Nature Biotechnology Covering the science and business of biotechnology. http://www.nature.com/nbt/current_issue/ Nature Publishing Group en © Nature Publishing Group Nature Biotechnology 1087-0156 1546-1696 © Nature Publishing Group permissions@nature.com Nature Biotechnology http://www.nature.com/includes/rj_globnavimages/nbt_logo.gif http://www.nature.com/nbt/ Protein microarrays with carbon nanotubes as multicolor Raman labels http://dx.doi.org/10.1038/nbt.1501 The picomolar sensitivity of fluorescence-based protein detection limits the use of protein arrays in research and clinical diagnosis. Chen et al. use antibody-tagged single-walled carbon nanotubes as multicolor Raman labels to detect femtomolar levels of serum analytes over a wide dynamic range. Protein microarrays with carbon nanotubes as multicolor Raman labels

Nature Biotechnology. doi:10.1038/nbt.1501

Authors: Zhuo Chen, Scott M Tabakman, Andrew P Goodwin, Michael G Kattah, Dan Daranciang, Xinran Wang, Guangyu Zhang, Xiaolin Li, Zhuang Liu, Paul J Utz, Kaili Jiang, Shoushan Fan & Hongjie Dai

]]> Protein microarrays with carbon nanotubes as multicolor Raman labels Zhuo Chen Scott M Tabakman Andrew P Goodwin Michael G Kattah Dan Daranciang Xinran Wang Guangyu Zhang Xiaolin Li Zhuang Liu Paul J Utz Kaili Jiang Shoushan Fan Hongjie Dai doi:10.1038/nbt.1501 Nature Biotechnology 2008-10-26 Nature Biotechnology 2008-10-26 Research Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes http://dx.doi.org/10.1038/nbt.1503 Aasen et al. boost the efficiency of human induced pluripotent stem (iPS) cell generation 100-fold by starting with keratinocytes rather than fibroblasts. They also produce iPS cells from plucked adult hair, an easily accessible source of cells that avoids the need for a biopsy. Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes

Nature Biotechnology. doi:10.1038/nbt.1503

Authors: Trond Aasen, Angel Raya, Maria J Barrero, Elena Garreta, Antonella Consiglio, Federico Gonzalez, Rita Vassena, Josipa Bilić, Vladimir Pekarik, Gustavo Tiscornia, Michael Edel, Stéphanie Boué & Juan Carlos Izpisú Belmonte

]]> Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes Trond Aasen Angel Raya Maria J Barrero Elena Garreta Antonella Consiglio Federico Gonzalez Rita Vassena Josipa Bilić Vladimir Pekarik Gustavo Tiscornia Michael Edel Stéphanie Boué Juan Carlos Izpisú Belmonte doi:10.1038/nbt.1503 Nature Biotechnology 2008-10-17 Nature Biotechnology 2008-10-17 Research Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2 http://dx.doi.org/10.1038/nbt.1502 One strategy for advancing induced pluripotent stem (iPS) cell technology toward the clinic is to replace the reprogramming genes with small molecules. Huangfu et al. show that the HDAC inhibitor valproic acid can substitute for the reprogramming gene Klf4, allowing human iPS cells to be generated with only two transgenes, Oct4 and Sox2. Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

Nature Biotechnology. doi:10.1038/nbt.1502

Authors: Danwei Huangfu, Kenji Osafune, René Maehr, Wenjun Guo, Astrid Eijkelenboom, Shuibing Chen, Whitney Muhlestein & Douglas A Melton

]]> Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2 Danwei Huangfu Kenji Osafune René Maehr Wenjun Guo Astrid Eijkelenboom Shuibing Chen Whitney Muhlestein Douglas A Melton doi:10.1038/nbt.1502 Nature Biotechnology 2008-10-12 Nature Biotechnology 2008-10-12 Research An integrated software system for analyzing ChIP-chip and ChIP-seq data http://dx.doi.org/10.1038/nbt.1505 Analyzing the massive and heterogenous datasets from genome-wide chromatin immunoprecipitation (ChIP) datasets presents several computational and statistical challenges. Ji et al. present a software suite that integrates all steps in ChIP-chip and ChIP-seq data analyses and illustrate the use of these tools by comparing the ability of the two platforms to identify transcription factor binding sites. An integrated software system for analyzing ChIP-chip and ChIP-seq data

Nature Biotechnology. doi:10.1038/nbt.1505

Authors: Hongkai Ji, Hui Jiang, Wenxiu Ma, David S Johnson, Richard M Myers & Wing H Wong

]]> An integrated software system for analyzing ChIP-chip and ChIP-seq data Hongkai Ji Hui Jiang Wenxiu Ma David S Johnson Richard M Myers Wing H Wong doi:10.1038/nbt.1505 Nature Biotechnology 2008-11-02 Nature Biotechnology 2008-11-02 Article Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors http://dx.doi.org/10.1038/nbt.1506 Fruit-specific overexpression of a pair of snapdragon transcription factors produces tomatoes that uniformly accumulate anthocyanins at levels unprecedented for metabolic engineering. When included as a dietary supplement, the purple tomatoes increase the life spans of tumorigenic p53 knockout mice. Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors

Nature Biotechnology. doi:10.1038/nbt.1506

Authors: Eugenio Butelli, Lucilla Titta, Marco Giorgio, Hans-Peter Mock, Andrea Matros, Silke Peterek, Elio G W M Schijlen, Robert D Hall, Arnaud G Bovy, Jie Luo & Cathie Martin

Dietary consumption of anthocyanins, a class of pigments produced by higher plants, has been associated with protection against a broad range of human diseases. However, anthocyanin levels in the most commonly eaten fruits and vegetables may be inadequate to confer optimal benefits. When we expressed two transcription factors from snapdragon in tomato, the fruit of the plants accumulated anthocyanins at levels substantially higher than previously reported for efforts to engineer anthocyanin accumulation in tomato and at concentrations comparable to the anthocyanin levels found in blackberries and blueberries. Expression of the two transgenes enhanced the hydrophilic antioxidant capacity of tomato fruit threefold and resulted in fruit with intense purple coloration in both peel and flesh. In a pilot test, cancer-susceptible Trp53−/− mice fed a diet supplemented with the high-anthocyanin tomatoes showed a significant extension of life span.

]]> Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors Eugenio Butelli Lucilla Titta Marco Giorgio Hans-Peter Mock Andrea Matros Silke Peterek Elio G W M Schijlen Robert D Hall Arnaud G Bovy Jie Luo Cathie Martin doi:10.1038/nbt.1506 Nature Biotechnology 2008-10-26 Nature Biotechnology 2008-10-26 Letter Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network http://dx.doi.org/10.1038/nbt.1499 Chechik et al. define activity motifs, which extend the concept of a network motif from the static to the dynamic realm. Mapping functional data onto network structure enables them to reveal new systems-level principles describing how yeast cells integrate exogenous signals and use transcriptional regulation to optimize metabolic responses to environmental perturbations. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

Nature Biotechnology. doi:10.1038/nbt.1499

Authors: Gal Chechik, Eugene Oh, Oliver Rando, Jonathan Weissman, Aviv Regev & Daphne Koller

]]> Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network Gal Chechik Eugene Oh Oliver Rando Jonathan Weissman Aviv Regev Daphne Koller doi:10.1038/nbt.1499 Nature Biotechnology 2008-10-26 Nature Biotechnology 2008-10-26 Analysis