scholarly journals Addressing evolutionary questions with synthetic biology

2021 ◽  
Author(s):  
Florian Baier ◽  
Yolanda Schaerli
Keyword(s):  
Synthetic Biology ◽  
Regulatory Networks ◽  
Biological Behavior ◽  
Natural Systems ◽  
Experimental Systems ◽  
Engineering Discipline ◽  
Regulatory Circuits ◽  
Evolutionary Advantage ◽  
Experimental Laboratory ◽  
Quantitative Manner

Synthetic biology emerged as an engineering discipline to design and construct artificial biological systems. Synthetic biological designs aim to achieve specific biological behavior, which can be exploited for biotechnological, medical and industrial purposes. In addition, mimicking natural systems using well-characterized biological parts also provides powerful experimental systems to study evolution at the molecular and systems level. A strength of synthetic biology is to go beyond nature’s toolkit, to test alternative versions and to study a particular biological system and its phenotype in isolation and in a quantitative manner. Here, we review recent work that implemented synthetic systems, ranging from simple regulatory circuits, rewired cellular networks to artificial genomes and viruses, to study fundamental evolutionary concepts. In particular, engineering, perturbing or subjecting these synthetic systems to experimental laboratory evolution provides a mechanistic understanding on important evolutionary questions, such as: Why did particular regulatory networks topologies evolve and not others? What happens if we rewire regulatory networks? Could an expanded genetic code provide an evolutionary advantage? How important is the structure of genome and number of chromosomes? Although the field of evolutionary synthetic biology is still in its teens, further advances in synthetic biology provide exciting technologies and novel systems that promise to yield fundamental insights into evolutionary principles in the near future.

Epistemic and Aleatory Uncertainty in Recommended, Generic Rock Kd Values used in Performance Assessment Studies

2006 ◽  
Vol 932 ◽  
Author(s):  
James Crawford ◽  
Ivars Neretnieks ◽  
Luis Moreno
Keyword(s):  
Performance Assessment ◽  
Laboratory Data ◽  
Scientific Basis ◽  
Performance Assessments ◽  
Aleatory Uncertainty ◽  
Transport Modelling ◽  
Natural Systems ◽  
Rock Types ◽  
Kd Values ◽  
Experimental Laboratory

ABSTRACTOver the past decade or so there has been an explosion in the number of sorption modelling approaches and applications of sorption modelling for understanding and predicting solute transport in natural systems. The most widely used and simplest of all models, however, is that employing a constant distribution coefficient (Kd) relating the sorbed concentration of a solute on a mineral surface and its aqueous concentration.There are a number of reasons why a constant partitioning coefficient is attractive to environmental modellers for predicting radionuclide retardation, and in spite of all the shortcomings and pitfalls associated with such an approach, it remains the leitmotif of most performance assessment transport modelling.This paper examines the scientific basis underpinning the Kd-approach and its broad defensibility in a performance assessment framework. It also examines sources of epistemic and aleatory uncertainty that undermine confidence in Kd-values reported in the open literature. The paper focuses particularly upon the use of so-called “generic” data for generalised rock types that may not necessarily capture the full material property characteristics of site-specific materials.From the examination of recent literature data, it appears that there are still a number of outstanding issues concerning interpretation of experimental laboratory data that need to be considered in greater detail before concluding that the recommended values used in performance assessments are indeed conservative.

scholarly journals Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

2019 ◽  
Vol 2 (2) ◽  
pp. 39 ◽  
Author(s):  
Dohyun Jeong ◽  
Melissa Klocke ◽  
Siddharth Agarwal ◽  
Jeongwon Kim ◽  
Seungdo Choi ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Free Expression ◽  
Dna Nanostructures ◽  
Expression Systems ◽  
Natural Systems ◽  
The Past ◽  
Current Cell ◽  
Recent Developments ◽  
Biological Circuits

Synthetic biology integrates diverse engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription–translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.

scholarly journals Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology

2018 ◽  
Vol 115 (36) ◽  
pp. E8509-E8517 ◽  
Author(s):  
Jianguo Yang ◽  
Xiaqing Xie ◽  
Nan Xiang ◽  
Zhe-Xian Tian ◽  
Ray Dixon ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Nitrogenase Activity ◽  
Klebsiella Oxytoca ◽  
Protein Splicing ◽  
Important Goal ◽  
Tobacco Etch Virus Protease ◽  
Regulatory Circuits ◽  
Number Of Genes ◽  
Eukaryotic Organisms ◽  
Diazotrophic Growth

Re-engineering of complex biological systems (CBS) is an important goal for applications in synthetic biology. Efforts have been made to simplify CBS by refactoring a large number of genes with rearranged polycistrons and synthetic regulatory circuits. Here, a posttranslational protein-splicing strategy derived from RNA viruses was exploited to minimize gene numbers of the classic nitrogenase system, where the expression stoichiometry is particularly important. Operon-basednifgenes fromKlebsiella oxytocawere regrouped into giant genes either by fusing genes together or by expressing polyproteins that are subsequently cleaved with Tobacco Etch Virus protease. After several rounds of selection based on protein expression levels and tolerance toward a remnant C-terminal ENLYFQ-tail, a system with only five giant genes showed optimal nitrogenase activity and supported diazotrophic growth ofEscherichia coli. This study provides an approach for efficient translation from an operon-based system into a polyprotein-based assembly that has the potential for portable and stoichiometric expression of the complex nitrogenase system in eukaryotic organisms.

scholarly journals RNA–protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity

Open Biology ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 190096 ◽  
Author(s):  
Anna Balcerak ◽  
Alicja Trebinska-Stryjewska ◽  
Ryszard Konopinski ◽  
Maciej Wakula ◽  
Ewa Anna Grzybowska
Keyword(s):  
Protein Interactions ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Binding Motifs ◽  
Coding Regions ◽  
Regulatory Circuits ◽  
Proteins Interactions

RNA–protein interactions are crucial for most biological processes in all organisms. However, it appears that the complexity of RNA-based regulation increases with the complexity of the organism, creating additional regulatory circuits, the scope of which is only now being revealed. It is becoming apparent that previously unappreciated features, such as disordered structural regions in proteins or non-coding regions in DNA leading to higher plasticity and pliability in RNA–protein complexes, are in fact essential for complex, precise and fine-tuned regulation. This review addresses the issue of the role of RNA–protein interactions in generating eukaryotic complexity, focusing on the newly characterized disordered RNA-binding motifs, moonlighting of metabolic enzymes, RNA-binding proteins interactions with different RNA species and their participation in regulatory networks of higher order.

Proposing "analogy experiment" as a sub-category of "analog experiment" in earth science

2020 ◽  
Author(s):  
Mie Ichihara
Keyword(s):  
Complex Dynamics ◽  
Earth Science ◽  
Experimental Studies ◽  
Natural Phenomena ◽  
Natural Systems ◽  
Natural Processes ◽  
Experimental Systems ◽  
Analog Experiment ◽  
Education And Outreach ◽  
Analog Experiments

<p>In the earth and planetary sciences, the term "analog experiment" indicates laboratory experiments that use analog materials to investigate natural processes. Scaled experiments constitute a representative sub-category of analog experiments. They are designed to have the same dominant dimensionless parameter in the same range as the targeted natural processes. Other primary uses of analog experiments are education and outreach. Reproducing similar phenomena in front of the audience is useful in explaining the essence of the complex dynamics of natural processes. However, it is often the case that we do not fully understand the physics of the experimental systems or the targeted natural phenomena. In such cases, especially when the process is complex, it is difficult to guarantee the scaling similarity. When we take such laboratory phenomena as a research subject of earth science, we encounter critical comments about the scaling issue.</p><p>Nevertheless, I think it scientifically important to consider questions like follows. What is the mechanism of the experimental phenomena? Why the behaviors of the experiment look similar to the natural phenomena? To what extent the laboratory and the natural systems are similar. To indicate experimental studies to elucidate these questions, I would like to define "analogy experiment" as a new sub-category of analog experiments.  Some recent experiments are presented as examples.</p>

scholarly journals Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

2016 ◽  
Vol 13 (117) ◽  
pp. 20151046 ◽  
Author(s):  
Fei He ◽  
Ettore Murabito ◽  
Hans V. Westerhoff
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Regulatory Networks ◽  
Computational Systems Biology ◽  
Control Engineering ◽  
Trade Offs ◽  
Metabolic Systems ◽  
Analytical Approaches

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo , not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

scholarly journals Whither life? Conjectures on the future evolution of biochemistry

2016 ◽  
Vol 12 (8) ◽  
pp. 20160269 ◽  
Author(s):  
Jodi L. Brewster ◽  
Thomas J. Finn ◽  
Miguel A. Ramirez ◽  
Wayne M. Patrick
Keyword(s):  
Synthetic Biology ◽  
Energy Generation ◽  
Sufficient Time ◽  
Evolutionary Time ◽  
Future Evolution ◽  
The Earth ◽  
Regulatory Circuits ◽  
Extant Species ◽  
The Future ◽  
Metabolic Biochemistry

Life has existed on the Earth for approximately four billion years. The sheer depth of evolutionary time, and the diversity of extant species, makes it tempting to assume that all the key biochemical innovations underpinning life have already happened. But we are only a little over halfway through the trajectory of life on our planet. In this Opinion piece, we argue: (i) that sufficient time remains for the evolution of new processes at the heart of metabolic biochemistry and (ii) that synthetic biology is providing predictive insights into the nature of these innovations. By way of example, we focus on engineered solutions to existing inefficiencies in energy generation, and on the complex, synthetic regulatory circuits that are currently being implemented.

scholarly journals Bio-electrical engineering: a promising frontier for synthetic biology

2019 ◽  
Vol 41 (3) ◽  
pp. 10-13 ◽  
Author(s):  
Robert Bradley
Keyword(s):  
Synthetic Biology ◽  
Molecular Mechanisms ◽  
Individual Cell ◽  
Electrical Engineering ◽  
Bacterial Biofilm ◽  
Biotechnological Applications ◽  
Music Festival ◽  
Natural Systems ◽  
Led Lights ◽  
A Current

What do the following have in common? The production of methane gas from farm waste; toilets at a music festival, lit with LED lights; a bacterial biofilm that is on the brink of starvation. All of these involve microbes that are making use of bio-electrical processes. Though it is difficult to define the limits of what can be called bio-electrical, these processes are typically responding to or creating a current or voltage, with the electrical effects extending beyond the limit of an individual cell. In the examples above, current is flowing between organisms of different species or between an organism and an abiotic material, or voltage changes are being sensed and propagated across a colony of cells. Our appreciation of the extent of electrical phenomena in microbial biology has seen a recent revival, with studies revealing not just the variety of bioelectrical processes that exist but also defining the molecular mechanisms responsible. Now, we can begin to apply the approaches and techniques of synthetic biology. By re-engineering natural systems, we can hope to improve our understanding of how their components function and repurpose them for exciting biotechnological applications.

scholarly journals Reconstruction of the global neural crest gene regulatory networkin vivo

2018 ◽  
Author(s):  
Ruth M Williams ◽  
Ivan Candido-Ferreira ◽  
Emmanouela Repapi ◽  
Daria Gavriouchkina ◽  
Upeka Senanayake ◽  
...  
Keyword(s):  
Neural Crest ◽  
Regulatory Networks ◽  
Transcriptome Profiling ◽  
Integrated Approach ◽  
Precise Control ◽  
Regulatory Circuits ◽  
A Genome ◽  
Gene Regulatory ◽  
Cell Transcriptome

AbstractPrecise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-widein vivoreconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineeringin vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, noveltrans-factors andcis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuitsin vivo, has broad implications for GRN discovery and investigation.

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