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�A synthetic mammalian electro-genetic transcription circuit. � Weber W,�Luzi S,�Karlsson M,�Sanchez-Bustamante CD,�Frey U,�Hierlemann A,�Fussenegger M. �Nucleic Acids Res.�2009 Mar;37(4):e33. Epub 2009 Feb 3. ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, CH-4058 Basel, Switzerland. Electric signal...
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Enzymatic assembly of DNA molecules up to several hundred kilobases. Gibson DG,�Young L,�Chuang RY,�Venter JC,�Hutchison CA 3rd,�Smith HO. Nat Methods.�2009 May;6(5):343-5. Epub 2009 Apr 12. The J. Craig Venter Institute, Synthetic Biology Group, Rockville, Maryland, USA. [email protected] We describe an isothermal, single-reaction method for...
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Automated unrestricted multigene recombineering for multiprotein complex production. Bieniossek C,�Nie Y,�Frey D,�Olieric N,�Schaffitzel C,�Collinson I,�Romier C,�Berger P,�Richmond TJ,�Steinmetz MO,Berger I. �Nat Methods.�2009 Jun;6(6):447-450. Epub 2009 May 3. [1] European Molecular Biology Laboratory, Grenoble Outstation,...
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At loose ends: resecting a double-strand break. Cell.�2009 May 29;137(5):807-10. Bernstein KA,�Rothstein R. Columbia University Medical Center, Department of Genetics & Development, New York, NY 10032, USA. Double-strand break (DSB) repair is critical for maintaining genomic integrity and requires the processing of the 5' DSB ends. Recent studies have shed...
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A general strategy for the production of difficult-to-express inducer-dependent bacterial repressor proteins in Escherichia coli. Christen EH,�Karlsson M,�Kämpf MM,�Weber CC,�Fussenegger M,�Weber W. �Protein Expr Purif.�2009 Aug;66(2):158-64. Epub 2009 Mar 24. Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse...
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Protein sequencing gone awry: 1 sample, 27 labs, 20 results One of the more recent fields to pick up an -omics designation, proteomics, is intended to identify all the proteins in a single sample. But a new study shows that the field is suffering growing pains due to a variety of inconsistencies in procedures and analyses. By�John Timmer�| Last...
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Nat Methods. 2009 May 3. [Epub ahead of print]   Automated unrestricted multigene recombineering for multiprotein complex production. Bieniossek C, Nie Y, Frey D, Olieric N, Schaffitzel C, Collinson I, Romier C, Berger P, Richmond TJ, Steinmetz MO,Berger I. [1] European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, Grenoble, France. [2] Unit of Virus Host-Cell...
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Nat Methods. 2009 May;6(5):331-8. Imaging intracellular RNA distribution and dynamics in living cells. Tyagi S. Public Health Research Institute, New Jersey Medical School, University of Medicine & Dentistry of New Jersey, Newark, New Jersey, USA. [email protected] Powerful methods now allow the imaging of specific mRNAs in living cells. These methods enlist fluorescent proteins to...
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Nat Methods. 2009 May;6(5):351-3. Epub 2009 Apr 6. An ultramarine fluorescent protein with increased photostability and pH insensitivity. Tomosugi W, Matsuda T, Tani T, Nemoto T, Kotera I, Saito K, Horikawa K, Nagai T. Laboratory for Nanosystems Physiology, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido, Japan. We report a pH-insensitive and...
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Curr Opin Biotechnol. 2009 Mar 17. Engineered luciferases for molecular sensing in living cells. Binkowski B, Fan F, Wood K. Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, United States. As a means for visualizing molecular physiology within living cells, new strategies are emerging for engineering luciferases into intracellular biosensors. These biosensors can be...
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Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP. Publication Date: 2008 Nov PMID: 18794860 Authors: Biteen, J. S. - Thompson, M. A. - Tselentis, N. K. - Bowman, G. R. - Shapiro, L. - Moerner, W. E. Journal: Nat Methods The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit...
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Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Publication Date: 2008 Dec PMID: 19029906 Authors: Huang, B. - Jones, S. A. - Brandenburg, B. - Zhuang, X. Journal: Nat Methods The ability to directly visualize nanoscopic cellular structures and their spatial relationship in all three dimensions will greatly enhance our understanding...
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F-pili dynamics by live-cell imaging. Publication Date: 2008 Nov 18 PMID: 19004777 Authors: Clarke, M. - Maddera, L. - Harris, R. L. - Silverman, P. M. Journal: Proc Natl Acad Sci U S A Bacteria have evolved numerous mechanisms for cell-cell communication, many of which have important consequences for human health. Among these is conjugation, the direct transfer of DNA from one cell to...
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Cationic gold microparticles for biolistic delivery of nucleic acids. Publication Date: 2008 Nov PMID: 19007338 Authors: Svarovsky, S. - Borovkov, A. - Sykes, K. Journal: Biotechniques Here we report preparation and properties of positively charged gold microparticles, and their use for biolistic DNA delivery. Micron-sized gold microparticles were modified by building self-assembling...
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Nature Methods 5, 683 (2008). doi:10.1038/nmeth.1235 Authors: Hidekazu Tsutsui, Satoshi Karasawa, Yasushi Okamura & Atsushi Miyawaki We used two new coral fluorescent proteins as fluorescence resonance energy transfer (FRET) donor and acceptor to develop a voltage sensor, named Mermaid, that displays ∼40% changes in emission ratio per 100 mV, allowing for direct visualization of...
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Publication Date: 2008 Jul 16 PMID: 18621983 Authors: Bayle, V. - Nussaume, L. - Bhat, R. A. Journal: Plant Physiol Forster resonance energy transfer (FRET) measurements based on fluorescence lifetime imaging microscopy (FLIM) are increasingly being used to assess molecular conformations and associations in living systems. Reduction in the excited state lifetime of the donor...
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Publication Date: 2008 Aug 5 PMID: 18667691 Authors: Strickland, D. - Moffat, K. - Sosnick, T. R. Journal: Proc Natl Acad Sci U S A An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that...
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Nature Methods 5, 605 (2008). doi:10.1038/nmeth.1220 Authors: Julia Riedl, Alvaro H Crevenna, Kai Kessenbrock, Jerry Haochen Yu, Dorothee Neukirchen, Michal Bista, Frank Bradke, Dieter Jenne, Tad A Holak, Zena Werb, Michael Sixt & Roland Wedlich-Soldner Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches...
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RNA techniques for bacteria.: "Publication Date: 2007 Jun 14 PMID: 17574902 Authors: Charpentier, E. - Schroeder, R. Journal: Curr Opin Microbiol post to: CiteULike" (Via current opinion in microbiology.)
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Peptide signals encode protein localization.: "Publication Date: 2007 Nov PMID: 17766408 Authors: Russell, J. H. - Keiler, K. C. Journal: J Bacteriol Many bacterial proteins are localized to precise intracellular locations, but in most cases the mechanism for encoding localization information is not known. Screening libraries of peptides fused to green fluorescent protein identified...
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Specific and efficient cleavage of fusion proteins by recombinant plum pox virus NIa protease.: "Publication Date: 2007 Oct 22 PMID: 18024078 Authors: Zheng, N. - Perez, J. D. - Zhang, Z. - Dominguez, E. - Garcia, J. A. - Xie, Q. Journal: Protein Expr Purif Site-specific proteases are the most popular kind of enzymes for removing the fusion tags from fused target proteins. Nuclear...
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A better fluorescent protein for whole-body imaging.: "Publication Date: 2007 Nov 21 PMID: 18037177 Authors: Hoffman, R. M. Journal: Trends Biotechnol Whole-body imaging with fluorescent proteins is a powerful technology with many applications in small animals. Brighter, red-shifted proteins can make whole-body imaging more sensitive owing to reduced absorption by tissues and less...
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Gene synthesis by circular assembly amplification.: "Publication Date: 2007 Nov 25 PMID: 18037891 Authors: Bang, D. - Church, G. M. Journal: Nat Methods Here we report the development of a gene-synthesis technology, circular assembly amplification. In this approach, we first constructed exonuclease-resistant circular DNA via simultaneous ligation of oligonucleotides. Exonuclease- and...
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The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a 70/+96 mRNA region with respect to the translation initiation codon.: "Publication Date: 2007 Dec 15 PMID: 18084029 Authors: Care, S. - Bignon, C. - Pelissier, M. C. - Blanc, E. - Canard, B. - Coutard, B. Journal: Nucleic Acids Res Recombinant protein...
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A secreted luciferase for ex vivo monitoring of in vivo processes: " A secreted luciferase for ex vivo monitoring of in vivo processes Nature Methods 5, 171 (2008). doi:10.1038/nmeth.1177 Authors: Thomas Wurdinger, Christian Badr, Lisa Pike, Ruben de Kleine, Ralph Weissleder, Xandra O Breakefield & Bakhos A Tannous Luciferases are widely used to monitor biological...
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Fluorescent Proteins Developed For Live Cell Imaging, Biosensor Design: "Scientists have developed new 'fluorogen activating proteins' that will become a key component of novel molecular biosensor technology. The FAPs can be used to monitor biological activities of individual proteins and other biomolecules within living cells in real time. Researchers designed the FAPs to emit...
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Fluorogen-activating single-chain antibodies for imaging cell surface proteins: " Fluorogen-activating single-chain antibodies for imaging cell surface proteins Nature Biotechnology 26, 235 (2008). doi:10.1038/nbt1368 Authors: Christopher Szent-Gyorgyi, Brigitte A Schmidt, Yehuda Creeger, Gregory W Fisher, Kelly L Zakel, Sally Adler, James A J Fitzpatrick, Carol A Woolford, Qi...
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GFP-like Proteins Stably Accumulate in Lysosomes.: "Publication Date: 2008 Feb 6 PMID: 18256512 Authors: Katayama, H. - Yamamoto, A. - Mizushima, N. - Yoshimori, T. - Miyawaki, A. Journal: Cell Struct Funct Green fluorescent protein (GFP) from the jellyfish Aequorea victoria, its GFP variants (Aequorea GFPs), and more recently the novel GFP-like proteins from Anthozoa have greatly...
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Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression: " Introns that elevate mRNA accumulation have been found in a wide range of eukaryotes. However, not all introns affect gene expression, and direct testing is currently the only way to identify stimulatory introns. Our genome-wide analysis in Arabidopsis thaliana...
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Current status of binary vectors and superbinary vectors.: "Publication Date: 2007 Dec PMID: 18056865 Authors: Komori, T. - Imayama, T. - Kato, N. - Ishida, Y. - Ueki, J. - Komari, T. Journal: Plant Physiol
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Diolistics: incorporating fluorescent dyes into biological samples using a gene gun.: "Publication Date: 2007 Oct 16 PMID: 17945370 Authors: O'Brien, J. A. - Lummis, S. C. Journal: Trends Biotechnol The hand-held gene gun provides a rapid and efficient method of incorporating fluorescent dyes into cells, a technique that is becoming known as diolistics. Transporting fluorescent dyes...
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Engineered minichromosomes in plants.: "Publication Date: 2007 Oct 29 PMID: 17977710 Authors: Yu, W. - Han, F. - Birchler, J. A. Journal: Curr Opin Biotechnol Genetic engineering for complex or combined traits requires the simultaneous expression of multiple genes, and has been considered as the bottleneck for the next generation of genetic engineering in plants. Minichromosome...
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Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets: " Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets Nature Protocols 3, 41 (2008). doi:10.1038/nprot.2007.491 Authors: Luke E Berchowitz & Gregory P Copenhaver In most...
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Novel plant transformation vectors containing the superpromoter.: "Publication Date: 2007 Dec PMID: 17932307 Authors: Lee, L. Y. - Kononov, M. E. - Bassuner, B. - Frame, B. R. - Wang, K. - Gelvin, S. B. Journal: Plant Physiol We developed novel plasmids and T-DNA binary vectors that incorporate a modified and more useful form of the superpromoter. The superpromoter consists of a...
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PlantGDB: a resource for comparative plant genomics.: "Publication Date: 2007 Dec 6 PMID: 18063570 Authors: Duvick, J. - Fu, A. - Muppirala, U. - Sabharwal, M. - Wilkerson, M. D. - Lawrence, C. J. - Lushbough, C. - Brendel, V. Journal: Nucleic Acids Res PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB...
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ppdb: a plant promoter database.: "Publication Date: 2007 Oct 18 PMID: 17947329 Authors: Yamamoto, Y. Y. - Obokata, J. Journal: Nucleic Acids Res ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been...
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The pCLEAN Dual Binary Vector System for Agrobacterium-Mediated Plant Transformation.: "Publication Date: 2007 Dec PMID: 17932303 Authors: Thole, V. - Worland, B. - Snape, J. W. - Vain, P. Journal: Plant Physiol The development of novel transformation vectors is essential to the improvement of plant transformation technologies. Here, we report the construction and testing of a new...
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Improved multiple displacement amplification with varphi29 DNA polymerase for genotyping of single human cells.: "Publication Date: 2008 Jun PMID: 18533898 Authors: Kumar, G. - Garnova, E. - Reagin, M. - Vidali, A. Journal: Biotechniques The ability to genotype multiple loci of single cells would be of significant benefit to investigations of cellular processes such as oncogenesis,...
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Improving the photostability of bright monomeric orange and red fluorescent proteins.: "Publication Date: 2008 May 4 PMID: 18454154 Authors: Shaner, N. C. - Lin, M. Z. - McKeown, M. R. - Steinbach, P. A. - Hazelwood, K. L. - Davidson, M. W. - Tsien, R. Y. Journal: Nat Methods All organic fluorophores undergo irreversible photobleaching during prolonged illumination. Although fluorescent...
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pBINPLUS/ARS: an improved plant transformation vector based on pBINPLUS.: "Publication Date: 2008 May PMID: 18466145 Authors: Belknap, W. - Rockhold, D. - McCue, K. Journal: Biotechniques Binary plant transformation vectors are widely used for introduction of transgenes into plants via Agrobacterium tumefaciens-mediated transformation. We report the construction of a binary plant vector...
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