Working Backward

This paper discusses role of reverse engineering in biomedical and other bioscience applications. Reverse engineering is one of the most relevant examples of methods that have moved from engineering to find a role in biomedical and other bioscience applications. For an early introduction to the method's use in both biomedical and engineering fields, reverse engineering is commonly taught to biomedical undergraduates. Scientists in the biomedical hybrid fields of systems and synthetic biology call upon reverse engineering in ways that may look foreign to the practicing mechanical or electrical engineer—or even to the practicing biomedical engineer. The paper also highlights that synthetic biology, a new area of research, focuses solely on designing and building new biological systems. Synthetic biology often focuses on ways of taking parts of natural biological systems, characterizing and simplifying them, and using them as components of an engineered, biological system. According to critics, biological circuits can be integrated into organisms to change their interactions or products or, ultimately, to synthesize fundamentally new and possibly hazardous organisms. The new field of study—like all other fields encompassed by biomedical engineering—has seen fit to use reverse engineering as an everyday tool.

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

Communications Biology ◽

10.1038/s42003-021-02987-1 ◽

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.

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Biology by design: reduction and synthesis of cellular components and behaviour

Journal of The Royal Society Interface ◽

10.1098/rsif.2006.0206 ◽

2007 ◽

Vol 4 (15) ◽

pp. 607-623 ◽

Cited By ~ 42

Author(s):

Philippe Marguet ◽

Frederick Balagadde ◽

Cheemeng Tan ◽

Lingchong You

Keyword(s):

Synthetic Biology ◽

Biological System ◽

Biological Systems ◽

Cellular Systems ◽

Biological Research ◽

Future Directions ◽

Technological Advances ◽

Active Pursuit ◽

Cellular Components

Biological research is experiencing an increasing focus on the application of knowledge rather than on its generation. Thanks to the increased understanding of cellular systems and technological advances, biologists are more frequently asking not only ‘how can I understand the structure and behaviour of this biological system?’, but also ‘how can I apply that knowledge to generate novel functions in different biological systems or in other contexts?’ Active pursuit of the latter has nurtured the emergence of synthetic biology. Here, we discuss the motivation behind, and foundational technologies enabling, the development of this nascent field. We examine some early successes and applications while highlighting the challenges involved. Finally, we consider future directions and mention non-scientific considerations that can influence the field's growth.

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The Epistemology of Biomimetics: The Role of Models and of Morphogenetic Principles

Perspectives on Science ◽

10.1162/posc_a_00385 ◽

2021 ◽

pp. 583-601

Author(s):

Ulrich Krohs

Keyword(s):

Theoretical Model ◽

Synthetic Biology ◽

Biological System ◽

Function Form ◽

Technological Systems ◽

Technical Design ◽

Realization Problem ◽

Technical Function ◽

Technical Artifact

Abstract Form follows function, but it does not follow from function. Form is not derivable from the latter. To realize a desired technical function, a form must first be found that is able to realize it at all. Secondly, the question arises as to whether an envisaged form realizes the function in an appropriate way. Functions are multiply realizable—various different forms can bear the very same function. One needs to find a form of a technical artifact that realizes an envisaged function sufficiently efficient, robust, or whatever criteria might be imposed. This paper scrutinizes biomimetics as one way to find a good solution to the realization problem. Drawing on an approach from the philosophy of simulations, it reconstructs the biomimetic relation as being mediated by a theoretical model. It is shown that the robustness of the functioning system is usually reached in different ways in biological and in technological systems, which explains differences in morphogenetic mechanisms or principles found in these fields. This reconstruction helps to understand problems with robustness in synthetic biology that occur when technical design principles are implemented in a biological system. The mimetic relation between the biological and the technical realm is found to be asymmetric.

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Independent control of amplitude and period in the synthetic repressilator

10.21203/rs.3.rs-584751/v1 ◽

2021 ◽

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

Abstract Synthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, orthogonally 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 orthogonally 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 orthogonal control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.

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

Journal of Commercial Biotechnology ◽

10.5912/jcb327 ◽

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 â€˜genomic alchemyâ€™ 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 â€˜orâ€™ 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.

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Microbial Biofilms and Biotechnology – Some Perceptions

Current Biotechnology ◽

10.2174/2211550109999201026091512 ◽

2020 ◽

Vol 09 ◽

Author(s):

Subba Rao Toleti

Keyword(s):

Tissue Culture ◽

Synthetic Biology ◽

Industrial Effluents ◽

Aquatic Environments ◽

Biochemical Processes ◽

Microbial Biofilms ◽

Biofilm Bacteria ◽

Prophylactic Vaccines ◽

Design Construction

: The review is an attempt to introduce the readers in brief about biofilms and their implications as well as some new perceptions in biotechnology. Biofilms are adherent microbial communities, which are developed on submerged surfaces in aquatic environments. Biofilms play a significant role in exopolymer production, material deterioration and also cause harmful infections. Further, the role of corrosion causing biofilm bacteria in deterioration of different materials, microbial biofilms and their enzymatic processes in reducing the toxicity of pollutants in industrial effluents are elaborated, along with clean technologies for wastewater treatment. Biotechnology is defined as any technological application that uses biological systems to synthesize or modify products or processes. The applications include biochemical processes, medical care, cell and tissue culture as well as synthetic biology and others. Synthetic biology details about the design, construction of new biological components and systems for useful purposes. Finally, to overcome the limitations that are inherent to the use of cellular host’s, cell-free systems as critical platforms for synthetic biology applications. This mini-review also mentions about new diagnostic products based on enzymes, monoclonal antibodies and engineered proteins as well as novel prophylactic vaccines.

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Epigenetic transgenerational inheritance, Gametogenesis and Germline Development

Biology of Reproduction ◽

10.1093/biolre/ioab085 ◽

2021 ◽

Author(s):

Millissia Ben Maamar ◽

Eric E Nilsson ◽

Michael K Skinner

Keyword(s):

Developmental Biology ◽

Environmental Factors ◽

Biological System ◽

Developmental Stages ◽

Primordial Germ Cell ◽

Cell Types ◽

Transgenerational Inheritance ◽

Germline Development ◽

Current Review

Abstract One of the most important developing cell types in any biological system is the gamete (sperm and egg). The transmission of phenotypes and optimally adapted physiology to subsequent generations is in large part controlled by gametogenesis. In contrast to genetics, the environment actively regulates epigenetics to impact the physiology and phenotype of cellular and biological systems. The integration of epigenetics and genetics is critical for all developmental biology systems at the cellular and organism level. The current review is focused on the role of epigenetics during gametogenesis for both the spermatogenesis system in the male and oogenesis system in the female. The developmental stages from the initial primordial germ cell through gametogenesis to the mature sperm and egg are presented. How environmental factors can influence the epigenetics of gametogenesis to impact the epigenetic transgenerational inheritance of phenotypic and physiological change in subsequent generations is reviewed.

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