SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent genetic circuit designs, and it is based on capturing data using graphs. The language provides the syntax using a free text document which is accessible to humans only. Here, we provide SBOL-OWL, an ontology for a machine understandable definition of SBOL. This ontology acts as a semantic layer for genetic circuit designs. As a result, computational tools can understand the meaning of design entities in addition to parsing structured SBOL data. SBOL-OWL not only describes how genetic circuits can be constructed computationally, it also facilitates the use of several existing Semantic Web tooling for synthetic biology. Here, we demonstrate some of these features, for example, to validate designs and check for inconsistencies. Through the use of SBOL-OWL, queries are simplified and become more intuitive. Moreover, existing reasoners can be used to infer information about genetic circuit designs that can't be directly retrieved using existing querying mechanisms. This ontological representation of the SBOL standard provides a new perspective to the verification, representation and querying of information about synthetic genetic circuits and is important to incorporate complex design information via the integration of biological ontologies.

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CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli

Journal of Biological Engineering ◽

10.1186/s13036-019-0218-8 ◽

2019 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Stefano Vecchione ◽

Georg Fritz

Keyword(s):

Escherichia Coli ◽

Synthetic Biology ◽

Integrated Circuits ◽

High Efficiency ◽

Genetic Circuit ◽

Dna Assembly ◽

Chromosomal Integration ◽

Golden Gate ◽

Genetic Circuits ◽

E Coli

Abstract Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.

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SBOL Visual 2 Ontology

10.1101/2020.01.24.918417 ◽

2020 ◽

Author(s):

Göksel Misirli ◽

Jacob Beal ◽

Thomas E. Gorochowski ◽

Guy-Bart Stan ◽

Anil Wipat ◽

...

Keyword(s):

Synthetic Biology ◽

Web Service ◽

Visual Representation ◽

Biological Ontologies ◽

Visualization Tools ◽

Synthetic Biology Open Language

AbstractStandardising the visual representation of genetic parts and circuits is vital for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.Graphical TOC Entry

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Rosa26 docking sites for investigating genetic circuit silencing in stem cells

Synthetic Biology ◽

10.1093/synbio/ysaa014 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Michael Fitzgerald ◽

Mark Livingston ◽

Chelsea Gibbs ◽

Tara L Deans

Keyword(s):

Stem Cells ◽

Synthetic Biology ◽

Cell Lines ◽

Pluripotent Stem Cells ◽

Genetic Circuit ◽

Genetic Circuits ◽

Immortalized Cell Lines ◽

Site Specific Integration ◽

Docking Sites ◽

Immortalized Cell

Abstract Approaches in mammalian synthetic biology have transformed how cells can be programmed to have reliable and predictable behavior, however, the majority of mammalian synthetic biology has been accomplished using immortalized cell lines that are easy to grow and easy to transfect. Genetic circuits that integrate into the genome of these immortalized cell lines remain functional for many generations, often for the lifetime of the cells, yet when genetic circuits are integrated into the genome of stem cells gene silencing is observed within a few generations. To investigate the reactivation of silenced genetic circuits in stem cells, the Rosa26 locus of mouse pluripotent stem cells was modified to contain docking sites for site-specific integration of genetic circuits. We show that the silencing of genetic circuits can be reversed with the addition of sodium butyrate, a histone deacetylase inhibitor. These findings demonstrate an approach to reactivate the function of genetic circuits in pluripotent stem cells to ensure robust function over many generations. Altogether, this work introduces an approach to overcome the silencing of genetic circuits in pluripotent stem cells that may enable the use of genetic circuits in pluripotent stem cells for long-term function.

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Performance Evaluation of LSA, NMF and ILSA in Electronic Assessment of Free Text Document

Asian Journal of Research in Computer Science ◽

10.9734/ajrcos/2021/v9i130214 ◽

2021 ◽

pp. 46-56

Author(s):

M. M. Rufai ◽

A. O. Afolabi ◽

O. D. Fenwa ◽

F. A. Ajala

Keyword(s):

Latent Semantic Analysis ◽

Semantic Analysis ◽

Semantic Representation ◽

Free Text ◽

Test Question ◽

Text Document ◽

Electronic Assessment ◽

Term Similarity ◽

F Measure ◽

Improved Algorithm

Aims: To evaluate the performance of an Improved Latent Semantic Analysis (ILSA), Latent Semantic Analysis (LSA), Non-Negative Matrix Factorization (NMF) algorithms in an Electronic Assessment Application using metrics, Term Similarity, Precision, Recall and F-measure functions, Mean divergence, Assessment Accuracy and Adequacy in Semantic Representation. Methodology: The three algorithms were separately applied in developing an Electronic Assessment application. One hundred students’ responses to a test question in an introductory artificial intelligence course were used. Their performance was measured based on the following metrics, Term Similarity, Precision, Recall and F-measure functions, Mean divergence and Assessment Accuracy. Results: ILSA outperformed the LSA and NMF with an assessment accuracy of 96.64, mean divergence from manual score of 0.03, and recall, precision and f-measure value of 0.83, 0.85 and 0.87 respectively. Conclusion: The research observed the performance of an improved algorithm ILSA for electronic Assessment of free text document using Adequacy in Semantic Representation, Retrieval Quality and Assessment Accuracy as performance metrics. The results obtained from the experimental designs shows the adequacy of the improved algorithm in semantic representation, better retrieval quality and improved assessment accuracy.

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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information

ACS Synthetic Biology ◽

10.1021/acssynbio.8b00532 ◽

2019 ◽

Vol 8 (7) ◽

pp. 1498-1514 ◽

Cited By ~ 6

Author(s):

Göksel Mısırlı ◽

Renee Taylor ◽

Angel Goñi-Moreno ◽

James Alastair McLaughlin ◽

Chris Myers ◽

...

Keyword(s):

Synthetic Biology ◽

Semantic Representation ◽

Ontological Approach

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An Improved LSA Model for Electronic Assessment of Free Text Document

International Journal of Innovative Technology and Exploring Engineering - Special Issue ◽

10.35940/ijitee.d8536.0210421 ◽

2021 ◽

Vol 10 (4) ◽

pp. 152-159

Author(s):

Rufai Mohammed Mutiu ◽

A. O. Afolabi ◽

O. D. Fenwa ◽

F. A. Ajala

Keyword(s):

Semantic Analysis ◽

Semantic Representation ◽

Pearson Correlation ◽

Semantic Content ◽

Free Text ◽

Text Document ◽

Electronic Assessment ◽

Decision Variables ◽

Assessment Result ◽

Non Negative Matrix Factorization

Latent Semantic Analysis (LSA) is a statistical approach designed to capture the semantic content of a document which form the basis for its application in electronic assessment of free-text document in an examination context. The students submitted answers are transformed into a Document Term Matrix (DTM) and approximated using SVD-LSA for noise reduction. However, it has been shown that LSA still has remnant of noise in its semantic representation which ultimately affects the assessment result accuracy when compared to human grading. In this work, the LSA Model is formulated as an optimization problem using Non-negative Matrix Factorization(NMF)-Ant Colony Optimization (ACO). The factors of LSA are used to initialize NMF factors for quick convergence. ACO iteratively searches for the value of the decision variables in NMF that minimizes the objective function and use these values to construct a reduced DTM. The results obtained shows a better approximation of the DTM representation and improved assessment result of 91.35% accuracy, mean divergence of 0.0865 from human grading and a Pearson correlation coefficient of 0.632 which proved to be a better result than the existing ones.

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Rosa26 docking sites for investigating genetic circuit silencing in stem cells

10.1101/575266 ◽

2019 ◽

Author(s):

Michael Fitzgerald ◽

Mark Livingston ◽

Chelsea Gibbs ◽

Tara L. Deans

Keyword(s):

Stem Cells ◽

Synthetic Biology ◽

Cell Lines ◽

Pluripotent Stem Cells ◽

Genetic Circuit ◽

Genetic Circuits ◽

Immortalized Cell Lines ◽

Site Specific Integration ◽

Docking Sites ◽

Immortalized Cell

ABSTRACTApproaches in mammalian synthetic biology have transformed how cells can be programmed to have reliable and predictable behaviour, however, the majority of mammalian synthetic biology has been accomplished using immortalized cell lines that are easy to grow and easy to transfect. Genetic circuits that integrate into the genome of these immortalized cell lines remain functional for many generations, often for the lifetime of the cells, yet when genetic circuits are integrated into the genome of stem cells gene silencing is observed within a few generations. To investigate the reactivation of silenced genetic circuits in stem cells, the Rosa26 locus of mouse pluripotent stem cells was modified to contain docking sites for site-specific integration of genetic circuits. We show that the silencing of genetic circuits can be reversed with the addition of sodium butyrate, a histone deacetylase inhibitor. These findings demonstrate an approach to reactivate the function of genetic circuits in pluripotent stem cells to ensure robust function over many generations. Altogether, this work introduces an approach to overcome the silencing of genetic circuits in pluripotent stem cells that may enable the use of genetic circuits in pluripotent stem cells for long-term function.

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TXO: Transcription-Only genetic circuits as a novel cell-free approach for Synthetic Biology

10.1101/826230 ◽

2019 ◽

Author(s):

Felipe A. Millacura ◽

Mengxi Li ◽

Marcos Valenzuela-Ortega ◽

Christopher E. French

Keyword(s):

Synthetic Biology ◽

Real World ◽

Genetically Modified Organisms ◽

Rna Aptamers ◽

Genetic Circuit ◽

Environmental Concerns ◽

Genetic Circuits ◽

Transcriptional Units ◽

Biosensor Applications ◽

Real World Problems

AbstractWhile synthetic biology represents a promising approach to solve real-world problems, the use of genetically modified organisms is a cause of legal and environmental concerns. Cell-free systems have emerged as a possible solution but much work is needed to optimize their functionality and simplify their usage for Synthetic Biology. Here we present TXO, transcription-only genetic circuits, independent of translation or post-translation maturation. RNA aptamers are used as reaction output allowing the generation of fast, reliable and simple-to-design transcriptional units. TXO cell-free reactions and their possible applications are a promising new tool for fast and simple bench-to-market genetic circuit and biosensor applications.

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Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma

Neurosurgical FOCUS ◽

10.3171/2020.12.focus20855 ◽

2021 ◽

Vol 50 (2) ◽

pp. E10

Author(s):

Dileep D. Monie ◽

Archis R. Bhandarkar ◽

Ian F. Parney ◽

Cristina Correia ◽

Jann N. Sarkaria ◽

...

Keyword(s):

Systems Biology ◽

Synthetic Biology ◽

Laboratory Data ◽

Immunological Response ◽

Analytical Framework ◽

Oncolytic Viruses ◽

Genetic Circuit ◽

Genetic Circuits ◽

Synthetic Dna ◽

Network Analyses

Oncolytic viruses (OVs) are a class of immunotherapeutic agents with promising preclinical results for the treatment of glioblastoma (GBM) but have shown limited success in recent clinical trials. Advanced bioengineering principles from disciplines such as synthetic and systems biology are needed to overcome the current challenges faced in developing effective OV-based immunotherapies for GBMs, including off-target effects and poor clinical responses. Synthetic biology is an emerging field that focuses on the development of synthetic DNA constructs that encode networks of genes and proteins (synthetic genetic circuits) to perform novel functions, whereas systems biology is an analytical framework that enables the study of complex interactions between host pathways and these synthetic genetic circuits. In this review, the authors summarize synthetic and systems biology concepts for developing programmable, logic-based OVs to treat GBMs. Programmable OVs can increase selectivity for tumor cells and enhance the local immunological response using synthetic genetic circuits. The authors discuss key principles for developing programmable OV-based immunotherapies, including how to 1) select an appropriate chassis, a vector that carries a synthetic genetic circuit, and 2) design a synthetic genetic circuit that can be programmed to sense key signals in the GBM microenvironment and trigger release of a therapeutic payload. To illustrate these principles, some original laboratory data are included, highlighting the need for systems biology studies, as well as some preliminary network analyses in preparation for synthetic biology applications. Examples from the literature of state-of-the-art synthetic genetic circuits that can be packaged into leading candidate OV chassis are also surveyed and discussed.

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Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

Essays in Biochemistry ◽

10.1042/ebc20160015 ◽

2016 ◽

Vol 60 (4) ◽

pp. 303-313 ◽

Cited By ~ 30

Author(s):

Juhyun Kim ◽

Manuel Salvador ◽

Elizabeth Saunders ◽

Jaime González ◽

Claudio Avignone-Rossa ◽

...

Keyword(s):

Synthetic Biology ◽

Genetic Information ◽

Essential Element ◽

Model Organisms ◽

Biotechnological Applications ◽

Cell Models ◽

Genetic Circuits ◽

Metabolic Diversity ◽

Translational Machinery ◽

Metabolic Fluxes

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.

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