-476 Around the world in a month   p477 doi:10.1038/nbt0612-477 JOBS Act to jumpstart small business   p478 Jeffrey L Fox doi:10.1038/nbt0612-478a Wellcome partners to make drugs for India   p478 Killugudi Jayaraman doi:10.1038/nbt0612-478b Shire drops 'emergency' Fabry's disease drug   p478 Jeffrey L Fox doi:10.1038/nbt0612-478c Gintuit cell therapy approval signals shift at US regulator   p479 Charles Schmidt doi:10.1038/nbt0612-479 Newsmaker Cathay Industrial Biotech   p480 Emily Waltz doi:10.1038/nbt0612-480 This Chinese biotech exemplifies how companies in emerging markets can thrive in low-margin industrial applications. Obituary George Rathmann 1927-2012   p481 doi:10.1038/nbt0612-481 Not for nothing was the founding father of Amgen known as the Golden Throat. News Feature The gatekeepers of effectiveness   pp482 - 484 Mark Ratner doi:10.1038/nbt.2265 Comparative effectiveness, especially in its new guise of patient-centered outcomes research, is all the rage in US policy circles. Will it really make a difference to healthcare? Mark Ratner reports. Bioentrepreneur Top Reaching across the table   pp485 - 487 Pamela Cox and Benjamin Dibling doi:10.1038/nbt.2202 Opinion and Comment Top Correspondence Should preclinical studies be registered?   pp488 - 489 Jonathan Kimmelman and James A Anderson doi:10.1038/nbt.2261 The need for innovation in biomanufacturing   pp489 - 492 Uwe Gottschalk, Kurt Brorson and Abhinav A Shukla doi:10.1038/nbt.2263 European agricultural policy goes down the tubers   pp492 - 493 Christina Dixelius, Torbjorn Fagerstrom and J F Sundstrom doi:10.1038/nbt.2255 Transgenic insect resistance traits increase corn yield and yield stability   pp493 - 496 Michael D Edgerton, Jon Fridgen, John R Anderson Jr, Jenne Ahlgrim, Monty Criswell, Prabhakar Dhungana, Tom Gocken, Zheng Li, Sadayappan Mariappan, Clinton D Pilcher, Arnold Rosielle and Steven B Stark doi:10.1038/nbt.2259 Commentary Geron's quixotic fate   p497 Christopher Scott and Brady Huggett doi:10.1038/nbt.2253 Why did Geron—corporate standard bearer for regenerative medicine—fail, whereas technology pioneers in other areas persist? Features Top Patents Biomarker patents for diagnostics: problem or solution?   pp498 - 500 Michael M Hopkins and Stuart Hogarth doi:10.1038/nbt.2257 Patents on genes and other types of biomarkers have caused much controversy, but their importance to diagnostic innovation is in danger of being overlooked. Recent patent applications in pluripotent stem cells   p501 doi:10.1038/nbt.2272 News and Views Top Next-generation protein engineering targets influenza   pp502 - 504 Shoshana J Wodak doi:10.1038/nbt.2268 Computational design and high-throughput mutational scanning yield proteins with subnanomolar affinities for influenza hemagglutinin. See also: Research by Whitehead et al. Dissecting genomic regulatory elements in vivo    pp504 - 506 Vanja Haberle and Boris Lenhard doi:10.1038/nbt.2266 Three high-throughput methods allow regulatory sequences to be analyzed at single-nucleotide resolution in living cells. See also: Research by Sharon et al. Nanopores as protein sensors   pp506 - 507 Stefan Howorka and Zuzanna S Siwy doi:10.1038/nbt.2264 Two studies describe progress in designing nanopores capable of detecting single protein molecules. Biotechnology JOBS of the week Exploitation of biodiversity and of biotechnologies for a high-quality and environmentally friendly durum wheat breeding. Università degli Studi della Tuscia Research or Post-Doc position in Bio-informatics Flemish Institute for Biotechnology (VIB) Invitation for Top Talent in Research and Academics for Regular Positions National Institute of Animal Biotechnology (NIAB) The Arturo Falaschi ICGEB Flexible Fellowships International Centre for Genetic Engineering and Biotechnology Biotechnology IASVM-CAAS More Science jobs from Biotechnology EVENT IBS 2012(International Biotechnology Symposium & Exhibition) September 16-21, 2012 Daegu, Korea More science events from Research Highlights Top Anti-stress therapy for muscular dystrophy | Safer lentiviral vectors | Protein characterization via aptamers | Rare-cell signature predicts heart attack | Mapping the newest epigenetic mark Computational Biology Top News Feature My data are your data   pp509 - 511 Vivien Marx doi:10.1038/nbt.2243 Encouraging more broad and inclusive data sharing in today's world will involve concerted community efforts to overcome technical barriers and human foibles. Vivien Marx investigates. Research Top Perspective Unlocking the potential of metagenomics through replicated experimental design   pp513 - 520 Rob Knight, Janet Jansson, Dawn Field, Noah Fierer, Narayan Desai, Jed A Fuhrman, Phil Hugenholtz, Daniel van der Lelie, Folker Meyer, Rick Stevens, Mark J Bailey, Jeffrey I Gordon, George A Kowalchuk and Jack A Gilbert doi:10.1038/nbt.2235 Articles Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters   pp521 - 530 Eilon Sharon, Yael Kalma, Ayala Sharp, Tali Raveh-Sadka, Michal Levo, Danny Zeevi, Leeat Keren, Zohar Yakhini, Adina Weinberger and Eran Segal doi:10.1038/nbt.2205 Analyzing the effects of multiple promoter motifs on gene expression can be a laborious process. Sharon et al. present a high-throughput method to measure the expression of thousands of designed yeast promoters in a single experiment and use it to reveal new features of transcriptional regulation. See also: News and Views by Haberle & Lenhard Isolation of primitive endoderm, mesoderm, vascular endothelial and trophoblast progenitors from human pluripotent stem cells   pp531 - 542 Micha Drukker, Chad Tang, Reza Ardehali, Yuval Rinkevich, Jun Seita, Andrew S Lee, Adriane R Mosley, Irving L Weissman and Yoav Soen doi:10.1038/nbt.2239 Drukker and colleagues differentiated human embryonic stem (ES) cells for 3 days and screened the cells for labeling by >400 antibodies. They identified cell-surface markers expressed on four classes of early progenitor cell. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing   pp543 - 548 Timothy A Whitehead, Aaron Chevalier, Yifan Song, Cyrille Dreyfus, Sarel J Fleishman, Cecilia De Mattos, Chris A Myers, Hetunandan Kamisetty, Patrick Blair, Ian A Wilson and David Baker doi:10.1038/nbt.2214 To increase the affinity of designed protein inhibitors for influenza hemagglutinin, Whitehead et al. use yeast display and deep sequencing to measure the effects on binding of ~1,000 amino-acid substitutions. Rare beneficial mutations are then combined and screened, yielding inhibitors with ~25-fold lower dissociation constants. See also: News and Views by Wodak Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential   pp549 - 554 Gengyun Zhang, Xin Liu, Zhiwu Quan, Shifeng Cheng, Xun Xu, Shengkai Pan, Min Xie, Peng Zeng, Zhen Yue, Wenliang Wang, Ye Tao, Chao Bian, Changlei Han, Qiuju Xia, Xiaohua Peng, Rui Cao, Xinhua Yang, Dongliang Zhan, Jingchu Hu, Yinxin Zhang, Henan Li, Hua Li, Ning Li, Junyi Wang, Chanchan Wang, Renyi Wang, Tao Guo, Yanjie Cai, Chengzhang Liu, Haitao Xiang, Qiuxiang Shi, Ping Huang, Qingchun Chen, Yingrui Li, Jun Wang, Zhihai Zhao and Jian Wang doi:10.1038/nbt.2195 Completion of genome sequences for the diploid Setaria italica reveals features of C4 photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. Reference genome sequence of the model plant Setaria   pp555 - 561 Jeffrey L Bennetzen, Jeremy Schmutz, Hao Wang, Ryan Percifield, Jennifer Hawkins, Ana C Pontaroli, Matt Estep, Liang Feng, Justin N Vaughn, Jane Grimwood, Jerry Jenkins, Kerrie Barry, Erika Lindquist, Uffe Hellsten, Shweta Deshpande, Xuewen Wang, Xiaomei Wu, Therese Mitros, Jimmy Triplett, Xiaohan Yang, Chu-Yu Ye, Margarita Mauro-Herrera, Lin Wang, Pinghua Li, Manoj Sharma, Rita Sharma, Pamela C Ronald, Olivier Panaud, Elizabeth A Kellogg, Thomas P Brutnell, Andrew N Doust, Gerald A Tuskan, Daniel Rokhsar and Katrien M Devos doi:10.1038/nbt.2196 Completion of genome sequences for the diploid Setaria italica reveals features of C4 photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. Errata Top Reinventing clinical trials   p562 Malorye Allison doi:10.1038/nbt0612-562a Parallel genome universes   p562 Tom Misteli doi:10.1038/nbt0612-562b BASF moves GM crop research to US   p562 Lucas Laursen doi:10.1038/nbt0612-562c In Their Words   p562 doi:10.1038/nbt0612-562d Corrigenda Top Performance comparison of whole-genome sequencing platforms   p562 Hugo Y K Lam, Michael J Clark, Rui Chen, Rong Chen, Georges Natsoulis, Maeve O'Huallachain, Frederick E Dewey, Lukas Habegger, Euan A Ashley, Mark B Gerstein, Atul J Butte, Hanlee P Ji and Michael Snyder doi:10.1038/nbt0612-562e Performance comparison of benchtop high-throughput sequencing platforms   p562 Nicholas J Loman, Raju V Misra, Timothy J Dallman, Chrystala Constantinidou, Saheer E Gharbia, John Wain and Mark J Pallen doi:10.1038/nbt0612-562f Careers and Recruitment Top The importance of matching talented leadership with the growth stage of your life-sciences company   pp563 - 565 J Michael Honeysett and Richard Metheny doi:10.1038/nbt.2267 In the life sciences' rapidly changing business climate, it is imperative that companies find innovative, effective and enlightened leadership. People People   p566 doi:10.1038/nbt.2271 Top Advertisement Frontiers in Plant Biology: From Discovery to Applications   October 3-5, 2012 - Ghent, Belgium This conference will focus on the recent breakthroughs in plant biology, enabled by the latest methodological developments. For more information and to register, visit: http://www.nature.com/natureconferences/fpb2012/index.html     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.