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Advanced micro- and nanofabrication technologies for tissue engineering

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by
Shapira A, Kim DH, Dvir T.

"The ability of the living body to heal and regenerate itself following trauma is astonishing. Numerous events of repair and regeneration occur during our lifetime, most of which we are never aware of. Unfortunately, in some cases, the injury or defect cannot be adequately repaired solely by nature and medical intervention is required. Tissue engineering is a multidisciplinary field of science that integrates knowledge from engineering, biology, chemistry and medicine [1]. It focuses on the development of functional tissues or organs that can be used to repair or substitute their defected, injured or diseased natural counterparts. As opposed to superficial growth of cells in a culture dish, cells that populate a functional tissue are usually integrated in a complex, three-dimensional (3D) architecture of extracellular matrix (ECM) and vasculature. With the recent advances in cellular biology research, it becomes increasingly clear that the micro- and nanoscale cues in the surrounding microenvironment of the cells have a profound effect on their growth, differentiation, morphology and metabolic state [2, 3]. At a higher hierarchical level, the cues provided by the ECM can direct the morphogenesis of the whole tissue. When they recognized the importance of chemical and biomechanical signals in tissue organization, scientists began to develop materials and methods for mimicking the natural cellular microenvironment. In this special section of Biofabrication , we bring together original research articles from top scientists in the field of biomaterials and regenerative medicine. Each presents state-of-the-art micro- and nanotechnologies and developments in biofabrication for tissue engineering. Great emphasis is currently given to the biofabrication of biomimetic 3D scaffolds that replicate the architecture and mechanical properties of the natural ECM. Fabrication methods such as self-assembly, particulate-leaching, freeze-drying, phase-separation and electrospinning were developed to produce biodegradable, porous polymeric scaffolds from natural or synthetic materials. The fabricated scaffolds can also be further modified to improve cell adherence or present and deliver chemical cues that can 'guide' the cells toward their desired fate (e.g. proliferation, differentiation, migration, regulation of a specific cellular function, etc). The porous scaffold is then populated with cells that secrete a structural protein network and thus create their own ECM. This traditional approach, which is called 'top-down' or 'solid-scaffold-based tissue engineering', is demonstrated in this special issue by Szymanski and Feinberg [4]. In their paper, a method for the fabrication of an alginate and alginate-fibrin-based microfibrous structure with tunable geometries is described. The authors used photolithography in order to fabricate an elastic stamp for imprinting the biomaterial onto a thermally sensitive sacrificial layer. Subsequently, the material was cross-linked and the microstructures were released from the support. The resulting fine fabric supported the polarization of myoblasts and the formation of interconnected cell strands. Another example of using a lithographic method for fabrication of biodegradable scaffold is reported by Kim et al [5]. The group used UV-assisted capillary force lithography to fabricate nanopatterned cell culture substrates for vascular tissue engineering. By varying the amount and ratio of the constituents of poly(ethylene glycol)-gelatin methacrylate hydrogel, the elasticity and degradation rate of the composite structure could be tuned. Importantly, in comparison to an unpatterned substrate, endothelial cells showed better attachment and native vascular cell-like morphology when seeded on the patterned scaffold. The pattern also promoted rapid migration and anisotropic organization of the cells. Together, these two lithography-assisted techniques could be applied in a wide range of tissue engineering applications when a controllable and precise fabrication of fine geometries is required. In order to closely mimic the natural 3D extracellular environment and attain improved substrate-specific cell adhesion and spreading, a unique composite scaffold made of biofunctionalized, electrospun fibers and a hydrogel was fabricated by Schulte et al [6]. Following a short period of pre-culturing on the functionalized fibers, the cell-seeded matrix was covered with a protective semi-synthetic hyaluronic acid-based hydrogel that further supported cell proliferation and spreading along the embedded fibers. While embedding an originally superficial cell-seeded fibrous matrix in a hydrogel represents an intriguing strategy for mimicking the natural 3D environment of the cells, the native architecture of the ECM may also be mimicked by spatial fabrication of the fibers themselves. For instance, Park et al [7] developed a method to fabricate fibrous, 3D cell-laden alginate scaffolds using a single microfluidic platform. The authors showed the capability of their set-up to control the shape, volume and porosity of the scaffolds while preserving their delicate structure. Moreover, the porous nature of the scaffolds, which permits a high diffusion rate, was found to be superior in maintaining cell viability when compared to a 3D alginate non-fibrous block. Another creative strategy for the fabrication of 3D fibrous scaffolds was developed by Park et al [8]. The authors describe a hybrid process for thermal fusion of uniaxially oriented electrospun nanofibers by algorithm-directed molten polymer deposition. The aligned fibers were bound together by thermally extruded microstructures to create 2D mats that can be used as one-layer fibrous substrates or can be stacked to produce 3D multilayer constructs. The feasibility of these composite scaffolds for application in muscle tissue engineering was demonstrated by obtaining viable and highly aligned cultured myoblasts. Overall, the aforementioned studies describe three elegant strategies for fabricating fibrous 3D scaffolds. The morphological and biochemical resemblance of these scaffolds to the native ECM, together with their biocompatibility and biodegradability, underline their potential to serve as biomimetic substrates for tissue engineering applications. The solid-scaffold-based approach of populating a pre-fabricated scaffold with cells was also utilized by Zieber et al [9]. Recognizing the importance of prevascularization of engineered tissues for maintenance of cell viability and for effective integration with the host, the researchers have used a CO2 laser engraving system to create an array of microscale channels within alginate macroporous scaffolds. The channels were then decorated with adhesion peptides and angiogenic factors to create a blood-vessel-supporting microenvironment. Upon sequential seeding of endothelial cells, cardiomyocytes and fibroblasts, the unique architecture and the biochemical cues promoted the generation of vessel-like networks within an engineered cardiac patch. Another important aspect for engineering functional cardiac tissues is the structural and functional anisotropy of the tissue. In order to control these parameters, Bian et al [10] have applied a high aspect ratio soft lithography technique to generate network-like tissue patches composed of cardiomyocytes. The authors have shown that the alignment of the cells and secreted ECM proteins can be enhanced by extending the transverse diameter of the elliptical pores that crossed the patch networks. The improved alignment resulted in increased anisotropy of the action potential propagation and augmented contractile forces. While synthetic scaffolds made of biocompatible materials can be fabricated to closely mimic the ECM structure, they still lack much of the fine, complex architecture and biochemical cues that can be found in the native ECM. In a study by Shevach et al [11], the omentum, a double sheet of peritoneum, was manipulated to serve as a natural, autologous scaffold for engineering functional cardiac tissue. It was found that the biochemical and mechanical properties of the processed omental tissue could support the survival and assembly of cardiac cells into a contractile patch. The patch could then be populated with endothelial cells to generate a vascularized tissue for better integration with the host. Since the omentum can easily and safely be extracted from patients, this approach might be utilized to engineer autologous patches. To prove this concept, the authors also showed that the omentum-based matrices can support the growth of induced pluripotent and mesenchymal stem cells, which in theory can also be isolated from the same patient. Whereas fabrication of ECM-like scaffolds is a key process in tissue engineering for regenerative medicine, it can also be utilized for construction of 3D tissue models for more basic research. Ock and Li [12] have used a laser foaming technique to fabricate an array of micro-scale porous polylactic acid scaffolds for high throughput, tissue-based biomedical assays. The authors have studied the effects of the process parameters on the resulting internal architecture of the scaffolds and demonstrated enhanced cell viability within the scaffolds. The fabricated microarray represents a more biologically relevant model for drug screening than the common 2D cultures. While the 'top-down' approach is mostly suitable for engineering thin, non-vascularized artificial tissues, the construction of thicker, complex tissues with micro- and nanoscale architectural characteristics is still a challenge. The emerging 'bottom-up' or 'modular' approach aims to overcome this issue. This concept is based on the generation of microscale tissue building blocks that incorporate complex artificial micro- and nano-architectures resembling those of a native tissue. The tissue components can be fabricated by using various methods such as self-assembled cell aggregates, generation of cell sheets and fabrication of cell-laden hydrogels. These building blocks are then assembled to form a large tissue construct using methods such as random packing, stacking of layers and 3D bioprinting. For example, in their article Lee et al [13] used a 3D printing method for reconstruction of the external ear. The authors encapsulated chondrocytes and adipocytes in an alginate hydrogel and dispensed them into ear-shaped structures made of sacrificial-layer-supported polycaprolactone. Using this strategy, both the shape and the composition of the ear were faithfully mimicked. Importantly, the adipocytes and chondrocytes survived the printing process, proliferated and showed both adipogenesis and chondrogenesis, respectively. Without doubt, this study has the potential to broaden the current arsenal of practical methods used in reconstructive medicine, especially in cases when the target tissue or organ has a complex structure. Another example of harnessing the power of 3D printing for tissue fabrication was reported by Bertassoni et al [14]. The authors demonstrate a strategy for 3D bioprinting using a modified set-up that uses a photolabile cell-laden methacrylated gelatin as 'bioink' for fabrication of pre-polymerized hydrogel fibers. After assessing the effect of the biopolymer concentration and cell density on the fabrication process, the authors proved the ability of their method to fabricate and control macroscale architectures and to support the viability of the printed cells. A different strategy of 3D bioprinting involves the fabrication of 'scaffold-free' constructs using tissue spheroids as bioink. In this process, the basic building blocks of the tissue are spherical bodies composed of spontaneous self-assembled cells. Upon deposition in a pre-defined architecture, the spheroids fuse into a 3D tissue structure. In their paper, Tan et al [15] describe a technique for direct 3D mold printing for fabrication of scaffold-free tissue engineering constructs. Using algorithm-directed deposition of alginate micro-droplets on a calcium-containing substrate, the group managed to construct hydrogels with defined 3D architecture. The resulting structure then served as a mold into which tissue spheroids were deposited and eventually fused together to form an artificial, tissue-like structure. The promising results from these three studies demonstrate the emerging role of 3D printing technology as an effective means of implementing the modular approach. By performing a precise, algorithm-guided deposition of cells and biomaterials, 'bottom-up' fabrication of composite constructs has become feasible. Whether the fabrication method of choice is based on the 'top-down' or 'bottom-up' approach, the subsequent step is usually an incubation period in a bioreactor to support the organization and maturation of the construct into a functioning tissue. In this issue Miklas et al [16] report on the development of a bioreactor that offers both mechanical and electrical stimuli to engineered cardiac tissues and allows the researcher to study the physiology of the patch by providing on-line measurements of contraction force. In summary, the articles in this special section demonstrate selected current advances in the fabrication of biomaterials in the context of tissue engineering. The recent achievements in this evolving, multidisciplinary field bring the scientific community another step toward the goal of faithfully imitating the fine and complex architecture of a functional human tissue. Finding the most appropriate cell source and engineering a thick, vascularized tissue are still a challenge. Nevertheless, the intense work and vast efforts that are being invested in research and development of artificial tissues for treatment of damaged or malfunctioning organs give hope to many patients that currently relay on organ transplantation from scarce donors. Acknowledgment TD acknowledges support from the European Union FP7 program (Marie Curie, CIG), Alon Fellowship, the Israeli Science Foundation and the Nicholas and Elizabeth Slezak Super Center for Cardiac Research and Biomedical Engineering at Tel Aviv University. DHK acknowledges support from the American Heart Association Scientist Development Grant, the Muscular Dystrophy Association, Perkins Coie Award for Discovery and KSEA Young Investigator Award. Research reported in this publication was also supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under Award Number R21 AR064395-01A1."

 http://1.usa.gov/1gQyFvM

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Improvement in the production of the human recombinant enzyme N-acetylgalactosamine-6-sulfatase (rhGALNS) in Escherichia coli using synthetic biology approaches

Previously, we demonstrated production of an active recombinant human N-acetylgalactosamine-6-sulfatase (rhGALNS) enzyme in Escherichia coli as a potential therapeutic alternative for mucopolysaccharidosis IVA. However, most of the rhGALNS produced was present as protein aggregates. Here, several methods were investigated to improve production and activity of rhGALNS. These methods involved the use of physiologically-regulated promoters and alternatives to improve protein folding including global stress responses (osmotic shock), overexpression of native chaperones, and enhancement of cytoplasmic disulfide bond formation. Increase of rhGALNS activity was obtained when a promoter regulated under σ s was implemented. Additionally, improvements were observed when osmotic shock was applied. Noteworthy, overexpression of chaperones did not have any effect on rhGALNS activity, suggesting that the effect of osmotic shock was probably due to a general stress response and not to the action of an individual chaperone. Finally, it was observed that high concentrations of sucrose in conjunction with the physiological-regulated promoter proU mod significantly increased the rhGALNS production and activity. Together, these results describe advances in the current knowledge on the production of human recombinant enzymes in a prokaryotic system such as E. coli, and could have a significant impact on the development of enzyme replacement therapies for lysosomal storage diseases.
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CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness

Elife. 2017 Jul 18;6. pii: e28129. doi: 10.7554/eLife.28129. [Epub ahead of print]
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Twin-primer non-enzymatic DNA assembly: an efficient and accurate multi-part DNA assembly method

DNA assembly forms the cornerstone of modern synthetic biology. Despite the numerous available methods, scarless multi-fragment assembly of large plasmids remains challenging. Furthermore, the upcoming wave in molecular biological automation demands a rethinking of how we perform DNA assembly. To streamline automation workflow and minimize operator intervention, a non-enzymatic assembly method is highly desirable. Here, we report the optimization and operationalization of a process called Twin-Primer Assembly (TPA), which is a method to assemble polymerase chain reaction-amplified fragments into a plasmid without the use of enzymes. TPA is capable of assembling a 7 kb plasmid from 10 fragments at ∼80% fidelity and a 31 kb plasmid from five fragments at ∼50% fidelity. TPA cloning is scarless and sequence independent. Even without the use of enzymes, the performance of TPA is on par with some of the best in vitro assembly methods currently available. TPA should be an invaluable addition to a synthetic biologist's toolbox.
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Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells

ACS Synth Biol. 2017 Jun 27. doi: 10.1021/acssynbio.7b00115. [Epub ahead of print]
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Tissue engineering pioneer Michael Sefton to lead Medicine by Design as executive director - Medicine by Design

Tissue engineering pioneer Michael Sefton to lead Medicine by Design as executive director - Medicine by Design | SynBioFromLeukipposInstitute | Scoop.it
Sefton, who also heads a collaborative team project focused on using novel biomaterials to stimulate skeletal muscle to repair itself, begins his five-year term on July 1, 2017.
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Neuron-integrated nanotubes to repair nerve fibers

Neuron-integrated nanotubes to repair nerve fibers | SynBioFromLeukipposInstitute | Scoop.it
Carbon nanotubes exhibit interesting characteristics rendering them particularly suited to the construction of special hybrid devices consisting of biological issue and synthetic material. These could re-establish connections between nerve cells at the spinal level that were lost due to lesions or trauma. This is the result of research published in the scientific journal Nanomedicine: Nanotechnology, Biology, and Medicine conducted by a multi-disciplinary team comprising SISSA (International School for Advanced Studies), the University of Trieste, ELETTRA Sincrotrone and two Spanish institutions, Basque Foundation for Science and CIC BiomaGUNE.
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iGEM 2017 Manchester: On the Mission to Save Phosphorus Reserves and Clean Water

iGEM 2017 Manchester: On the Mission to Save Phosphorus Reserves and Clean Water | SynBioFromLeukipposInstitute | Scoop.it
iGEM Manchester 2017 is a team of nine students participating in iGEM, the
biggest synthetic biology competition in the world. In their project, iGEM
Manchester aims to solve two imminent environmental dangers, which threaten
our ecosystem: eutrophication and rapid depletion of phosphorus rese
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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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A Synthetic Circuit for Mercury Bioremediation Using Self-Assembling Functional Amyloids

Synthetic biology approaches to bioremediation are a key sustainable strategy to leverage the self-replicating and programmable aspects of biology for environmental stewardship. The increasing spread of anthropogenic mercury pollution into our habitats and food chains is a pressing concern. Here, we explore the use of programmed bacterial biofilms to aid in the sequestration of mercury. We demonstrate that by integrating a mercury-responsive promoter and an operon encoding a mercury-absorbing self-assembling extracellular protein nanofiber, we can engineer bacteria that can detect and sequester toxic Hg2+ ions from the environment. This work paves the way for the development of on-demand biofilm living materials that can operate autonomously as heavy-metal absorbents.
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Bacteria Are the New Hard Drives

Bacteria Are the New Hard Drives | SynBioFromLeukipposInstitute | Scoop.it
DNA is the densest known storage medium in the universe - and Harvard University researchers have managed to use it to store GIFs inside bacteria.
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4th International Synthetic & Systems Biology Summer School - SSBSS 2017

The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Robinson Colleg
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Researchers develop yeast-based tool for worldwide pathogen detection

Researchers develop yeast-based tool for worldwide pathogen detection | SynBioFromLeukipposInstitute | Scoop.it
Columbia University researchers have developed a tool that is likely to revolutionize the way we detect and treat pathogens in everything from human health to agriculture to water. Using only common household baker's yeast
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MIT Media Lab's Journal of Design and Science Is a Radical New Kind of Publication

MIT Media Lab's Journal of Design and Science Is a Radical New Kind of Publication | SynBioFromLeukipposInstitute | Scoop.it
The MIT Media Lab has launched a new kind of academic journal that embodies its "antidisciplinary" ethos.
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New book on Synthetic Biology from Cold Spring Harbor Laboratory Press - EurekAlert (press release) | CodonOps

New book on Synthetic Biology from Cold Spring Harbor Laboratory Press - EurekAlert (press release) | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
EurekAlert (press release)New book on Synthetic Biology from Cold Spring Harbor Laboratory PressEurekAlert (press release)Cold Spring Harbor, NY -- Cold Spring Harbor Laboratory Press (CSHLP) today announced the release of Synthetic Biology: Tools for Engineering Biological Systems, availabl
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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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