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

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Patrick M. Boyle ◽  
Pamela A. Silver

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.

2016 ◽  
Vol 60 (4) ◽  
pp. 303-313 ◽  
Author(s):  
Juhyun Kim ◽  
Manuel Salvador ◽  
Elizabeth Saunders ◽  
Jaime González ◽  
Claudio Avignone-Rossa ◽  
...  

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.


2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengyu Zhang ◽  
Yanhong Sun ◽  
Yihao Zhang ◽  
Wenting Shen ◽  
Shujing Wang ◽  
...  

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.


Author(s):  
David J. Hand

Biological systems pose particularly challenging measurement issues. This is partly because the biological domain is characterized by complexity and diversity. As a consequence, the results of measuring biological organisms will often result in a distribution of values. A further complication in medicine is that much measurement is of attributes or characteristics relating to internal or subjective phenomena such as of pain, anxiety, and dizziness. ‘Measurement in the life sciences, medicine, and health’ considers the scope of medical measurement, how to measure patients, and how to measure the health of populations. In modern medicine, there are many different reasons for taking a measurement, and hence many different types of measurement.


2019 ◽  
Vol 16 (2) ◽  
Author(s):  
Curtis Madsen ◽  
Angel Goni Moreno ◽  
Zachary Palchick ◽  
Umesh P ◽  
Nicholas Roehner ◽  
...  

AbstractPeople who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.


2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick

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.


2020 ◽  
Vol 11 (1) ◽  
pp. 23-31
Author(s):  
Maxwell S. DeNies ◽  
Allen P. Liu ◽  
Santiago Schnell

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.


Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1252-1254 ◽  
Author(s):  
Petra Schwille

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.


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

2016 ◽  
Vol 8 (4) ◽  
pp. 394-408 ◽  
Author(s):  
Le-Zhi Wang ◽  
Fuqing Wu ◽  
Kevin Flores ◽  
Ying-Cheng Lai ◽  
Xiao Wang

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


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