scholarly journals Network visualisation of synthetic biology designs

2021 ◽  
Author(s):  
Matthew Crowther ◽  
Anil Wipat ◽  
Angel Goñi-Moreno
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Design Information ◽  
Complex Information ◽  
Linear Sequence ◽  
Hidden Data ◽  
Proteins Interactions ◽  
Visualisation Technique

Visualising the complex information captured by synthetic biology designs is still a major challenge. The popular glyph approach where each genetic part is displayed on a linear sequence allows researchers to generate diagrams and visualise abstract designs, but only represents a single, static representation that results in visualisation that is not specific to the requirements of a user resulting in a one-size-fits-all visualisation. We developed a network visualisation technique that automatically turns all design information into a graph, displaying otherwise hidden data. The structure of the resulting graphs can be dynamically adjusted according to specific visualisation requirements, such as highlighting proteins, interactions or hierarchy. Since biological systems have an inherent affinity with network visualisation, we advocate for adopting this approach to standardise and automate the representation of complex information.

scholarly journals Independent control of amplitude and period in a synthetic oscillator circuit with modified repressilator

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengyu Zhang ◽  
Yanhong Sun ◽  
Yihao Zhang ◽  
Wenting Shen ◽  
Shujing Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Biological Systems ◽  
Reporter Genes ◽  
Quantitative Model ◽  
Theoretical Level ◽  
Independent Control ◽  
Oscillator Circuit ◽  
Biological Circuits

AbstractSynthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, independently controlling the oscillation of reporter genes in terms of their amplitude and period is only on theoretical level. Here, we introduce a new oscillator circuit that can be independently controlled by two inducers in Escherichia coli. Some control components, including σECF11 and NahR, were added to the circuit. By systematically tuning the concentration of the inducers, salicylate and IPTG, the amplitude and period can be modulated independently. Furthermore, we constructed a quantitative model to forecast the regulation results. Under the guidance of the model, the expected oscillation can be regulated by choosing the proper concentration combinations of inducers. In summary, our work achieved independent control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.

Integrating the whole from the sum of the parts: vignettes in computational biology

2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Personalized Medicine ◽  
Computational Biology ◽  
Biological Systems ◽  
Deep Understanding ◽  
Biological Processes ◽  
Practical Applications ◽  
Biological Variables

As is typical of contemporary cutting-edge interdisciplinary fields, computational biology touches and impacts many disciplines ranging from fundamental studies in the areas of genomics, proteomics transcriptomics, lipidomics to practical applications such as personalized medicine, drug discovery, and synthetic biology. This editorial examines the multifaceted role computational biology plays. Using the tools of deep learning, it can make powerful predictions of many biological variables, which may not provide a deep understanding of what factors contribute to the phenomena. Alternatively, it can provide the how and the why of biological processes. Most importantly, it can help guide and interpret what experiments and biological systems to study.

scholarly journals Are the biomedical sciences ready for synthetic biology?

2020 ◽  
Vol 11 (1) ◽  
pp. 23-31
Author(s):  
Maxwell S. DeNies ◽  
Allen P. Liu ◽  
Santiago Schnell
Keyword(s):  
Synthetic Biology ◽  
Biomedical Research ◽  
Molecular Level ◽  
Biological Systems ◽  
Science Research ◽  
Functional System ◽  
Biomedical Sciences ◽  
Present Evidence ◽  
Experimental Control ◽  
Discovery Science

AbstractThe ability to construct a functional system from its individual components is foundational to understanding how it works. Synthetic biology is a broad field that draws from principles of engineering and computer science to create new biological systems or parts with novel function. While this has drawn well-deserved acclaim within the biotechnology community, application of synthetic biology methodologies to study biological systems has potential to fundamentally change how biomedical research is conducted by providing researchers with improved experimental control. While the concepts behind synthetic biology are not new, we present evidence supporting why the current research environment is conducive for integration of synthetic biology approaches within biomedical research. In this perspective we explore the idea of synthetic biology as a discovery science research tool and provide examples of both top-down and bottom-up approaches that have already been used to answer important physiology questions at both the organismal and molecular level.

Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1252-1254 ◽  
Author(s):  
Petra Schwille
Keyword(s):  
Synthetic Biology ◽  
Life Science ◽  
Biological Systems ◽  
Living Systems ◽  
Design Features ◽  
Literal Interpretation ◽  
Bottom Up ◽  
Systematic Construction ◽  
Science Discipline ◽  
Recent Developments

How synthetic can “synthetic biology” be? A literal interpretation of the name of this new life science discipline invokes expectations of the systematic construction of biological systems with cells being built module by module—from the bottom up. But can this possibly be achieved, taking into account the enormous complexity and redundancy of living systems, which distinguish them quite remarkably from design features that characterize human inventions? There are several recent developments in biology, in tight conjunction with quantitative disciplines, that may bring this literal perspective into the realm of the possible. However, such bottom-up engineering requires tools that were originally designed by nature’s greatest tinkerer: evolution.

Mammalian Synthetic Biology: Engineering Biological Systems

2017 ◽  
Vol 19 (1) ◽  
pp. 249-277 ◽  
Author(s):  
Joshua B. Black ◽  
Pablo Perez-Pinera ◽  
Charles A. Gersbach
Keyword(s):  
Synthetic Biology ◽  
Biological Systems

scholarly journals Harnessing nature's toolbox: regulatory elements for synthetic biology

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Patrick M. Boyle ◽  
Pamela A. Silver
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Regulatory Elements ◽  
Biological Regulation ◽  
Metabolic Fluxes ◽  
Biological Organisms

Synthetic biologists seek to engineer complex biological systems composed of modular elements. Achieving higher complexity in engineered biological organisms will require manipulating numerous systems of biological regulation: transcription; RNA interactions; protein signalling; and metabolic fluxes, among others. Exploiting the natural modularity at each level of biological regulation will promote the development of standardized tools for designing biological systems.

scholarly journals Build to understand: synthetic approaches to biology

2016 ◽  
Vol 8 (4) ◽  
pp. 394-408 ◽  
Author(s):  
Le-Zhi Wang ◽  
Fuqing Wu ◽  
Kevin Flores ◽  
Ying-Cheng Lai ◽  
Xiao Wang
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Genetic Circuits ◽  
Naturally Occurring ◽  
Synthetic Approaches

In this review we discuss how synthetic biology facilitates the task of investigating genetic circuits that are observed in naturally occurring biological systems.

scholarly journals Network Structure of a System coded by Groups

1980 ◽  
Vol 35 (5) ◽  
pp. 526-530
Author(s):  
H. G. Busse ◽  
B. H. Havsteen
Keyword(s):  
Kinetic Model ◽  
Network Structure ◽  
Biological Systems ◽  
Free Groups ◽  
Chemical Kinetic ◽  
Mathematical Tool ◽  
Systematic Treatment ◽  
Chemical Kinetic Model ◽  
Linear Sequence ◽  
Context Free

Abstract A system may be characterized by its dynamics as well as by its structure. Several kinds of schematic drawings have been proposed to represent the structure of a system. Here, the representation of the structure by free groups is discussed. Free groups are an abstract mathematical tool, which permits the systematic treatment of a structure. The suggestion is exemplified by its application to a chemical kinetic model. The structure of the model is given (coded) by a linear sequence of symbols. The interaction of the environment with the structure (mutation) and the relation between structure and systemic boundaries (finiteness) are treated. The concept probably also applies to biological systems. Also, context-free languages could be used as alternate representations of system structures.

scholarly journals A Synthetic Microbial Operational Amplifier

2017 ◽  
Author(s):  
Ji Zeng ◽  
Jaewook Kim ◽  
Areen Banerjee ◽  
Rahul Sarpeshkar
Keyword(s):  
Transcription Factor ◽  
Synthetic Biology ◽  
Operational Amplifier ◽  
Biological Systems ◽  
Logic Gates ◽  
Living Cells ◽  
Output Stage ◽  
Cellular Circuits ◽  
Differential Transcription ◽  
Insight Into

AbstractSynthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.One Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.

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