Synthetic Biology:Articles
This list was downloaded from citeulike on 2007/10/09.
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<bibtex> @article{citeulike:1595409, author = {Henkel, Joachim and Maurer, Stephen M. }, citeulike-article-id = {1595409}, doi = {10.1038/msb4100161}, journal = {Mol Syst Biol}, keywords = {syntheticbiology}, month = {June}, title = {The economics of synthetic biology}, url = {http://dx.doi.org/10.1038/msb4100161}, volume = {3}, year = {2007} }
@article{citeulike:1526398, author = {Wong, Wilson W. and Tsai, Tony Y. and Liao, James C. }, citeulike-article-id = {1526398}, doi = {10.1038/msb4100172}, journal = {Mol Syst Biol}, keywords = {degradation protein singlecell ssra synthetic syntheticbiology tag}, month = {July}, title = {Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator}, url = {http://dx.doi.org/10.1038/msb4100172}, volume = {3}, year = {2007} }
@article{citeulike:1595400, author = {Anderson, Christopher J. and Voigt, Christopher A. and Arkin, Adam P. }, citeulike-article-id = {1595400}, doi = {10.1038/msb4100173}, journal = {Mol Syst Biol}, keywords = {gates logic modularity syntheticbiology}, title = {Environmental signal integration by a modular AND gate}, url = {http://dx.doi.org/10.1038/msb4100173}, volume = {3}, year = {2007} }
@article{citeulike:211037, author = {Church, George M. }, citeulike-article-id = {211037}, doi = {10.1038/msb4100007}, journal = {Molecular Systems Biology}, keywords = {church simulation syntheticbiology sysbio systemsbiology thoughtleaders}, month = {March}, number = {1}, pages = {msb4100007-E1--msb4100007-E2}, publisher = {Nature Publishing Group}, title = {From systems biology to synthetic biology}, url = {http://dx.doi.org/10.1038/msb4100007}, volume = {1}, year = {2005} }
@article{citeulike:142488, abstract = {Accurately predicting noise propagation in gene networks is crucial for understanding signal fidelity in natural networks and designing noise-tolerant gene circuits. To quantify how noise propagates through gene networks, we measured expression correlations between genes in single cells. We found that noise in a gene was determined by its intrinsic fluctuations, transmitted noise from upstream genes, and global noise affecting all genes. A model was developed that explains the complex behavior exhibited by the correlations and reveals the dominant noise sources. The model successfully predicts the correlations as the network is systematically perturbed. This approach provides a step toward understanding and manipulating noise propagation in more complex gene networks.}, author = {Pedraza, Juan M. and van Oudenaarden, Alexander }, citeulike-article-id = {142488}, doi = {10.1126/science.1109090}, journal = {Science}, keywords = {avano_lab experiment expression fluctuations gene genecircuits gene_expression gene-expression gene-networks geneticnetworks genevariation n networks noise stochastic stochasticity syntheticbiology}, month = {March}, number = {5717}, pages = {1965--1969}, title = {Noise Propagation in Gene Networks}, url = {http://dx.doi.org/10.1126/science.1109090}, volume = {307}, year = {2005} }
@article{citeulike:687437, abstract = {Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered ligases can 'read' one sequence and then 'write' (by ligation) a separate, distinct sequence, which can in turn be uniquely amplified. The binary deoxyribozymes show great specificity, can discriminate against a small number of mutations in the effector, and can read and recode DNA information with high fidelity even in the presence of excess obscuring genomic DNA. In addition, the binary deoxyribozymes can read non-natural nucleotides and write natural sequence information. The binary deoxyribozyme ligases could potentially be used in a variety of applications, including the detection of single nucleotide polymorphisms in genomic DNA or the identification of short nucleic acids such as microRNAs.}, address = {Center for Systems and Synthetic Biology and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.}, author = {Tabor, J. J. and Levy, M. and Ellington, A. D. }, citeulike-article-id = {687437}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {ecoli rna syntheticbiology}, number = {8}, pages = {2166--2172}, title = {Deoxyribozymes that recode sequence information.}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=pubmed\&dopt=Abstract\&list_uids=16648360}, volume = {34}, year = {2006} }
@article{citeulike:521084, author = {Parikh, Monal R. and Greene, Dina N. and Woods, Kristen K. and Matsumura, Ichiro }, citeulike-article-id = {521084}, doi = {10.1093/protein/gzj010}, issn = {1741-0126}, journal = {Protein Engineering, Design and Selection}, keywords = {biology ecoli efficiency energy pathway rubisco salvage synthetic syntheticbiology}, month = {March}, number = {3}, pages = {113--119}, publisher = {Oxford University Press}, title = {Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli}, url = {http://dx.doi.org/10.1093/protein/gzj010}, volume = {19}, year = {2006} }
@article{citeulike:682586, author = {Misawa, N. and Satomi, Y. and Kondo, K. and Yokoyama, A. and Kajiwara, S. and Saito, T. and Ohtani, T. and Miki, W. }, citeulike-article-id = {682586}, journal = {J. Bacteriol.}, keywords = {ecoli energy syntheticbiology}, month = {November}, number = {22}, pages = {6575--6584}, title = {Structure and functional analysis of a marine bacterial carotenoid biosynthesis gene cluster and astaxanthin biosynthetic pathway proposed at the gene level}, url = {http://jb.asm.org/cgi/content/abstract/177/22/6575}, volume = {177}, year = {1995} }
@article{citeulike:2837, author = {Shaner, Nathan C. and Campbell, Robert E. and Steinbach, Paul A. and Giepmans, Ben N. G. and Palmer, Amy E. and Tsien, Roger Y. }, citeulike-article-id = {2837}, doi = {10.1038/nbt1037}, journal = {Nature Biotechnology}, keywords = {bacteria detection discosoma dsred fluorescence fluorescent fluorescentreporter gfp mcherry monomeric orange protein red rfp syntheticbiology tmars yellow}, month = {November}, number = {12}, pages = {1567+}, title = {Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein}, url = {http://dx.doi.org/10.1038/nbt1037}, volume = {22}, year = {2004} }
@article{citeulike:306413, abstract = {Gene function is typically evaluated by sampling the continuum of gene expression at only a few discrete points corresponding to gene knockout or overexpression. We argue that this characterization is incomplete and present a library of engineered promoters of varying strengths obtained through mutagenesis of a constitutive promoter. A multifaceted characterization of the library, especially at the single-cell level to ensure homogeneity, permitted quantitative assessment correlating the effect of gene expression levels to improved growth and product formation phenotypes in Escherichia coli. Integration of these promoters into the chromosome can allow for a quantitative accurate assessment of genetic control. To this end, we used the characterized library of promoters to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase levels on lycopene production. The multifaceted characterization of promoter strength enabled identification of optimal expression levels for ppc and dxs, which maximized the desired phenotype. Additionally, in a strain preengineered to produce lycopene, the response to deoxy-xylulose-P synthase levels was linear at all levels tested, indicative of a rate-limiting step, unlike the parental strain, which exhibited an optimum expression level, illustrating that optimal gene expression levels are variable and dependent on the genetic background of the strain. This promoter library concept is illustrated as being generalizable to eukaryotic organisms (Saccharomyces cerevisiae) and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.}, address = {Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139.}, author = {Alper, Hal and Fischer, Curt and Nevoigt, Elke and Stephanopoulos, Gregory }, citeulike-article-id = {306413}, doi = {10.1073/pnas.0504604102}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {genecircuits promoters syntheticbiology synthetic_biology transcription}, month = {August}, title = {Tuning genetic control through promoter engineering.}, url = {http://dx.doi.org/10.1073/pnas.0504604102}, year = {2005} }
@article{citeulike:141524, abstract = {The quantitative relation between transcription factor concentrations and the rate of protein production from downstream genes is central to the function of genetic networks. Here we show that this relation, which we call the gene regulation function (GRF), fluctuates dynamically in individual living cells, thereby limiting the accuracy with which transcriptional genetic circuits can transfer signals. Using fluorescent reporter genes and fusion proteins, we characterized the bacteriophage lambda promoter P(R) in Escherichia coli. A novel technique based on binomial errors in protein partitioning enabled calibration of in vivo biochemical parameters in molecular units. We found that protein production rates fluctuate over a time scale of about one cell cycle, while intrinsic noise decays rapidly. Thus, biochemical parameters, noise, and slowly varying cellular states together determine the effective single-cell GRF. These results can form a basis for quantitative modeling of natural gene circuits and for design of synthetic ones.}, address = {Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel.}, author = {Rosenfeld, N. and Young, J. W. and Alon, U. and Swain, P. S. and Elowitz, M. B. }, citeulike-article-id = {141524}, doi = {10.1126/science.1106914}, issn = {1095-9203}, journal = {Science}, keywords = {adaptive-systems cell ecophysiology elowitz experiment expression fluctuations gene genecircuits gene_expression gene-expression genevariation mesophysics molbio molecular-general molecular-signaling morphogenesis n noise no-tag single single_cell single-cell stochasticity syntheticbiology}, month = {March}, number = {5717}, pages = {1962--1965}, title = {Gene regulation at the single-cell level.}, url = {http://dx.doi.org/10.1126/science.1106914}, volume = {307}, year = {2005} }
@article{citeulike:464453, abstract = {Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. Using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. None of the 43 RNA-coding genes were disrupted. Herein, we identify 382 of the 482 M. genitalium protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport. Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth.}, author = {Glass, John I. and Assad-Garcia, Nacyra and Alperovich, Nina and Yooseph, Shibu and Lewis, Matthew R. and Maruf, Mahir and Hutchison, Clyde A. and Smith, Hamilton O. and Venter, Craig J. }, citeulike-article-id = {464453}, doi = {10.1073/pnas.0510013103}, journal = {PNAS}, keywords = {biology creation essential-genes evolution genome minimalgenome minimal_genome minimal-genome religion synthetic syntheticbiology}, month = {January}, number = {2}, pages = {425--430}, title = {Essential genes of a minimal bacterium}, url = {http://dx.doi.org/10.1073/pnas.0510013103}, volume = {103}, year = {2006} }
@article{citeulike:524531, abstract = {Bacteria can sense their environment, distinguish between cell types, and deliver proteins to eukaryotic cells. Here, we engineer the interaction between bacteria and cancer cells to depend on heterologous environmental signals. We have characterized invasin from Yersinia pseudotuburculosis as an output module that enables Escherichia coli to invade cancer-derived cells, including HeLa, HepG2, and U2OS lines. To environmentally restrict invasion, we placed this module under the control of heterologous sensors. With the Vibrio fischeri lux quorum sensing circuit, the hypoxia-responsive fdhF promoter, or the arabinose-inducible araBAD promoter, the bacteria invade cells at densities greater than 10(8)bacteria/ml, after growth in an anaerobic growth chamber or in the presence of 0.02% arabinose, respectively. In the process, we developed a technique to tune the linkage between a sensor and output gene using ribosome binding site libraries and genetic selection. This approach could be used to engineer bacteria to sense the microenvironment of a tumor and respond by invading cancerous cells and releasing a cytotoxic agent.}, address = {Howard Hughes Medical Institute, California Institute of Quantitative Biology Department of Bioengineering, University of California, 717 Potter Street, Room 257 Berkeley, CA 94720, USA.}, author = {Anderson, J. C. and Clarke, E. J. and Arkin, A. P. and Voigt, C. A. }, citeulike-article-id = {524531}, doi = {10.1016/j.jmb.2005.10.076}, issn = {0022-2836}, journal = {J Mol Biol}, keywords = {bacteria bioengineering cancer cpjc ecoli syntheticbiology synthetic_biology}, month = {January}, number = {4}, pages = {619--627}, title = {Environmentally controlled invasion of cancer cells by engineered bacteria.}, url = {http://dx.doi.org/10.1016/j.jmb.2005.10.076}, volume = {355}, year = {2006} } </bibtex>
