Trouble at the office - pp967 - 969

Malorye Allison

doi:10.1038/nbt0908-967

The FDA's Office of Oncology Products has come in for stinging criticism from drug developers, advocates and even a US legislator over the use of surrogate endpoints. Has the agency struck the right balance between speed and caution? Malorye Allison investigates.

Abstract - | Full Text - Trouble at the office | PDF (159 KB) - Trouble at the office

Building for an exit (or not) - pp971 - 973

Thomas G Gunning

doi:10.1038/bioe.2008.8

PDF (115 KB) - Building for an exit (or not)

Auf Wiedersehen, agbiotech - pp974 - 975

Henry I Miller

doi:10.1038/nbt0908-974

Full Text - Auf Wiedersehen, agbiotech | PDF (165 KB) - Auf Wiedersehen, agbiotech

Trace and traceability—a call for regulatory harmony - pp975 - 978

Koreen Ramessar, Teresa Capell, Richard M Twyman, Hector Quemada & Paul Christou

doi:10.1038/nbt0908-975

Full Text - Trace and traceability—a call for regulatory harmony | PDF (160 KB) - Trace and traceability—a call for regulatory harmony

Do-it-yourself (DIY) pathology - pp978 - 979

Tan A Ince, Jerrold M Ward, Victor E Valli, Dennis Sgroi, Alexander Yu Nikitin, Massimo Loda, Stephen M Griffey, Christopher P Crum, James M Crawford, Roderick T Bronson & Robert D Cardiff

doi:10.1038/nbt0908-978

Full Text - Do-it-yourself (DIY) pathology | PDF (193 KB) - Do-it-yourself (DIY) pathology

Reply to Do-it-yourself (DIY) pathology - p979

doi:10.1038/nbt0908-979a

Full Text - Reply to Do-it-yourself (DIY) pathology | PDF (122 KB) - Reply to Do-it-yourself (DIY) pathology

Bypassing consent for research on biological material - pp979 - 980

Bjørn M Hofmann

doi:10.1038/nbt0908-979b

Full Text - Bypassing consent for research on biological material | PDF (132 KB) - Bypassing consent for research on biological material

Reply to Bypassing consent for research on biological material - pp980 - 981

doi:10.1038/nbt0908-980

Full Text - Reply to Bypassing consent for research on biological material | PDF (91 KB) - Reply to Bypassing consent for research on biological material

Cost/success projections for US biodefense countermeasure development - pp981 - 983

Jason Matheny, Michael Mair & Bradley Smith

doi:10.1038/nbt0908-981

Full Text - Cost/success projections for US biodefense countermeasure development | PDF (156 KB) - Cost/success projections for US biodefense countermeasure development | Supplementary information

Data completeness—the Achilles heel of drug-target networks - pp983 - 984

Jordi Mestres, Elisabet Gregori-Puigjané, Sergi Valverde & Ricard V Solé

doi:10.1038/nbt0908-983

Full Text - Data completeness—the Achilles heel of drug-target networks | PDF (233 KB) - Data completeness—the Achilles heel of drug-target networks

DNA-based patents: an empirical analysis - pp993 - 995

Ann E Mills & Patti Tereskerz

doi:10.1038/nbt0908-993

The perception of rising litigation rates is driving the push for patent reform.

Abstract - | Full Text - DNA-based patents: an empirical analysis | PDF (221 KB) - DNA-based patents: an empirical analysis

Recent patent applications in tissue culture - p996

doi:10.1038/nbt0908-996

Full Text - Recent patent applications in tissue culture | PDF (57 KB) - Recent patent applications in tissue culture

Network-based prediction of human tissue-specific metabolism - pp1003 - 1010

Tomer Shlomi, Moran N Cabili, Markus J Herrgård, Bernhard Ø Palsson & Eytan Ruppin

doi:10.1038/nbt.1487

Metabolic network modeling in multicellular organisms is confounded by the existence of multiple tissues with distinct metabolic functions. By integrating a genome-scale metabolic network with tissue-specific gene- and protein-expression data, Shlomi et al. adapt constraint-based approaches used for microorganisms to predicting metabolism in ten human tissues. Their computational approach should facilitate interpretation of expression data in the context of metabolic disorders.

Abstract - | Full Text - Network-based prediction of human tissue-specific metabolism | PDF (609 KB) - Network-based prediction of human tissue-specific metabolism | Supplementary information

What are decision trees? - pp1011 - 1013

Carl Kingsford & Steven L Salzberg

doi:10.1038/nbt0908-1011

Decision trees have been applied to problems such as assigning protein function and predicting splice sites. How do these classifiers work, what types of problems can they solve and what are their advantages over alternatives?

Abstract - | Full Text - What are decision trees? | PDF (355 KB) - What are decision trees?

T-DNA–mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants - pp1015 - 1017

Bekir Ülker, Yong Li, Mario G Rosso, Elke Logemann, Imre E Somssich & Bernd Weisshaar

doi:10.1038/nbt.1491

Backbone fragments of the Agrobacterium tumor-inducing (Ti) plasmid that bears transgenes of interest have occasionally been reported to be transferred to plant genomes. Now, Ülker et al. show that Agrobacterium chromosomal DNA can also be integrated into transgenic plants at a low frequency. Gene-bearing chromosomal fragments as large as 18 kb are found in T-DNA–tagged populations of Arabidopsis thaliana.

First Paragraph - | Full Text - T-DNA–mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants | PDF (207 KB) - T-DNA–mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants | Supplementary information

See also: News and Views by Gelvin

Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis - pp1019 - 1027

Shirit Einav, Doron Gerber, Paul D Bryson, Ella H Sklan, Menashe Elazar, Sebastian J Maerkl, Jeffrey S Glenn & Stephen R Quake

doi:10.1038/nbt.1490

New hepatitis C treatments are urgently needed. Working with a high-throughput microfluidic affinity assay for RNA-protein interactions, Quake and colleagues identify a small molecule that negatively affects HCV replication in cell culture by inhibiting the binding between the nonstructural protein 4B and the viral RNA genome.

Abstract - | Full Text - Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis | PDF (463 KB) - Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis | Supplementary information

High-resolution metagenomics targets specific functional types in complex microbial communities - pp1029 - 1034

Marina G Kalyuzhnaya, Alla Lapidus, Natalia Ivanova, Alex C Copeland, Alice C McHardy, Ernest Szeto, Asaf Salamov, Igor V Grigoriev, Dominic Suciu, Samuel R Levine, Victor M Markowitz, Isidore Rigoutsos, Susannah G Tringe, David C Bruce, Paul M Richardson, Mary E Lidstrom & Ludmila Chistoserdova

doi:10.1038/nbt.1488

Metagenomics, or shotgun sequencing of environmental DNA, is used to study complex microbial communities. Kalyuzhnaya et al. describe a method for targeting specific microbial subpopulations in environmental samples and use it to analyze microbes that metabolize C₁ compounds.

First Paragraph - | Full Text - High-resolution metagenomics targets specific functional types in complex microbial communities | PDF (347 KB) - High-resolution metagenomics targets specific functional types in complex microbial communities | Supplementary information

See also: News and Views by Dinsdale & Rohwer

Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy - pp1035 - 1040

Martin Andresen, Andre C Stiel, Jonas Fölling, Dirk Wenzel, Andreas Schönle, Alexander Egner, Christian Eggeling, Stefan W Hell & Stefan Jakobs

doi:10.1038/nbt.1493

The current reversibly switchable fluorescent proteins (RSFPs) can not be multiplexed. Jakobs and colleagues create two RSFPs with novel switching characteristics that can be used simultaneously in fluorescence microscopy experiments using only one detection color.

First Paragraph - | Full Text - Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy | PDF (478 KB) - Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy | Supplementary information

Predicting PDZ domain–peptide interactions from primary sequences - pp1041 - 1045

Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler & Gavin MacBeath

doi:10.1038/nbt.1489

PDZ domains represent one of the largest families of interaction domains. Chen et al. develop a scoring matrix that enables prediction of peptide–PDZ domain interactions. Unlike previous methods, the model works to some extent for PDZ domains that were not part of the training set.

First Paragraph - | Full Text - Predicting PDZ domain–peptide interactions from primary sequences | PDF (682 KB) - Predicting PDZ domain–peptide interactions from primary sequences | Supplementary information

Growing the bioscience career pipeline - pp1047 - 1048

Christine Shapard

doi:10.1038/nbt0908-1047

A new program connects local science teachers with the bioscience industry.

Abstract - | Full Text - Growing the bioscience career pipeline | PDF (165 KB) - Growing the bioscience career pipeline

People - p1050

doi:10.1038/nbt0908-1050

Full Text - People | PDF (112 KB) - People