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An Evolutionary Approach to Synthetic Biology - Zen and the Art of Creating Life - Abstract - UK PubMed Central

An Evolutionary Approach to Synthetic Biology - Zen and the Art of Creating Life - Abstract - UK PubMed Central | SynBioFromLeukipposInstitute | Scoop.it

"Our concepts of biology, evolution and complexity are constrained by having observed only a single instance of life, life on Earth. A truly comparative biology is needed to extend these concepts. Because we can not observe life on other planets, we are left with the alternative of creating artificial life forms on Earth. I will discuss the approach of inoculating evolution by natural selection into the medium of the digital computer. This is not a physical/chemical medium, it is a logical/informational medium. Thus these new instances of evolution are not subject to the same physical laws as organic evolution (e.g., the laws of thermodynamics), and therefore exist in what amounts to another universe, governed by the "physical laws" of the logic of the computer. This exercise gives us a broader perspective on what evolution is and what it does. An evolutionary approach to synthetic biology consists of inoculating the process of evolution by natural selection into an artificial medium. E..."

 
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Multiplex recording of cellular events over time on CRISPR biological tape

Multiplex recording of cellular events over time on CRISPR biological tape | SynBioFromLeukipposInstitute | Scoop.it
While dynamics underlie many biological processes, our ability to robustly and accurately profile time-varying biological signals and regulatory programs remains limited. Here, we describe a framework to store temporal biological information directly into the genomes of a cell population. A “biological tape recorder” is developed in which biological signals trigger intracellular DNA production that is then recorded by the CRISPR-Cas adaptation system. This approach enables stable recording over multiple days and accurate reconstruction of temporal and lineage information by sequencing CRISPR arrays. We further demonstrate a multiplexing strategy to simultaneously record the temporal availability of three metabolites (copper, trehalose, fucose) in the environment of a cell population over time. This work enables the temporal measurement of dynamic cellular states and environmental changes and suggests new applications for chronicling biological events on a large scale.
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Did a Swedish researcher eat the first CRISPR meal ever served?

Did a Swedish researcher eat the first CRISPR meal ever served? | SynBioFromLeukipposInstitute | Scoop.it
In what Swedish plant scientist Stefan Jansson declares “maybe” a historic event, he cultivated, grew, and ate a plant that had its genome edited with CRISPR-Cas9. Umeå University, where Jansson studies how trees know it’s autumn and how proteins allow plants to harvest light, released a 5 September press release about his meal, a pasta dish that included 300 grams of cabbage he grew from seeds that had been genetically modified with CRISPR-Cas9. The revolutionary technology vastly simplifies the editing of genes, and has triggered many debates about whether its plant products should be considered a genetically modified organism (GMO) and subject to regulation.

As noted by Science Daily and other media outlets, Jansson enjoyed the lunch with Gustaf Klarin, host of a Radio Sweden gardening show, which broadcast it earlier this week (in Swedish). “To our delight—and to some extent to my surprise—the meal turned out really nice,” Jannson wrote in a blog entry on 16 August, the actual day that history might have been made. “Both of us ate with great relish. Gustaf even thought the cabbage was the best tasting vegetable on the plate. And I agreed.”

Jansson’s lab did not create the seed, but he told ScienceInsider he received it from a colleague “in another country” who wants to remain unidentified. As Jansson notes, the European Union has yet to determine whether CRISPR-Cas9 modification that eliminates a gene should be classified as a GMO and thus illegal to grow. But he received approval from the Swedish Board of Agriculture to grow a similar CRISPR-Cas9 seed that his lab had engineered, which the authorities determined was not a GMO as long as it didn’t contain foreign DNA. Jansson told Science that because the plant they ate was by definition not a GMO, “we do of course not need to ask for a permit or even inform them.”
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Webinar | CRISPR unleashed: New tools and applications in live-cell imaging

Webinar | CRISPR unleashed: New tools and applications in live-cell imaging | SynBioFromLeukipposInstitute | Scoop.it
The CRISPR/Cas9 gene editing system has been a boon for researchers, enabling them to manipulate a broad range of genomes quickly and accurately. This novel, versatile tool has been used with great precision for DNA editing as well as a multitude of other applications. Recent enhancements have expanded its abilities; one example is a new, hyperaccurate Cas9 variant that demonstrates high specificity across the genome without compromising on-target activity in human cells. Another is a modification of Cas9 called CRISPRainbow, a system that can more easily label multiple genomic loci in living cells, allowing researchers to better study chromatin dynamics. The unprecedented flexibility of the CRISPR toolset makes it possible to capture imaging phenomena happening at very small scales of space and time. An essential piece of this technology is a camera that captures the fine structure necessary to see the modified DNA (and distinguish it from the background). It must be capable of functioning in challenging environments in living cells, which require cutting-edge light manipulation and detection technologies optimized for light-starved conditions. During this webinar, our experts will examine some of the latest enhancements to the CRISPR/Cas9 system and explain how they are being applied in the lab today.
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Editorial overview: Synthetic biology: Frontiers in synthetic biology

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Rational Design of Evolutionarily Stable Microbial Kill Switches

The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable. Both kill switches were shown to maintain functionality in vitro for at least 140 generations. Additionally, cryodeath was shown to control the growth environment of a population, with an escape frequency of less than 1 in 105 after 10 days of growth in the mammalian gut.
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Multiscale memory and bioelectric error correction in the cytoplasm-cytoskeleton-membrane system

A fundamental aspect of life is the modification of anatomy, physiology, and behavior in the face of changing conditions. This is especially illustrated by the adaptive regulation of growth and form that underlies the ability of most organisms-from single cells to complex large metazoa-to develop, remodel, and regenerate to specific anatomical patterns. What is the relationship of the genome and other cellular components to the robust computations that underlie this remarkable pattern homeostasis? Here we examine the role of constraints defined at the cellular level, especially endogenous bioelectricity, in generating and propagating biological information. We review evidence that the genome is only one of several multi-generational biological memories. Focusing on the cell membrane and cytoplasm, which is physically continuous across all of life in evolutionary timeframes, we characterize the environment as an interstitial space through which messages are passed via bioelectric and biochemical codes. We argue that biological memory is a fundamental phenomenon that cannot be understood at any one scale, and suggest that functional studies of information propagated in non-genomic cellular structures will not only strongly impact evolutionary developmental biology, but will also have implications for regenerative medicine and synthetic bioengineering. For further resources related to this article, please visit the WIREs website.
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CRISPR-Cas9D10A Nickase-Assisted Genome Editing in Lactobacillus casei

Lactobacillus casei has drawn increasing attention as a health-promoting probiotic, while effective genetic manipulation tools are often not available, e.g., the single-gene knockout in L. casei still depends on the classic homologous recombination-dependent double-crossover strategy, which is quite labor-intensive and time-consuming. In the present study, a rapid and precise genome editing plasmid, pLCNICK, was established for L. casei genome engineering based on CRISPR-Cas9D10A. In addition to the P23-Cas9D10A and Pldh-sgRNA (single guide RNA) expression cassettes, pLCNICK includes the homologous arms of the target gene as repair templates. The ability and efficiency of chromosomal engineering using pLCNICK were evaluated by in-frame deletions of four independent genes and chromosomal insertion of an enhanced green fluorescent protein (eGFP) expression cassette at the LC2W_1628 locus. The efficiencies associated with in-frame deletions and chromosomal insertion is 25 to 62%. pLCNICK has been proved to be an effective, rapid, and precise tool for genome editing in L. casei, and its potential application in other lactic acid bacteria (LAB) is also discussed in this study.
IMPORTANCE The lack of efficient genetic tools has limited the investigation and biotechnological application of many LAB. The CRISPR-Cas9D10A nickase-based genome editing in Lactobacillus casei, an important food industrial microorganism, was demonstrated in this study. This genetic tool allows efficient single-gene deletion and insertion to be accomplished by one-step transformation, and the cycle time is reduced to 9 days. It facilitates a rapid and precise chromosomal manipulation in L. casei and overcomes some limitations of previous methods. This editing system can serve as a basic technological platform and offers the possibility to start a comprehensive investigation on L. casei. As a broad-host-range plasmid, pLCNICK has the potential to be adapted to other Lactobacillus species for genome editing.
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Growing DNA Strands

Growing DNA Strands | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biologists and nanobiologists are repurposing DNA as a smart and stable self-assembling material to build nanofactories, drug-delivering nanostructures and molecular devices that can sense their environment and respond in different ways by, for example, detecting inflammation in the body...
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Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli

Inducible gene expression systems are widely used in microbial host strains for protein and commodity chemical production because of their extensive characterization and ease of use. However, some of these systems have disadvantages such as leaky expression, lack of dynamic control, and the prohibitively high costs of inducers associated with large-scale production. Quorum sensing (QS) systems in bacteria control gene expression in response to population density, and the LuxI/R system from Vibrio fischeri is a well-studied example. A QS system could be ideal for biofuel production strains as it is self-regulated and does not require the addition of inducer compounds, which reduce operational costs for inducer. In this study, a QS system was developed for inducer-free production of the biofuel compound bisabolene from engineered E. coli. Seven variants of the Sensor plasmid, which carry the luxI-luxR genes, and four variants of the Response plasmid, which carry bisabolene producing pathway genes under the control of the PluxI promoter, were designed for optimization of bisabolene production. Furthermore, a chromosome-integrated QS strain was engineered with the best combination of Sensor and Response plasmid and produced bisabolene at a titer of 1.1g/L without addition of external inducers. This is a 44% improvement from our previous inducible system. The QS strain also displayed higher homogeneity in gene expression and isoprenoid production compared to an inducible-system strain.
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Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing | SynBioFromLeukipposInstitute | Scoop.it
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Synthetic circuits can harvest light energy

Synthetic circuits can harvest light energy | SynBioFromLeukipposInstitute | Scoop.it
By organizing pigments on a DNA scaffold, an MIT-led team of researchers has designed a light-harvesting material that closely mimics the structure of naturally occurring photosynthetic structures. This type of structure could be incorporated into materials such as glass or textiles, enabling them to harvest or store energy from sunlight.
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Hypersymbiont Dress

Hypersymbiont Dress | SynBioFromLeukipposInstitute | Scoop.it
Photo: Photo: Installation view (detail) with video mapping at “Technology and Emotions”, Oslo
The Hypersymbiont Dress is a dress stained and video mapped with bacteria that may have the potentia
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Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Front Microbiol. 2017 Oct 24;8:2060. doi: 10.3389/fmicb.2017.02060. eCollection 2017. Review
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This robot made of algae can swim through your body—thanks to magnets

This robot made of algae can swim through your body—thanks to magnets | SynBioFromLeukipposInstitute | Scoop.it
For decades, engineers have been trying to build medical robots that can deliver drugs or do surgery inside the human body—a somewhat less fantastic version of the 1966 sci-fi film Fantastic Voyage. Now, scientists have manipulated spirulina, a microscopic plant and food supplement, to travel through people in response to magnetic signals. The biohybrid robot could one day carry drugs to specific parts of the body, minimizing side effects. What’s more, the robot—and its magnetic coat—appear to kill cancer cells.

Spirulina, an alga, looks like a tiny coiled spring at the microscopic level. Researchers had been trying, and succeeding to various degrees, to build bots out of rods, tubes, spheres, and even cages no bigger than a cell. Outfitting these tiny devices with an ample power supply has been quite a challenge, as most potential fuels are toxic to humans. Another problem is steering such a microrobot through the body’s maze of proteins and other molecules, which requires both a way to control its movements and to see where it is.

So Li Zhang, a materials scientist at the Chinese University of Hong Kong in Shatin, turned to magnetism—and living organisms. Magnetic fields created outside the body can penetrate living tissue without harm, allowing researchers to move magnetized objects around inside. For maximum mobility, a helical body propelled by twirling works best. Enter spirulina. “It’s surprising that you can find in nature such a convenient structure and that it can behave so nicely,” says Peer Fischer, a physical chemist at the Max Planck Institute for Intelligent Systems in Stuttgart, Germany, who was not involved in the study.
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RNA editing with CRISPR-Cas13

RNA editing with CRISPR-Cas13 | SynBioFromLeukipposInstitute | Scoop.it
Precise transcriptome engineering
Efficient and precise RNA editing to correct disease-relevant transcripts holds great promise for treating genetic disease. Cox et al. took advantage of the ability of Cas13b, an effector from a type VI CRISPR-Cas system, to target specific RNAs directly (see the Perspective by Yang and Chen). They fused Cas13b with the ADAR2 adenosine deaminase domain and used rational protein engineering to improve the resultant enzyme. These approaches yielded an RNA knockdown and editing platform that allowed efficient and specific RNA depletion and correction in mammalian cells.
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Synthetic biology platforms for natural product biosynthesis and disco

Plants are a rich source of unique scaffolds, including 25% of natural-product-derived drugs. However, the discovery, synthesis, and overall material supply chains for sourcing plant natural products and their derivatives remain ad hoc, biased, and tedious. While microbial biosynthesis presents compelling alternatives to traditional approaches based on extraction from natural plant hosts, many challenges exist in the reconstruction of plant specialized metabolic pathways in microbial hosts. My laboratory has developed approaches to address the challenges that arise in the reconstruction of complex biosynthesis schemes, including spatial engineering strategies to direct the activities and specificities of pathway enzymes and recoding strategies to address folding, processing, and stability issues that may arise with the expression of plant enzymes in heterologous microbial hosts. We have utilized these strategies to develop yeast-based production platforms for an important class of plant alkaloids, the benzylisoquinoline alkaloids, including the medicinal opioids. These synthetic biology platforms will lead to transformative advances in natural product discovery, drug development, and production.
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WU iGEM Team wins gold at international competition

WU iGEM Team wins gold at international competition | SynBioFromLeukipposInstitute | Scoop.it
Washington University’s genetic-engineering undergraduate research team won a gold medal at the international iGEM Giant Jamboree competition in Boston, held
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CRIPSR-Cas expands dynamic range of gene expression from T7RNAP promoters

Abstract
BACKGROUND:
Reducing leaky gene expression is critical for improving protein yield of recombinant bacteria and stability of engineered cellular circuits in synthetic biology. Leaky gene expression occurs when a genetic promoter is not fully repressed, leading to unintended protein synthesis in the absence of stimuli. Existing work has devised specific molecular strategies for reducing leaky gene expression of each promoter. Main Method and Results: In contrast, we describe a repurposed, modular CRISPRi system that attenuates leaky gene expression using a series of single-guide RNAs targeting the PT7/LacO1 . Furthermore, we demonstrate the efficacy of CRISPRi to significantly increase the dynamic range of T7 RNA Polymerase (T7RNAP) promoters. In addition, we demonstrate that the CRISPRi system can be applied to enhance growth of bacteria that suffer from leaky expression of a toxic protein.
CONCLUSIONS AND IMPLICATIONS:
Our work establishes a new application of CRISPRi in genomic engineering to improve the control of recombinant gene expression. The approach is potentially generalizable to other gene expression system by changing the single-guide RNAs.
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Discovery and design of self-assembling peptides

eptides are ubiquitous in nature and useful in many fields, from agriculture as pesticides, in medicine as antibacterial and antifungal drugs founded in the innate immune systems, to medicinal chemistry as hormones. However, the concept of peptides as materials was not recognized until 1990 when a self-assembling peptide as a repeating segment in a yeast protein was serendipitously discovered. Peptide materials are so called because they have bona fide materials property and are made from simple amino acids with well-ordered nanostructures under physiological conditions. These structures include well-ordered nanofibres, nanotubes and nanovesicles. These peptide materials have been used for: (i) three-dimensional tissue cell cultures of primary cells and stem cells, (ii) three-dimensional tissue printing, (iii) sustained releases of small molecules, growth factors, monoclonal antibody and siRNA, (iv) accelerated wound healing in reparative and regenerative medicine as well as tissue engineering, (v) used to stabilize membrane proteins including difficult G-protein coupled receptors and photosystem I for designing nanobiodevices, (vi) a few self-assembling peptides have been used in human clinical trials for accelerated wound healings in surgical uses and (vii) in human clinical trials for siRNA delivery for treatment of cancers. It is likely that these self-assembling peptides will open doors for more and more diverse uses. The field of self-assembling peptides is growing in a number of directions in areas of materials, synthetic biology, and clinical medicine and beyond.
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Scientists invent new way of folding and protecting recombinant proteins

Scientists invent new way of folding and protecting recombinant proteins | SynBioFromLeukipposInstitute | Scoop.it
November 13, 2017 A team from the NUS Yong Loo Lin School of Medicine (NUS Medicine) has invented a fundamentally new way of folding and protecting recombinant proteins. Sourced from the rapidly expanding field of synthetic biology, this protein-in-a-protein technology can improve functional...
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RNA-based dynamic genetic controllers: development strategies and applications

Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.
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CRISPR Can Now Edit Genes Using Nanoparticles Instead of Viruses

CRISPR Can Now Edit Genes Using Nanoparticles Instead of Viruses | SynBioFromLeukipposInstitute | Scoop.it
The new delivery mechanism completely turned off a gene responsible for high cholesterol in mice.
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Zipping DNA

Zipping DNA | SynBioFromLeukipposInstitute | Scoop.it
ETH researchers have developed a method that allows large amounts of genetic information to be compressed and then decompressed again in cells. This could aid in the development of new therapies.
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Researchers fold a protein within a protein

Researchers fold a protein within a protein | SynBioFromLeukipposInstitute | Scoop.it
A team from the NUS Yong Loo Lin School of Medicine (NUS Medicine) has invented a fundamentally new way of folding and protecting recombinant proteins. Sourced from the rapidly expanding field of synthetic biology, this protein-in-a-protei
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A New Method for the 3-D Printing of Living Tissues

The approach could revolutionize regenerative medicine
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