Nature Biotechnology 26, 541 (2008). doi:10.1038/nbt1360

Authors: Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude dePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank Oliver Glöckner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E Lewis, Kelvin Li, Allyson L Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson & Anil Wipat

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Nature Biotechnology 26, 549 (2008). doi:10.1038/nbt1399

Authors: Stephen C Hyde, Ian A Pringle, Syahril Abdullah, Anna E Lawton, Lee A Davies, Anusha Varathalingam, Graciela Nunez-Alonso, Anne-Marie Green, Reto P Bazzani, Stephanie G Sumner-Jones, Mario Chan, Hongyu Li, Nelson S Yew, Seng H Cheng, A Christopher Boyd, Jane C Davies, Uta Griesenbach, David J Porteous, David N Sheppard, Felix M Munkonge, Eric W F W Alton & Deborah R Gill

Pulmonary delivery of plasmid DNA (pDNA)/cationic liposome complexes is associated with an acute unmethylated CG dinucleotide (CpG)-mediated inflammatory response and brief duration of transgene expression. We demonstrate that retention of even a single CpG in pDNA is sufficient to elicit an inflammatory response, whereas CpG-free pDNA vectors do not. Using a CpG-free pDNA expression vector, we achieved sustained (≥56 d) in vivo transgene expression in the absence of lung inflammation.

Nature Biotechnology 26, 571 (2008). doi:10.1038/nbt1400

Authors: David C Chang, Wen J Liu, Itaru Anraku, David C Clark, Christopher C Pollitt, Andreas Suhrbier, Roy A Hall & Alexander A Khromykh

DNA vaccines encoding replication-defective viruses are safer than inactivated or live attenuated viruses but may fail to stimulate an immune response sufficient for effective vaccination. We augment the protective capacity of a capsid-deleted flavivirus DNA vaccine by co-expressing the capsid protein from a separate promoter. In transfected cells, the capsid-deleted RNA transcript is replicated and translated to produce secreted virus-like particles lacking the nucleocapsid. This RNA is also packaged with the help of co-expressed capsid protein to form secreted single-round infectious particles (SRIPs) that deliver the RNA into neighboring cells. In SRIP-infected cells, the RNA is replicated again and produces additional virus-like particles, but in the absence of capsid RNA no SRIPs are formed and no further spread occurs. Compared with an otherwise identical construct that does not encode capsid, our vaccine offers better protection to mice after lethal West Nile virus infection. It also elicits virus-neutralizing antibodies in horses. This approach may enable vaccination against pathogenic flaviviruses other than West Nile virus.

Nature Biotechnology 26, 578 (2008). doi:10.1038/nbt1404

Authors: Hakim Tafer, Stefan L Ameres, Gregor Obernosterer, Christoph A Gebeshuber, Renée Schroeder, Javier Martinez & Ivo L Hofacker

Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.

Nature Biotechnology 26, 475 (2008). doi:10.1038/nbt0508-475

Amgen's retrospective sortie into personalized Vectibix treatment poses some difficult questions for regulators concerning the oversight of companion diagnostics.

Nature Biotechnology 26, 476 (2008). doi:10.1038/nbt0508-476

Based on one company's past poor publishing practices, a top-tier medical journal misguidedly stigmatizes any paper from industry.

Nature Biotechnology 26, 487 (2008). doi:10.1038/nbt0508-487

Author: Randy Osborne

The special protocol assessment introduced only six years ago by the US Food and Drug Administration (FDA) to facilitate clinical trials is gaining popularity. Randy Osborne finds out why.

Nature Biotechnology 26, 491 (2008). doi:10.1038/bioe.2008.4

Authors: Tim Sparey & Francesca Gliubich

An industry academic liaison officer and a university technology-transfer professional in the UK canvass their peers to provide some pointers for how to streamline the technology-transfer process between companies and academia.

Nature Biotechnology 26, 509 (2008). doi:10.1038/nbt0508-509

Author: Malorye Allison

It's no gold rush, but dozens of players are emerging in personalized medicine, with biotechs, big and small, leading the way. Some big pharma companies and even payers remain skeptical, but economics aside, the real winners will be patients.

Nature Biotechnology 26, 519 (2008). doi:10.1038/nbt0508-519

Author: Shyh-Jen Wang

An analysis of US Federal Circuit decisions shows strategies for designing around patents.

Nature Biotechnology 26, 525 (2008). doi:10.1038/nbt0508-525

Author: Alan D T Barrett

Immunization with single-round infectious particles enhances potency of a DNA vaccine against West Nile virus.

Nature Biotechnology 26, 526 (2008). doi:10.1038/nbt0508-526

Authors: Patrick Guye & Ron Weiss

Engineering protein scaffolds creates signaling networks with novel properties.

Nature Biotechnology 26, 528 (2008). doi:10.1038/nbt0508-528

Author: Roy Bicknell

A regulator of VEGF signaling shows therapeutic potential for retinal disease.

Nature Biotechnology 26, 585 (2008). doi:10.1038/nbt0508-585

Author: Bruce Rychlik

Strategies for finding the right hire in life-science recruiting.