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Trending Papers in synthetic biology

A synthetic DNA gene therapy injected into a specific tissue can mitigate symptoms of autoimmune diseases
From Paper: Synthetic DNA Delivery of an Engineered Arginase Enzyme Can Modulate Specific Immunity In Vivo
Published: Jun 2020
  • Pretreatment of animals with the synthetic DNA-encoded arginase led to significant decreases in skin acanthosis, proinflammatory cytokines, and costimulatory molecules in extracted macrophages and dendritic cells
  • Significant in vivo immunosuppression was observed in the presence of DNA-encoded arginase
Submitted by Will McBurnie
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Programmable protein circuits in living cells
  • The authors demonstrate Boolean logic using their CHOMP circuits
  • Viral proteases are highly specific for short cognate sites and there is wide natural diversity - the authors focused on tobacco etch virus protease (TEVP) and related proteases to build a complex protein circuit in HEK293 cells
Submitted by Arye Lipman
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Engineering Stem Cell Self-organization to Build Better Organoids
Published: Jun 2019
  • Four areas of focus are needed to generate better organoids: 1) controlling initial culture conditions 2) directing symmetry breaking 3) imposing boundary conditions to guide cellular self-patterning 4) rationally engineered scale-up
  • Self organization can be engineered by spatiotemporally controlling cell to cell and cell to extra-cellular matrix interaction - this should allow better in vitro organogenesis
Submitted by Arye Lipman
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A novel protocol for transforming skin cells into cells that make up the human retina in order to treat diseases like macular degeneration
From Paper: Inducing Human Retinal Pigment Epithelium-like Cells from Somatic Tissue
Woogeng, Ivo Ngundu, et al
Published: Jul 2020
  • The authors anticipate that their system may enable robust retinal cell induction for regenerative medicine research and affordable autologous human RPE tissue for cell therapy
  • iRPE cells showed features of modern RPE benchmarks and significant in-vivo integration in transplanted chimeric hosts
Submitted by Patrick Joyce
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Plant Synthetic Biology: Quantifying the “Known Unknowns” and Discovering the “Unknown Unknowns”
Jennifer Nemhauser
  • This paper reviews this state of the art in measuring plant signaling, using principles and tools borrowed from and inspired by engineering, as well as efforts to use this knowledge to enable rapid, rational re-engineering of plant development.
  • Sensitive, genetically encoded reporters (biosensors), in combination with emerging single-cell transcriptomics approaches, are providing increasingly detailed molecular descriptions of cells undergoing developmental transitions
Submitted by Patrick Joyce
A novel technique allows for blue-light dependent gene expression, which will give scientists unprecedented spatial and temporal control of gene expression in animal studies
From Paper: A monogenic and fast-responding Light-Inducible Cre recombinase as a novel optogenetic switch
  • Compared to other light-inducible Cre recombinases, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark
  • This paper reports the development of LiCre, a novel light-inducible Cre recombinase - that allows for toggleable gene expression only in tissues actively exposed to blue light
Submitted by Patrick Joyce
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Simulate gold crystals in a way compatible with proteins
From Paper: GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
Published: Jan 2013
Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolPCHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field,compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and firstprinciples data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem. 2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp2 hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett. 2004, 92, 246401−1. Thonhauser, T.; et al. Phys. Rev. B 2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings.
Submitted by Robert Rhinehart
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Fighting aging with light-controlled gene expression of gut bacteria in C. elegans
From Paper: Optogenetic control of gut bacterial metabolism to promote longevity
The gut microbiota has been strongly implicated to play a role in the rate of aging. This paper describes an optogenetic method to fine-tune gene-expression of gut bacteria in C. elegans
Submitted by Patrick Joyce
Synthetic genetic circuits with expression that can be fine-tuned based on environmental variables
From Paper: Tunable genetic devices through simultaneous control of transcription and translation
Published: Jul 2019
  • This paper describes a tunable expression system (TES) that is able to modulate input sensor sensitivity between 4.5-28 fold
  • A genetic circuit with separate promoters controlling transcription and translation allow for dynamic tuning of genetic circuits after their construction
Submitted by Patrick Joyce
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Plasmid vectors that result in persistent transferred gene expression in mammals
From Paper: Minicircle DNA vectors devoid of bacterial DNA result in persistent and high-level transgene expression in vivo
Published: Jul 2003
  • Minicircles hold great promise as a tool for gene therapy applications in humans
  • Minicircle vectors resulted in effective and persistent (120d +) expression of human genes when injected into mice
Submitted by Tristan Roberts
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