scholarly journals Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

Author(s):  
Vittorio Bartoli ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski

Biological systems often need to operate in complex environments where conditions can rapidly change. This is possible due to their inherent ability to sense changes and adapt by adjusting their behavior in response. Here, we detail recent advances in the creation of synthetic genetic parts and circuits whose behaviors can be dynamically tuned through a variety of intra- and extra-cellular signals. We show how this capability lays the foundation for implementing control engineering schemes in living cells and allows for the creation of biological systems that are able to self-adapt, ensuring their functionality is maintained in the face of varying environmental and physiological conditions. We end by discussing some of the broader implications of this technology for the safe deployment of synthetic biology.

Author(s):  
Vittorio Bartoli ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski

Biological systems often need to operate in complex environments where conditions can rapidly change. This is possible due to their inherent ability to sense changes and adapt their behavior in response. Here, we detail recent advances in the creation of synthetic genetic parts and circuits whose behaviors can be dynamically tuned through a variety of intra- and extra-cellular signals. We show how this capability lays the foundation for implementing control engineering schemes in living cells and allows for the creation of biological systems that are able to self-adapt, ensuring their functionality is maintained in the face of varying environmental and physiological conditions. We end by discussing some of the broader implications of this technology for the safe deployment of synthetic biology.


2017 ◽  
Author(s):  
Ji Zeng ◽  
Jaewook Kim ◽  
Areen Banerjee ◽  
Rahul Sarpeshkar

AbstractSynthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.One Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.


Soft Matter ◽  
2017 ◽  
Vol 13 (38) ◽  
pp. 6672-6677 ◽  
Author(s):  
Malte Winnacker

Recent strategies for the synthesis of functional materials by living cells are highlighted, elucidating the potential of the interface of materials science and synthetic biology.


Author(s):  
Arlindo Oliveira

This chapter describes how computers played a decisive role in the sequencing and understanding of the genomes of humans and other organisms. The discovery of the structure of DNA, by Watson and Crick, opened the way to a systematic approach to biology, based on the study of the way DNA encodes the proteins in all living cells. The area that became known as computational biology, or bioinformatics, aims at modelling, simulating, and understanding the behaviour of biological systems, using computer models and algorithms. Such a deep understanding will enable us to create computer models of cells and of entire organisms and even, in the future, open the doors to the creation of entirely new lifeforms, a field known as synthetic biology.


Author(s):  
Jill Grimme ◽  
Travis King ◽  
Kyoo Dong Jo ◽  
Don Cropek ◽  
Aaron T. Timperman

In today's world, there is an ever growing need for lightweight, portable sensor systems to detect chemical toxicants and biological toxins. The challenges encountered with such detection systems are numerous, as there are a myriad of potential targets in various sample matrices that are often present at trace-level concentrations. At ERDC-CERL, the Lab-on-a-Chip (LoaC) group is working with a number of academic and small business collaborators to develop solutions to meet these challenges. This report will focus on recent advances in three distinct areas: (1) the development of a flexible platform to allow fieldable LoaC analyses of water samples, (2) cell-, organelle-, and synthetic biology-based toxicity sensors, and (3) nanofluidic/microfluidic interface (NMI) sample enrichment devices. To transition LoaC-based sensors from the laboratory bench to the field, a portable hardware system capable of operating a wide variety of microfluidic chip-based assays has been developed. As a demonstration of the versatility of this approach assays for the separation and quantitation of anionic contaminants (i.e., perchlorate), quantitation of heavy metals (Pb and Cd), and cell-based toxicity sensors have been developed and demonstrated. Sensors harboring living cells provide a rapid means of assessing water toxicity. Cell-based sensors exploit the sensitivity of a living cell to discrete changes in its environment to report the presence of toxicants. However, this sensitivity of cells to environmental changes also hinders their usability in nonlaboratory settings. Therefore, isolating intact organelles (i.e., mitochondria) offers a nonliving alternative that preserves the sensitivity of the living cells and allows the electrochemical reporting of the presence of a contaminant. Pursuing a synthetic biology approach has also allowed the development of nonliving reporting mechanisms that utilize engineered biological pathways for novel sensing and remediation applications. To help overcome the challenges associated with the detection of target species at trace-level concentrations, NMIs are being developed for the enrichment of charged species in solution. NMI concentrators can be classified as either electroosmotic flow or electrophoresis-dominant devices. Further advances in electrophoresis-dominant concentrators will aid in the analysis of samples that contain proteins and other substances prone to surface adsorption. These recent advances illustrate how LoaC systems provide a suitable platform for development of fieldable sensors to detect a broad range of chemical/biological pollutants and threats.


2020 ◽  
Vol 9 (2) ◽  
pp. 330-347
Author(s):  
Hugo Agra

O artigo analisa um tema pouco abordado na literatura brasileira de relações internacionais: a atuação das políticas externas do Brasil e do México para a criação do Grupo de Contadora (1983), Grupo de Apoio à Contadora (1985) e do Grupo do Rio (1987). Esses grupos tiveram papéis importantes nas tentativas de estabilização dos problemas políticos, econômicos e sociais da América Central a partir dos anos 1980. O artigo está dividido em quatro partes: i) compreensão da criação do Grupo de Contadora, do Grupo de Apoio à Contadora e a atuação do Brasil e do México, ii) destaque aos principais objetivos desses dois grupos, iii) explica o “dilema” das políticas externas do Brasil e do México diante das ações estadunidenses para a América Central e iv) e descreve a criação e os objetivos do Grupo do Rio. Por meio de uma pesquisa explicativa, onde é fundamental reunir informações sobre vários assuntos para entender de forma mais abrangente um tema específico, o artigo faz uso de fontes secundárias que analisam as relações internacionais da América Latina e os processos decisórios das políticas externas do Brasil e do México na década de 1980, além de algumas fontes primárias, como documentos oficiais dos acordos celebrados e declarações presidenciais disponíveis em arquivos dos sites eletrônicos da presidência ou chancelaria dos países. Conclui-se mostrando que os dois países foram fundamentais para o processo de estabilização política, principalmente na região centro-americana, não só pela importância histórica, política e econômica de cada um, mas também pelo fato de que a formação desses grupos foram importantes para dirimir litígios, acelerar a resolução de conflitos entre os países do continente, além de ter sido um período de aproximação e fortalecimento da relação bilateral Brasil-México.         ABSTRACT: The article analyzes a theme little addressed in the Brazilian literature of international relations: the performance of the foreign policies of Brazil and Mexico for the creation of the Contadora Group (1983), the Contadora Support Group (1985) and the Rio Group (1987). These groups played important roles in attempts to stabilize the political, economic and social problems of Central America from the 1980s onwards. The article is divided into four parts: i) an understanding of the creation of the Contadora Group, the Contadora Support Group and the actions of Brazil and Mexico, ii) highlighting the main objectives of these two groups, iii) explaining the "dilemma" of the foreign policies of Brazil and Mexico in the face of US actions for Central America, and iv) describing the creation and objectives of the Rio Group. By means of an explanatory survey, where it is essential to gather information on various subjects in order to understand more comprehensively a specific theme, the article makes use of secondary sources that analyze the international relations of Latin America and the decision-making processes of the foreign policies of Brazil and Mexico in the 1980s, in addition to some primary sources, such as official documents of the agreements signed and presidential declarations available on the archives of the electronic sites of the presidency or chancellery of the countries. It concludes by showing that both countries were fundamental to the process of political stabilization, especially in the Central American region, not only because of their historical, political and economic importance, but also because the formation of these groups was important to settle disputes, accelerate the resolution of conflicts between the countries of the continent, and was a period of rapprochement and strengthening of the bilateral relationship between Brazil and Mexico. Keywords: International Relations; Latin America; Contadora Group; Rio Group.       Aprovado em: setembro/2019. Recebido em: agosto/2020.


2021 ◽  
Vol 62 ◽  
pp. 68-75
Author(s):  
Giansimone Perrino ◽  
Andreas Hadjimitsis ◽  
Rodrigo Ledesma-Amaro ◽  
Guy-Bart Stan

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.


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