Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging

Gilad, Assaf A.; Shapiro, Mikhail G.

doi:10.1007/s11307-017-1062-1

Cited by 30 publications

(22 citation statements)

References 77 publications

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“…In addition, as the first genetically encodable contrast agents for ultrasound and hyperpolarized xenon MRI, they offer the possibility of being developed as reporter genes 16 , creating new opportunities for non-invasive imaging at the molecular and cellular level.…”

Section: Introductionmentioning

confidence: 99%

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI

et al. 2017

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Gas vesicles are a unique class of gas-filled protein nanostructures whose physical properties allow them to serve as highly sensitive imaging agents for ultrasound and magnetic resonance imaging (MRI), detectable at sub-nanomolar concentrations. Here we provide a protocol for isolating gas vesicles from native and heterologous host organisms, functionalizing these nanostructures with moieties for targeting and fluorescence, characterizing their biophysical properties and imaging them using ultrasound and magnetic resonance imaging. Gas vesicles can be isolated from natural cyanobacterial and haloarchaeal host organisms or from E. coli expressing a heterologous gas vesicle gene cluster, and purified using buoyancy-assisted techniques. They can then be modified by replacing surface-bound proteins with engineered, heterologously expressed variants, or through chemical conjugation, resulting in altered mechanical, surface and targeting properties. Pressurized absorbance spectroscopy is used to characterize their mechanical properties, while dynamic light scattering and transmission electron microscopy are used to determine nanoparticle size and morphology, respectively. Gas vesicles can then be imaged with ultrasound in vitro and in vivo using pulse sequences optimized for their detection versus background. They can also be imaged with hyperpolarized xenon MRI using chemical exchange saturation transfer between gas vesicle-bound and dissolved xenon – a technique currently implemented in vitro. Taking 3–8 days to prepare, these genetically encodable nanostructures enable multi-modal, noninvasive biological imaging with high sensitivity and potential for molecular targeting.

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Section: Introductionmentioning

confidence: 99%

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI

et al. 2017

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“…From this standpoint, new reporter proteins such as aquaporins and gas vesicles could serve as the basis for developing biomolecular sensors by leveraging tools and principles of protein engineering and synthetic biology [109], as has been done with T 1 , T 2 and CEST-based sensors [9, 18, 32]. In addition, a new mechanism for modulating MRI contrast, called MRET [110], may provide another avenue towards dynamic MRI sensors analogous to optical reporters based on Förster resonance energy transfer (FRET).…”

Section: Discussionmentioning

confidence: 99%

Biomolecular MRI reporters: Evolution of new mechanisms

Mukherjee

Davis

Ramesh

et al. 2017

Progress in Nuclear Magnetic Resonance Spectroscopy

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Magnetic resonance imaging (MRI) is a powerful technique for observing the function of specific cells and molecules inside living organisms. However, compared to optical microscopy, in which fluorescent protein reporters are available to visualize hundreds of cellular functions ranging from gene expression and chemical signaling to biomechanics, to date relatively few such reporters are available for MRI. Efforts to develop MRI-detectable biomolecules have mainly focused on proteins containing or transporting paramagnetic metals for T1 and T2 relaxation enhancement or large numbers of exchangeable protons for chemical exchange saturation transfer. While these pioneering developments established several key uses of biomolecular MRI, such as imaging of gene expression and functional biosensing, they also revealed that low molecular sensitivity poses a major challenge for broader adoption in biology and medicine. Recently, new classes of biomolecular reporters have been developed based on alternative contrast mechanisms, including enhancement of spin diffusivity, interactions with hyperpolarized nuclei, and modulation of blood flow. These novel reporters promise to improve sensitivity and enable new forms of multiplexed and functional imaging.

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“…Central to our system is the data model, which defines how the measurement data is organized and labelled (figure 2, table 1). The basic unit of data is the measurement, which typically consists of readout of fluorescent, luminescent or colorimetric reporter level, 40,41 and estimates of biomass or density. Each measurement refers to a particular sample at a specific time, and each sample is measured at multiple time points, possibly reading mul- Figure 2: Flapjack's data model.…”

Section: Data Modelmentioning

confidence: 99%

Flapjack: a data management and analysis tool for genetic circuit characterization

Feliu

Gomez

Berrocal

et al. 2020

Preprint

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Characterization is fundamental to the design, build, test, learn (DBTL) cycle for engineering synthetic genetic circuits. Components must be described in such a way as to account for their behavior in a range of contexts. Measurements and associated metadata, including part composition, constitute the test phase of the DBTL cycle. These data may consist of measurements of thousands of circuits, measured in hundreds of conditions, in multiple assays potentially performed in different labs and using different techniques. In order to inform the learn phase this large volume of data must be filtered, collated, and analyzed. Characterization consists of using this data to parameterize models of component function in different contexts, and combining them to predict behaviors of novel circuits. Tools to store, organize, share, and analyze large volumes of measurement and metadata are therefore essential to linking the test phase to the build and learn phases, closing the loop of the DBTL cycle. Here we present such a system, implemented as a web app with a backend data registry and analysis engine. An interactive frontend provides powerful querying, plotting and analysis tools, and we provide a REST API and Python package for full integration with external build and learn software. All measurements are associated to circuit part composition via SBOL. We demonstrate our tool by characterizing a range of genetic components and circuits according to composition and context.

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Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging

Cited by 30 publications

References 77 publications

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI

Biomolecular MRI reporters: Evolution of new mechanisms

Flapjack: a data management and analysis tool for genetic circuit characterization

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