Designing biological systems: Systems Engineering meets Synthetic Biology

2012 ◽  
Vol 69 (1) ◽  
pp. 1-29 ◽  
Author(s):  
Sascha Rollié ◽  
Michael Mangold ◽  
Kai Sundmacher
Keyword(s):  
Synthetic Biology ◽  
Systems Engineering ◽  
Biological Systems

Commercializing synthetic biology: Socio-ethical concerns and challenges under intellectual property regime

1969 ◽  
Vol 16 (2) ◽  
Author(s):  
Trichi Saukshmya ◽  
Archana Chugh
Keyword(s):  
Biological Sciences ◽  
Intellectual Property ◽  
Synthetic Biology ◽  
Systems Engineering ◽  
Human Life ◽  
Biological Systems ◽  
Ethical Implications ◽  
Synthetic Organisms ◽  
Property Regime

Synthetic biology also termed as ‘genomic alchemy’ represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It focuses on building, modelling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. As discussed in the present study, synthetic biology is an elegant consequence of amalgamation of various branches of science. It is speculated that the resulting synthetic organisms can successfully provide solutions for the problems where natural biological systems have failed. These artificially synthesized organisms can be tutored to meet diverse applications such as production of various biodrugs and creation of tailor-made metabolic pathways. Evidently, this revolutionary technology has the potential to transform human life directly and indirectly. The article provides an insight into the tremendous commercialization ability of synthetic biology in various sectors (bioenergy, medicine, and so on) as demonstrated by various initiatives, collaborative projects with huge investments. It is noteworthy that synthetic biology tools and organisms can be used for saving, creating ‘or’ destroying life; hence the study further deals with the socio-ethical implications of this rapidly advancing field of biology and also assesses the challenging role of intellectual property regime in commercialization of synthetic biology.

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.

scholarly journals A Spiral Curriculum Approach To The Implementation Of Instrumentation In Biological Systems Engineering

2020 ◽  
Author(s):  
Kumar Mallikarjunan ◽  
Anand Lakshmikanth ◽  
John Cundiff ◽  
Andrew Fulton
Keyword(s):  
Systems Engineering ◽  
Biological Systems ◽  
Spiral Curriculum

Biomolecular Systems Engineering: Unlocking the Potential of Engineered Allostery via the Lactose Repressor Topology

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Thomas M. Groseclose ◽  
Ronald E. Rondon ◽  
Ashley N. Hersey ◽  
Prasaad T. Milner ◽  
Dowan Kim ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Systems Engineering ◽  
Gene Networks ◽  
Chemical Engineering ◽  
Publication Date ◽  
Biomolecular Systems ◽  
Lactose Repressor ◽  
Unit Operations ◽  
Allosteric Communication ◽  
Logical Operations

Allosteric function is a critical component of many of the parts used to construct gene networks throughout synthetic biology. In this review, we discuss an emerging field of research and education, biomolecular systems engineering, that expands on the synthetic biology edifice—integrating workflows and strategies from protein engineering, chemical engineering, electrical engineering, and computer science principles. We focus on the role of engineered allosteric communication as it relates to transcriptional gene regulators—i.e., transcription factors and corresponding unit operations. In this review, we ( a) explore allosteric communication in the lactose repressor LacI topology, ( b) demonstrate how to leverage this understanding of allostery in the LacI system to engineer non-natural BUFFER and NOT logical operations, ( c) illustrate how engineering workflows can be used to confer alternate allosteric functions in disparate systems that share the LacI topology, and ( d) demonstrate how fundamental unit operations can be directed to form combinational logical operations. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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 Taming the Beast of Biology: Synthetic Biology and Biological Systems Engineering

2020 ◽  
Vol 74 (5) ◽  
pp. 402-406
Author(s):  
Sven Panke
Keyword(s):  
Synthetic Biology ◽  
Directed Evolution ◽  
Continuous Improvement ◽  
Systems Engineering ◽  
Large Scale ◽  
Strain Engineering ◽  
Stepping Stones ◽  
Omics Technologies ◽  
Molecular Systems ◽  
Genome Wide

Despite the availability of a variety of ' -omics ' technologies to support the system-wide analysis of industrially relevant microorganisms, the manipulation of strains towards an economically relevant goal remains a challenge. Remarkably, our ability to catalogue the participants in and model ever more comprehensive aspects of a microorganism's physiology is now complemented by technologies that permanently expand the scope of engineering interventions that can be imagined. In fact, genome-wide editing and re-synthesis of microbial and even eukaryotic chromosomes have become widely applied methods. At the heart of this emerging system-wide engineering approach, often labelled ' Synthetic Biology ' , is the continuous improvement of large-scale DNA synthesis, which is put to two-fold use: (i) starting ever more ambitious efforts to re-write existing and coding novel molecular systems, and (ii) designing and constructing increasingly sophisticated library technologies, which has led to a renaissance of directed evolution in strain engineering. Here, we briefly review some of the critical concepts and technological stepping-stones of Synthetic Biology on its way to becoming a mature industrial technology.

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
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