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Synthetic Biology - Science topic

A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems.
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Publications related to Synthetic Biology (10,000)
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The immune system is capable of remarkably potent and specific efficacy against infectious diseases. For decades, investigators sought to leverage those characteristics to create immune-based therapies (immunotherapy) that might be far more effective and less toxic than conventional chemotherapy and radiation therapy for cancer. Those studies revea...
Article
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Site-specific recombination systems are widely used as bioengineering tools. However, the traditional site-specific recombination system requires a consensus sequence for the specific site. Such sequence-level constraints limit effective recombination between sites. Therefore, in order to develop an efficient site-specific recombination system, we...
Article
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Infectious clone technology is universally applied for biological characterization and engineering of viruses. This protocol describes procedures that implement synthetic biology advances for streamlined assembly of virus infectious clones. Here, I detail homology-based cloning using biological material, as well as SynViP assembly using type IIS re...
Article
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Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, t...
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Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working co...
Article
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In current years, natural pigments are facing a fast-growing global market due to the increase of people’s awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to t...
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The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency. An increasing number of plant species have been subjected to site-directed gene editing through this technology. However, the applic...
Article
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Objective MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli . The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we in...
Article
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Synthetic biology has boosted the rapid development on using non-methylotrophy as chassis for value added chemicals production from one-carbon feedstocks, such as methanol and formic acid. The one-carbon dissimilation pathway can provide more NADH than monosaccharides including glucose, which is conducive for reductive chemicals production, such as...
Article
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Nature has a vast array of biomineralization mechanisms. The commonly shared mechanism by many living organisms to form hardened tissues is the nucleation of mineral structures via proteins. Living materials, thanks to synthetic biology, are providing many opportunities to program cells for many functionalities. Here we have demonstrated a living m...
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Synthetic biology has played a key role in responding to the current pandemic. Biofoundries are critical synthetic biology infrastructure which should be available to all nations as a part of their independent bioengineering, biosecurity, and countermeasure response systems.
Preprint
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Predicting the dynamics of mutation spread in engineered cell populations is a sought-after goal in synthetic biology. Until now, models that capture these processes have been lacking, either by failing to account for the diversity of mutation types, or by failing to link the growth rate of a cell to the consumption of shared cellular resources by...
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Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research fields. With the aim to extend the biotechnological applications, the genetic tractability of the BC producers within the Komagataeibacter genus and its potential as an alternative host...
Article
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Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell‐free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supp...
Article
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New materials with a low environmental load are expected to be generated through synthetic biology. To widely utilize this technology, it is important to create cells with designed biological functions and to control the expression of multiple enzymes. In this study, we constructed a cell-free evaluation system for multiple protein expression, in w...
Preprint
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Synthetic biology holds immense promise to tackle key problems we are facing, for instance in resource use, environmental health, and human health care. However, comprehensive safety measures are needed to deploy genetically engineered microorganisms in open-environment applications. Here, we describe a genetic biocontainment system based on condit...
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Therapies with genetically modified T cells that express chimeric antigen receptors (CARs) specific for CD19 or B cell maturation antigen (BCMA) are approved to treat certain B cell malignancies. However, translating these successes into treatments for patients with solid tumours presents various challenges, including the risk of clinically serious...
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A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performan...
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Members of the phylum Actinomycetota (formerly Actinobacteria) have historically been the most prolific providers of small bioactive molecules. Although the genus Streptomyces is the best-known member for this issue, other genera, such as Gordonia, have shown interesting potential in their specialized metabolism. Thus, we combined herein the result...
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Synthetic biology tools have become increasingly prevalent as we look to nature for biological approaches to complex problems. With an ever-growing global population, issues of food safety and security, as well as addressing pollution and striving for sustainability are of the utmost importance. In this review, we first highlight synthetic biology...
Preprint
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Plant synthetic biology and genetic engineering depend on the controlled expression of transgenes of interest, which is relying heavily on the use of Agrobacterium-mediated transformation. Here we establish a novel split selectable marker system using protein splicing elements called "inteins" for Agrobacterium-mediated co-transformation in plants....
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There is an on-going demand in recent years for safer and “greener” hair coloring agents with the global consumer awareness of the adverse effects of synthetic hair dyes. The belief in sustainability and health benefits has focused the attention of the scientific community towards natural colorants that serve to replace their synthetic toxic counte...
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Cyanobacteria are of particular interest for chemical production as they can assimilate CO2 and use solar energy to power chemical synthesis. However, unlike the model microorganism of Escherichia coli, the availability of genetic toolboxes for rapid proof-of-concept studies in cyanobacteria is generally lacking. In this study, we first characteriz...
Article
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With the rapid development of synthetic biology, the production of 2′-fucosyllactose by biological fermentation gradually has the basis for industrialization. However, the lack of efficient downstream technology of biological fermentation, especially purification technology, has become the main factor limiting its commercialization. In this study,...
Article
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Artificial cells are developed to redesign novel biological functions in a programmable and tunable manner. Although it aims to reconstitute living cell features and address ‘origin of life' related questions, rapid development over the years has transformed artificial cells into an engineering tool with huge potential in applied biotechnology. Alt...
Article
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Heterologous gene activation causes non-physiological burden on cellular resources that cells are unable to adjust to. Here, we introduce a feedforward controller that actuates growth rate upon activation of a gene of interest (GOI) to compensate for such a burden. The controller achieves this by activating a modified SpoT enzyme (SpoTH) with sole...
Article
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Gram-positive bacteria are a nascent platform for synthetic biology and metabolic engineering that can provide new opportunities for the production of biomolecules. However, the lack of standardized methods and genetic parts is a major obstacle towards attaining the acceptance and widespread use of Gram-positive bacterial chassis for industrial bio...
Preprint
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General approaches for designing sequence-specific peptide binding proteins would have wide utility in proteomics and synthetic biology. Although considerable progress has been made in designing proteins which bind to other proteins, the general peptide binding problem is more challenging as most peptides do not have defined structures in isolation...
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While science is mandated for discovering "life", we are engaged in the 'chemistry-as-life' or 'physics-as-life' paradigm with machine-metaphor everywhere! The whole explanation of photosynthesis by plants and quorum sensing in the bacterial colony is based on chemistry and physics. The focus is on signal-based automated molecular robots directed b...
Preprint
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Fashion industry is the second most polluting industry in the world representing a 2 trillion dollars and growing valuation (Pal, 2017). This dual context makes its challenges hard to address. From one side, fashion design education and practice systems have been perpetuating an industrial-focused approach which relies mostly in the economic improv...
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Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their hig...
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Background Natural life systems can be significantly modified at the genomic scale by human intervention, demonstrating the great innovation capacity of genome engineering. Large epi-chromosomal DNA structures were established in Escherichia coli cells, but some of these methods were inconvenient, using heterologous systems, or relied on engineered...
Preprint
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NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms are unique in treating complex and test tube ensembles containing arb...
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Recent studies have shown that the reconstituted cell-free DNA replisome and in vitro transcription and translation systems from Escherichia coli are highly important in applied and synthetic biology. To date, no attempt has been made to combine those two systems. Here, we study the performance of the mixed two separately exploited systems commerci...
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Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. Here, we s...
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The in-depth study of fungal secondary metabolites (SMs) over the past few years has led to the discovery of a vast number of novel fungal SMs, some of which possess good biological activity. However, because of the limitations of the traditional natural product mining methods, the discovery of new SMs has become increasingly difficult. In recent y...
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Post-secondary education is falling behind in delivering the talent and skills development needed to support the growth of biology-based economies and the demands of professional and research-based graduate degree programs. Here, we describe an applied research program, the BioExperience Research and Entrepreneurship Challenge, launched in May 2020...
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Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide...
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Ganoderma sinense, with more than 2000 years of medicinal history, is a fungus of the basidiomycetes that is rich in polysaccharides and terpenoids. However, the biosynthesis of terpenes, especially sesquiterpenes, has been little studied. The functional identification of sesquiterpene synthases from G. sinense is of great significance to the study...
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Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants i...
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The delivery of colloidal particles in dead-end microstructures is very challenging, since these geometries do not allow net flows of particle-laden fluids; meanwhile, diffusive transport is slow and inefficient. Recently, we introduced a novel particle manipulation strategy, based on diffusiophoresis, whereby the salt concentration gradient betwee...
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Polysaccharides synthesized by microorganisms (bacterial cellulose, dextran, pullulan, xanthan, etc.) have a set of valuable properties, such as being antioxidants, detoxifying, structuring, being biodegradable, etc., which makes them suitable for a variety of applications. Biocatalysts are the key substances used in producing such polysaccharides;...
Conference Paper
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Background Tumor-infiltrating lymphocyte (TIL) therapy can mediate tumor regression in a range of solid cancers, most notably in melanoma. However, its wider application and efficacy has been limited by the low frequency and exhausted phenotype of tumor-specific T cells in the final product. Here, we developed a personalized, neoantigen-specific TC...
Preprint
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Chemical inducer of dimerization (CID) modules can be used effectively as molecular switches to control biological processes, and thus there is significant interest within the synthetic biology community in identifying novel CID systems. To date, CID modules have been used primarily in engineering cells for in vitro applications. To broaden their u...
Article
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The ability to externally control gene expression has been paradigm shifting for all areas of biological research, especially for synthetic biology. Such control typically occurs at the transcriptional and translational level, while technologies enabling control at the DNA copy level are limited by either (i) relying on a handful of plasmids with f...
Article
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Background Ginsenosides are Panax plant-derived triterpenoid with wide applications in cardiovascular protection and immunity-boosting. However, the saponins content of Panax plants is fairly low, making it time-consuming and unsustainable by direct extraction. Protopanaxadiol (PPD) is a common precursor of dammarane-type saponins, and its sufficie...
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Yeasts are increasingly employed in synthetic biology as chassis strains, including conventional and non-conventional species. It is still unclear how genomic evolution determines metabolic diversity among various yeast species and strains. In this study, we constructed draft GEMs for 332 yeast species using two alternative procedures from the tool...
Preprint
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Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as potential inputs to biotechnological processes. We previously demonstrated that activation of the galactose (GAL...
Article
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Bacillus genetics need more versatile promoters for gene circuit engineering. UP elements are widely distributed in noncoding regions and interact with the α-subunit of RNA polymerase (RNAP). They can be applied as a standard element for synthetic biology. Characterization of the binding motif between UP elements and RNAP may assist with rational a...
Article
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Real-time chemical sensing is crucial for applications in environmental and health monitoring¹. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal2–4. However, the process of protein expression limits the speed of this sen...
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Bottom-up synthetic biology provides new means to understand living matter by constructing minimal life-like systems. This principle can also be applied to study infectious diseases. Here we summarize approaches and ethical considerations for the bottom-up assembly of viral replication cycles. Synthetic biology encompasses engineering approaches to...
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Microbiota-derived metabolites have biological importance for their host. Spermidine, a metabolite described for its protective effect in age-related diseases, is now studied for its role in the resolution of inflammation and gut homeostasis. Strategies to modulate its production in the gastrointestinal tract are of interest to increase host spermi...
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Natural products have multifarious bioactivities against bacteria, fungi, viruses, cancers and other diseases due to their diverse structures. Nearly 65% of anticancer drugs are natural products or their derivatives. Thus, natural products play significant roles in clinical cancer therapy. With the development of biosynthetic technologies, an incre...
Article
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Circular bacteriocins are antimicrobial peptides produced by bacteria that after synthesis undergo a head-to-tail circularization. Compared to their linear counterparts, circular bacteriocins are, in general, very stable to temperature and pH changes and more resistant to proteolytic enzymes, being considered as one of the most promising groups of...
Article
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In synthetic biology, small molecules are commonly used for altering gene expression through the (in)activation of gene switches. Current switches, however, have a narrow species range, are non-titratable, or use non-inert inducers which evoke important side effects. Universal gene switches (XRs) that have dynamic ranges without interference with t...