scholarly journals Spatio-temporal patterning of living cells with extracellular DNA programs

Author(s):  
Marc Van Der Hofstadt ◽  
Jean-Christophe Galas ◽  
André Estevez-Torres

AbstractReactive extracellular media focus on engineering reaction networks outside the cell to control intracellular chemical composition across time and space. However, current implementations lack the feedback loops and out-of-equilibrium molecular dynamics for encoding spatio-temporal control. Here, we demonstrate that enzyme-DNA molecular programs combining these qualities are functional in an extracellular medium where human cells can grow. With this approach, we construct an internalization program that delivers fluorescent DNA inside living cells and remains functional for at least 48 h. Its non-equilibrium dynamics allows us to control both the time and position of cell internalization. In particular, a spatially inhomogeneous version of this program generates a tunable reaction-diffusion two-band pattern of cell internalization. This demonstrates that a synthetic extracellular program can provide temporal and positional information to living cells, emulating archetypal mechanisms observed during embryo development. We foresee that non-equilibrium reactive extracellular media could be advantageously applied to in vitro biomolecular tracking, tissue engineering or smart bandages.

2012 ◽  
Vol 100 (4) ◽  
pp. 46004 ◽  
Author(s):  
M. Marcuzzi ◽  
A. Gambassi ◽  
M. Pleimling

2018 ◽  
Author(s):  
Mukul Tewary ◽  
Dominika Dziedzicka ◽  
Joel Ostblom ◽  
Laura Prochazka ◽  
Nika Shakiba ◽  
...  

AbstractIn vitro models of post-implantation human development are valuable to the fields of regenerative medicine and developmental biology. Here, we report characterization of a robust in vitro platform that enabled high-content screening of multiple human pluripotent stem cell (hPSC) lines for their ability to undergo peri-gastrulation-like fate patterning upon BMP4 treatment of geometrically-confined colonies and observed significant heterogeneity in their differentiation propensities along a gastrulation associable and neuralization associable axis. This cell line associated heterogeneity was found to be attributable to endogenous nodal expression, with upregulation of Nodal correlated with expression of a gastrulation-associated gene profile, and Nodal downregulation correlated with a neurulation-associated gene profile expression. We harness this knowledge to establish a platform of pre-neurulation-like fate patterning in geometrically confined hPSC colonies that arises due to a stepwise activation of reaction-diffusion and positional-information. Our work identifies a Nodal signalling dependent switch in peri-gastrulation versus pre-neurulation-associated fate patterning in hPSC cells, provides a technology to robustly assay hPSC differentiation outcomes, and suggests conserved mechanisms of self-organized fate specification in differentiating epiblast and ectodermal tissues.


2017 ◽  
Author(s):  
Niccoló Parenti ◽  
Ambra Del Grosso ◽  
Claudia Antoni ◽  
Marco Cecchini ◽  
Renato Corradetti ◽  
...  

It is now widely accepted that oligomers consisting of Aβ peptide are the cytotoxic species contributing mostly to the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro. By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal, respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β-secretase BACE1 fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP.


2017 ◽  
Author(s):  
Niccoló Parenti ◽  
Ambra Del Grosso ◽  
Claudia Antoni ◽  
Marco Cecchini ◽  
Renato Corradetti ◽  
...  

It is now widely accepted that oligomers consisting of Aβ peptide are the cytotoxic species contributing mostly to the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro. By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal, respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β-secretase BACE1 fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP.


2019 ◽  
Author(s):  
Matthew J. Varga ◽  
Spencer Loggia ◽  
Yiben Fu ◽  
Osman N Yogurtcu ◽  
Margaret E. Johnson

AbstractCurrently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular models cannot capture minutes-long cellular dynamics that couple distinct components with active processes, while reaction-diffusion models lack sufficient detail for capturing assembly structures. Here we introduce the Non-Equilibrium Reaction-Diffusion Self-assembly Simulator (NERDSS), which addresses this gap by integrating a structure-resolved reaction-diffusion algorithm with rule-based model construction. By representing proteins as rigid, multi-site molecules that adopt well-defined orientations upon binding, NERDSS simulates formation of large reversible structures with sites that can be acted on by reaction rules. We show how NERDSS allows for directly comparing and optimizing models of multi-component assembly against time-dependent experimental data. Applying NERDSS to assembly steps in clathrin-mediated endocytosis, we capture how the formation of clathrin caged structures can be driven by modulating the strength of clathrin-clathrin interactions, by adding cooperativity, or by localizing clathrin to the membrane. NERDSS further predicts how clathrin lattice disassembly can be driven by enzymes that irreversibly change lipid populations on the membrane. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the wide usability and adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.


PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3086 ◽  
Author(s):  
Niccoló Parenti ◽  
Ambra Del Grosso ◽  
Claudia Antoni ◽  
Marco Cecchini ◽  
Renato Corradetti ◽  
...  

Alzheimer’s disease is a multifactorial disorder caused by the interaction of genetic, epigenetic and environmental factors. The formation of cytotoxic oligomers consisting of Aβ peptide is widely accepted as being one of the main key events triggering the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro. By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal (mChAPPmGFP), respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β-secretase BACE1, or the α-secretase ADAM10, fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. In order to allow the discrimination between the α- and the β-secretase activity, we have created a variant of mChAPPmGFP with a mutation that inhibits the α-secretase cleavage without perturbing the β-secretase processing. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP.


2021 ◽  
Author(s):  
Lijuan Liu ◽  
Shengting Zhang ◽  
Xiaodan Zheng ◽  
Hongmei Li ◽  
Qi Chen ◽  
...  

Fusobacterium nucleatum has been employed for the first time to synthesize fluorescent carbon dots which could be applied for the determination of Fe3+ ions in living cells and bioimaging in vitro and in vivo with excellent biocompatibility.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marco Baity-Jesi ◽  
Enrico Calore ◽  
Andrés Cruz ◽  
Luis Antonio Fernandez ◽  
José Miguel Gil-Narvion ◽  
...  

AbstractExperiments featuring non-equilibrium glassy dynamics under temperature changes still await interpretation. There is a widespread feeling that temperature chaos (an extreme sensitivity of the glass to temperature changes) should play a major role but, up to now, this phenomenon has been investigated solely under equilibrium conditions. In fact, the very existence of a chaotic effect in the non-equilibrium dynamics is yet to be established. In this article, we tackle this problem through a large simulation of the 3D Edwards-Anderson model, carried out on the Janus II supercomputer. We find a dynamic effect that closely parallels equilibrium temperature chaos. This dynamic temperature-chaos effect is spatially heterogeneous to a large degree and turns out to be controlled by the spin-glass coherence length ξ. Indeed, an emerging length-scale ξ* rules the crossover from weak (at ξ ≪ ξ*) to strong chaos (ξ ≫ ξ*). Extrapolations of ξ* to relevant experimental conditions are provided.


2021 ◽  
pp. 129929
Author(s):  
Francisco Fueyo-González ◽  
Rosario Herranz ◽  
Simona Plesselova ◽  
Maria D. Giron ◽  
Rafael Salto ◽  
...  
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