Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Nature Biotechnology 27, 633 (2009). doi:10.1038/nbt.1546

Authors: Terri A Addona, Susan E Abbatiello, Birgit Schilling, Steven J Skates, D R Mani, David M Bunk, Clifford H Spiegelman, Lisa J Zimmerman, Amy-Joan L Ham, Hasmik Keshishian, Steven C Hall, Simon Allen, Ronald K Blackman, Christoph H Borchers, Charles Buck, Helene L Cardasis, Michael P Cusack, Nathan G Dodder, Bradford W Gibson, Jason M Held, Tara Hiltke, Angela Jackson, Eric B Johansen, Christopher R Kinsinger, Jing Li, Mehdi Mesri, Thomas A Neubert, Richard K Niles, Trenton C Pulsipher, David Ransohoff, Henry Rodriguez, Paul A Rudnick, Derek Smith, David L Tabb, Tony J Tegeler, Asokan M Variyath, Lorenzo J Vega-Montoto, Åsa Wahlander, Sofia Waldemarson, Mu Wang, Jeffrey R Whiteaker, Lei Zhao, N Leigh Anderson, Susan J Fisher, Daniel C Liebler, Amanda G Paulovich, Fred E Regnier, Paul Tempst & Steven A Carr

Nature Biotechnology 27, 659 (2009). doi:10.1038/nbt.1549

Authors: Joseph Lehár, Andrew S Krueger, William Avery, Adrian M Heilbut, Lisa M Johansen, E Roydon Price, Richard J Rickles, Glenn F Short III, Jane E Staunton, Xiaowei Jin, Margaret S Lee, Grant R Zimmermann & Alexis A Borisy

Nature Biotechnology 27, 652 (2009). doi:10.1038/nbt.1551

Authors: Doron Lipson, Tal Raz, Alix Kieu, Daniel R Jones, Eldar Giladi, Edward Thayer, John F Thompson, Stan Letovsky, Patrice Milos & Marie Causey

Nature Biotechnology 27, 643 (2009). doi:10.1038/nbt.1547

Authors: Jennifer A MacDiarmid, Nancy B Amaro-Mugridge, Jocelyn Madrid-Weiss, Ilya Sedliarou, Stefanie Wetzel, Kartini Kochar, Vatsala N Brahmbhatt, Leo Phillips, Scott T Pattison, Carlotta Petti, Bruce Stillman, Robert M Graham & Himanshu Brahmbhatt

Nature Biotechnology 27, 667 (2009). doi:10.1038/nbt.1550

Authors: Debashish Ray, Hilal Kazan, Esther T Chan, Lourdes Peña Castillo, Sidharth Chaudhry, Shaheynoor Talukder, Benjamin J Blencowe, Quaid Morris & Timothy R Hughes

Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation, require significant time and labor investment. Here we introduce RNAcompete, a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4 and YB1). RNAcompete identified expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than are conventional motif models. We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.

Nature Biotechnology 27, 627 (2009). doi:10.1038/nbt.1552

Author: Nikos C Kyrpides

As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise for far-reaching advancements in microbiology as well as in diverse, related sciences. But realizing that potential will require meeting the challenges that have accompanied the rapid development of the underlying technology and the exponential growth of data. New technologies provide unprecedented opportunities but also call for conceptual shifts. Experience gained in the first decade of genomics can guide the improved approaches now needed for the selection of genome sequencing projects and their funding, for genome publication and annotation, as well as for data analysis and access. Equipped with these new tools and policies, microbiologists will have a unique opportunity for unprecedented exploration of our microbial planet.

Nature Biotechnology 27, 606 (2009). doi:10.1038/nbt0709-606

Authors: Melissa K Carpenter, Joyce Frey-Vasconcells & Mahendra S Rao

Translation of human pluripotent stem cells into cell therapies will require the development of standardized tests for product consistency, stability, tumorigenicity, toxicity and immunogenicity.

Nature Biotechnology 27, 595 (2009). doi:10.1038/bioe.2009.5

Authors: Francesco De Rubertis, Roman Fleck & Werner Lanthaler

What are the core elements of a successful biotech?

Nature Biotechnology 27, 620 (2009). doi:10.1038/nbt0709-620

Authors: Emmanouil D Karagiannis & Daniel G Anderson

Bacterially derived minicells loaded with siRNA reverse drug resistance in tumor xenografts.

Nature Biotechnology 27, 622 (2009). doi:10.1038/nbt0709-622

Authors: Martin McIntosh & Matthew Fitzgibbon

A multilaboratory study demonstrates the potential for establishing quantitative targeted proteomic assays for moderately to highly abundant plasma proteins.

Nature Biotechnology 27, 624 (2009). doi:10.1038/nbt0709-624

Authors: Bradley W Rice & Christopher H Contag

A near-infrared fluorescent protein opens a window into the mammalian body.

Nature Biotechnology 27, 592 (2009). doi:10.1038/nbt0709-592

Author: Gunjan Sinha

Several European countries continue to defy EU law and ban genetically modified maize. Will the stalemate ever be resolved? Gunjan Sinha investigates.

Nature Biotechnology 27, 614 (2009). doi:10.1038/nbt0709-614

Authors: Harry Thangaraj, Craig J van Dolleweerd, Edward G McGowan & Julian K-C Ma

Examining the relationships between invention disclosure type in industry and academia and geographical disclosure trends, using plant-made pharmaceuticals as a single-sector model for the biopharmaceutical industry.

Nature Biotechnology 27, 579 (2009). doi:10.1038/nbt0709-579

A universal tagging system that links data sets with the author(s) that generated them is essential to promote data sharing within the proteomics and other research communities.