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. 

 
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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At the Advances in Genome Biology and Technology 2012 conference (AGBT), Oxford Nanopore Technologies Ltd. announced it is entering the gene-sequencing battle with a disposable DNA sequencer that will sell for under $900 in the second half of 2012. The USB-size sequencer is called the MinION (min-ion), and has already demonstrated the potential to bring genome sequencing and personalized...
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rsTagRFP is the first monomeric red fluorescent protein (FP) with reversibly photoswitchable absorbance spectra. The switching is realized by irradiation of rsTagRFP with blue (440 nm) and yellow (567 nm) light, turning the protein fluorescence ON and OFF, respectively. It is perhaps the most useful probe in this color class that has yet been reported. Because of the photoswitchable absorbance,...
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Copepods are the dominant taxa in zooplankton communities of the ocean world-wide. Although bioluminescence of certain copepods has been known for more than a hundred years, there is very limited information about the structure and evolutionary history of copepod luciferase genes. Here we report the cDNA sequences of 11 copepod luciferases isolated from the superfamily Augaptiloidea in the order...
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Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics...
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Megabase-sized DNA is crucial to modern genomics research of all organisms. Among the preparation methods developed, the nuclei method is the simplest and most widely used for preparing high-quality megabase-sized DNA from divergent organisms. In this method, nuclei are first isolated by physically grinding the... Preparation of megabase-sized DNA from a variety of organisms using the nuclei...
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Protein expression in Escherichia coli at 15-25 degrees C is widely used to increase the solubility of recombinant proteins. However, many recombinant proteins are insolubly expressed even at those low temperatures. Here, we show that recombinant proteins can be expressed as soluble forms by simply lowering temperature to 6-10 degrees C without cold adapted chaperon systems. By using E. coli...
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This shows a model of the "threading tetra-intercalator " bound up in the double helix of a DNA sequence. Chemists at The University of Texas at Austin have created a molecule that's so good at tangling itself inside the double helix of a DNA sequence that it can stay there for up to 16 days before the DNA liberates itself, much longer than any other molecule reported. New molecule can tangle...
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New England Biolabs, Inc. (NEB) and Synthetic Genomics, Inc. (SGI) jointly announce that they have entered into a licensing agreement whereby NEB will introduce a master mix based on Gibson Assembly™, a revolutionary technology developed by Dr. Daniel Gibson and his colleagues at the J. Craig Venter Institute (JCVI) as part of a program sponsored by SGI. Gibson Assembly enables the rapid...
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Tobacco etch virus (TEV) protease is widely used to remove tags from recombinant fusion proteins because of its stringent sequence specificity. It is generally accepted that the high concentrations of salts or other special agents in most protein affinity chromatography buffers can affect enzyme activity, including that of TEV protease. Consequently, tedious desalination or the substitution of...
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In bacteria, many small regulatory RNAs (sRNAs) are induced in response to specific environmental signals or stresses and act by base-pairing with mRNA targets to affect protein translation or mRNA stability. In Escherichia coli, the gene for the sRNA IS061/IsrA, here renamed McaS, was predicted to reside in an intergenic region between abgR, encoding a transcription regulator and ydaL, encoding...
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Xenogeneic silencing proteins facilitate horizontal gene transfer by silencing expression of AT-rich sequences. By virtue of their activity these proteins serve as master regulators of a variety of important functions including motility, drug resistance, and virulence. Three families of silencers have been identified to date: the H-NS like proteins of Gram-negative bacteria, the MvaT like...
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Quorum-sensing systems mediate chemical communication between bacterial cells, coordinating cell-density-dependent processes like biofilm formation and virulence-factor expression. In the proteobacterial LuxI/LuxR quorum sensing paradigm, a signaling molecule generated by an enzyme (LuxI) diffuses between cells and allosterically stimulates a transcriptional regulator (LuxR) to activate its...
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ABSTRACT: BACKGROUND: In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary...
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Error correction in gene synthesis technology.: "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...
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Expression and purification of E. coli BirA biotin ligase for in vitro biotinylation.: "Publication Date: 2012 Jan 2 PMID: 22227598 Authors: Li, Y. - Sousa, R. Journal: Protein Expr Purif The extremely tight binding between biotin and avidin or streptavidin makes labeling proteins with biotin a useful tool for many applications. BirA is the Escherichia coli biotin ligase that site-specifically...
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SLiCE: a novel bacterial cell extract-based DNA cloning method.: "Publication Date: 2012 Jan 12 PMID: 22241772 Authors: Zhang, Y. - Werling, U. - Edelmann, W. Journal: Nucleic Acids Res We describe a novel cloning method termed SLiCE (Seamless Ligation Cloning Extract) that utilizes easy to generate bacterial cell extracts to assemble multiple DNA fragments into recombinant DNA molecules in a...
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Although the focus on CES is on consumer technology, it's not unusual to see announcements for products that companies will use to provide services to consumers. Even by that standard, one of the announcements made at the show this year was rather unusual, since it was for a consumer service that's not quite there yet: personal genomics. Right now, two companies are pushing hard to become the...
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It’s Easy Being Green Now RNA can glow in the cell, as only proteins could in the past. Finding out where specific RNA molecules are located in a cell just got a whole lot easier. Green fluorescent protein (GFP), makes protein localization in living cells, or even in whole animals, as simple as cloning a gene. But until now, there wasn’t an equivalent for RNA. The number of...
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Unipro UGENE - free full-featured software for manipulation of DNA sequences Download from http://ugene.unipro.ru/ List of Features: • Creating, editing and annotating nucleic acid and protein sequences • Search through online databases: NCBI, PDB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL • Multiple sequence alignment: Clustal, MUSCLE, Kalign, MAFFT, T-Coffee • Online and...
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A snapshot of the most highly ranked articles in genomics, genetics and related areas, from Faculty of 1000 By Sabrina Richards | September 19, 2011 from: http://the-scientist.com/2011/09/19/top-7-in-genomics-genetics/ HIV budding from cell membrane.WIKIMEDIA COMMONS, NIH 1. Lighting up RNA A novel technique for tagging and following RNA processes in live cells promises to...
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