DNAhelix (140)DNA assembly and standardisation of biological components

 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. 

 
Interactions among neighboring cells underpin many physiological processes ranging from early development to immune responses. When these interactions do not function properly, numerous pathologies, including infection and cancer, can result. Molecular imaging technologies, especially optical imaging, are uniquely suited to illuminate complex cellular interactions within the context of living...
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Synthetic single-strand oligonucleotides (oligos) with homology to genomic DNA have proved to be highly effective for constructing designed mutations in targeted genomes, a process referred to as recombineering. The cellular functions important for this type of homologous recombination have yet to be determined. Towards this end, we have identified Escherichia coli functions that process the...
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Publication Date: 2013 Apr 29 PMID: 23630273 Authors: Uphoff, S. - Reyes-Lamothe, R. - Garza de Leon, F. - Sherratt, D. J. - Kapanidis, A. N. Journal: Proc Natl Acad Sci U S A Cellular DNA damage is reversed by balanced repair pathways that avoid accumulation of toxic intermediates. Despite their importance, the organization of DNA repair pathways and the function of repair enzymes in vivo have...
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Publication Date: 2013 Apr 29 PMID: 23630319 Authors: Williams, K. - Savageau, M. A. - Blumenthal, R. M. Journal: Nucleic Acids Res Restriction-modification (RM) systems are extremely widespread among bacteria and archaea, and are often specified by mobile genetic elements. In type II RM systems, where the restriction endonuclease (REase) and protective DNA methyltransferase (MTase) are separate...
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Nature Protocols 8, 1019 (2013). doi:10.1038/nprot.2013.060 Authors: Daphne H E W Huberts, Sung Sik Lee, Javier Gonzáles, Georges E Janssens, Ima Avalos Vizcarra & Matthias Heinemann This protocol describes the production and operation of a microfluidic dissection platform for long-term, high-resolution imaging of budding yeast cells. At the core of this platform is an array of micropads...
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Nature Methods 10, 407 (2013). doi:10.1038/nmeth.2413 Authors: Nathan C Shaner, Gerard G Lambert, Andrew Chammas, Yuhui Ni, Paula J Cranfill, Michelle A Baird, Brittney R Sell, John R Allen, Richard N Day, Maria Israelsson, Michael W Davidson & Jiwu Wang We report a monomeric yellow-green fluorescent protein, mNeonGreen, derived from a tetrameric fluorescent protein from the cephalochordate...
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Nature Methods 10, 410 (2013). doi:10.1038/nmeth.2433 Authors: Bogumil J Karas, Jelena Jablanovic, Lijie Sun, Li Ma, Gregory M Goldgof, Jason Stam, Adi Ramon, Micah J Manary, Elizabeth A Winzeler, J Craig Venter, Philip D Weyman, Daniel G Gibson, John I Glass, Clyde A Hutchison, Hamilton O Smith & Yo Suzuki Transfer of genomes into yeast facilitates genome engineering for genetically...
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Publication Date: 2013 Apr 26 PMID: 23625964 Authors: Muller, K. - Engesser, R. - Schulz, S. - Steinberg, T. - Tomakidi, P. - Weber, C. C. - Ulm, R. - Timmer, J. - Zurbriggen, M. D. - Weber, W. Journal: Nucleic Acids Res The emergence and future of mammalian synthetic biology depends on technologies for orchestrating and custom tailoring complementary gene expression and signaling processes in a...
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Publication Date: 2013 Apr 24 PMID: 23614576 Authors: Faure, E. - Peter, I. S. - Davidson, E. H. Journal: J Comput Biol Abstract The efficacy of a newly created software package for predictive modeling of developmental gene regulatory networks (GRNs) has recently been demonstrated (Peter et al., 2012 ). The program GeNeTool computes spatial gene expression patterns based on GRN interactions and...
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Publication Date: 2013 Mar 24 PMID: 23524394 Authors: Gebhardt, J. C. - Suter, D. M. - Roy, R. - Zhao, Z. W. - Chapman, A. R. - Basu, S. - Maniatis, T. - Xie, X. S. Journal: Nat Methods Imaging single fluorescent proteins in living mammalian cells is challenged by out-of-focus fluorescence excitation. To reduce out-of-focus fluorescence we developed reflected light-sheet microscopy (RLSM), a...
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Publication Date: 2013 Apr 1 PMID: 23576716 Authors: Alvarez-Ponce, D. - Lopez, P. - Bapteste, E. - McInerney, J. O. Journal: Proc Natl Acad Sci U S A The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the...
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Publication Date: 2013 Mar 31 PMID: 23542886 Authors: Karas, B. J. - Jablanovic, J. - Sun, L. - Ma, L. - Goldgof, G. M. - Stam, J. - Ramon, A. - Manary, M. J. - Winzeler, E. A. - Venter, J. C. - Weyman, P. D. - Gibson, D. G. - Glass, J. I. - Hutchison, C. A. 3rd - Smith, H. O. - Suzuki, Y. Journal: Nat Methods Transfer of genomes into yeast facilitates genome engineering for genetically...
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How-To: DIY Bioprinter: "Interesting Instructable from Dr. Patrik D'haeseleer, Harvard-trained computational biologist and denizen of Sunnyvale biotech hackerspace BioCurious. Bioprinting, which is basically 3D printing with living cells, has been much in the news lately, with breathless tales of fully 3D-printed living organs and replacement body parts. There is of course a fair bit of hype...
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Protein engineering has traditionally relied on random mutagenesis strategies to generate diverse libraries, which require high-throughput screening or selection methods to identify rare variants. Alternatively, approaches to semi-rational library construction can be used to minimize the screening load and enhance the efficiency by which improved mutants may be identified. Such methods are...
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University of Oxford chemists custom-built a 3D printer that fabricates 'synthetic tissue,' or rather structures with tissue-like functions. Eventually, the technology could be used to crank out replacement tissue that could replace damaged human tissue or be used in new drug delivery systems. The material consist of a network of water droplets encapsulated in lipids, or fat molecules. 'The...
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Panasonic, together with the Belgium-based research institution IMEC, has developed a DNA testing chip that automates all stages of obtaining genetic information, including preprocessing. This development is expected to enable personalized, tailor-made therapy to become widespread. ‘This is the chip we’ve actually developed. As you can see, it’s less than half the size of a business...
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L2 annotations Hide 1 2 GEORGE DVORSKY These spectacular images show why they call it the ‘OMG’ microscope Back in 2011, GE unveiled DeltaVision OMX Blaze, a state-of-the art microscope that uses a combination of optics and powerful computer algorithms. Using a technique called 3D structured illumination microscopy (SIM), OMX can see objects as small as 100...
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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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Publication Date: 2012 Jun 22 PMID: 22726436 Authors: Kraemer, J. A. - Erb, M. L. - Waddling, C. A. - Montabana, E. A. - Zehr, E. A. - Wang, H. - Nguyen, K. - Pham, D. S. - Agard, D. A. - Pogliano, J. Journal: Cell Tubulins are essential for the reproduction of many eukaryotic viruses, but historically, bacteriophage were assumed not to require a cytoskeleton. Here, we identify a tubulin-like...
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Publication Date: 2012 Jun 7 PMID: 22676326 Authors: Anzaldi, L. J. - Munoz-Fernandez, D. - Erill, I. Journal: BMC Bioinformatics ABSTRACT: BACKGROUND: Manipulation, editing and basic processing of DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed...
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Publication Date: 2012 Jun 16 PMID: 22705793 Authors: Kim, H. - Han, H. - Ahn, J. - Lee, J. - Cho, N. - Jang, H. - Kim, H. - Kwon, S. - Bang, D. Journal: Nucleic Acids Res We developed a highly scalable 'shotgun' DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin...
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Publication Date: 2012 Jun 26 PMID: 22740649 Authors: Briggs, A. W. - Rios, X. - Chari, R. - Yang, L. - Zhang, F. - Mali, P. - Church, G. M. Journal: Nucleic Acids Res DNA built from modular repeats presents a challenge for gene synthesis. We present a solid surface-based sequential ligation approach, which we refer to as iterative capped assembly (ICA), that adds DNA repeat monomers...
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Publication Date: 2012 Jun 19 PMID: 22718978 Authors: Ham, T. S. - Dmytriv, Z. - Plahar, H. - Chen, J. - Hillson, N. J. - Keasling, J. D. Journal: Nucleic Acids Res 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 of recording information about 'legacy' parts, such as...
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TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction.: "Publication Date: 2012 Jun 12 PMID: 22693217 Authors: Doyle, E. L. - Booher, N. J. - Standage, D. S. - Voytas, D. F. - Brendel, V. P. - Vandyk, J. K. - Bogdanove, A. J. Journal: Nucleic Acids Res Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant...
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Publication Date: 2011 Dec 28 PMID: 22209624 Authors: Ma, S. - Saaem, I. - Tian, J. Journal: Trends Biotechnol Accurate, economical and high-throughput gene and genome synthesis is essential to the development of synthetic biology and biotechnology. New large-scale gene synthesis methods harnessing the power of DNA microchips have recently been demonstrated. Yet, the technology is still...
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Publication Date: 2012 Mar 9 PMID: 22403384 Authors: Paige, J. S. - Nguyen-Duc, T. - Song, W. - Jaffrey, S. R. Journal: Science Genetically encoded sensors are powerful tools for imaging intracellular metabolites and signaling molecules. However, developing sensors is challenging because they require proteins that undergo conformational changes upon binding the desired target molecule. We...
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J Biol Eng. 2012 Feb 28;6(1):1 Authors: Chen J, Densmore D, Ham TS, Keasling JD, Hillson NJ Abstract ABSTRACT: BACKGROUND: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must...
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Methods Mol Biol. 2012;852:197-213 Authors: Villalobos A, Welch M, Minshull J Abstract The promise of synthetic biology lies in the creation of novel function from the proper combination of genetic elements. De novo gene synthesis has become a cost-effective method for building virtually any conceptualized genetic construct, removing the constraints of extant sequences, and greatly...
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Methods Mol Biol. 2012;852:11-21 Authors: Gibson DG Abstract The yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp and can be as long as 200 nucleotides in length to produce kilobase-sized synthetic DNA molecules....
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Methods Mol Biol. 2012;852:151-63 Authors: Linshiz G, Yehezkel TB, Shapiro E Abstract Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology, and synthetic biology. We developed an error-correcting recursive construction procedure that attempts to address this challenge. Making DNA molecules from synthetic...
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Scientists have discovered how bacteriophages - viruses that infect bacteria - manage to pierce the bacterial membrane: with an iron spike. When they crystallized this smaller protein fragment, the x-rays were finally able to resolve its structure, and from this the team had the very first picture of the tip of the spike: a single iron atom held ...
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