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  1 / 1914 MEDLINE  
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[PMID]:29389936
[Au] Autor:Mahajan T; Rai K
[Ad] Endereço:Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, India.
[Ti] Título:A novel optogenetically tunable frequency modulating oscillator.
[So] Source:PLoS One;13(2):e0183242, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Synthetic biology has enabled the creation of biological reconfigurable circuits, which perform multiple functions monopolizing a single biological machine; Such a system can switch between different behaviours in response to environmental cues. Previous work has demonstrated switchable dynamical behaviour employing reconfigurable logic gate genetic networks. Here we describe a computational framework for reconfigurable circuits in E.coli using combinations of logic gates, and also propose the biological implementation. The proposed system is an oscillator that can exhibit tunability of frequency and amplitude of oscillations. Further, the frequency of operation can be changed optogenetically. Insilico analysis revealed that two-component light systems, in response to light within a frequency range, can be used for modulating the frequency of the oscillator or stopping the oscillations altogether. Computational modelling reveals that mixing two colonies of E.coli oscillating at different frequencies generates spatial beat patterns. Further, we show that these oscillations more robustly respond to input perturbations compared to the base oscillator, to which the proposed oscillator is a modification. Compared to the base oscillator, the proposed system shows faster synchronization in a colony of cells for a larger region of the parameter space. Additionally, the proposed oscillator also exhibits lesser synchronization error in the transient period after input perturbations. This provides a strong basis for the construction of synthetic reconfigurable circuits in bacteria and other organisms, which can be scaled up to perform functions in the field of time dependent drug delivery with tunable dosages, and sets the stage for further development of circuits with synchronized population level behaviour.
[Mh] Termos MeSH primário: Biologia Sintética
[Mh] Termos MeSH secundário: Escherichia coli/genética
Modelos Teóricos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180202
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0183242


  2 / 1914 MEDLINE  
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[PMID]:28457785
[Au] Autor:Glushakova LG; Alto BW; Kim MS; Bradley A; Yaren O; Benner SA
[Ad] Endereço:Firebird Biomolecular Sciences LLC,13709 Progress Blvd, Box 17, Alachua, FL 32615, United States.
[Ti] Título:Detection of chikungunya viral RNA in mosquito bodies on cationic (Q) paper based on innovations in synthetic biology.
[So] Source:J Virol Methods;246:104-111, 2017 Aug.
[Is] ISSN:1879-0984
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Chikungunya virus (CHIKV) represents a growing and global concern for public health that needs inexpensive and convenient methods to collect mosquitoes as potential carriers so that they can be preserved, stored and transported for later and/or remote analysis. Reported here is a cellulose-based paper, derivatized with quaternary ammonium groups ("Q-paper") that meets these needs. In a series of tests, infected mosquito bodies were squashed directly on Q-paper. Aqueous ammonia was then added on the mosquito bodies to release viral RNA that adsorbed on the cationic surface via electrostatic interactions. The samples were then stored (frozen) or transported. For analysis, the CHIKV nucleic acids were eluted from the Q-paper and PCR amplified in a workflow, previously developed, that also exploited two nucleic acid innovations, ("artificially expanded genetic information systems", AEGIS, and "self-avoiding molecular recognition systems", SAMRS). The amplicons were then analyzed by a Luminex hybridization assay. This procedure detected CHIKV RNA, if present, in each infected mosquito sample, but not in non-infected counterparts or ddH O samples washes, with testing one week or ten months after sample collection.
[Mh] Termos MeSH primário: Aedes/virologia
Vírus Chikungunya/genética
Vírus Chikungunya/isolamento & purificação
Papel
RNA Viral/isolamento & purificação
Biologia Sintética/métodos
[Mh] Termos MeSH secundário: Animais
Hibridização de Ácido Nucleico/métodos
Preservação Biológica
Compostos de Amônio Quaternário/química
RNA Viral/genética
Manejo de Espécimes/instrumentação
Manejo de Espécimes/métodos
Biologia Sintética/instrumentação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Quaternary Ammonium Compounds); 0 (RNA, Viral)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE


  3 / 1914 MEDLINE  
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[PMID]:28470621
[Au] Autor:Wallace S; Balskus EP
[Ad] Endereço:Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
[Ti] Título:Interfacing Biocompatible Reactions with Engineered Escherichia coli.
[So] Source:Methods Mol Biol;1586:409-421, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Biocompatible chemistry represents a new way of merging chemical and biological synthesis by interfacing nonenzymatic reactions with metabolic pathways. This approach can enable the production of nonnatural molecules directly from renewable starting materials via microbial fermentation. When developing a new biocompatible reaction certain criteria must be satisfied, i.e., the reaction must be (1) functional in aqueous growth media at ambient temperature and pH, (2) nontoxic to the producing microorganism, and (3) have negligible effects on the targeted metabolic pathway. This chapter provides a detailed outline of two biocompatible reaction procedures (hydrogenation and cyclopropanation), and describes some of the chemical and microbiological experiments and considerations required during biocompatible reaction development.
[Mh] Termos MeSH primário: Escherichia coli/genética
Escherichia coli/metabolismo
Engenharia Metabólica/métodos
[Mh] Termos MeSH secundário: Catálise
Ciclopropanos/metabolismo
Escherichia coli/crescimento & desenvolvimento
Fermentação
Glucose
Hidrogenação
Redes e Vias Metabólicas
Biologia Sintética/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cyclopropanes); 99TB643425 (cyclopropane); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-6887-9_27


  4 / 1914 MEDLINE  
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[PMID]:28470613
[Au] Autor:Rues RB; Gräwe A; Henrich E; Bernhard F
[Ad] Endereço:Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany.
[Ti] Título:Membrane Protein Production in E. coli Lysates in Presence of Preassembled Nanodiscs.
[So] Source:Methods Mol Biol;1586:291-312, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cell-free expression allows to synthesize membrane proteins in completely new formats that can relatively easily be customized for particular applications. Amphiphilic superstructures such as micelles, lipomicelles, or nanodiscs can be provided as nano-devices for the solubilization of membrane proteins. Defined empty bilayers in the form of nanodiscs offer native like environments for membrane proteins, supporting functional folding, proper oligomeric assembly as well as stability. Even very difficult and detergent-sensitive membrane proteins can be addressed by the combination of nanodisc technology with efficient cell-free expression systems as the direct co-translational insertion of nascent membrane proteins into supplied preassembled nanodiscs is possible. This chapter provides updated protocols for the synthesis of membrane proteins in presence of preassembled nanodiscs suitable for emerging applications such as screening of lipid effects on membrane protein function and the modulation of oligomeric complex formation.
[Mh] Termos MeSH primário: Sistema Livre de Células/metabolismo
Escherichia coli/genética
Bicamadas Lipídicas/química
Proteínas de Membrana/genética
Nanoestruturas/química
Biologia Sintética/métodos
[Mh] Termos MeSH secundário: Detergentes/química
Expressão Gênica
Lipídeos/química
Proteínas de Membrana/química
Proteínas de Membrana/isolamento & purificação
Dobramento de Proteína
Solubilidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Detergents); 0 (Lipid Bilayers); 0 (Lipids); 0 (Membrane Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-6887-9_19


  5 / 1914 MEDLINE  
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[PMID]:29302054
[Au] Autor:Wijnands SPW; Engelen W; Lafleur RPM; Meijer EW; Merkx M
[Ad] Endereço:Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
[Ti] Título:Controlling protein activity by dynamic recruitment on a supramolecular polymer platform.
[So] Source:Nat Commun;9(1):65, 2018 01 04.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins. Specific recruitment of DNA-conjugated proteins on the supramolecular polymer results in a 1000-fold increase in protein complex formation, while at the same time enabling their rapid exchange along the BTA polymer. Our results establish supramolecular BTA polymers as a generic protein recruitment platform and demonstrate how assembly of protein complexes along the supramolecular polymer allows efficient and dynamic control of protein activity.
[Mh] Termos MeSH primário: Benzamidas/metabolismo
DNA/metabolismo
Nanoestruturas
Polímeros/metabolismo
Proteínas/metabolismo
[Mh] Termos MeSH secundário: Simulação de Dinâmica Molecular
Biologia Sintética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Benzamides); 0 (Polymers); 0 (Proteins); 0 (benzene-1,3,5-tricarboxamide); 9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180106
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02559-0


  6 / 1914 MEDLINE  
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[PMID]:29326254
[Au] Autor:Cohen J
[Ti] Título:How a horror story haunts science.
[So] Source:Science;359(6372):148-150, 2018 Jan 12.
[Is] ISSN:1095-9203
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Pesquisa Biomédica
Literatura Moderna
Editoração
Ciência na Literatura
[Mh] Termos MeSH secundário: Pesquisa Biomédica/ética
Ética em Pesquisa
História do Século XIX
Literatura Moderna/história
Ciência na Literatura/história
Biologia Sintética
[Pt] Tipo de publicação:HISTORICAL ARTICLE; JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180113
[St] Status:MEDLINE
[do] DOI:10.1126/science.359.6372.148


  7 / 1914 MEDLINE  
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[PMID]:28461174
[Au] Autor:Dalonso N; Savoldi M; França PHC; Reis TF; Goldman GH; Gern RMM
[Ad] Endereço:Programa de Pós Graduação em Saúde e Meio Ambiente, Universidade da Região de Joinville, UNIVILLE, Joinville, SC 89201-972, Brazil. Electronic address: nenidalo@yahoo.com.br.
[Ti] Título:Sequence-independent cloning methods for long DNA fragments applied to synthetic biology.
[So] Source:Anal Biochem;530:5-8, 2017 08 01.
[Is] ISSN:1096-0309
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Simplified methods to assemble DNA fragments by independent cloning sequence have helped in the progress of synthetic biology, allowing some biotechnological processes to become economically viable by genetic improvement of microorganisms. We compared three methods of assembling six DNA fragments: PCR fusion-based, isothermal NEBuilder and circular polymerase extension cloning (CPEC). Double and triple fusion occurs directly with the PCR products using PCR fusion-based and NEBuilder methods. For multiple fragments the results showed higher efficiency by the CPEC method which allowed assembly of six fragments previously purified by agarose gel extraction, after a sequence of 20 annealing/extension cycles without any primer.
[Mh] Termos MeSH primário: Clonagem Molecular/métodos
DNA/química
DNA/genética
Reação em Cadeia da Polimerase/métodos
Biologia Sintética/métodos
[Mh] Termos MeSH secundário: Ligases/metabolismo
Transformação Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA); EC 6.- (Ligases)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE


  8 / 1914 MEDLINE  
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[PMID]:28467058
[Au] Autor:Bouzon M; Perret A; Loreau O; Delmas V; Perchat N; Weissenbach J; Taran F; Marlière P
[Ad] Endereço:CEA, Genoscope , 2 rue Gaston Crémieux, 91000 Evry, France.
[Ti] Título:A Synthetic Alternative to Canonical One-Carbon Metabolism.
[So] Source:ACS Synth Biol;6(8):1520-1533, 2017 Aug 18.
[Is] ISSN:2161-5063
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:One-carbon metabolism is an ubiquitous metabolic pathway that encompasses the reactions transferring formyl-, hydroxymethyl- and methyl-groups bound to tetrahydrofolate for the synthesis of purine nucleotides, thymidylate, methionine and dehydropantoate, the precursor of coenzyme A. An alternative cyclic pathway was designed that substitutes 4-hydroxy-2-oxobutanoic acid (HOB), a compound absent from known metabolism, for the amino acids serine and glycine as one-carbon donors. It involves two novel reactions, the transamination of l-homoserine and the transfer of a one-carbon unit from HOB to tetrahydrofolate releasing pyruvate as coproduct. Since canonical reactions regenerate l-homoserine from pyruvate by carboxylation and subsequent reduction, every one-carbon moiety made available for anabolic reactions originates from CO . The HOB-dependent pathway was established in an Escherichia coli auxotroph selected for prototrophy using long-term cultivation protocols. Genetic, metabolic and biochemical evidence support the emergence of a functional HOB-dependent one-carbon pathway achieved with the recruitment of the two enzymes l-homoserine transaminase and HOB-hydroxymethyltransferase and of HOB as an essential metabolic intermediate. Escherichia coli biochemical reprogramming was achieved by minimally altering canonical metabolism and leveraging on natural selection mechanisms, thereby launching the resulting strain on an evolutionary trajectory diverging from all known extant species.
[Mh] Termos MeSH primário: Acetoacetatos/metabolismo
Carbono/metabolismo
Proteínas de Escherichia coli/metabolismo
Escherichia coli/metabolismo
Melhoramento Genético/métodos
Engenharia Metabólica/métodos
Redes e Vias Metabólicas/genética
[Mh] Termos MeSH secundário: Escherichia coli/genética
Proteínas de Escherichia coli/genética
Glicina/genética
Glicina/metabolismo
Ácido Pirúvico/metabolismo
Serina/genética
Serina/metabolismo
Biologia Sintética/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Acetoacetates); 0 (Escherichia coli Proteins); 452VLY9402 (Serine); 4ZI204Y1MC (acetoacetic acid); 7440-44-0 (Carbon); 8558G7RUTR (Pyruvic Acid); TE7660XO1C (Glycine)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180201
[Lr] Data última revisão:
180201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1021/acssynbio.7b00029


  9 / 1914 MEDLINE  
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[PMID]:28459541
[Au] Autor:Shopera T; He L; Oyetunde T; Tang YJ; Moon TS
[Ad] Endereço:Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis , St. Louis, Missouri 63130, United States.
[Ti] Título:Decoupling Resource-Coupled Gene Expression in Living Cells.
[So] Source:ACS Synth Biol;6(8):1596-1604, 2017 Aug 18.
[Is] ISSN:2161-5063
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Synthetic biology aspires to develop frameworks that enable the construction of complex and reliable gene networks with predictable functionalities. A key limitation is that increasing network complexity increases the demand for cellular resources, potentially causing resource-associated interference among noninteracting circuits. Although recent studies have shown the effects of resource competition on circuit behaviors, mechanisms that decouple such interference remain unclear. Here, we constructed three systems in Escherichia coli, each consisting of two independent circuit modules where the complexity of one module (Circuit 2) was systematically increased while the other (Circuit 1) remained identical. By varying the expression level of Circuit 1 and measuring its effect on the expression level of Circuit 2, we demonstrated computationally and experimentally that indirect coupling between these seemingly unconnected genetic circuits can occur in three different regulatory topologies. More importantly, we experimentally verified the computational prediction that negative feedback can significantly reduce resource-coupled interference in regulatory circuits. Our results reveal a design principle that enables cells to reliably multitask while tightly controlling cellular resources.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/genética
Escherichia coli/genética
Regulação Bacteriana da Expressão Gênica/genética
Redes Reguladoras de Genes/genética
Genes Bacterianos/genética
Modelos Genéticos
Transdução de Sinais/genética
[Mh] Termos MeSH secundário: Simulação por Computador
Retroalimentação Fisiológica/fisiologia
Biologia Sintética/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Escherichia coli Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180201
[Lr] Data última revisão:
180201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1021/acssynbio.7b00119


  10 / 1914 MEDLINE  
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[PMID]:29293531
[Au] Autor:Andreou AI; Nakayama N
[Ad] Endereço:SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom.
[Ti] Título:Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.
[So] Source:PLoS One;13(1):e0189892, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
[Mh] Termos MeSH primário: DNA/genética
[Mh] Termos MeSH secundário: Biologia Sintética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180129
[Lr] Data última revisão:
180129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189892



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