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Collecting synthetic biology – an iGEM of an idea | Stories from the stores

Collecting synthetic biology – an iGEM of an idea | Stories from the stores | SynBioFromLeukipposInstitute | Scoop.it
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*Collecting synthetic biology – an iGEM of an idea* 

by anonymous / Science Museum’

"Collecting stuff is generally the bit I like most about my job. That’s probably why I’ve got a bit over excited about the new acquisitions we’ve made related to synthetic biology – from no other than Tom Knight widely described as the “father” of the discipline.

 Synthetic biology is research that combines biology and engineering. Sounds like genetic engineering by another name? Well yes, but it goes much further. It looks to create new biological functions not found in nature, designing them according to engineering principles.  Some see the field as the ultimate achievement of knowledge, citing the engineer-mantra of American physicist Richard Feynman, “What I cannot create, I do not understand”...."


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Mammalian synthetic biology in the age of genome editing and personalized medicine

The recent expansion of molecular tool kits has propelled synthetic biology toward the design of increasingly sophisticated mammalian systems. Specifically, advances in genome editing, protein engineering, and circuitry design have enabled the programming of cells for diverse applications, including regenerative medicine and cancer immunotherapy. The ease with which molecular and cellular interactions can be harnessed promises to yield novel approaches to elucidate genetic interactions, program cellular functions, and design therapeutic interventions. Here, we review recent advancements in the development of enabling technologies and the practical applications of mammalian synthetic biology.
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Sequential self-assembly of DNA functionalized droplets

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.Natural complex systems are often constructed by sequential assembly but this is not readily available for synthetic systems. Here, the authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands.

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A standard-enabled workflow for synthetic biology

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

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Synthetic biology engineering of biofilms as nanomaterials factories

Bottom-up fabrication of nanoscale materials has been a significant focus in materials science for expanding our technological frontiers. This assembly concept, however, is old news to biology - all living organisms fabricate themselves using bottom-up principles through a vast self-organizing system of incredibly complex biomolecules, a marvelous dynamic that we are still attempting to unravel. Can we use what we have gleaned from biology thus far to illuminate alternative strategies for designer nanomaterial manufacturing? In the present review article, new synthetic biology efforts toward using bacterial biofilms as platforms for the synthesis and secretion of programmable nanomaterials are described. Particular focus is given to self-assembling functional amyloids found in bacterial biofilms as re-engineerable modular nanomolecular components. Potential applications and existing challenges for this technology are also explored. This novel approach for repurposing biofilm systems will enable future technologies for using engineered living systems to grow artificial nanomaterials.

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SB7.0 The Seventh International Meeting on Synthetic Biology: Days 1 and 2

SB7.0 The Seventh International Meeting on Synthetic Biology: Days 1 and 2 | SynBioFromLeukipposInstitute | Scoop.it
From ethical dilemmas about preservation of wildlife to the innovation of thousands of different variants of a single biological organism, SB7.0 has covered it all!Over the past 2 days, experts from around the globe have convened at the National University of Singapore’s University Cultural Center to discuss
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Synthetic biology applications in industrial microbiology

Exponentially increasing information on biological organisms coupled with increasing computational power in the past decade have broadened the perspective of fundamental biological research, bringing about considerable promise and unprecedented potential for practical applications in biotechnology. As one emergent discipline, synthetic biology aims to design and engineer novel biologically-based parts, devices, and systems, in addition to redesigning existing, natural biological systems. Although previously relegated to demonstration studies, more recent research in synthetic biology has focused on the rational engineering of industrial microorganisms with the potential to address many of society’s critical challenges. Within the realm of industrial microbiology, progress in the field of synthetic biology has enabled the development of, for example, new biosynthetic pathways for the production of renewable fuels and chemicals, programmable logic controls to regulate and optimize cell function, and robust microbes for the destruction of harmful environmental contaminants. Some of the exciting examples included producing anti-malarial drug, anti- cancer taxol precursor and various biofuel molecules in E. coli and yeast. In addition, these researches have also greatly enhanced our understanding of the cellular machinery and its regulation in some of the industry important microbes, laying an important foundation for further design and engineering of biological function for even greater application. For these reasons, we present here a collection of articles from the leading edge of the field of synthetic biology, with a specific focus on the development in industrial microorganisms. It is the intent of this collection to reach a wide audience whose interests and expertise spans from development of novel synthetic biology methodologies and theories (both experimental and computational) to practical applications seeking to address issues facing the world today.
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A decade of discovery: CRISPR functions and applications

A decade of discovery: CRISPR functions and applications | SynBioFromLeukipposInstitute | Scoop.it
This year marks the tenth anniversary of the identification of the biological function of CRISPR–Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR–Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.
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A DNA-programmed liposome fusion cascade

Chemically engineered and functionalized nanoscale compartments are used in bottom-up synthetic biology to construct compartmentalized chemical processes. Progressively more complex designs demand for spatial and temporal control over entrapped species. Here, we address this demand by a DNA-encoded design for successive fusion of multiple liposome populations. Three individual stages of fusion are induced by orthogonally hybridizing sets of membrane-anchored oligonucleotides. Each fusion event leads to efficient content mixing and transfer of the recognition unit for the subsequent stage. In contrast to fusion protein-dependent eukaryotic vesicle processing, this artificial fusion cascade exploits the versatile encoding-potential of DNA hybridization and is generally applicable to small and giant unilamellar vesicles. Thus, our platform will enable numerous applications in artificial cellular systems and liposome-based synthetic pathways.
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Synthetic biology: step by step towards its democratization | PLOS Synthetic Biology Community

Synthetic biology: step by step towards its democratization | PLOS Synthetic Biology Community | SynBioFromLeukipposInstitute | Scoop.it
An interview with Julie Legault: Founder and CEO or Amino Labs Inc
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Applications of CRISPR-Cas for synthetic biology and genetic recording

The epic arms race between microbes and their predators was the driving force behind the evolution and diversification of the truly remarkable microbial adaptive immune system CRISPR-Cas. CRISPR-Cas systems mediate defense through three stages: recording of nucleic acid species, multiplexed RNA expression and processing, and eventually RNA-guided cleavage of hostile genetic elements. The entire process is orchestrated by a plethora of effector proteins endowed with specialized functions for manipulating genetic material. Investigating this treasure trove substantially fostered the development of the RNA-guided DNA endonuclease Cas9 into a versatile molecular tool for synthetic biology and biomedicine. Here, we review the developments of Cas9 and other CRISPR-Cas components for applications in synthetic biology as well as highlight emerging CRISPR-Cas-based genetic recorders and memory devices.
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Multiplex genome editing by natural transformation (MuGENT) for synthetic biology in Vibrio natriegens

Vibrio natriegens has recently emerged as an alternative to Escherichia coli for molecular biology and biotechnology, but low-efficiency genetic tools hamper its development. Here, we uncover how to induce natural competence in V. natriegens and describe methods for multiplex genome editing by natural transformation (MuGENT). MuGENT promotes integration of multiple genome edits at high-efficiency on unprecedented timescales. Also, this method allows for generating highly complex mutant populations, which can be exploited for metabolic engineering efforts. As a proof-of-concept, we attempted to enhance production of the value added chemical poly-β-hydroxybutyrate (PHB) in V. natriegens by targeting the expression of nine genes involved in PHB biosynthesis via MuGENT. Within 1 week, we isolated edited strains that produced ~100 times more PHB than the parent isolate and ~3.3 times more than a rationally designed strain. Thus, the methods described here should extend the utility of this species for diverse academic and industrial applications.
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Metabolic engineering and synthetic biology approaches driving isoprenoid production in Escherichia coli

Isoprenoids comprise the largest family of natural organic compounds with many useful applications in the pharmaceutical, nutraceutical, and industrial fields. Rapid developments in metabolic engineering and synthetic biology have facilitated the engineering of isoprenoid biosynthetic pathways in Escherichia coli to induce high levels of production of many different isoprenoids. In this review, the stem pathways for synthesizing isoprene units as well as the branch pathways deriving diverse isoprenoids from the isoprene units have been summarized. The review also highlights the metabolic engineering efforts made for the biosynthesis of hemiterpenoids, monoterpenoids, sesquiterpenoids, diterpenoids, carotenoids, retinoids, and coenzyme Q10 in E. coli. Perspectives and future directions for the synthesis of novel isoprenoids, decoration of isoprenoids using cytochrome P450 enzymes, and secretion or storage of isoprenoids in E. coli have also been included.
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A Safety and Efficacy Study of TALEN and CRISPR/Cas9 in the Treatment of HPV-related Cervical Intraepithelial Neoplasia

This is an open-label and triple cohort study of the safety and efficacy of TALEN and CRISPR/Cas9 to possibly treat HPV Persistency and human cervical intraepithelial neoplasiaⅠwithout invasion.
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ComplexInsight's curator insight, June 5, 3:01 PM
If your tracking CRISPR/Cas9 applications - this is worth reviewing.
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Cell-free synthetic biology for in vitro prototype engineering

Cell-free synthetic biology for in vitro prototype engineering | SynBioFromLeukipposInstitute | Scoop.it
Cell-free transcription–translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells.
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Controlling microbial PHB synthesis via CRISPRi

Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively. Depending on the binding location and the number of sgRNA on phaC, CRISPRi was able to control the phaC transcription and thus PhaC activity. It was found that PHB content, molecular weight, and polydispersity were approximately in direct and reverse proportion to the PhaC activity, respectively. The higher the PhaC activity, the more the intracellular PHB accumulation, yet the less the PHB molecular weights and the wider the polydispersity. This study allowed the PHB contents to be controlled in the ranges of 1.47-75.21% cell dry weights, molecular weights from 2 to 6 millions Dalton and polydispersity of 1.2 to 1.43 in 48 h shake flask studies. This result will be very important for future development of ultrahigh molecular weight PHA useful to meet high strength application requirements.

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Cell-free synthetic biology for in vitro prototype engineering

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells.

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Robustness of synthetic oscillators in growing and dividing cells

Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator. More recently, Stricker et al. [Nature (London) 456, 516 (2008)NATUAS0028-083610.1038/nature07389] presented another synthetic oscillator, called the dual-feedback oscillator, which is more stable. Detailed studies have been carried out to determine how the stability of these oscillators is affected by the intrinsic noise of the interactions between the components and the stochastic expression of their genes. However, as all biological oscillators reside in growing and dividing cells, an important question is how these oscillators are perturbed by the cell cycle. In previous work we showed that the periodic doubling of the gene copy numbers due to DNA replication can couple not only natural, circadian oscillators to the cell cycle [Paijmans et al., Proc. Natl. Acad. Sci. (USA) 113, 4063 (2016)PNASA60027-842410.1073/pnas.1507291113], but also these synthetic oscillators. Here we expand this study. We find that the strength of the locking between oscillators depends not only on the positions of the genes on the chromosome, but also on the noise in the timing of gene replication: noise tends to weaken the coupling. Yet, even in the limit of high levels of noise in the replication times of the genes, both synthetic oscillators show clear signatures of locking to the cell cycle. This work enhances our understanding of the design of robust biological oscillators inside growing and diving cells.

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Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors

Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include multiplexed detection using microfluidics. Synthetic biology can be used to engineer new biological biosensors with improved characteristics. Although there have been few biosensors developed for bioprocessing thus far, emerging trends can be applied in the future. A range of new platform technologies will enable rapid engineering of new biosensors based on transcriptional activation, riboswitches, and Förster Resonance Energy Transfer. However, translation to industry remains a challenge and more research into the robustness biosensors at scale is needed.
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Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion

We report on entirely man-made nano-bio architecture fabricated through non-covalent assembly of cell-free expressed transmembrane proton pump and TiO2 semiconductor nanoparticles as an efficient nanophotocatalyst for H2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H2 (μmol protein)-1 h-1 and 17.74 mmol of H2 (μmol protein)-1 h-1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robsutness and flexibility of this approach allows for systemic manipulation at nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.
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Metabolic engineering and synthetic biology approaches driving isoprenoid production in Escherichia coli

Isoprenoids comprise the largest family of natural organic compounds with many useful applications in the pharmaceutical, nutraceutical, and industrial fields. Rapid developments in metabolic engineering and synthetic biology have facilitated the engineering of isoprenoid biosynthetic pathways in Escherichia coli to induce high levels of production of many different isoprenoids. In this review, the stem pathways for synthesizing isoprene units as well as the branch pathways deriving diverse isoprenoids from the isoprene units have been summarized. The review also highlights the metabolic engineering efforts made for the biosynthesis of hemiterpenoids, monoterpenoids, sesquiterpenoids, diterpenoids, carotenoids, retinoids, and coenzyme Q10 in E. coli. Perspectives and future directions for the synthesis of novel isoprenoids, decoration of isoprenoids using cytochrome P450 enzymes, and secretion or storage of isoprenoids in E. coli have also been included.
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Dynamics of problem setting and framing in citizen discussions on synthetic biology

Synthetic biology is an emerging scientific field where engineers and biologists design and build biological systems for various applications. Developing synthetic biology responsibly in the public interest necessitates a meaningful societal dialogue. In this article, we argue that facilitating such a dialogue requires an understanding of how people make sense of synthetic biology. We performed qualitative research to unravel the underlying dynamics of problem setting and framing in citizen discussions on synthetic biology. We found that most people are not inherently for or against synthetic biology as a technology or development in itself, but that their perspectives are framed by core values about our relationships with science and technology and that sensemaking is much dependent on the context and general feelings of (dis)content. Given that there are many assumptions focused on a more binary idea of the public's view, we emphasize the need for frame awareness and understanding in a meaningful dialogue.
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CRISPR-Cas Genome Surgery in Ophthalmology

Genetic disease affecting vision can significantly impact patient quality of life. Gene therapy seeks to slow the progression of these diseases by treating the underlying etiology at the level of the genome. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated systems (Cas) represent powerful tools for studying diseases through the creation of model organisms generated by targeted modification and by the correction of disease mutations for therapeutic purposes. CRISPR-Cas systems have been applied successfully to the visual sciences and study of ophthalmic disease – from the modification of zebrafish and mammalian models of eye development and disease, to the correction of pathogenic mutations in patient-derived stem cells. Recent advances in CRISPR-Cas delivery and optimization boast improved functionality that continues to enhance genome-engineering applications in the eye. This review provides a synopsis of the recent implementations of CRISPR-Cas tools in the field of ophthalmology.
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SYSTEMS AND METHODS FOR SYNTHETIC BIOLOGY DESIGN AND HOST CELL SIMULATION

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CRISPR-Cas Genome Surgery in Ophthalmology

Genetic disease affecting vision can significantly impact patient quality of life. Gene therapy seeks to slow the progression of these diseases by treating the underlying etiology at the level of the genome. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated systems (Cas) represent powerful tools for studying diseases through the creation of model organisms generated by targeted modification and by the correction of disease mutations for therapeutic purposes. CRISPR-Cas systems have been applied successfully to the visual sciences and study of ophthalmic disease - from the modification of zebrafish and mammalian models of eye development and disease, to the correction of pathogenic mutations in patient-derived stem cells. Recent advances in CRISPR-Cas delivery and optimization boast improved functionality that continues to enhance genome-engineering applications in the eye. This review provides a synopsis of the recent implementations of CRISPR-Cas tools in the field of ophthalmology.
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ComplexInsight's curator insight, June 5, 2:59 PM
While the promise of CRISPR was not that it would change how genetics and biology behaved its quickly becoming hyped that way in popular press.  The fact that the Cas9 protein can be used as a cheap and fast technique to co-localize with specific DNA sequences is undoubtedly incredibly useful. As researchers discover mechanisms where they can exploit co-localization and modification at specific sites using DNA cleavage capabilities it is important we get well informed reviews of actual applications as well as coverage of potential ones.  This paper gives a good summary of recent developments and insights to applications of CRISPR-CAS in ophthalmology  for both better understanding visual systems and potential treatments for ophthalmic disease. 
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Microsoft Plans to Have a DNA-Based Computer by 2020

Microsoft Plans to Have a DNA-Based Computer by 2020 | SynBioFromLeukipposInstitute | Scoop.it
It’s durable, exponentially scalable, and it’ll last millennia, if not millions of years.
 
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