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Synthetic biology: advancing biological frontiers by building synthetic systems
Advances in synthetic biology are contributing
to diverse research areas, from basic biology to
biomanufacturing and disease therapy. We discuss the
theoretical foundation, applications, and potential of
this emerging field
Synthetic Biology: A Bridge between Artificial and Natural Cells.
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications
Synthetic biology and microdevices : a powerful combination
Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there has been a shift from the optimization of the abiotic components, for example, the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will also improve the robustness and speed of their response towards applied signals. To this end, the development of new genetic circuits has to be guided by computational design methods that enable to tune and optimize the circuit response. As the successful design of genetic circuits is highly dependent on the quality and reliability of its composing elements, intense characterization of standard biological parts will be crucial for an efficient rational design process in the development of new genetic circuits. Microengineered devices can thereby offer a new analytical approach for the study of complex biological parts and systems. By summarizing the recent techniques in creating new synthetic circuits and in integrating biology with microdevices, this review aims at emphasizing the power of combining synthetic biology with microfluidics and microelectronics
Synthetic associative learning in engineered multicellular consortia
Associative learning is one of the key mechanisms displayed by living
organisms in order to adapt to their changing environments. It was early
recognized to be a general trait of complex multicellular organisms but also
found in "simpler" ones. It has also been explored within synthetic biology
using molecular circuits that are directly inspired in neural network models of
conditioning. These designs involve complex wiring diagrams to be implemented
within one single cell and the presence of diverse molecular wires become a
challenge that might be very difficult to overcome. Here we present three
alternative circuit designs based on two-cell microbial consortia able to
properly display associative learning responses to two classes of stimuli and
displaying long and short-term memory (i. e. the association can be lost with
time). These designs might be a helpful approach for engineering the human gut
microbiome or even synthetic organoids, defining a new class of decision-making
biological circuits capable of memory and adaptation to changing conditions.
The potential implications and extensions are outlined.Comment: 5 figure
Chemical communication between synthetic and natural cells: a possible experimental design
The bottom-up construction of synthetic cells is one of the most intriguing
and interesting research arenas in synthetic biology. Synthetic cells are built
by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the
synthesis of one or more functional proteins. Thanks to the in situ synthesized
proteins, synthetic cells become able to perform several biomolecular
functions, which can be exploited for a large variety of applications. This
paves the way to several advanced uses of synthetic cells in basic science and
biotechnology, thanks to their versatility, modularity, biocompatibility, and
programmability. In the previous WIVACE (2012) we presented the
state-of-the-art of semi-synthetic minimal cell (SSMC) technology and
introduced, for the first time, the idea of chemical communication between
synthetic cells and natural cells. The development of a proper synthetic
communication protocol should be seen as a tool for the nascent field of
bio/chemical-based Information and Communication Technologies (bio-chem-ICTs)
and ultimately aimed at building soft-wet-micro-robots. In this contribution
(WIVACE, 2013) we present a blueprint for realizing this project, and show some
preliminary experimental results. We firstly discuss how our research goal
(based on the natural capabilities of biological systems to manipulate chemical
signals) finds a proper place in the current scientific and technological
contexts. Then, we shortly comment on the experimental approaches from the
viewpoints of (i) synthetic cell construction, and (ii) bioengineering of
microorganisms, providing up-to-date results from our laboratory. Finally, we
shortly discuss how autopoiesis can be used as a theoretical framework for
defining synthetic minimal life, minimal cognition, and as bridge between
synthetic biology and artificial intelligence.Comment: In Proceedings Wivace 2013, arXiv:1309.712
Roadmap on semiconductor-cell biointerfaces.
This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world
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