DNA assembly and standardisation of biological components

DNAhelix (140)

The use of standardised components is found in all fields of engineering, where it allows the benefits of abstraction, decoupling and insulation from unnecessary detail in the design of complex systems. The ability to construct new DNA sequences has far outpaced our capacity to design the genetic circuits that these might encode. Synthetic Biology promises simplified design using modular standardised DNA components. 

 
Publication Date: 2013 Mar PMID: 23505358 Authors: Amin, M. - Porter, S. L. - Soyer, O. S. Journal: PLoS Comput Biol Bacteria sense and respond to their environment through signaling cascades generally referred to as two-component signaling networks. These networks comprise histidine kinases and their cognate response regulators. Histidine kinases have a number of biochemical activities: ATP...
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Publication Date: 2013 Mar 19 PMID: 23511967 Authors: Cambray, G. - Guimaraes, J. C. - Mutalik, V. K. - Lam, C. - Mai, Q. A. - Thimmaiah, T. - Carothers, J. M. - Arkin, A. P. - Endy, D. Journal: Nucleic Acids Res The reliable forward engineering of genetic systems remains limited by the ad hoc reuse of many types of basic genetic elements. Although a few intrinsic prokaryotic transcription...
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Publication Date: 2013 Mar 14 PMID: 23496817 Authors: Cheng, J. - Zeng, X. - Ren, G. - Liu, Z. Journal: BMC Bioinformatics BACKGROUND: Chloroplast is an essential organelle in plants which contains independent genome. Chloroplast genomes have been widely used for plant phylogenetic inference recently. The number of complete chloroplast genomes increases rapidly with the development of various...
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Publication Date: 2013 Mar 7 PMID: 23497278 Authors: Zhong, Y. - Wan, Y. W. - Pang, K. - Chow, L. M. - Liu, Z. Journal: BMC Bioinformatics Gene expression analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles....
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Publication Date: 2013 Mar 16 PMID: 23511112 Authors: Albus, C. A. - Rishal, I. - Fainzilber, M. Journal: Trends Cell Biol Neurons exhibit great size differences, and must coordinate biosynthesis rates in cell bodies with the growth needs of different lengths of axons. Classically, axon growth has been viewed mainly as a consequence of extrinsic influences. However, recent publications have...
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Publication Date: 2013 Mar 10 PMID: 23474465 Authors: Mutalik, V. K. - Guimaraes, J. C. - Cambray, G. - Lam, C. - Christoffersen, M. J. - Mai, Q. A. - Tran, A. B. - Paull, M. - Keasling, J. D. - Arkin, A. P. - Endy, D. Journal: Nat Methods An inability to reliably predict quantitative behaviors for novel combinations of genetic elements limits the rational engineering of biological systems. We...
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Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.1 Authors: Carlos F Lopez, Jeremy L Muhlich, John A Bachman & Peter K Sorger Programming biological models in Python using PySB (Via Molecular Systems Biology.)
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Publication Date: 2013 Mar PMID: 23477381 Authors: Matsumura, I. Journal: Biotechniques Gene Splicing by Overlap Extension (SOE), described in a BioTechniques Research Report 23 years ago, is still widely used today in spite of changes in technology and scientific fashion. The history of SOE offers practical lessons for those who seek the best techniques, and for those who strive to develop...
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Functional genomics requires vector construction for protein expression and functional characterization of target genes; therefore, a simple, flexible, and low-cost molecular manipulation strategy will be highly advantageous for genomics approaches. Here, we describe a ohm-PCR strategy that enables multiple types of sequence modification, including precise insertion, deletion and substitution, in...
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Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR- and csrA-repressed S17-1) capable of producing 2...
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Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have...
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 Felix Salazar's macro photography of a coral reef offers a serene and colorful tour through an almost alien universe. Seen up close and in such brilliant colors, it's each to forget that these are creatures from our own planet. So head over to Salazar's website, scroll through the photos, and forget about Earth for a minute or two. More » Macro photos of coral take us to underwater alien...
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Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.: "Publication Date: 2012 Dec 23 PMID: 23263691 Authors: Hocine, S. - Raymond, P. - Zenklusen, D. - Chao, J. A. - Singer, R. H. Journal: Nat Methods Live-cell imaging of mRNA yields important insights into gene expression, but it has generally been limited to the labeling of one RNA species and has never been...
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ERISdb: a Database of Plant Splice Sites and Splicing Signals.: "Publication Date: 2013 Jan 7 PMID: 23299413 Authors: Szczesniak, M. W. - Kabza, M. - Pokrzywa, R. - Gudys, A. - Makalowska, I. Journal: Plant Cell Physiol Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. There are numerous factors that affect the process...
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Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli.: "Publication Date: 2012 Dec PMID: 23271961 Authors: Brewster, R. C. - Jones, D. L. - Phillips, R. Journal: PLoS Comput Biol One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will. As a step in that direction, we have...
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Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012 Jun 19; Authors: Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD Abstract The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable...
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A synthetic biology framework for programming eukaryotic transcription functions.: " Related Articles Cell. 2012 Aug 3;150(3):647-58 Authors: Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ Abstract Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for...
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Molecular code cracked: "The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins. When a gene is switched on, it is copied into RNA. This RNA is then used to make proteins that are required by the organism for all of its vital functions. If a gene is defective, its RNA copy and the proteins made from this will...
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A synthetic biology framework for programming eukaryotic transcription functions. Cell. 2012 Aug 3;150(3):647-58 Authors: Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ Abstract Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing...
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Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res. 2012 Jun 28; Authors: Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA Abstract Synthetic genetic sensors and circuits enable programmable control over the timing and conditions of gene expression. They are being increasingly incorporated into the control of complex, multigene pathways and...
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