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Inserting "artificial" chromosome into world's first synthetic yeast

Inserting "artificial" chromosome into world's first synthetic yeast | SynBioFromLeukipposInstitute | Scoop.it
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"- A UK team is building an “artificial” chromosome to be inserted into the world’s first synthetic yeast.

 Teams worldwide are making the other parts of its genome, which will be assembled to make the yeast strain Saccharomyces cerevisiae. Once complete, new strains of synthetic yeast could help make products such as vaccines, biofuels and chemicals. The UK government has announced a grant of almost £1m towards the project, which aims to be complete by 2017. Synthetic biology involves assembling artificial genes to create new materials in a similar way that engineers build machines using many parts. Some even think it can form the basis of a new industrial revolution. Teams worldwide are making the other parts of its genome, which will be assembled to make the yeast strain Saccharomyces cerevisiae. Once complete, new strains of synthetic yeast could help make products such as vaccines, biofuels and chemicals. The UK government has announced a grant of almost £1m towards the project, which aims to be complete by 2017. Synthetic biology involves assembling artificial genes to create new materials in a similar way that engineers build machines using many parts. Some even think it can form the basis of a new industrial revolution."




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Complex cellular logic computation using ribocomputing devices

Complex cellular logic computation using ribocomputing devices | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative technologies1. Synthetic gene circuits that combine DNA, protein, and RNA components have demonstrated a range of functions such as bistability2, oscillation3, 4, feedback5, 6, and logic capabilities7, 8, 9, 10, 11, 12, 13, 14, 15. However, it remains challenging to scale up these circuits owing to the limited number of designable, orthogonal, high-performance parts, the empirical and often tedious composition rules, and the requirements for substantial resources for encoding and operation. Here, we report a strategy for constructing RNA-only nanodevices to evaluate complex logic in living cells. Our ‘ribocomputing’ systems are composed of de-novo-designed parts and operate through predictable and designable base-pairing rules, allowing the effective in silico design of computing devices with prescribed configurations and functions in complex cellular environments. These devices operate at the post-transcriptional level and use an extended RNA transcript to co-localize all circuit sensing, computation, signal transduction, and output elements in the same self-assembled molecular complex, which reduces diffusion-mediated signal losses, lowers metabolic cost, and improves circuit reliability. We demonstrate that ribocomputing devices in Escherichia coli can evaluate two-input logic with a dynamic range up to 900-fold and scale them to four-input AND, six-input OR, and a complex 12-input expression (A1 AND A2 AND NOT A1*) OR (B1 AND B2 AND NOT B2*) OR (C1 AND C2) OR (D1 AND D2) OR (E1 AND E2). Successful operation of ribocomputing devices based on programmable RNA interactions suggests that systems employing the same design principles could be implemented in other host organisms or in extracellular settings.
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Bio-inspired materials—borrowing from nature's playbook

Bio-inspired materials—borrowing from nature's playbook | SynBioFromLeukipposInstitute | Scoop.it
Nature provides myriad examples of unique materials and structures developed for specialized applications or adaptations. An interdisciplinary group of researchers at the U.S. Department of Energy's Ames Laboratory is tryin
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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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Scientists Build DNA From Scratch to Alter Life's Blueprint

Scientists Build DNA From Scratch to Alter Life's Blueprint | SynBioFromLeukipposInstitute | Scoop.it
At Jef Boeke's lab, you can whiff an odor that seems out of place, as if they were baking bread here.

But he and his colleagues are cooking up something else altogether: yeast that works with chunks of man-made DNA.

Scientists have long been able to make specific changes in the DNA code. Now, they're taking the more radical step of starting over, and building redesigned life forms from scratch. Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to "rewrite" the yeast genome, following a detailed plan they published in March.

Their work is part of a bold and controversial pursuit aimed at creating custom-made DNA codes to be inserted into living cells to change how they function, or even provide a treatment for diseases. It could also someday help give scientists the profound and unsettling ability to create entirely new organisms.

The genome is the entire genetic code of a living thing. Learning how to make one from scratch, Boeke said, means "you really can construct something that's completely new."

The research may reveal basic, hidden rules that govern the structure and functioning of genomes. But it also opens the door to life with new and useful characteristics, like microbes or mammal cells that are better than current ones at pumping out medications in pharmaceutical factories, or new vaccines. The right modifications might make yeast efficiently produce new biofuels, Boeke says.

Some scientists look further into the future and see things like trees that purify water supplies and plants that detect explosives at airports and shopping malls.

Also on the horizon is redesigning human DNA. That's not to make genetically altered people, scientists stress. Instead, the synthetic DNA would be put into cells, to make them better at pumping out pharmaceutical proteins, for example, or perhaps to engineer stem cells as a safer source of lab-grown tissue and organs for transplanting into patients.

Some have found the idea of remaking human DNA disconcerting, and scientists plan to get guidance from ethicists and the public before they try it.

Still, redesigning DNA is alarming to some. Laurie Zoloth of Northwestern University, a bioethicist who's been following the effort, is concerned about making organisms with "properties we cannot fully know." And the work would disturb people who believe creating life from scratch would give humans unwarranted power, she said.

"It is not only a science project," Zoloth said in an email. "It is an ethical and moral and theological proposal of significant proportions."

Rewritten DNA has already been put to work in viruses and bacteria. Australian scientists recently announced that they'd built the genome of the Zika virus in a lab, for example, to better understand it and get clues for new treatments.

At Harvard University, Jeffrey Way and Pamela Silver are working toward developing a harmless strain of salmonella to use as a vaccine against food poisoning from salmonella and E. coli, as well as the diarrhea-causing disease called shigella.

A key goal is to prevent the strain from turning harmful as a result of picking up DNA from other bacteria. That requires changing its genome in 30,000 places.

"The only practical way to do that," Way says, "is to synthesize it from scratch."

The cutting edge for redesigning a genome, though, is yeast. Its genome is bigger and more complex than the viral and bacterial codes altered so far. But it's well-understood and yeast will readily swap man-made DNA for its own.

Still, rewriting the yeast genome is a huge job.
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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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