{"topic":"synthetic-biology","sort":"top","limit":25,"offset":0,"count":25,"papers":[{"id":"doi:10.1038/nrg2775","kind":"review","title":"Synthetic biology: applications come of age","authors":["Ahmad S. Khalil","James J. Collins"],"author_count":2,"year":2010,"published":"2010-04-16","venue":"Nature Reviews Genetics","cited_by":1381,"doi":"10.1038/nrg2775","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nrg2775","archive_url":"https://space-kitty.com/papers/doi:10.1038/nrg2775","updated":null,"pmid":"20395970","pmcid":null,"openalex_id":"W2021099440","pdf_url":"https://www.nature.com/articles/nrg2775.pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Microbial Metabolic Engineering and Bioproduction"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nature08753","kind":"article","title":"A synchronized quorum of genetic clocks","authors":["Tal Danino","Octavio Mondragón-Palomino","Lev S. Tsimring","Jeff Hasty"],"author_count":4,"year":2010,"published":"2010-01-01","venue":"Nature","cited_by":995,"doi":"10.1038/nature08753","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature08753","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature08753","updated":null,"pmid":"20090747","pmcid":null,"openalex_id":"W2114228460","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1186/s12951-021-00806-7","kind":"review","title":"Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers","authors":["Nooraei S","Bahrulolum H","Hoseini ZS","Katalani C","Hajizade A","Easton AJ","Ahmadian G"],"author_count":7,"year":2021,"published":"2021-02-25","venue":"Journal of nanobiotechnology","cited_by":623,"doi":"10.1186/s12951-021-00806-7","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1186/s12951-021-00806-7","archive_url":"https://space-kitty.com/papers/doi:10.1186/s12951-021-00806-7","updated":null,"pmid":"33632278","pmcid":"PMC7905985","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC7905985/pdf","abstract":"Virus-like particles (VLPs) are virus-derived structures made up of one or more different molecules with the ability to self-assemble, mimicking the form and size of a virus particle but lacking the genetic material so they are not capable of infecting the host cell. Expression and self-assembly of the viral structural proteins can take place in various living or cell-free expression systems after which the viral structures can be assembled and reconstructed. VLPs are gaining in popularity in the field of preventive medicine and to date, a wide range of VLP-based candidate vaccines have been developed for immunization against various infectious agents, the latest of which is the vaccine against SARS-CoV-2, the efficacy of which is being evaluated. VLPs are highly immunogenic and are able to elicit both the antibody- and cell-mediated immune responses by pathways different from those elicited by conventional inactivated viral vaccines. However, there are still many challenges to this surface display system that need to be addressed in the future. VLPs that are classified as subunit vaccines are subdivided into enveloped and non- enveloped subtypes both of which are discussed in this review article. VLPs have also recently received attention for their successful applications in targeted drug delivery and for use in gene therapy. The development of more effective and targeted forms of VLP by modification of the surface of the particles in such a way that they can be introduced into specific cells or tissues or increase their half-life in the host is likely to expand their use in the future. Recent advances in the production and fabrication of VLPs including the exploration of different types of expression systems for their development, as well as their applications as vaccines in the prevention of infectious diseases and cancers resulting from their interaction with, and mechanism of activation of, the humoral and cellular immune systems are discussed in this review.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers\" by Nooraei S, Bahrulolum H, Hoseini ZS et al., https://doi.org/10.1186/s12951-021-00806-7, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1093/bioinformatics/btx345","kind":"article","title":"Protein-Sol: a web tool for predicting protein solubility from sequence","authors":["Hebditch M","Carballo-Amador MA","Charonis S","Curtis R","Warwicker J"],"author_count":5,"year":2017,"published":"2017-10-01","venue":"Bioinformatics (Oxford, England)","cited_by":641,"doi":"10.1093/bioinformatics/btx345","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1093/bioinformatics/btx345","archive_url":"https://space-kitty.com/papers/doi:10.1093/bioinformatics/btx345","updated":null,"pmid":"28575391","pmcid":"PMC5870856","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC5870856/pdf","abstract":"Motivation Protein solubility is an important property in industrial and therapeutic applications. Prediction is a challenge, despite a growing understanding of the relevant physicochemical properties. Results Protein-Sol is a web server for predicting protein solubility. Using available data for Escherichia coli protein solubility in a cell-free expression system, 35 sequence-based properties are calculated. Feature weights are determined from separation of low and high solubility subsets. The model returns a predicted solubility and an indication of the features which deviate most from average values. Two other properties are profiled in windowed calculation along the sequence: fold propensity, and net segment charge. The utility of these additional features is demonstrated with the example of thioredoxin. Availability and implementation The Protein-Sol webserver is available at http://protein-sol.manchester.ac.uk. Contact jim.warwicker@manchester.ac.uk.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Protein-Sol: a web tool for predicting protein solubility from sequence\" by Hebditch M, Carballo-Amador MA, Charonis S et al., https://doi.org/10.1093/bioinformatics/btx345, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1016/j.cell.2014.10.004","kind":"article","title":"Paper-Based Synthetic Gene Networks","authors":["Keith Pardee","Alexander A. Green","Tom Ferrante","D. Ewen Cameron","AJay DaleyKeyser","Peng Yin","James J. Collins"],"author_count":7,"year":2014,"published":"2014-10-24","venue":"Cell","cited_by":703,"doi":"10.1016/j.cell.2014.10.004","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2014.10.004","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2014.10.004","updated":null,"pmid":"25417167","pmcid":null,"openalex_id":"W4236366502","pdf_url":"http://www.cell.com/article/S0092867414012914/pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Biosensors and Analytical Detection"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1126/science.add9667","kind":"review","title":"Engineering bacteria as interactive cancer therapies","authors":["Candice R. Gurbatri","Nicholas Arpaia","Tal Danino"],"author_count":3,"year":2022,"published":"2022-11-24","venue":"Science","cited_by":456,"doi":"10.1126/science.add9667","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1126/science.add9667","archive_url":"https://space-kitty.com/papers/doi:10.1126/science.add9667","updated":null,"pmid":"36423303","pmcid":null,"openalex_id":"W4310251760","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10584033/pdf/nihms-1937712.pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Cancer Research and Treatments"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nature11516","kind":"article","title":"Genetic programs constructed from layered logic gates in single cells","authors":["Tae Seok Moon","Chunbo Lou","Alvin Tamsir","Brynne C. Stanton","Christopher A. Voigt"],"author_count":5,"year":2012,"published":"2012-10-07","venue":"Nature","cited_by":581,"doi":"10.1038/nature11516","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature11516","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature11516","updated":null,"pmid":"23041931","pmcid":null,"openalex_id":"W2083456183","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nrmicro.2015.24","kind":"review","title":"Synthetic biology to access and expand nature's chemical diversity","authors":["Michael J. Smanski","Hui Ling Zhou","Jan Claesen","Ben Shen","Michael Andrew Fischbach","Christopher A. Voigt"],"author_count":6,"year":2016,"published":"2016-02-15","venue":"Nature Reviews Microbiology","cited_by":483,"doi":"10.1038/nrmicro.2015.24","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nrmicro.2015.24","archive_url":"https://space-kitty.com/papers/doi:10.1038/nrmicro.2015.24","updated":null,"pmid":"26876034","pmcid":null,"openalex_id":"W2254470084","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Microbial Metabolic Engineering and Bioproduction"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1126/science.1203535","kind":"article","title":"A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice","authors":["Haifeng Ye","Marie Daoud‐El Baba","Ren‐Wang Peng","Martin Fussenegger"],"author_count":4,"year":2011,"published":"2011-06-24","venue":"Science","cited_by":469,"doi":"10.1126/science.1203535","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1126/science.1203535","archive_url":"https://space-kitty.com/papers/doi:10.1126/science.1203535","updated":null,"pmid":"21700876","pmcid":null,"openalex_id":"W2011083779","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["Photoreceptor and optogenetics research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.3389/fbioe.2019.00001","kind":"review","title":"Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies","authors":["Giordano Rampioni","Francesca D’Angelo","Livia Leoni","Pasquale Stano"],"author_count":4,"year":2019,"published":"2019-01-17","venue":"Frontiers in Bioengineering and Biotechnology","cited_by":446,"doi":"10.3389/fbioe.2019.00001","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.3389/fbioe.2019.00001","archive_url":"https://space-kitty.com/papers/doi:10.3389/fbioe.2019.00001","updated":null,"pmid":"30705882","pmcid":null,"openalex_id":"W2909219982","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbioe.2019.00001/pdf","abstract":"The bottom-up branch of synthetic biology includes – among others – innovative studies that combine cell-free protein synthesis with liposome technology to generate cell-like systems of minimal complexity, often referred to as synthetic cells. The functions of this type of synthetic cell derive from gene expression, hence they can be programmed in a modular, progressive and customizable manner by means of ad hoc designed genetic circuits. This experimental scenario is rapidly expanding and synthetic cell research already counts numerous successes. Here we present a review focused on the exchange of chemical signals between liposome-based synthetic cells (operating by gene expression) and biological cells, as well as between two populations of synthetic cells. The review includes a short presentation of the “molecular communication technologies”, briefly discussing their promises and challenges.","abstract_license":"CC-BY (publisher license, via OpenAlex)","license":"cc-by","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Molecular Communication and Nanonetworks"],"details":null,"provenance":"openalex","attribution":"Abstract of \"Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies\" by Giordano Rampioni, Francesca D’Angelo, Livia Leoni et al., https://doi.org/10.3389/fbioe.2019.00001, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/nature12148","kind":"article","title":"Synthetic analog computation in living cells","authors":["Ramiz Daniel","Jacob R. Rubens","Rahul Sarpeshkar","Timothy K. Lu"],"author_count":4,"year":2013,"published":"2013-05-14","venue":"Nature","cited_by":456,"doi":"10.1038/nature12148","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature12148","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature12148","updated":null,"pmid":"23676681","pmcid":null,"openalex_id":"W1993546274","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.ymben.2011.09.002","kind":"review","title":"Cell-free synthetic biology: Thinking outside the cell","authors":["C. Eric Hodgman","Michael C. Jewett"],"author_count":2,"year":2011,"published":"2011-09-18","venue":"Metabolic Engineering","cited_by":427,"doi":"10.1016/j.ymben.2011.09.002","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.ymben.2011.09.002","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.ymben.2011.09.002","updated":null,"pmid":"21946161","pmcid":null,"openalex_id":"W1963611162","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Microbial Metabolic Engineering and Bioproduction"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41578-020-00265-w","kind":"review","title":"Materials design by synthetic biology","authors":["Tzu‐Chieh Tang","Bolin An","Yuan‐Yuan Huang","Sangita Vasikaran","Yanyi Wang","Xiaoyu Jiang","Timothy K. Lu","Chao Zhong"],"author_count":8,"year":2020,"published":"2020-12-23","venue":"Nature Reviews Materials","cited_by":389,"doi":"10.1038/s41578-020-00265-w","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41578-020-00265-w","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41578-020-00265-w","updated":null,"pmid":null,"pmcid":null,"openalex_id":"W3117273886","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1177/0748730417728663","kind":"article","title":"Guidelines for Genome-Scale Analysis of Biological Rhythms","authors":["Hughes ME","Abruzzi KC","Allada R","Anafi R","Arpat AB","Asher G","Baldi P","de Bekker C","Bell-Pedersen D","Blau J","Brown S","Ceriani MF","Chen Z","Chiu JC","Cox J","Crowell AM","DeBruyne JP","Dijk DJ","DiTacchio L","Doyle FJ","Duffield GE","Dunlap JC","Eckel-Mahan K","Esser KA","FitzGerald GA"],"author_count":93,"year":2017,"published":"2017-10-01","venue":"Journal of biological rhythms","cited_by":237,"doi":"10.1177/0748730417728663","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1177/0748730417728663","archive_url":"https://space-kitty.com/papers/doi:10.1177/0748730417728663","updated":null,"pmid":"29098954","pmcid":"PMC5692188","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC5692188/pdf","abstract":"Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding \"big data\" that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Guidelines for Genome-Scale Analysis of Biological Rhythms\" by Hughes ME, Abruzzi KC, Allada R et al., https://doi.org/10.1177/0748730417728663, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/ncomms1516","kind":"article","title":"Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology","authors":["Baojun Wang","Richard Ian Kitney","Nicolas Joly","Martin Buck"],"author_count":4,"year":2011,"published":"2011-10-18","venue":"Nature Communications","cited_by":426,"doi":"10.1038/ncomms1516","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/ncomms1516","archive_url":"https://space-kitty.com/papers/doi:10.1038/ncomms1516","updated":null,"pmid":"22009040","pmcid":null,"openalex_id":"W2149778176","pdf_url":"https://www.nature.com/articles/ncomms1516.pdf","abstract":null,"abstract_license":null,"license":"cc-by-nc-nd","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41573-021-00285-3","kind":"review","title":"Engineering living therapeutics with synthetic biology","authors":["Andrés Cubillos-Ruiz","Tingxi Guo","Anna Sokolovska","Paul Miller","James J. Collins","Timothy K. Lu","José M. Lora"],"author_count":7,"year":2021,"published":"2021-10-06","venue":"Nature Reviews Drug Discovery","cited_by":360,"doi":"10.1038/s41573-021-00285-3","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41573-021-00285-3","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41573-021-00285-3","updated":null,"pmid":"34616030","pmcid":null,"openalex_id":"W3204862058","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.cell.2018.05.047","kind":"article","title":"The Inner Nuclear Membrane Is a Metabolically Active Territory that Generates Nuclear Lipid Droplets","authors":["Romanauska A","Köhler A"],"author_count":2,"year":2018,"published":"2018-06-21","venue":"Cell","cited_by":228,"doi":"10.1016/j.cell.2018.05.047","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2018.05.047","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2018.05.047","updated":null,"pmid":"29937227","pmcid":"PMC6371920","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC6371920/pdf","abstract":"The inner nuclear membrane (INM) encases the genome and is fused with the outer nuclear membrane (ONM) to form the nuclear envelope. The ONM is contiguous with the endoplasmic reticulum (ER), the main site of phospholipid synthesis. In contrast to the ER and ONM, evidence for a metabolic activity of the INM has been lacking. Here, we show that the INM is an adaptable membrane territory capable of lipid metabolism. S. cerevisiae cells target enzymes to the INM that can promote lipid storage. Lipid storage involves the synthesis of nuclear lipid droplets from the INM and is characterized by lipid exchange through Seipin-dependent membrane bridges. We identify the genetic circuit for nuclear lipid droplet synthesis and a role of these organelles in regulating this circuit by sequestration of a transcription factor. Our findings suggest a link between INM metabolism and genome regulation and have potential relevance for human lipodystrophy.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"The Inner Nuclear Membrane Is a Metabolically Active Territory that Generates Nuclear Lipid Droplets\" by Romanauska A, Köhler A, https://doi.org/10.1016/j.cell.2018.05.047, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/nature10722","kind":"article","title":"A sensing array of radically coupled genetic ‘biopixels’","authors":["Arthur B. Prindle","Phillip Samayoa","Ivan Razinkov","Tal Danino","Lev S. Tsimring","Jeff Hasty"],"author_count":6,"year":2011,"published":"2011-12-18","venue":"Nature","cited_by":400,"doi":"10.1038/nature10722","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature10722","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature10722","updated":null,"pmid":"22178928","pmcid":null,"openalex_id":"W2141564052","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nrmicro3253","kind":"review","title":"Biotechnological domestication of pseudomonads using synthetic biology","authors":["Pablo I. Nikel","Esteban Martínez‐García","Vı́ctor de Lorenzo"],"author_count":3,"year":2014,"published":"2014-04-16","venue":"Nature Reviews Microbiology","cited_by":381,"doi":"10.1038/nrmicro3253","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nrmicro3253","archive_url":"https://space-kitty.com/papers/doi:10.1038/nrmicro3253","updated":null,"pmid":"24736795","pmcid":null,"openalex_id":"W1998369603","pdf_url":null,"abstract":null,"abstract_license":null,"license":"other-oa","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Microbial Metabolic Engineering and Bioproduction"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"arxiv:0907.3976","kind":"article","title":"TinkerCell: Modular CAD Tool for Synthetic Biology","authors":["Deepak Chandran","Frank T. Bergmann","Herbert M. Sauro"],"author_count":3,"year":2009,"published":"2009-07-23","venue":"Journal of Biological Engineering","cited_by":186,"doi":"10.1186/1754-1611-3-19","arxiv_id":"0907.3976","nct_id":null,"source_url":"https://arxiv.org/abs/0907.3976","archive_url":"https://space-kitty.com/papers/arxiv:0907.3976","updated":"2009-07-23","pmid":null,"pmcid":null,"openalex_id":"W2101506009","pdf_url":"https://arxiv.org/pdf/0907.3976","abstract":"Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.","abstract_license":"CC0-1.0 (arXiv descriptive metadata)","license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["q-bio.MN","q-bio.QM"],"details":null,"provenance":"arxiv","attribution":"Abstract: arXiv descriptive metadata (CC0). Thank you to arXiv for use of its open access interoperability. This service was not reviewed or approved by, nor does it necessarily express or reflect the policies or opinions of, arXiv."},{"id":"doi:10.1093/nar/gky884","kind":"article","title":"Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design","authors":["Shuyi Zhang","Christopher A. Voigt"],"author_count":2,"year":2018,"published":"2018-09-20","venue":"Nucleic Acids Research","cited_by":166,"doi":"10.1093/nar/gky884","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1093/nar/gky884","archive_url":"https://space-kitty.com/papers/doi:10.1093/nar/gky884","updated":null,"pmid":"30289463","pmcid":"PMC6237744","openalex_id":"W2894806694","pdf_url":"https://academic.oup.com/nar/article-pdf/46/20/11115/26578084/gky884.pdf","abstract":"Large synthetic genetic circuits require the simultaneous expression of many regulators. Deactivated Cas9 (dCas9) can serve as a repressor by having a small guide RNA (sgRNA) direct it to bind a promoter. The programmability and specificity of RNA:DNA basepairing simplifies the generation of many orthogonal sgRNAs that, in theory, could serve as a large set of regulators in a circuit. However, dCas9 is toxic in many bacteria, thus limiting how high it can be expressed, and low concentrations are quickly sequestered by multiple sgRNAs. Here, we construct a non-toxic version of dCas9 by eliminating PAM (protospacer adjacent motif) binding with a R1335K mutation (dCas9*) and recovering DNA binding by fusing it to the PhlF repressor (dCas9*_PhlF). Both the 30 bp PhlF operator and 20 bp sgRNA binding site are required to repress a promoter. The larger region required for recognition mitigates toxicity in Escherichia coli, allowing up to 9600 ± 800 molecules of dCas9*_PhlF per cell before growth or morphology are impacted, as compared to 530 ± 40 molecules of dCas9. Further, PhlF multimerization leads to an increase in average cooperativity from n = 0.9 (dCas9) to 1.6 (dCas9*_PhlF). A set of 30 orthogonal sgRNA-promoter pairs are characterized as NOT gates; however, the simultaneous use of multiple sgRNAs leads to a monotonic decline in repression and after 15 are co-expressed the dynamic range is <10-fold. This work introduces a non-toxic variant of dCas9, critical for its use in applications in metabolic engineering and synthetic biology, and exposes a limitation in the number of regulators that can be used in one cell when they rely on a shared resource.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"other-oa","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["CRISPR and Genetic Engineering"],"details":null,"provenance":"openalex+europepmc","attribution":"Abstract of \"Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design\" by Shuyi Zhang, Christopher A. Voigt, https://doi.org/10.1093/nar/gky884, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/nchem.2644","kind":"article","title":"Engineering genetic circuit interactions within and between synthetic minimal cells","authors":["Katarzyna P. Adamala","Daniel A. Martin-Alarcon","Katriona R. Guthrie-Honea","Edward S. Boyden"],"author_count":4,"year":2016,"published":"2016-11-14","venue":"Nature Chemistry","cited_by":359,"doi":"10.1038/nchem.2644","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nchem.2644","archive_url":"https://space-kitty.com/papers/doi:10.1038/nchem.2644","updated":null,"pmid":"28430194","pmcid":null,"openalex_id":"W2549541186","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Gene Regulatory Network Analysis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"arxiv:q-bio/0501002","kind":"article","title":"Nonlinear Protein Degradation and the Function of Genetic Circuits","authors":["Nicolas E. Buchler","Ulrich Gerland","Terence Hwa"],"author_count":3,"year":2005,"published":"2005-01-03","venue":"Proceedings of the National Academy of Sciences","cited_by":169,"doi":"10.1073/pnas.0409553102","arxiv_id":"q-bio/0501002","nct_id":null,"source_url":"https://arxiv.org/abs/q-bio/0501002","archive_url":"https://space-kitty.com/papers/arxiv:q-bio/0501002","updated":"2005-01-03","pmid":null,"pmcid":null,"openalex_id":"W2123511816","pdf_url":"https://arxiv.org/pdf/q-bio/0501002","abstract":"The functions of most genetic circuits require sufficient degrees of cooperativity in the circuit components. While mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this study, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as cooperative stability. For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus cooperative stability can effectively widen the accessible range of protein levels in vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. These results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits.","abstract_license":"CC0-1.0 (arXiv descriptive metadata)","license":null,"is_open_access":false,"retracted":false,"peer_reviewed":null,"categories":["q-bio.MN","q-bio.BM"],"details":null,"provenance":"arxiv","attribution":"Abstract: arXiv descriptive metadata (CC0). Thank you to arXiv for use of its open access interoperability. This service was not reviewed or approved by, nor does it necessarily express or reflect the policies or opinions of, arXiv."},{"id":"doi:10.3791/50762","kind":"article","title":"Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology","authors":["Zachary Z. Sun","Clarmyra A. Hayes","Jonghyeon Shin","Filippo Caschera","Richard M. Murray","Vincent Noireaux"],"author_count":6,"year":2013,"published":"2013-09-16","venue":"Journal of Visualized Experiments","cited_by":352,"doi":"10.3791/50762","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.3791/50762","archive_url":"https://space-kitty.com/papers/doi:10.3791/50762","updated":null,"pmid":"24084388","pmcid":null,"openalex_id":"W2153067536","pdf_url":"https://www.jove.com/pdf/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["RNA and protein synthesis mechanisms"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41467-017-02473-5","kind":"article","title":"Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors","authors":["Chen Y","Ho JML","Shis DL","Gupta C","Long J","Wagner DS","Ott W","Josić K","Bennett MR"],"author_count":9,"year":2018,"published":"2018-01-04","venue":"Nature communications","cited_by":148,"doi":"10.1038/s41467-017-02473-5","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41467-017-02473-5","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41467-017-02473-5","updated":null,"pmid":"29302024","pmcid":"PMC5754348","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC5754348/pdf","abstract":"One challenge for synthetic biologists is the predictable tuning of genetic circuit regulatory components to elicit desired outputs. Gene expression driven by ligand-inducible transcription factor systems must exhibit the correct ON and OFF characteristics: appropriate activation and leakiness in the presence and absence of inducer, respectively. However, the dynamic range of a promoter (i.e., absolute difference between ON and OFF states) is difficult to control. We report a method that tunes the dynamic range of ligand-inducible promoters to achieve desired ON and OFF characteristics. We build combinatorial sets of AraC-and LasR-regulated promoters containing -10 and -35 sites from synthetic and Escherichia coli promoters. Four sequence combinations with diverse dynamic ranges were chosen to build multi-input transcriptional logic gates regulated by two and three ligand-inducible transcription factors (LacI, TetR, AraC, XylS, RhlR, LasR, and LuxR). This work enables predictable control over the dynamic range of regulatory components.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors\" by Chen Y, Ho JML, Shis DL et al., https://doi.org/10.1038/s41467-017-02473-5, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."}],"next":"https://space-kitty.com/api/v1/topics/synthetic-biology/papers?sort=top&limit=25&offset=25"}