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 Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

2016 ◽  
Vol 60 (4) ◽  
pp. 303-313 ◽  
Author(s):  
Juhyun Kim ◽  
Manuel Salvador ◽  
Elizabeth Saunders ◽  
Jaime González ◽  
Claudio Avignone-Rossa ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
Essential Element ◽  
Model Organisms ◽  
Biotechnological Applications ◽  
Cell Models ◽  
Genetic Circuits ◽  
Metabolic Diversity ◽  
Translational Machinery ◽  
Metabolic Fluxes

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.

scholarly journals Societal impact of synthetic biology: responsible research and innovation (RRI)

2016 ◽  
Vol 60 (4) ◽  
pp. 371-379 ◽  
Author(s):  
Daniel Gregorowius ◽  
Anna Deplazes-Zemp
Keyword(s):  
Synthetic Biology ◽  
Technology Assessment ◽  
Ethical Issues ◽  
Responsible Research And Innovation ◽  
Societal Impact ◽  
Biotechnological Applications ◽  
Research And Innovation ◽  
Challenges And Opportunities ◽  
Living Organisms ◽  
Responsible Research

Synthetic biology is an emerging field at the interface between biology and engineering, which has generated many expectations for beneficial biomedical and biotechnological applications. At the same time, however, it has also raised concerns about risks or the aim of producing new forms of living organisms. Researchers from different disciplines as well as policymakers and the general public have expressed the need for a form of technology assessment that not only deals with technical aspects, but also includes societal and ethical issues. A recent and very influential model of technology assessment that tries to implement these aims is known as RRI (Responsible Research and Innovation). In this paper, we introduce this model and its historical precursor strategies. Based on the societal and ethical issues which are presented in the current literature, we discuss challenges and opportunities of applying the RRI model for the assessment of synthetic biology.

scholarly journals Antimicrobial Resistance in Oral biofilm: Challenges and Alternatives

2021 ◽  
Vol 12 (1) ◽  
pp. 349-356
Author(s):  
Satish Kumar Sharma ◽  
Shmmon Ahmad
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Infections ◽  
Molecular Mechanisms ◽  
Resistance Mechanisms ◽  
Bacterial Biofilm ◽  
Bacterial Biofilms ◽  
Target Cells ◽  
Bacterial Cells ◽  
Antimicrobial Drugs ◽  
Oral Infections

Bacterial biofilm has been a major contributor to severe bacterial infections in humans. Oral infections have also been associated with biofilm-forming microbes. Several antimicrobial strategies have been developed to combat bacterial biofilms. However, the complexity of the oral cavity has made it difficult to use common drug treatments. Most effective ways to control normal bacterial infections are rendered ineffective for bacterial biofilms. Due to limited drug concentration availability, drug neutralization or altered phenotype of bacterial cells, different drug have been ineffective to identify the target cells. This leads to the development of the multifaceted phenomenon of antimicrobial resistance (AMR). Biofilm research done so far has been focused on using antimicrobial drugs to target molecular mechanisms of cells. The severity and resistance mechanisms of extracellular matrix (ECM) have been underestimated. The present study describes different antimicrobial strategies with respect to their applications in dental or oral infections. A prospective strategy has been proposed targeting ECM which is expected to provide an insight on biofilm obstinacy and antimicrobial resistance.

scholarly journals Self-Propulsion Strategies for Artificial Cell-Like Compartments

Nanomaterials ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1680 ◽  
Author(s):  
Ibon Santiago ◽  
Friedrich C. Simmel
Keyword(s):  
Synthetic Biology ◽  
Biomedical Engineering ◽  
Recent Progress ◽  
Emulsion Droplet ◽  
Artificial Cells ◽  
Droplet Motion ◽  
Active Particles ◽  
Artificial Cell ◽  
Catalytically Active ◽  
A Current

Reconstitution of life-like properties in artificial cells is a current research frontier in synthetic biology. Mimicking metabolism, growth, and sensing are active areas of investigation; however, achieving motility and directional taxis are also challenging in the context of artificial cells. To tackle this problem, recent progress has been made that leverages the tools of active matter physics in synthetic biology. This review surveys the most significant achievements in designing motile cell-like compartments. In this context, strategies for self-propulsion are summarized, including, compartmentalization of catalytically active particles, phoretic propulsion of vesicles and emulsion droplet motion driven by Marangoni flows. This work showcases how the realization of motile protocells may impact biomedical engineering while also aiming at answering fundamental questions in locomotion of prebiotic cells.

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 Glycan-decorated protocells: novel features for rebuilding cellular processes

2019 ◽  
Vol 9 (2) ◽  
pp. 20180084 ◽  
Author(s):  
Ramin Omidvar ◽  
Winfried Römer
Keyword(s):  
Synthetic Biology ◽  
Membrane Fusion ◽  
Molecular Mechanisms ◽  
Lipid Vesicles ◽  
Cross Linking ◽  
Membrane Systems ◽  
Biophysical Characterization ◽  
Characterization Methods ◽  
Cellular Processes ◽  
Shed Light

In synthetic biology approaches, lipid vesicles are widely used as protocell models. While many compounds have been encapsulated in vesicles (e.g. DNA, cytoskeleton and enzymes), the incorporation of glycocalyx components in the lipid bilayer has attracted much less attention so far. In recent years, glycoconjugates have been integrated in the membrane of giant unilamellar vesicles (GUVs). These minimal membrane systems have largely contributed to shed light on the molecular mechanisms of cellular processes. In this review, we first introduce several preparation and biophysical characterization methods of GUVs. Then, we highlight specific applications of protocells investigating glycolipid-mediated endocytosis of toxins, viruses and bacteria. In addition, we delineate how prototissues have been assembled from glycan-decorated protocells by using lectin-mediated cross-linking of opposed glycoreceptors (e.g. glycolipids and glycopeptides). In future applications, glycan-decorated protocells might be useful for investigating cell–cell interactions (e.g. adhesion and communication). We also speculate about the implication of lectin–glycoreceptor interactions in membrane fusion processes.

Disease resistance: Molecular mechanisms and biotechnological applications

Plant Science ◽  
2014 ◽  
Vol 228 ◽  
pp. 1-2 ◽  
Author(s):  
Kathryn Kamo ◽  
Dilip Lakshman ◽  
Keerti Rathore
Keyword(s):  
Disease Resistance ◽  
Molecular Mechanisms ◽  
Biotechnological Applications

scholarly journals Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Mark J. Lee ◽  
Alexander M. Geller ◽  
Natalie C. Bamford ◽  
Hong Liu ◽  
Fabrice N. Gravelat ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Fungal Pathogens ◽  
Molecular Mechanisms ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Bacterial Biofilm ◽  
Invasive Infection ◽  
Biosynthetic Gene ◽  
Adhesive Properties

ABSTRACTThe moldAspergillus fumigatuscauses invasive infection in immunocompromised patients. Recently, galactosaminogalactan (GAG), an exopolysaccharide composed of galactose andN-acetylgalactosamine (GalNAc), was identified as a virulence factor required for biofilm formation. The molecular mechanisms underlying GAG biosynthesis and GAG-mediated biofilm formation were unknown. We identified a cluster of five coregulated genes that were dysregulated in GAG-deficient mutants and whose gene products share functional similarity with proteins that mediate the synthesis of the bacterial biofilm exopolysaccharide poly-(β1-6)-N-acetyl-d-glucosamine (PNAG). Bioinformatic analyses suggested that the GAG cluster geneagd3encodes a protein containing a deacetylase domain. Because deacetylation ofN-acetylglucosamine residues is critical for the function of PNAG, we investigated the role of GAG deacetylation in fungal biofilm formation. Agd3 was found to mediate deacetylation of GalNAc residues within GAG and render the polysaccharide polycationic. As with PNAG, deacetylation is required for the adherence of GAG to hyphae and for biofilm formation. Growth of the Δagd3mutant in the presence of culture supernatants of the GAG-deficient Δuge3mutant rescued the biofilm defect of the Δagd3mutant and restored the adhesive properties of GAG, suggesting that deacetylation is an extracellular process. The GAG biosynthetic gene cluster is present in the genomes of members of thePezizomycotinasubphylum of theAscomycotaincluding a number of plant-pathogenic fungi and a single basidiomycete species,Trichosporon asahii, likely a result of recent horizontal gene transfer. The current study demonstrates that the production of cationic, deacetylated exopolysaccharides is a strategy used by both fungi and bacteria for biofilm formation.IMPORTANCEThis study sheds light on the biosynthetic pathways governing the synthesis of galactosaminogalactan (GAG), which plays a key role inA. fumigatusvirulence and biofilm formation. We find that bacteria and fungi use similar strategies to synthesize adhesive biofilm exopolysaccharides. The presence of orthologs of the GAG biosynthetic gene clusters in multiple fungi suggests that this exopolysaccharide may also be important in the virulence of other fungal pathogens. Further, these studies establish a molecular mechanism of adhesion in which GAG interacts via charge-charge interactions to bind to both fungal hyphae and other substrates. Finally, the importance of deacetylation in the synthesis of functional GAG and the extracellular localization of this process suggest that inhibition of deacetylation may be an attractive target for the development of novel antifungal therapies.

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.

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