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ACS Synthetic Biology

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https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#1
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28441476/sboldesigner-2-an-intuitive-tool-for-structural-genetic-design
#2
Michael Zhang, James Alastair McLaughlin, Anil Wipat, Chris J Myers
As the Synthetic Biology Open Language (SBOL) data and visual standards gain acceptance for describing genetic designs in a detailed and reproducible way, there is an increasing need for an intuitive sequence editor tool that biologists can use that supports these standards. This paper describes SBOLDesigner 2, a genetic design automation (GDA) tool that natively supports both the SBOL data model (Version 2.1) and SBOL Visual (Version 1.0). This software is enabled to fetch and store parts and designs from SBOL repositories, such as SynBioHub...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28441472/repurposing-a-two-component-system-based-biosensor-for-the-killing-of-vibrio-cholerae
#3
Premkumar Jayaraman, Maciej Bartosz Holowko, Jing Wui Yeoh, Sierin Lim, Chueh Loo Poh
New strategies to control cholera are urgently needed. This study develops an in vitro proof-of-concept sense-and-eradicate system in a wild-type Escherichia coli strain to target the causative pathogen Vibrio cholerae using a synthetic biology approach. Our engineered E. coli specifically detects V. cholerae via its quorum-sensing molecule CAI-1 and responds by expressing the lysis protein (YebF-Art-085), thereby self-lysing to release the killing protein (Art-085) to eradicate V. cholerae. For this report, we individually characterized the YebF-Art-085 and Art-085 expression and their activities when coupled to our previously developed V...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28414914/designing-uniquely-addressable-bio-orthogonal-synthetic-scaffolds-for-dna-and-rna-origami
#4
Jerzy Kozyra, Alessandro Ceccarelli, Emanuela Torelli, Annunziata Lopiccolo, Jing-Ying Gu, Harold Fellermann, Ulrich Stimming, Natalio Krasnogor
Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28438021/a-new-improved-and-extended-version-of-the-multicell-bacterial-simulator-gro
#5
Martín Eduardo Gutiérrez, Paula Gregorio-Godoy, Guillermo Pérez Del Pulgar, Luis Enrique Muñoz, Sandra Sáez, Alfonso Rodriguez-Paton
gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use and provide new functionalities. The new version of gro is between one and two orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 10(5) cells in less than 20 minutes...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28437108/design-of-a-toolbox-of-rna-thermometers
#6
Shaunak Sen, Divyansh Apurva, Rohit Satija, Dan Siegal, Richard M Murray
Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. While RNA-based sensors, called 'thermometers', have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature, differing in sensitivities and thresholds. We address this issue by constructing a library of RNA thermometers, based on thermodynamic computations, and experimentally measuring their activities in cell-free biomolecular 'breadboards'...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28437094/rational-design-of-an-ultrasensitive-quorum-sensing-switch
#7
Weiqian Zeng, Pei Du, Qiuli Lou, Lili Wu, Haoqian M Zhang, Chunbo Lou, Hongli Wang, Qi Ouyang
One of the purposes of synthetic biology is to develop rational methods that accelerate the design of genetic circuits, saving time and effort spent on experiments and providing reliably predictable circuit performance. We applied a reverse engineering approach to design an ultrasensitive transcriptional quorum-sensing switch. We want to explore how systems biology can guide synthetic biology in the choice of specific DNA sequences and their regulatory relations to achieve a targeted function. The workflow comprises network enumeration that achieves the target function robustly, experimental restriction of the obtained candidate networks, global parameter optimization via mathematical analysis, selection and engineering of parts based on these calculations, and finally, circuit construction based on the principles of standardization and modularization...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28418644/emma-an-extensible-mammalian-modular-assembly-toolkit-for-the-rapid-design-and-production-of-diverse-expression-vectors
#8
Andrea Martella, Mantas Matjusaitis, Jamie Auxillos, Steven M Pollard, Yizhi Cai
Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28430408/amplifying-riboswitch-signal-output-using-cellular-wiring
#9
Michael S Goodson, Annastacia C Bennett, Brenton R Jennewine, Emily Briskin, Svetlana V Harbaugh, Nancy Kelley-Loughnane
If fieldable riboswitch-based biological sensors are to fulfil their potential, it is necessary to increase their signal output. Here we report a novel modular amplification system using a riboswitch to initiate signaling between a sensing strain and a reporter strain of E. coli. A quorum sensing signaling molecule biologically wires the sensing and reporter strains together. The amplification circuit increased the amount of fluorescence generated on ligand binding compared to when the riboswitch controlled fluorescence expression directly...
April 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28419802/programming-post-translational-control-over-the-metabolic-labeling-of-cellular-proteins-with-a-non-canonical-amino-acid
#10
Emily E Thomas, Naresh Pandey, Sarah E Knudsen, Zachary T Ball, Jonathan J Silberg
Transcriptional control can be used to program cells to label proteins with non-canonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity...
April 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28418635/enhancing-protein-production-yield-from-cho-cells-by-crispr-interference-crispri
#11
Chih-Che Shen, Li-Yu Sung, Shih-Yeh Lin, Mei-Wei Lin, Yu-Chen Hu
CHO cell is an important host for biopharmaceutical production. Generation of stable CHO cell typically requires co-integration of dhfr and foreign gene into chromosomes and subsequent methotrexate (MTX) selection for co-amplification of dhfr and foreign gene. CRISPR interference (CRISPRi) is an emerging system that effectively suppresses gene transcription through the coordination of dCas9 protein and guide RNA (gRNA). However, CRISPRi has yet to be exploited in CHO cells. Here we constructed vectors expressing the functional CRISPRi system and proved effective CRISPRi-mediated suppression of dhfr transcription in CHO cells...
April 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28414905/application-of-an-acyl-coa-ligase-from-streptomyces-aizunensis-for-lactam-biosynthesis
#12
Jingwei Zhang, Jesus F Barajas, Mehmet Burdu, George Wang, Edward E K Baidoo, Jay D Keasling
ε-caprolactam and δ-valerolactam are important commodity chemicals used in the manufacture of nylons, with millions of tons produced annually. Biological production of these highly valued chemicals has been limited due to a lack of enzymes that cyclize ω-amino fatty acid precursors to corresponding lactams under ambient conditions. In this study, we demonstrated production of these chemicals using ORF26, an acyl-CoA ligase involved in the biosynthesis of ECO-02301 in Streptomyces aizunensis. This enzyme has a broad substrate spectrum and can cyclize 4-aminobutyric acid into γ-butyrolactam, 5-aminovaleric acid into δ-valerolactam and 6-aminocaproic acid into ε-caprolactam...
April 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28414903/nanopore-logic-operation-with-dna-to-rna-transcription-in-a-droplet-system
#13
Masayuki Ohara, Masahiro Takanoue, Ryuji Kawano
This paper describes an AND logic operation with amplification and transcription from DNA to RNA using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore at the single-molecule level. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic gates into electrochemical devices is necessary to obtain output information in a human-recognizable form...
April 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28355056/deconvolution-of-gene-expression-noise-into-spatial-dynamics-of-transcription-factor-promoter-interplay
#14
Ángel Goñi-Moreno, Ilaria Benedetti, Juhyun Kim, Víctor de Lorenzo
Gene expression noise is not only the mere consequence of stochasticity, but also a signal that reflects the upstream physical dynamics of the cognate molecular machinery. Soil bacteria facing recalcitrant pollutants exploit noise of catabolic promoters to deploy beneficial phenotypes such as metabolic bet-hedging and/or division of biochemical labor. Although the role of upstream promoter-regulator interplay in the origin of this noise is little understood, its specifications are probably ciphered in flow cytometry data patterns...
April 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28350462/automated-design-framework-for-synthetic-biology-exploiting-pareto-optimality
#15
Irene Otero-Muras, Julio R Banga
In this work we consider Pareto optimality for automated design in synthetic biology. We present a generalized framework based on a mixed-integer dynamic optimization formulation that, given design specifications, allows the computation of Pareto optimal sets of designs, that is, the set of best trade-offs for the metrics of interest. We show how this framework can be used for (i) forward design, that is, finding the Pareto optimal set of synthetic designs for implementation, and (ii) reverse design, that is, analyzing and inferring motifs and/or design principles of gene regulatory networks from the Pareto set of optimal circuits...
April 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28398719/deep-sequencing-analysis-of-aptazyme-variants-based-on-a-pistol-ribozyme
#16
Shungo Kobori, Kei Takahashi, Yohei Yokobayashi
Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element...
April 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28375596/efficient-transcriptional-gene-repression-by-type-v-a-crispr-cpf1-from-eubacterium-eligens
#17
Seong Keun Kim, Haseong Kim, Woo-Chan Ahn, Kwang-Hyun Park, Eui-Jeon Woo, Dae-Hee Lee, Seung-Goo Lee
Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is an emerging technology for artificial gene regulation. Type II CRISPR-Cas endonuclease Cas9 is the most widely used protein for gene regulation with CRISPRi. Here, we present type V-A CRISPR-Cas endonuclease Cpf1-based CRISPRi. We constructed an l-rhamnose-inducible CRISPRi system with DNase-deactivated Cpf1 from Eubacterium eligens (EedCpf1) and compared its performance with catalytically deactivated Cas9 from Streptococcus pyogenes (SpdCas9)...
April 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28391682/centromeric-dna-facilitates-nonconventional-yeast-genetic-engineering
#18
Mingfeng Cao, Meirong Gao, Carmen Lorena Lopez-Garcia, Yutong Wu, Arun Somwarpet Seetharam, Andrew Josef Severin, Zengyi Shao
Many nonconventional yeast species have highly desirable features that are not possessed by model yeasts despite that significant technology hurdles to effectively manipulate them lay in front. Scheffersomyces stipitis is one of the most important exemplary nonconventional yeasts in biorenewables industry, which has the highest native xylose utilization capacity. Recent study suggested its much better potential than Saccharomyces cerevisiae as a well-suited microbial biomanufacturing platform for producing high-value compounds derived from shikimate pathway, many of which are associated with potent nutraceutical or pharmaceutical properties...
April 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28372360/a-modular-high-throughput-in-vivo-screening-platform-based-on-chimeric-bacterial-receptors
#19
Christina E Lehning, Jan B Heidelberger, John Reinhard, Morten H H Nørholm, Roger R Draheim
Multidrug resistance (MDR) is a globally relevant problem that requires novel approaches. Two-component systems are a promising, yet untapped target for novel antibacterials. They are prevalent in bacteria and absent in mammals, and their activity can be modulated upon perception of various stimuli. Screening pre-existing compound libraries could reveal small molecules that inhibit stimulus-perception by virulence-modulating receptors, reduce signal output from essential receptors or identify artificial stimulatory ligands for novel SHKs that are involved in virulence...
April 7, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28383905/construction-and-rescue-of-a-functional-synthetic-baculovirus
#20
Yu Shang, Manli Wang, Gengfu Xiao, Xi Wang, Dianhai Hou, Kai Pan, Shurui Liu, Jiang Li, Jun Wang, Basil M Arif, Just M Vlak, Xinwen Chen, Hualin Wang, Fei Deng, Zhihong Hu
Synthetic viruses provide a powerful platform to delve deeper into the nature and function of viruses as well as to engineer viruses with novel properties. So far, most synthetic viruses have been RNA viruses (<30 kb) and small DNA viruses, such as bacteriophage phiX174. Baculoviruses contain a large circular dsDNA genome of 80-180 kb and have been used as biocontrol agents and protein expression vectors. Here, we report on the first synthesis of a baculovirus based on the type species Autographa californica nucleopolyhedrovirus, AcMNPV, by a combination of PCR and transformation-associated recombination in yeast...
April 6, 2017: ACS Synthetic Biology
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