scholarly journals Synthetic biology projects in vitro

2006 ◽  
Vol 17 (1) ◽  
pp. 1-6 ◽  
Author(s):  
A. C. Forster ◽  
G. M. Church
Keyword(s):  
Synthetic Biology

scholarly journals Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

2019 ◽  
Vol 2 (2) ◽  
pp. 39 ◽  
Author(s):  
Dohyun Jeong ◽  
Melissa Klocke ◽  
Siddharth Agarwal ◽  
Jeongwon Kim ◽  
Seungdo Choi ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Free Expression ◽  
Dna Nanostructures ◽  
Expression Systems ◽  
Natural Systems ◽  
The Past ◽  
Current Cell ◽  
Recent Developments ◽  
Biological Circuits

Synthetic biology integrates diverse engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription–translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.

scholarly journals Strains, Mechanism, and Perspective:Salmonella-Based Cancer Therapy

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Cheng-Zhi Wang ◽  
Robert A. Kazmierczak ◽  
Abraham Eisenstark
Keyword(s):  
Synthetic Biology ◽  
Tumor Targeting ◽  
Tumor Therapy ◽  
The Other ◽  
Cancer Therapies ◽  
Chemotherapeutic Drugs ◽  
Serovar Typhimurium ◽  
Candidate Strain

Recently, investigation of bacterial-based tumor therapy has regained focus due to progress in molecular, cellular, and microbial biology. Many bacteria such asSalmonella,Listeria,Escherichia, andClostridiumhave proved to have tumor targeting and in some cases even tumor-destroying phenotypes. Furthermore, bacterial clinical treatments for cancer have been improved by combination with other therapeutic methods such as chemotherapeutic drugs and radioactive agents. Synthetic biology techniques have also driven the development of new bacterial-based cancer therapies. However, basic questions about the mechanisms of bacterial-mediated tumor targeting and destruction are still being elucidated. In this review, we focus on three tumor-therapeuticSalmonellamodels, the most intensively studied bacterial genus in this field. One of theseSalmonellamodels is ourSalmonella entericaserovar Typhimurium LT2 derived strain CRC2631, engineered to minimize toxicity but maximize tumor-targeting and destruction effects. The other two are VNP20009 and A1-R. We compare the means by which these therapeutic candidate strain models were selected for study, their tumor targeting and tumor destruction phenotypesin vitroandin vivo, and what is currently known about the mechanisms by which they target and destroy tumors.

scholarly journals An exploration of synthetic biology: A preliminary Christian ethical assessment of the advantages and disadvantages of synthetic biology

2014 ◽  
Vol 48 (2) ◽  
Author(s):  
Riaan A.L. Rheeder
Keyword(s):  
Synthetic Biology ◽  
Genetic Manipulation ◽  
Positive Outcomes ◽  
Ethical Assessment ◽  
Advantages And Disadvantages ◽  
Natural Function ◽  
Mycoplasma Capricolum ◽  
Mycoplasma Mycoides ◽  
Point Of Departure

On 20 May 2010, the Venter Institute in America announced that they have fully synthesised the genome of the organism Mycoplasma mycoides whilst in vitro by using a computer connected to a machine that synthesises genes. Thereafter, the genome was placed back into the casing of another organism (Mycoplasma capricolum) and it was reported that the synthesised organism and the genome functioned normally. This synthesised organism was reconstructed to function as a minute little factory with the aim of producing and secreting fuel and medicine − something that is not the natural function of this organism. There are certain potential dangers inherent in this kind of technology. Scientists fear that this technology may contaminate or infect humans, animals or the environment, and that it can as such be extremely harmful, or even lead to the destruction of humans. Other scientists are concerned that terrorists can use this technology to kill innocent citizens. Some ethicists are of the opinion that the consequences of synthetic biology is currently unpredictable and that it is therefore risky. In opposition to the potential dangers, one has to mention that synthetic biology indeed can result in far-reaching positive outcomes such as the manufacturing of biofuel and medication. Most scientists and ethicists are of the opinion that the potential dangers involved in synthetic biology should be evaluated in light of the fact that genetic manipulation has not caused any biological devastation over the last 30 years. From a Christian point of departure, the opinion is currently that synthetic biology is not an irresponsible science and technology.’n Verkenning van sintetiese biologie: ’n Voorlopige Christelik-etiese beoordeling van die voor- en nadele van sintetiese biologie. Op 20 Mei 2010 het die Venter-instituut (in Amerika) aangekondig dat hulle die genoom van die organisme Mycoplasma mycoides ten volle in vitro gesintetiseer het (deur middel van ’n rekenaar, gekoppel aan ’n masjien wat gene sintetiseer). Die berig het verder gelei dat die genoom daarna teruggeplaas is in die omhulsel van ’n ander organisme (Mycoplasma capricolum) − en dat die gesintetiseerde genoom en organisme normaal gefunksioneer het. Hierdie gesintetiseerde organisme word gerekonstrueer om as minuskule fabriek te funksioneer met die doel om brandstof en medisyne te produseer en te sekreer − wat nie die natuurlike funksie van die organisme is nie. Aan hierdie tegnologie is daar ook bepaalde potensiële gevare verbonde. Wetenskaplikes is bang dat hierdie tegnologie mens, dier en omgewing kan kontamineer of infekteer en op dié wyse groot skade kan aanrig − en selfs tot mense se dood kan lei. Ander wetenskaplikes is weer bekommerd dat hierdie tegnologie deur terroriste gebruik kan word om onskuldige burgers dood te maak. Sommige etici is oortuig dat die gevolge van sintetiese biologie tans onvoorspelbaar, en daarom riskant is. Teenoor die potensiële gevare moet gestel word dat sintetiese biologie inderdaad omvangryke positiewe uitkomste soos die vervaardiging van biobrandstof en medisyne tot gevolg kan hê. Meeste wetenskaplikes en etici is van mening dat die potensiële gevare verbonde aan sintetiese biologie beoordeel moet word in die lig van die feit dat genetiese manipulasie in die afgelope 30 jaar geen biologiese ramp veroorsaak het nie. Uit ’n Christelike oogpunt word voorlopig geoordeel dat sintetiese biologie nie ’n onverantwoordelike wetenskap en tegnologie is nie.

scholarly journals Bioinspired genotype–phenotype linkages: mimicking cellular compartmentalization for the engineering of functional proteins

2015 ◽  
Vol 5 (4) ◽  
pp. 20150035 ◽  
Author(s):  
Liisa D. van Vliet ◽  
Pierre-Yves Colin ◽  
Florian Hollfelder
Keyword(s):  
Synthetic Biology ◽  
Directed Evolution ◽  
Enzyme Catalysis ◽  
Darwinian Evolution ◽  
Oil Droplets ◽  
Shell Beads ◽  
Cellular Compartmentalization ◽  
In Cells

The idea of compartmentalization of genotype and phenotype in cells is key for enabling Darwinian evolution. This contribution describes bioinspired systems that use in vitro compartments—water-in-oil droplets and gel-shell beads—for the directed evolution of functional proteins. Technologies based on these principles promise to provide easier access to protein-based therapeutics, reagents for processes involving enzyme catalysis, parts for synthetic biology and materials with biological components.

scholarly journals Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Shue Wang ◽  
Sagardip Majumder ◽  
Nicholas J Emery ◽  
Allen P Liu
Keyword(s):  
Synthetic Biology ◽  
Real Time ◽  
Protein Dynamics ◽  
Mammalian Cell ◽  
Locked Nucleic Acid ◽  
Free Expression ◽  
Reporter Protein ◽  
Bottom Up ◽  
Lna Probe

Abstract Transcription and translation are two critical processes during eukaryotic gene expression that regulate cellular activities. The development of mammalian cell-free expression (CFE) systems provides a platform for studying these two critical processes in vitro for bottom-up synthetic biology applications such as construction of an artificial cell. Moreover, real-time monitoring of the dynamics of synthesized mRNA and protein is key to characterize and optimize gene circuits before implementing in living cells or in artificial cells. However, there are few tools for measurement of mRNA and protein dynamics in mammalian CFE systems. Here, we developed a locked nucleic acid (LNA) probe for monitoring transcription in a HeLa-based CFE system in real-time. By using this LNA probe in conjunction with a fluorescent reporter protein, we were able to simultaneously monitor mRNA and protein dynamics in bulk reactions and cell-sized single-emulsion droplets. We found rapid production of mRNA transcripts that decreased over time as protein production ensued in bulk reactions. Our results also showed that transcription in cell-sized droplets has different dynamics compared to the transcription in bulk reactions. The use of this LNA probe in conjunction with fluorescent proteins in HeLa-based mammalian CFE system provides a versatile in vitro platform for studying mRNA dynamics for bottom-up synthetic biology applications.

scholarly journals Regulating synthetic gene networks in 3D materials

2012 ◽  
Vol 109 (38) ◽  
pp. 15217-15222 ◽  
Author(s):  
Tara L. Deans ◽  
Anirudha Singh ◽  
Matthew Gibson ◽  
Jennifer H. Elisseeff
Keyword(s):  
Synthetic Biology ◽  
Gene Networks ◽  
Materials Science ◽  
Genetic Circuits ◽  
Therapeutic Applications ◽  
Regulatory Processes ◽  
Cellular Events ◽  
The Matrix

Combining synthetic biology and materials science will enable more advanced studies of cellular regulatory processes, in addition to facilitating therapeutic applications of engineered gene networks. One approach is to couple genetic inducers into biomaterials, thereby generating 3D microenvironments that are capable of controlling intrinsic and extrinsic cellular events. Here, we have engineered biomaterials to present the genetic inducer, IPTG, with different modes of activating genetic circuits in vitro and in vivo. Gene circuits were activated in materials with IPTG embedded within the scaffold walls or chemically linked to the matrix. In addition, systemic applications of IPTG were used to induce genetic circuits in cells encapsulated into materials and implanted in vivo. The flexibility of modifying biomaterials with genetic inducers allows for patterned placement of these inducers that can be used to generate distinct patterns of gene expression. Together, these genetically interactive materials can be used to characterize genetic circuits in environments that more closely mimic cells’ natural 3D settings, to better explore complex cell–matrix and cell–cell interactions, and to facilitate therapeutic applications of synthetic biology.

scholarly journals Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

2016 ◽  
Vol 13 (117) ◽  
pp. 20151046 ◽  
Author(s):  
Fei He ◽  
Ettore Murabito ◽  
Hans V. Westerhoff
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Regulatory Networks ◽  
Computational Systems Biology ◽  
Control Engineering ◽  
Trade Offs ◽  
Metabolic Systems ◽  
Analytical Approaches

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo , not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

scholarly journals A synthetic biology platform for the reconstitution and mechanistic dissection of LINC complex assembly

2018 ◽  
Author(s):  
Sagardip Majumder ◽  
Patrick T. Willey ◽  
Maxwell S. DeNies ◽  
Allen P. Liu ◽  
G.W. Gant Luxton
Keyword(s):  
Synthetic Biology ◽  
Lipid Bilayers ◽  
Transmembrane Domain ◽  
Experimental System ◽  
Free Expression ◽  
Supported Lipid Bilayers ◽  
Linc Complex ◽  
Complex Assembly ◽  
Complex Core

ABSTRACTThe linker of nucleoskeleton and cytoskeleton (LINC) is a conserved nuclear envelope-spanning molecular bridge that is responsible for the mechanical integration of the nucleus with the cytoskeleton. LINC complexes are formed by a transluminal interaction between the outer and inner nuclear membrane KASH and SUN proteins, respectively. Despite recent structural insights, our mechanistic understanding of LINC complex assembly remains limited by the lack of an experimental system for its in vitro reconstitution and manipulation. Here, we describe artificial nuclear membranes (ANMs) as a synthetic biology platform based on mammalian cell-free expression for the rapid reconstitution of SUN proteins in supported lipid bilayers. We demonstrate that SUN1 and SUN2 are oriented in ANMs with solvent-exposed C-terminal KASH-binding SUN domains. We also find that SUN2 possesses a single transmembrane domain, while SUN1 possesses three. Finally, SUN protein-containing ANMs bind synthetic KASH peptides, thereby reconstituting the LINC complex core. This work represents the first in vitro reconstitution of KASH-binding SUN proteins in supported lipid bilayers using cell-free expression, which will be invaluable for testing proposed models of LINC complex assembly and its regulation.

scholarly journals Synthetic Perturbations in IL6 Biological Circuit Induces Dynamical Cellular Response

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 124
Author(s):  
Bhavnita Soni ◽  
Shailza Singh
Keyword(s):  
Synthetic Biology ◽  
Cellular Response ◽  
Leishmania Major ◽  
Early Stage ◽  
Macrophage Polarization ◽  
Janus Kinase ◽  
Cytokine Signaling ◽  
Macrophage Phenotype ◽  
Stat Pathway

Macrophage phenotype plays a crucial role in the pathogenesis of Leishmanial infection. Pro-inflammatory cytokines signals through the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway that functions in parasite killing. Suppression of cytokine signaling (SOCS) is a well-known negative feedback regulator of the JAK/STAT pathway. However, change in the expression levels of SOCSs in correlation with the establishment of infection is not well understood. IL6 is a pleotropic cytokine that induces SOCS1 and SOCS3 expression through JAK-STAT signaling. Mathematical modeling of the TLR2 and IL6 signaling pathway has established the immune axis of SOCS1 and SOCS3 functioning in macrophage polarization during the early stage of Leishmania major infection. The ratio has been quantified both in silico and in vitro as 3:2 which is required to establish infection during the early stage. Furthermore, phosphorylated STAT1 and STAT3 have been established as an immunological cross talk between TLR2 and IL6 signaling pathways. Using synthetic biology approaches, peptide based immuno-regulatory circuits have been designed to target the activity of SOCS1 which can restore pro-inflammatory cytokine expression during infection. In a nutshell, we explored the potential of synthetic biology to address and rewire the immune response from Th2 to Th1 type during the early stage of leishmanial infection governed by SOCS1/SOCS3 immune axis.

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