scholarly journals What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Part 1

Cell Systems ◽  
2017 ◽  
Vol 4 (4) ◽  
pp. 370-372
Keyword(s):  
Synthetic Biology ◽  
Circuit Design

scholarly journals Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology

2010 ◽  
Vol 2010 ◽  
pp. 1-16 ◽  
Author(s):  
Yuting Zheng ◽  
Ganesh Sriram
Keyword(s):  
Mathematical Modeling ◽  
Synthetic Biology ◽  
Circuit Design ◽  
Central Component ◽  
Transcription Network ◽  
Phenotype Analysis ◽  
Synthetic Circuit ◽  
Gene Regulatory ◽  
Mathematical Techniques

Mathematical modeling plays an important and often indispensable role in synthetic biology because it serves as a crucial link between the concept and realization of a biological circuit. We review mathematical modeling concepts and methodologies as relevant to synthetic biology, including assumptions that underlie a model, types of modeling frameworks (deterministic and stochastic), and the importance of parameter estimation and optimization in modeling. Additionally we expound mathematical techniques used to analyze a model such as sensitivity analysis and bifurcation analysis, which enable the identification of the conditions that cause a synthetic circuit to behave in a desired manner. We also discuss the role of modeling in phenotype analysis such as metabolic and transcription network analysis and point out some available modeling standards and software. Following this, we present three case studies—a metabolic oscillator, a synthetic counter, and a bottom-up gene regulatory network—which have incorporated mathematical modeling as a central component of synthetic circuit design.

Microbial Biofilms and Biotechnology – Some Perceptions

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.

Engineering as Normative Practice

2015 ◽  
pp. 12-21
Author(s):  
Marc J. de Vries
Keyword(s):  
Synthetic Biology ◽  
Social Practice ◽  
Business Practice ◽  
Complex Situation ◽  
Technological Developments ◽  
Normative Practice ◽  
Normative Practices ◽  
Ethical Norms ◽  
Ethical Reflections

The concept of social practice was introduced by Alisdair Macintyre as a means for ethical reflections for professional situations. This concept has been extended by Hoogland and Jochemsen to include different types of norms. The term “normative practice” indicates that practices are determined by the norms by which they are defined. Engineering is such a normative practice, one that is part of a more complex situation of technological developments, in which other normative practices are also involved (e.g., a government practice, a business practice, a consumer practice). The norms in a normative practice are not only ethical norms but also include task descriptions. In this chapter, the role of both non-ethical and ethical norms in engineering as normative practices is analyzed. This is illustrated by two case studies: one from military ethics (with a specific focus on the role of technology) and one from synthetic biology.

scholarly journals Spatial localisation meets biomolecular networks

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Govind Menon ◽  
J. Krishnan
Keyword(s):  
Synthetic Biology ◽  
Pattern Formation ◽  
Circuit Design ◽  
Systematic Approach ◽  
Temporal Networks ◽  
Spatial Organisation ◽  
Biomolecular Networks ◽  
Systems Chemistry ◽  
Spatial Localisation ◽  
Systems Framework

AbstractSpatial organisation through localisation/compartmentalisation of species is a ubiquitous but poorly understood feature of cellular biomolecular networks. Current technologies in systems and synthetic biology (spatial proteomics, imaging, synthetic compartmentalisation) necessitate a systematic approach to elucidating the interplay of networks and spatial organisation. We develop a systems framework towards this end and focus on the effect of spatial localisation of network components revealing its multiple facets: (i) As a key distinct regulator of network behaviour, and an enabler of new network capabilities (ii) As a potent new regulator of pattern formation and self-organisation (iii) As an often hidden factor impacting inference of temporal networks from data (iv) As an engineering tool for rewiring networks and network/circuit design. These insights, transparently arising from the most basic considerations of networks and spatial organisation, have broad relevance in natural and engineered biology and in related areas such as cell-free systems, systems chemistry and bionanotechnology.

scholarly journals Biomedically relevant circuit‐design strategies in mammalian synthetic biology

2013 ◽  
Vol 9 (1) ◽  
pp. 691 ◽  
Author(s):  
William Bacchus ◽  
Dominique Aubel ◽  
Martin Fussenegger
Keyword(s):  
Synthetic Biology ◽  
Circuit Design ◽  
Design Strategies
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