.png)
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.
|
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...
| 1528 hits
| Read more
|
|
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...
| 1474 hits
| Read more
|
|
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...
| 1300 hits
| Read more
|
|
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...
| 1464 hits
| Read more
|
|
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...
| 1646 hits
| Read more
|
|
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...
| 1378 hits
| Read more
|
 |
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...
| 1337 hits
| Read more
|
 |
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...
| 1602 hits
| Read more
|
.png) |
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...
| 1278 hits
| Read more
|
 |
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...
| 1936 hits
| Read more
|
 |
A new device for directing fluids is designed to deliver chemical cues directly to petri dishes without disturbing cells.
http://the-scientist.com/2011/10/04/next-generation-microfluidics-for-the-dish/
Microfluidic quadrupoleMOHAMMAD AMEEN QASAIMEH, MCGILL UNIVERSITY
THE DEVICE: Microfluidic devices offer precise, small-scale methods of delivering fluids to organisms, tissues,...
| 1479 hits
| Read more
|
|
Building enhancers from the ground up: a synthetic biologyapproach.
Amit R, Garcia HG, Phillips R, Fraser SE.
Source
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA.
Cell. 2011 Jul 8;146(1):105-18.
Abstract
A challenge of the synthetic...
| 1259 hits
| Read more
|
|
Transcription activator like effectors (TALEs) are natural typeIII effector proteins secreted by numerous species of Xanthomonas to modulate gene expression in host plants and to facilitate bacterial colonization and survival. Recent studies of TALEs have revealed an elegant code linking the repetitive region of TALEs with their target DNA-binding site (Boch et al., Science 2009; Moscou et...
| 1312 hits
| Read more
|
|
Haley Bridger, February 8th, 2011
http://www.broadinstitute.org/blog/tale-tal-effectors
Species of Xanthomonas bacteria cause blight in many types of plants, including plum and cherry plants. These bacteria use TAL effectors as a weapon against their hosts. Image courtesy of University of Georgia Plant Pathology Archive, University of Georgia, Bugwood.org
Two years ago, researchers in Germany...
| 4740 hits
| Read more
|
|
Bioeng Bugs. 2010 7;1(4):274-281
Authors: Chandran D, Bergmann FT, Sauro HM
Synthetic biology is an engineering discipline that builds on modeling practices from systems biology and wet-lab techniques from genetic engineering. As synthetic biology advances, efficient procedures will be developed that will allow a synthetic biologist to design, analyze and build biological networks. In this...
| 4506 hits
| Read more
|
|
Conf Proc IEEE Eng Med Biol Soc. 2010;1:768-74
Authors: Hallinan JS, Misirli G, Wipat A
Biological systems are inherently stochastic, a fact which is often ignored when simulating genetic circuits. Synthetic biology aims to design genetic circuits de novo, and cannot therefore afford to ignore the effects of stochastic behavior. Since computational design tools will be essential for...
| 4453 hits
| Read more
|
|
Nat Nanotechnol. 2011 Feb;6(2):116-20
Authors: Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H
Synthetic nanostructures consisting of biomacromolecules such as nucleic acids have been constructed using bottom-up approaches. In particular, Watson-Crick base pairing has been used to construct a variety of two- and three-dimensional DNA nanostructures....
| 4452 hits
| Read more
|
|
Cell. 2011 Jan 7;144(1):119-31
Authors: O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA
The flexibility of MAPK cascade responses enables regulation of a vast array of cell fate decisions, but elucidating the mechanisms underlying this plasticity is difficult in endogenous signaling networks. We constructed insulated mammalian MAPK cascades in yeast to explore how intrinsic and extrinsic...
| 4265 hits
| Read more
|
|
Integr Biol (Camb). 2011 Feb 8;3(2):97-108
Authors: Macdonald JT, Barnes C, Kitney RI, Freemont PS, Stan GB
A proliferation of new computational methods and software tools for synthetic biology design has emerged in recent years but the field has not yet reached the stage where the design and construction of novel synthetic biology systems has become routine. To a large degree this is due to...
| 1344 hits
| Read more
|
|
Nat Protoc. 2011 Jan;6(1):89-96
Authors: Noskov VN, Chuang RY, Gibson DG, Leem SH, Larionov V, Kouprina N
Circular yeast artificial chromosomes (YACs) provide significant advantages for cloning and manipulating large segments of genomic DNA in Saccharomyces cerevisiae. However, it has been difficult to exploit these advantages, because circular YACs are difficult to isolate and purify. Here we...
| 4348 hits
| Read more
|
|
Int J Biochem Cell Biol. 2010 Nov 23;
Authors: Marchisio MA, Rudolf F
An essential feature of synthetic biology devices is the conversion of signals from the exterior of the cell into specific cellular events such as the synthesis of a fluorescent protein. In the first synthetic gene circuits, signal transduction was accomplished via inducible or repressible transcription factors. Today, these...
| 4273 hits
| Read more
|
|
Bioeng Bugs. 2010 9;1(5):303-308
Authors: Berry DA
Volatile fuel costs, the need to reduce greenhouse gas emissions and fuel security concerns are driving efforts to produce sustainable renewable fuels and chemicals. Petroleum comes from sunlight, CO(2) and water converted via a biological intermediate into fuel over a several million year timescale. It stands to reason that using biology to...
| 4040 hits
| Read more
|
|
Biotechnol J. 2011 Feb 16;
Authors: Krivoruchko A, Siewers V, Nielsen J
Constant progress in genetic engineering has given rise to a number of promising areas of research that facilitated the expansion of industrial biotechnology. The field of metabolic engineering, which utilizes genetic tools to manipulate microbial metabolism to enhance the production of compounds of interest, has had a...
| 4255 hits
| Read more
|
|
Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler.
Mol Biosyst. 2011 Feb 16;
Authors: Shao Z, Luo Y, Zhao H
We report a synthetic biology strategy for rapid genetic manipulation of natural product biosynthetic pathways. Based on DNA assembler, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the...
| 3951 hits
| Read more
|
|
Synthetic biology: A foundation for multi-scale molecular biology.
Bioeng Bugs. 2010 9;1(5):309-312
Authors: Bower AG, McClintock MK, Fong SS
The field of synthetic biology has made rapid progress in a number of areas including method development, novel applications and community building. In seeking to make biology 'engineerable,' synthetic biology is increasing the accessibility of...
| 1218 hits
| Read more
|
 |
Alan Turing’s Patterns in Nature, and Beyond
By Brandon Keim at Wired
February 22, 2011
View as gallery
Alan Turing's Biology Paper
Near the end of his life, the great mathematician Alan Turing wrote his first and last paper on biology and chemistry, about how a certain type of chemical reaction ought to produce many patterns seen in nature.
Called "The Chemical Basis of...
| 2462 hits
| Read more
|
 |
Mussels are remarkable creatures, not only in how good they taste steamed and buttered, but also in their ability to cling to rocks that are pounded by ocean waves. Their tenacious grip comes courtesy of byssal holdfast fibers that are secreted by the mussels themselves. Last year, scientists from Germany’s Max Planck Institute for Colloids and Interfaces analyzed these fibers in an...
| 6624 hits
| Read more
|
 |
Scientists have used gelatinous hydrogel to create an inexpensive new type of biochemical sensor that is highly sensitive, sturdy, long-lasting, and has few moving parts. The gel expands or contracts according to the acidity of its environment, a quality that allows the sensor to measure changes in pH down to one one-thousandth on the pH scale. This amount of accuracy, along with its...
| 6430 hits
| Read more
|
|
Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics.: "Publication Date: 2011 Jan 15 PMID: 21242078 Authors: Wu, B. - Piatkevich, K. D. - Lionnet, T. - Singer, R. H. - Verkhusha, V. V. Journal: Curr Opin Cell Biol Recent developments in reagent design can address problems in single cells that were not previously approachable. We have...
| 1222 hits
| Read more
|
|
Molecular design of the microbial cell surface toward the recovery of metal ions.: "Publication Date: 2011 Jan 17 PMID: 21247751 Authors: Kuroda, K. - Ueda, M. Journal: Curr Opin Biotechnol The genetic engineering of microorganisms to adsorb metal ions is an attractive method to facilitate the environmental cleanup of metal pollution and to enrich the recovery of metal ions such as rare metal...
| 2763 hits
| Read more
|
|
The silica-binding Si-tag functions as an affinity tag even under denaturing conditions.: "Publication Date: 2011 Jan 28 PMID: 21277372 Authors: Ikeda, T. - Motomura, K. - Agou, Y. - Ishida, T. - Hirota, R. - Kuroda, A. Journal: Protein Expr Purif We recently reported a one-step affinity purification method using a silica-binding protein, designated Si-tag, as a fusion partner and silica...
| 2683 hits
| Read more
|
|
The role of codon selection in regulation of translation efficiency deduced from synthetic libraries.: "Publication Date: 2011 Feb 1 PMID: 21284851 Authors: Navon, S. - Pilpel, Y. Journal: Genome Biol ABSTRACT: BACKGROUND: Translation efficiency is affected by a diversity of parameters, including secondary structure of the transcript and its codon usage. Here we examined the effects of codon...
| 2660 hits
| Read more
|
|
Directed evolution of a protein container.: "Publication Date: 2011 Feb 4 PMID: 21292977 Authors: Worsdorfer, B. - Woycechowsky, K. J. - Hilvert, D. Journal: Science Confinement of enzymes in protein nanocompartments represents a potentially powerful strategy for controlling catalytic activity in cells. By using a simple electrostatically based tagging system for protein encapsulation, we...
| 2754 hits
| Read more
|
|
Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns.: "Publication Date: 2011 Feb 6 PMID: 21297621 Authors: Hampel, S. - Chung, P. - McKellar, C. E. - Hall, D. - Looger, L. L. - Simpson, J. H. Journal: Nat Methods We developed a multicolor neuron labeling technique in Drosophila melanogaster that combines the power to specifically...
| 2601 hits
| Read more
|
|
Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster.: "Publication Date: 2011 Feb 6 PMID: 21297619 Authors: Hadjieconomou, D. - Rotkopf, S. - Alexandre, C. - Bell, D. M. - Dickson, B. J. - Salecker, I. Journal: Nat Methods To facilitate studies of neural network architecture and formation, we generated three Drosophila melanogaster variants of the...
| 2730 hits
| Read more
|
|
Indole transport across Escherichia coli membranes.: "Publication Date: 2011 Feb 4 PMID: 21296966 Authors: Pinero-Fernandez, S. - Chimerel, C. - Keyser, U. F. - Summers, D. K. Journal: J Bacteriol Indole has many, diverse roles in bacterial signaling. It regulates the transition from exponential to stationary phase, it is involved in the control of plasmid stability, and it influences biofilm...
| 2748 hits
| Read more
|
|
Development of an artificial cell, from self-organization to computation and self-reproduction [Biophysics and Computational Biology]: "This article describes the state and the development of an artificial cell project. We discuss the experimental constraints to synthesize the most elementary cell-sized compartment that can self-reproduce using synthetic genetic information. The original idea was...
| 2535 hits
| Read more
|
|
Transcription in action:
In a work just published at Nature, Churchman and Weissman (2011) describe a new method for directly capturing and sequencing elongating, or nascent, RNA transcripts. The authors then use this method to provide a detailed look at the transcriptional process in action, revealing a histone modification-dependent mechanism that constrains genome-wide antisense...
| 2305 hits
| Read more
|
|
Rapid blue-light-mediated induction of protein interactions in living cells.: "Publication Date: 2010 Dec PMID: 21037589 Authors: Kennedy, M. J. - Hughes, R. M. - Peteya, L. A. - Schwartz, J. W. - Ehlers, M. D. - Tucker, C. L. Journal: Nat Methods Dimerizers allowing inducible control of protein-protein interactions are powerful tools for manipulating biological processes. Here we describe...
| 3172 hits
| Read more
|
 |
Geneious 5.3.0
Geneiousis research software for biologists, not computer scientists.
Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution! Its ease of use makes bioinformatics accessible to any biologist. It even runs on all major operating systems and is very affordable.
Features include: Sequence alignment, Contig assembly,...
| 3915 hits
| Read more
|
 |
The Cambridge iGEM2010 team built a set of BioBricks to allow bioluminescence in a wide range of colours which have applications both as reporters for biosensors and as natural light sources. They adopted a number of strategies to extend the use of firefly luciferase: (i) codon optimisation for increased light output, (ii) use of a luciferin regenerating enzyme and (iii) mutagenesis to create...
| 1385 hits
| Read more
|
 |
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10)
Recent advances in the study of natural products made by bacteria have laid the foundation for engineering these molecules and for developing cost-effective ways to manufacture them. In our lab, we study a number of natural...
| 7526 hits
| Read more
|
|
Multifactorial determinants of protein expression in prokaryotic open reading frames.: "Publication Date: 2010 Oct 8 PMID: 20727358 Authors: Allert, M. - Cox, J. C. - Hellinga, H. W. Journal: J Mol Biol A quantitative description of the relationship between protein expression levels and open reading frame (ORF) nucleotide sequences is important for understanding natural systems, designing...
| 3576 hits
| Read more
|
|
Design, construction and characterization of a set of insulated bacterial promoters.: "Publication Date: 2010 Sep 15 PMID: 20843779 Authors: Davis, J. H. - Rubin, A. J. - Sauer, R. T. Journal: Nucleic Acids Res We have generated a series of variable-strength, constitutive, bacterial promoters that act predictably in different sequence contexts, span two orders of magnitude in strength and...
| 1301 hits
| Read more
|
|
A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization.: "Publication Date: 2010 Sep 3 PMID: 20603133 Authors: Hoi, H. - Shaner, N. C. - Davidson, M. W. - Cairo, C. W. - Wang, J. - Campbell, R. E. Journal: J Mol Biol The use of green-to-red photoconvertible fluorescent proteins (FPs) enables researchers to highlight a subcellular population of a fusion...
| 3716 hits
| Read more
|
|
Bathy phytochromes in rhizobial soil bacteria.: "Publication Date: 2010 Oct PMID: 20675484 Authors: Rottwinkel, G. - Oberpichler, I. - Lamparter, T. Journal: J Bacteriol Phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. Prototypical phytochromes have a Pr ground state that absorbs in the red spectral range and is converted by light into the Pfr form,...
| 3623 hits
| Read more
|
|
Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the Eut-BMC.: "Publication Date: 2010 Sep 17 PMID: 20851901 Authors: Takenoya, M. - Nikolakakis, K. - Sagermann, M. Journal: J Bacteriol The ethanolamine utilizing microcompartment of E. coli (Eut-BMC) is a polyhedrally shaped organelle that harbors specific enzymes for the catabolic...
| 3535 hits
| Read more
|
|
Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the Eut-BMC.: "Publication Date: 2010 Sep 17 PMID: 20851901
Authors: Takenoya, M. - Nikolakakis, K. - Sagermann, M.
Journal: J Bacteriol
The ethanolamine utilizing microcompartment of E. coli (Eut-BMC) is a polyhedrally shaped organelle that harbors specific enzymes for...
| 3526 hits
| Read more
|
|
The Carboxysome Shell Is Permeable to Protons.: "Publication Date: 2010 Sep 24 PMID: 20870775 Authors: Menon, B. B. - Heinhorst, S. - Shively, J. M. - Cannon, G. C. Journal: J Bacteriol Bacterial microcompartments (BMCs) are polyhedral organelles found in an increasingly wide variety of bacterial species. These structures, as typified by carboxysomes of cyanobacteria and many chemoautotrophs,...
| 3441 hits
| Read more
|
|
A new tagged-TEV protease: Construction, optimisation of production, purification and test activity.
A new tagged-TEV protease: Construction, optimisation of production, purification and test activity.: "Publication Date: 2010 Sep 9 PMID: 20817099 Authors: Miladi, B. - Bouallagui, H. - Dridi, C. - El Marjou, A. - Boeuf, G. - Di Martino, P. - Dufour, F. - Elm'selmi, A. Journal: Protein Expr Purif The Tobacco Etch Virus (TEV) protease is frequently used in the cleavage of recombinant fusion...
| 3517 hits
| Read more
|
Page 2 of 4