Interdisciplinary Interconnections in Synthetic Biology

Synthetic biology (SynBio) is a rapidly growing scientific discipline. In the Netherlands, various universities and companies are tackling a variety of opportunities and challenges within this field. In this perspective article, we review the current synthetic biology landscape in the Netherlands across academia, industry, politics, and society. Especially within Dutch academia there is an active, though only partially connected, research community involved in various domains of SynBio. Mostly supported by governmental funding, academic research is focusing on top-down synthetic biology, involving the engineering of, for example, bacteria and yeast for bioproduction, as well as bottom-up and cell-free synthetic biology aiming to understand life and build synthetic cells. There is also a large number of talented and motivated students interested in the field, exemplified by the participation and success of Dutch teams in the international iGEM synthetic biology competition. Commercial synthetic biology activities are taking place in various large industrial companies, as well as in start-ups and spin-offs, mostly divided over several ‘SynBio hubs’ in the Netherlands. However, the investment, regulatory and public-perception landscape is not yet optimal to stimulate entrepreneurial activities in SynBio. The Dutch and global society can further benefit from the large promise of SynBio through better integration of people active in the Dutch SynBio field, frequent political and public dialogue, and more attention towards regulatory issues. The recently founded Dutch synthetic biology association SynBioNL aims to contribute to realizing a positive impact on society by stimulating advances of the field in the Netherlands and beyond.

EDITORIAL article Front. Microbiol., 11 January 2016Sec. Microbial Physiology and Metabolism Volume 6 - 2015 | https://doi.org/10.3389/fmicb.2015.01562

Synthetic biology is an interdisciplinary subject in which biologists, engineers and computer scientists collaborate with the aim to synthesize new organisms and engineer them to perform tasks, which the respective organism does not perform in nature. Synthetic biology overlaps with nanobiotechnology not only in certain technical aspects, but also concerning social, safety and ethical impacts. Both disciplines act at the intersection of biology and technology and challenge the boundary between living and non-living matter, as it has been understood hitherto. Possible applications for example in medicine and the danger for abuse in bioterrorism are common to synthetic biology and nanobiotechnology. We want to examine ethical and social implications of synthetic biology in comparison to nanobiotechnology. Thereby we aim to contribute to a better understanding of which issues are specific to nanobiotechnology and which are shared with other approaches in the field.

In this editorial, we situate the 17 chapters of the book in the context of ambivalences of synthetic biology: the uses of the label, the significance of the associated metaphors and visions, critical and public engagement, and reasons for unease. Hype and metaphors in synthetic biology may sometimes skew the debate, but they should nevertheless not be ignored: a balanced, realistic view of synthetic biology includes acknowledgment of the variety of research agendas and visions. The goals and agendas underlying engagement and evaluative activities are important aspects, too: in some cases, they are designed to increase acceptance. This can be a source of unease. Another major source of persistent unease is that synthetic biology takes to further extremes the worldview that allows humans to put life under their disposal. Is quoting grand visions for synthetic biology a good way to begin a book about its societal implications? Metaphors such as “living machines” and “digitizing life” have been ubiquitous in synthetic biology, but with ambivalent effects. For synthetic biology, on the one hand, futuristic—even biblical—visions have helped to establish the field and secure funding. On the other hand, the field needs to deliver; and vivid metaphors as well as “newness” make it an obvious subject for critical voices and regulatory initiatives. Beyond this political dimension, hype and metaphors of synthetic biology—including the label itself—have been inspiring for more nuanced evaluative efforts.

Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.

Although the field of synthetic biology is still in its infancy, there are expectations for great advances in the coming decades, both on Earth and potentially in space. Promising applications for long duration space missions include a variety of biologically engineered products and biologically aided processes and technologies, which will undoubtedly be scrutinized for risks and benefits in the broad context of ethical, legal and social realms. By comparing and contrasting features of Earth-based and space-applied synthetic biology, it is possible to identify the likely similarities and differences, and to identify possible challenges ahead for space applications that will require additional research, both in the short and long terms. Using an analytical framework associated with synthetic biology and new technologies on Earth, this paper analyses the kinds of issues and concerns ahead, and identifies those areas where space applications may require additional examination. In general, while Earth- and space-based synthetic biology share many commonalities, space applications have additional challenges such as those raised by space microbiology and environmental factors, legal complications, planetary protection, lack of decision-making infrastructure(s), long duration human missions, terraforming and the possible discovery of extraterrestrial (ET) life. For synthetic biology, the way forward offers many exciting opportunities, but is not without legitimate concerns – for life, environments and society, both on Earth and beyond.

With growing attention to societal issues and implications of synthetic biology, we investigate sources of social science publication knowledge in synthetic biology and probe what might be learned by comparison with earlier rounds of social science research in nanotechnology. “Social science” research is broadly defined to include publications in conventional social science as well as humanities, law, ethics, business, and policy fields. We examine the knowledge clusters underpinning social science publications in nanotechnology and synthetic biology using a methodology based on the analysis of cited references. Our analysis finds that social science research in synthetic biology already has traction and direction, rooted in an ethical, legal, and social implications framework. However, compared with nanotechnology, social science research in synthetic biology could further explore opportunities and openings for engagement, anticipatory, and downstream application perspectives that will help to build a wider platform for insights into current and future societal impacts.

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

Plastids (chloroplasts) harbor a small gene-dense genome that is amenable to genetic manipulation by transformation. During 1billion years of evolution from the cyanobacterial endosymbiont to present-day chloroplasts, the plastid genome has undergone a dramatic size reduction, mainly as a result of gene losses and the large-scale transfer of genes to the nuclear genome. Thus the plastid genome can be regarded as a naturally evolved miniature genome, the gradual size reduction and compaction of which has provided a blueprint for the design of minimum genomes. Furthermore, because of the largely prokaryotic genome structure and gene expression machinery, the high transgene expression levels attainable in transgenic chloroplasts and the very low production costs in plant systems, the chloroplast lends itself to synthetic biology applications that are directed towards the efficient synthesis of green chemicals, biopharmaceuticals and other metabolites of commercial interest. This review describes recent progress with the engineering of plastid genomes with large constructs of foreign or synthetic DNA, and highlights the potential of the chloroplast as a model system in bottom-up and top-down synthetic biology approaches.

As the nineteenth century was the age of iron and the twentieth belonged to silicon, the present century will be identified with carbon. CO2 is the iconic greenhouse gas, imprinted on our vocabulary with talk of carbon footprints and allowances and offsets. For synthetic biologists, however, the carbon debacle has counterintuitively positioned this debased element as our savior. The future they foresee will supplant grimy factories of concrete and steel with clean colonies of living cells. To use the terminology of Freeman Dyson, gray technology will be replaced by green. Among the most celebrated physicists of the twentieth century, Dyson has become one of the foremost promoters of synthetic biology, a field that technologically is to genetic engineering what genetic engineering is to crop cultivation. Conceptually the distinction is even more radical than that: whereas genetic engineering merely modifies preexisting creatures more precisely than selective breeding, synthetic biology aims to fabricate entirely new organisms from nonliving materials. Unconstrained by genetic history, these artificial life forms can be intelligently designed to produce fuels or pharmaceuticals with unprecedented efficiency. The sheer audacity of synthetic biology lends itself to hyperbole, aptly captured in a 2007 Nature editorial: “For the first time, God has competition.” Yet the language of synthetic biology, also known as bioengineering, hardly bespeaks a cosmic paradigm shift. DNA constructed at a so-called gene foundry gives specialized function to a generic cell referred to as a chassis. A Victorian industrialist would have no trouble following the metaphoric language. He might even find work as a bioengineering consultant: the quaint iron age phrasing reflects the old-fashioned framework underlying this brave new discipline. After all, radical as artificial life may be philosophically—and significant as it may be environmentally—it’s technically just a strenuous construction project, with manufacturing challenges akin to building a bridge or a steam engine. That may explain why one of the most successful synthetic biologists working today, the Stanford University professor Drew Endy, trained as a civil engineer. Together with colleagues at the Massachusetts Institute of Technology, Endy has methodically approached synthetic biology as a problem of developing reliable building blocks and assembly protocols.

Synthetic Biology demonstrates the integral relationship between biology, chemistry, mathematics and computer science. The field provides innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies. Synthetic biology involves construction of genetic circuits when DNA sequences are modified to include standard restriction enzyme sites making the DNA sequences interchangeable and allowing for construction of a variety of circuits. New tools and devices are constantly needed to enhance the already extensive list of BioBricks housed at the Registry of Standard Biological Parts. As proof of concept we constructed a new BioBricks based on the toluene sensor built by Stiner and Haverson (AEM, 2002) in Pseudomonas. Toluene is an environmental contaminant that is the byproduct of oil contamination. Biosensors generated from BioBrick parts yield more affordable, transportable, and faster methods of pollutant detection. The tbuT cassette from Stiner and Haverson's work was digested with XbaI and SpeI sites then ligated with the GFP reporter gene and cloned into iGEM BioBrick vectors in order to create a biosensor in Escherichia coli. These BioBricks can be readily used with a variety of reporter genes to create new versions of the biosensor. We expanded our biosensor construction to create a dual functional estrogen sensitive BioBrick. The presence of estrogenic compounds (endocrine‐disruptors, EDCs) in the water supply raises concerns about human and aquatic health. Current methods for detecting estrogen contamination require expensive, time‐consuming techniques such as liquid chromatography‐mass spectrometry and high performance liquid chromatography. Previously reported estrogen biosensors required multiple cloning and transformation steps for successful detection in bacteria. Our estrogen responsive plasmid contains parts that allow for both the constitutive expression of the estrogen receptor followed by an estrogen response element toggled to a reporter gene in a single vector. When the estrogen response element is activated the reporter gene, red fluorescent protein, will produce a color change in E.coli. We will present data demonstrating the efficiency of this dual‐functional biosensor and it effectiveness for estrogenic compounds in contaminated water.Support or Funding InformationNSF grant #NSF‐GPG‐1444406, GPG: Research Collaboration: REU Pilot: Synthetic Biology Boot camp

DNA assembly and transformation are crucial to the building process in synthetic biology. These steps are significant roadblocks when engineering increasingly complex biological systems. To address this, recent development of widespread 'biofoundry' facilities has employed automation equipment to expedite the synthetic biology workflow. Despite significant progress, there is a clear demand for lower-cost and smaller-footprint automation equipment. The field of microfluidics have emerged to provide automation capabilities to meet this demand. However, we still lack devices capable of building large multi-gene systems in a consolidated process. In response to this challenge, we have developed a digital microfluidic platform that performs "one-pot" Golden Gate DNA assembly of large plasmids and transformation of E coli. The system features a novel electrode geometry and modular design, which make these devices simple to fabricate and use, thus improving the accessibility of microfluidics. This device incorporates an impedance-based adaptive closed loop water replenishment system to compensate for droplet evaporation and maintain constant assembly reaction concentrations, which we found to be crucial to the DNA assembly efficiency. We also showcase a closed-loop temperature control system that generates precise thermodynamic profiles to optimize heat shock transformation. Moreover, we validated the system by assembling and transforming large and complex plasmids conferring a biosynthetic pathway, resulting in performance comparable to those of standard techniques. We propose that the methods described here will contribute to a new generation of accessible automation platforms aimed at speeding up the 'building' process, lowering reagent consumption and removing manual work from synthetic biology.

Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

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.