ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL).

abstract：:This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on t...

journal_title：ACS synthetic biology

authors： Sainz de Murieta I,Bultelle M,Kitney RI

更新日期：2016-08-19 00:00:00

abstract：:Directed evolution requires the creation of genetic diversity and subsequent screening or selection for improved variants. For DNA mutagenesis, conventional site-directed methods implicitly utilize the Boolean AND operator (creating all mutations simultaneously), producing a combinatorial explosion in the number of ge...

journal_title：ACS synthetic biology

authors： Currin A,Kwok J,Sadler JC,Bell EL,Swainston N,Ababi M,Day P,Turner NJ,Kell DB

更新日期：2019-06-21 00:00:00

abstract：:In response to emergent antibiotic resistance, new strategies are needed to enhance the effectiveness of existing antibiotics. Here, we describe a phagemid-delivered, RNA-mediated system capable of directly knocking down antibiotic resistance phenotypes. Small regulatory RNAs (sRNAs) were designed to specifically inhi...

journal_title：ACS synthetic biology

authors： Libis VK,Bernheim AG,Basier C,Jaramillo-Riveri S,Deyell M,Aghoghogbe I,Atanaskovic I,Bencherif AC,Benony M,Koutsoubelis N,Löchner AC,Marinkovic ZS,Zahra S,Zegman Y,Lindner AB,Wintermute EH

更新日期：2014-12-19 00:00:00

abstract：:As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evok...

journal_title：ACS synthetic biology

authors： Hannanta-Anan P,Chow BY

更新日期：2018-06-15 00:00:00

abstract：:Optogenetic control of endogenous signaling can be an important tool for probing cell behavior. Using the photoresponse of the LOV2 domain of Avena sativa phototropin 1, we developed analogues of kinase inhibitors whose activity is light dependent. Inhibitory peptides were appended to the Jα helix, where they potently...

journal_title：ACS synthetic biology

authors： Yi JJ,Wang H,Vilela M,Danuser G,Hahn KM

更新日期：2014-11-21 00:00:00

abstract：:This paper describes SBOLExplorer, a system that is used to provide intuitive searching within the SynBioHub genetic design repository. SynBioHub stores genetic constructs encoded in the SBOL data format. These constructs can represent genetic parts, circuits, and sequences. These constructs are often numerous, exist ...

journal_title：ACS synthetic biology

authors： Zhang M,Zundel Z,Myers CJ

更新日期：2019-10-18 00:00:00

abstract：:The measurement of gene expression using fluorescence markers has been a cornerstone of synthetic biology for the past two decades. However, the use of arbitrary units has limited the usefulness of these data for many quantitative purposes. Calibration of fluorescence measurements from flow cytometry and plate reader ...

journal_title：ACS synthetic biology

authors： Fedorec AJH,Robinson CM,Wen KY,Barnes CP

更新日期：2020-09-18 00:00:00

abstract：:A defining goal of synthetic biology is to develop biomaterials with superior performance and versatility. Here we introduce a purely genetically encoded and self-assembling biopolymer based on the SpyTag-SpyCatcher chemistry. We show the application of this polymer for highly efficient uranyl binding and extraction f...

journal_title：ACS synthetic biology

authors： Yang X,Wei J,Wang Y,Yang C,Zhao S,Li C,Dong Y,Bai K,Li Y,Teng H,Wang D,Lyu N,Li J,Chang X,Ning X,Ouyang Q,Zhang Y,Qian L

更新日期：2018-10-19 00:00:00

abstract：:Synonymous mutation of the N-terminal coding sequence (NCS) has been used to regulate gene expression. We here developed a statistical model to predict the effect of the NCSs on protein expression in Bacillus subtilis WB600. First, a synonymous mutation was performed within the first 10 residues of a superfolder green...

journal_title：ACS synthetic biology

authors： Xu K,Tong Y,Li Y,Tao J,Li J,Zhou J,Liu S

更新日期：2021-01-19 00:00:00

abstract：:We recently developed a technique for rapidly and reversibly inhibiting protein function through light-inducible sequestration of proteins away from their normal sites of action. Here, we adapt this method for inducible inactivation of Bem1, a scaffold protein involved in budding yeast polarity. We find that acute inh...

journal_title：ACS synthetic biology

authors： Jost AP,Weiner OD

更新日期：2015-10-16 00:00:00

abstract：:Constructing efficient cellular factories often requires integration of heterologous pathways for synthesis of novel compounds and improved cellular productivity. Few genomic sites are routinely used, however, for efficient integration and expression of heterologous genes, especially in nonmodel hosts. Here, a data-gu...

journal_title：ACS synthetic biology

authors： Brady JR,Tan MC,Whittaker CA,Colant NA,Dalvie NC,Love KR,Love JC

更新日期：2020-09-18 00:00:00

abstract：:The cellular response to hypoxia is orchestrated by HIF-1, a heterodimeric transcription factor composed of an α and a β subunit that enables cell survival under low oxygen conditions by altering the transcription of over 300 genes. There is significant evidence that inhibition of HIF-1 would be beneficial for cancer ...

journal_title：ACS synthetic biology

authors： Mistry IN,Tavassoli A

更新日期：2017-03-17 00:00:00

abstract：:Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic func...

journal_title：ACS synthetic biology

authors： Glover DJ,Lim S,Xu D,Sloan NB,Zhang Y,Clark DS

更新日期：2018-10-19 00:00:00

abstract：:As light-regulated actuators, sensory photoreceptors underpin optogenetics and numerous applications in synthetic biology. Protein engineering has been applied to fine-tune the properties of photoreceptors and to generate novel actuators. For the blue-light-sensitive light-oxygen-voltage (LOV) photoreceptors, mutation...

journal_title：ACS synthetic biology

authors： Diensthuber RP,Engelhard C,Lemke N,Gleichmann T,Ohlendorf R,Bittl R,Möglich A

更新日期：2014-11-21 00:00:00

abstract：:Microorganisms often use specific autoinducers other than common metabolites for quorum sensing (QS). Herein, we demonstrated that Escherichia coli produced sulfide (H2S, HS-, and S2-) with the concentrations proportionally correlated to its cell density. We then designed synthetic gene circuits that used H2S as an au...

journal_title：ACS synthetic biology

authors： Liu H,Fan K,Li H,Wang Q,Yang Y,Li K,Xia Y,Xun L

更新日期：2019-09-20 00:00:00

abstract：:Identification of the enzyme(s) involved in complex biosynthetic pathways can be challenging. An alternative approach might be to deliberately diverge from the original natural enzyme source and use promiscuous enzymes from other organisms. In this paper, we have tested the ability of a series of human and animal cyto...

journal_title：ACS synthetic biology

authors： Sarrade-Loucheur A,Ro DK,Fauré R,Remaud-Siméon M,Truan G

更新日期：2020-02-21 00:00:00

abstract：:Site directed RNA editing is an engineered tool for the posttranscriptional manipulation of RNA and proteins. Here, we demonstrate the inclusion of additional N- and C-terminal protein domains in an RNA editing-dependent manner to switch between protein isoforms in mammalian cell culture. By inclusion of localization ...

journal_title：ACS synthetic biology

authors： Vogel P,Hanswillemenke A,Stafforst T

更新日期：2017-09-15 00:00:00

abstract：:Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducib...

journal_title：ACS synthetic biology

authors： Didovyk A,Tonooka T,Tsimring L,Hasty J

更新日期：2017-12-15 00:00:00

abstract：:The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoter...

journal_title：ACS synthetic biology

authors： Koopal B,Kruis AJ,Claassens NJ,Nobrega FL,van der Oost J

更新日期：2019-02-15 00:00:00

abstract：:In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnol...

journal_title：ACS synthetic biology

authors： Carapezza G,Umeton R,Costanza J,Angione C,Stracquadanio G,Papini A,Lió P,Nicosia G

更新日期：2013-05-17 00:00:00

abstract：:The ability of RNA to sense, regulate, and store information is an attractive attribute for a variety of functional applications including the development of regulatory control devices for synthetic biology. RNA folding and function is known to be highly context sensitive, which limits the modularity and reuse of RNA ...

journal_title：ACS synthetic biology

authors： Kent R,Halliwell S,Young K,Swainston N,Dixon N

更新日期：2018-07-20 00:00:00

abstract：:Understanding the molecular mechanisms underlying antibiotic resistance requires concerted efforts in enzymology and medicinal chemistry. Here we describe a new synthetic biology approach to antibiotic development, where the presence of tetracycline antibiotics is linked to a life-death selection in Saccharomyces cere...

journal_title：ACS synthetic biology

authors： Scott LH,Mathews JC,Flematti GR,Filipovska A,Rackham O

更新日期：2018-08-17 00:00:00

abstract：:Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence sp...

journal_title：ACS synthetic biology

authors： Vilkhovoy M,Horvath N,Shih CH,Wayman JA,Calhoun K,Swartz J,Varner JD

更新日期：2018-08-17 00:00:00

abstract：:The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learn...

journal_title：ACS synthetic biology

authors： Gupta V,Irimia J,Pau I,Rodríguez-Patón A

更新日期：2017-07-21 00:00:00

abstract：:As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three ...

journal_title：ACS synthetic biology

authors： Li T,Ye J,Shen R,Zong Y,Zhao X,Lou C,Chen GQ

更新日期：2016-11-18 00:00:00

abstract：:In this work we report synthetic adhesins (SAs) enabling the rational design of the adhesion properties of E. coli. SAs have a modular structure comprising a stable β-domain for outer membrane anchoring and surface-exposed immunoglobulin domains with high affinity and specificity that can be selected from large repert...

journal_title：ACS synthetic biology

authors： Piñero-Lambea C,Bodelón G,Fernández-Periáñez R,Cuesta AM,Álvarez-Vallina L,Fernández LÁ

更新日期：2015-04-17 00:00:00

abstract：:Secondary structure formation of mRNA, caused by desynchronization of transcription and translation, is known to impact gene expression in vivo. Yet, inactivation of mRNA by secondary structures in cell-free protein expression is frequently overlooked. Transcription and translation rates are often not highly synchroni...

journal_title：ACS synthetic biology

authors： Hansen MM,Ventosa Rosquelles M,Yelleswarapu M,Maas RJ,van Vugt-Jonker AJ,Heus HA,Huck WT

更新日期：2016-12-16 00:00:00

abstract：:Synthetic biology involves reprogramming and engineering of regulatory genes in innovative ways for the implementation of novel tasks. Transcriptional gene regulation systems induced by small molecules in prokaryotes provide a rich source for logic gates. Cross-regulation, whereby a promoter is activated by different ...

journal_title：ACS synthetic biology

authors： Zhang D,Zhao Y,He Y,Wang Y,Zhao Y,Zheng Y,Wei X,Zhang L,Li Y,Jin T,Wu L,Wang H,Davison PA,Xu J,Huang WE

更新日期：2012-07-20 00:00:00

abstract：:There is a growing interest in mediating information transfer between biology and electronics. By the addition of redox mediators to various samples and cells, one can both electronically obtain a redox "portrait" of a biological system and, conversely, program gene expression. Here, we have created a cell-based synth...

journal_title：ACS synthetic biology

authors： VanArsdale E,Hörnström D,Sjöberg G,Järbur I,Pitzer J,Payne GF,van Maris AJA,Bentley WE

更新日期：2020-05-15 00:00:00

abstract：:The versatility of Ca2+ signals allows it to regulate diverse cellular processes such as migration, apoptosis, motility and exocytosis. In some receptors (e.g., VEGFR2), Ca2+ signals are generated upon binding their ligand(s) (e.g., VEGF-A). Here, we employed a design strategy to engineer proteins that generate a Ca2+...

journal_title：ACS synthetic biology

authors： Qudrat A,Truong K

更新日期：2017-03-17 00:00:00