Nature Biotechnology Contents: Volume 31 pp 85 - 176

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ReichertSPR.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Nature Biotechnology Focus on DNA Sequencing Technology Performance gains and falling costs have fueled diverse applications of high-throughput DNA sequencing. This focus issue summarizes the current status of these technologies as applied to life sciences and medical research. Click here to access the Focus! Produced with support from:   Editorial Top Dishing out cancer treatment   p85 doi:10.1038/nbt.2516 Despite their limitations, in vitro assays are a simple means for assessing the drug sensitivity of a patient's cancer. After consulting experts in the community, we think such assays deserve a second look. News Top Amgen punts on deCODE's genetics know-how   pp87 - 88 Cormac Sheridan doi:10.1038/nbt0213-87 Chinese investors tap US biotechs   p88 Hepeng Jia doi:10.1038/nbt0213-88 First novel anti-tuberculosis drug in 40 years   pp89 - 91 Randy Osborne doi:10.1038/nbt0213-89 Citizen microbiome   p90 Moheb Costandi doi:10.1038/nbt0213-90a Gilead widens cancer focus   p90 Malorye Allison doi:10.1038/nbt0213-90b Isis inks two antisense deals   p91 Malorye Allison doi:10.1038/nbt0213-91a Forty fight rust and rot   p91 Lucas Laursen doi:10.1038/nbt0213-91b Exelixis debuts in rare cancer   p92 Malini Guha doi:10.1038/nbt0213-92a First drug for short-bowel   p92 Emma Dorey doi:10.1038/nbt0213-92b Startups, inventors cheer European unified patent   pp92 - 93 Nuala Moran doi:10.1038/nbt0213-92c Egg-free flu vaccines   p93 Jeffrey L Fox doi:10.1038/nbt0213-93a UK science's Christmas gift   p93 Barbara Casassus doi:10.1038/nbt0213-93b BioTime acquires Geron's stem cell program   p94 Vicki Brower doi:10.1038/nbt0213-94a Brustle patent holds up in Germany   p94 Nuala Moran doi:10.1038/nbt0213-94b Industry backs biocatalysis for greener manufacturing   pp95 - 96 Susan Aldridge doi:10.1038/nbt0213-95 All conflicts of interest in one site   p97 Jeffrey L Fox doi:10.1038/nbt0213-97a Around the world in a month   p97 doi:10.1038/nbt0213-97b Editor's Pick Inovio   p98 Jennifer Rohn doi:10.1038/nbt0213-98 A Pennsylvania company hopes to turn synthetic DNA vaccines into rapid response agents against flu epidemics and cancer. Data Page 2012—Bullish for big biotech   p99 Walter Yang doi:10.1038/nbt.2504 News Feature Fresh from the biotech pipeline—2012   pp100 - 103 Randy Osborne doi:10.1038/nbt.2498 FDA approvals hit a new high mark in 2012, with a December flurry of approvals. Orphan and fast-track drugs showed strong in the list. Randy Osborne reports. Bioentrepreneur Top Building a business Giving voice to India's entrepreneurs   pp104 - 107 Gayatri Saberwal doi:10.1038/nbt.2493 Opinion and Comment Top Correspondence Prize-based contests can provide solutions to computational biology problems   pp108 - 111 Karim R Lakhani, Kevin J Boudreau, Po-Ru Loh, Lars Backstrom, Carliss Baldwin, Eric Lonstein, Mike Lydon, Alan MacCormack, Ramy A Arnaout and Eva C Guinan doi:10.1038/nbt.2495 Commercialized transgenic traits, maize productivity and yield risk   pp111 - 114 Guanming Shi, Jean-Paul Chavas and Joseph Lauer doi:10.1038/nbt.2496 Commentary Liquid refreshment   p115 Christopher Scott doi:10.1038/nbt.2481 Compared with the long time horizons and diminished returns of traditional antibody startups, Ablexis gave investors a deal they couldn't refuse. Features Top Patents Intellectual property rights and user facility agreements   pp116 - 117 Francis Hane doi:10.1038/nbt.2494 Scientific collaborations can produce results greater than the sum of their parts, but determining who owns the IP rights to scientific results is of prime importance. Recent patent applications in polyethylene glycosylation   p118 doi:10.1038/nbt.2513 News and Views Top Epigenetic trigger for tomato ripening   pp119 - 120 Joseph R Ecker doi:10.1038/nbt.2497 The maturation of tomato fruits is accompanied by widespread reprogramming of the epigenome. See also: Research by Zhong et al. Discovery of antibiotic adjuvants   pp120 - 122 Maya A Farha and Eric D Brown doi:10.1038/nbt.2500 Modeling the production of reactive oxygen species in bacteria reveals targets for adjuvants that boost antibiotic activity. See also: Research by Brynildsen et al. RESEARCH HIGHLIGHTS   p122 doi:10.1038/nbt.2506 Pig genomics for biomedicine   pp122 - 124 Randall S Prather doi:10.1038/nbt.2490 The newly released swine genome assembly will aid research on disease models and xenotransplantation. Goat genome sequence by optical mapping   p123 H Craig Mak doi:10.1038/nbt.2502 See also: Research by Dong et al. Membrane channels built from DNA   p125 Markus Elsner doi:10.1038/nbt.2499 Biotechnology JOBS of the week Postdoctoral, Physical / Chemical Cornell University Postdoctoral Researcher in Organic Synthesis Uppsala University Postdoctoral fellow in Nanomedicine Ian Wark Research Institute Biotechnology Engineer SymbioTEK More Science jobs from Biotechnology EVENT Plant Genomes & Biotechnology: from Genes to Networks December 4-7, 2013 Cold Spring Harbor, US More science events from Computational Biology Top Analysis Evaluation of methods for modeling transcription factor sequence specificity   pp126 - 134 Matthew T Weirauch, Atina Cote, Raquel Norel, Matti Annala, Yue Zhao, Todd R Riley, Julio Saez-Rodriguez, Thomas Cokelaer, Anastasia Vedenko, Shaheynoor Talukder, Phaedra Agius, Aaron Arvey, Philipp Bucher, Curtis G Callan Jr, Cheng Wei Chang, Chien-Yu Chen, Yong-Syuan Chen, Yu-Wei Chu, Jan Grau, Ivo Grosse, Vidhya Jagannathan, Jens Keilwagen, Szymon M Kielbasa, Justin B Kinney, Holger Klein, Miron B Kursa, Harri Lahdesmaki, Kirsti Laurila, Chengwei Lei, Christina Leslie, Chaim Linhart, Anand Murugan, Alena Mysickova, William Stafford Noble, Matti Nykter, Yaron Orenstein, Stefan Posch, Jianhua Ruan, Witold R Rudnicki, Christoph D Schmid, Ron Shamir, Wing-Kin Sung, Martin Vingron, Zhizhuo Zhang, DREAM5 Consortium:  Phaedra Agius, Aaron Arvey, Philipp Bucher, Curtis G Callan Jr, Cheng Wei Chang, Chien-Yu Chen, Yong-Syuan Chen, Yu-Wei Chu, Jan Grau, Ivo Grosse, Vidhya Jagannathan, Jens Keilwagen, Szymon M Kielbasa, Justin B Kinney, Holger Klein, Miron B Kursa, Harri Lahdesmaki, Kirsti Laurila, Chengwei Lei, Christina Leslie, Chaim Linhart, Anand Murugan, Alena Mysickova, William Stafford Noble, Matti Nykter, Yaron Orenstein, Stefan Posch, Jianhua Ruan, Witold R Rudnicki, Christoph D Schmid, Ron Shamir, Wing-Kin Sung, Martin Vingron and Zhizhuo Zhang Harmen J Bussemaker, Quaid D Morris, Martha L Bulyk, Gustavo Stolovitzky and Timothy R Hughes doi:10.1038/nbt.2486 The most comprehensive analysis to date of models of transcription-factor binding specificity reveals the best methods for predicting in vivo binding from in vitro data. Research Top Articles Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) OPEN   pp135 - 141 Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Bertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao, Jun Wang and Wen Wang doi:10.1038/nbt.2478 An instrument for whole-genome optical mapping is used to assemble the genome of the domestic goat into super-long scaffolds. See also: News and Views by Mak Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis   pp142 - 147 Yun Liu, Martin J Aryee, Leonid Padyukov, M Daniele Fallin, Espen Hesselberg, Arni Runarsson, Lovisa Reinius, Nathalie Acevedo, Margaret Taub, Marcus Ronninger, Klementy Shchetynsky, Annika Scheynius, Juha Kere, Lars Alfredsson, Lars Klareskog, Tomas J Ekstrom and Andrew P Feinberg doi:10.1038/nbt.2487 Liu et al. use mediation analysis to find changes in DNA methylation that mediate the genetic risk for rheumatoid arthritis. Targeted zwitterionic near-infrared fluorophores for improved optical imaging   pp148 - 153 Hak Soo Choi, Summer L Gibbs, Jeong Heon Lee, Soon Hee Kim, Yoshitomo Ashitate, Fangbing Liu, Hoon Hyun, GwangLi Park, Yang Xie, Soochan Bae, Maged Henary and John V Frangioni doi:10.1038/nbt.2468 Diagnostic and surgical procedures that rely on optical imaging are improved by using near-infrared fluorescent probes with low background signal. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening   pp154 - 159 Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper, Bao Liu, Jenny Xiang, Ying Shao and James J Giovannoni doi:10.1038/nbt.2462 Whole-genome bisulfite sequencing reveals that global reprogramming of the epigenome occurs during the maturation of tomato fruits, potentially identifying new targets for breeders. See also: News and Views by Ecker Letters Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production   pp160 - 165 Mark P Brynildsen, Jonathan A Winkler, Catherine S Spina, I Cody MacDonald and James J Collins doi:10.1038/nbt.2458 The first global metabolic models that incorporate reactive oxygen species in E. coli reveal targets for potentiating the action of antibacterials. See also: News and Views by Farha & Brown High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire   pp166 - 169 Brandon J DeKosky, Gregory C Ippolito, Ryan P Deschner, Jason J Lavinder, Yariv Wine, Brandon M Rawlings, Navin Varadarajan, Claudia Giesecke, Thomas Dorner, Sarah F Andrews, Patrick C Wilson, Scott P Hunicke-Smith, C Grant Willson, Andrew D Ellington and George Georgiou doi:10.1038/nbt.2492 A new method facilitates high-throughput sequencing of the repertoire of immunoglobulin heavy-light chain pairs in human B cells. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs   pp170 - 174 Dokyun Na, Seung Min Yoo, Hannah Chung, Hyegwon Park, Jin Hwan Park and Sang Yup Lee doi:10.1038/nbt.2461 Synthetic small RNAs are designed for use in metabolic pathway optimization in bacteria. Careers and Recruitment Top Fourth-quarter biotech job picture   p175 Michael Francisco doi:10.1038/nbt.2505 People People   p176 doi:10.1038/nbt.2511 Top Advertisement Epigenetics: Why histone modifications matter in health and disease   February 26 10am EST | 3pm GMT Histones are an integral part of chromatin as they make up the 'protein spools' DNA is wound around. Two prominent speakers will explore one of the key questions in chromatin biology: how the language of post translational modifications on histones influences gene expression.  Register for FREE      Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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