scholarly journals Barcoding biological reactions with DNA-functionalized vesicles

2019 ◽  
Author(s):  
Justin A. Peruzzi ◽  
Miranda L. Jacobs ◽  
Timothy Q. Vu ◽  
Neha P. Kamat
Keyword(s):  
Temporal Dynamics ◽  
Phase Segregation ◽  
Vesicle Fusion ◽  
Cellular Systems ◽  
Membrane Phase ◽  
Aqueous Environments ◽  
New Strategy ◽  
Spatio Temporal ◽  
Direct Fusion

AbstractTargeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase-segregated membranes, promote fusion between specific vesicle populations. We show that membrane phase-segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA-mediated fusion events. Using this system, we show that orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. We then demonstrate that vesicle fusion between DNA-tethered vesicles can be used to initiatein vitroprotein expression that leads to the synthesis of model soluble and membrane proteins. The ability to engineer orthogonal fusion events between DNA-tethered vesicles will provide a new strategy to control the spatio-temporal dynamics of cell-free reactions, expanding opportunities to engineer artificial cellular systems.

scholarly journals Role of β-Catenin Activation Levels and Fluctuations in Controlling Cell Fate

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 176 ◽  
Author(s):  
Elisa Pedone ◽  
Lucia Marucci
Keyword(s):  
Signaling Pathway ◽  
Cell Fate ◽  
Temporal Dynamics ◽  
Cellular Systems ◽  
Future Research ◽  
Somatic Cell Reprogramming ◽  
Development In Vitro ◽  
Pluripotency Maintenance

Cells have developed numerous adaptation mechanisms to external cues by controlling signaling-pathway activity, both qualitatively and quantitatively. The Wnt/β-catenin pathway is a highly conserved signaling pathway involved in many biological processes, including cell proliferation, differentiation, somatic cell reprogramming, development, and cancer. The activity of the Wnt/β-catenin pathway and the temporal dynamics of its effector β-catenin are tightly controlled by complex regulations. The latter encompass feedback loops within the pathway (e.g., a negative feedback loop involving Axin2, a β-catenin transcriptional target) and crosstalk interactions with other signaling pathways. Here, we provide a review shedding light on the coupling between Wnt/β-catenin activation levels and fluctuations across processes and cellular systems; in particular, we focus on development, in vitro pluripotency maintenance, and cancer. Possible mechanisms originating Wnt/β-catenin dynamic behaviors and consequently driving different cellular responses are also reviewed, and new avenues for future research are suggested.

The relationship between histone H3 phosphorylation and acetylation throughout the mammalian cell cycleThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 640-657 ◽  
Author(s):  
Kirk J. McManus ◽  
Michael J. Hendzel
Keyword(s):  
Cell Cycle ◽  
Temporal Dynamics ◽  
Peer Review Process ◽  
Histone H3 ◽  
Specific Cell ◽  
Cell Cycle Time ◽  
Post Translational Modifications ◽  
Amino Terminal ◽  
Spatio Temporal

During interphase, histone amino-terminal tails play important roles in regulating the extent of DNA compaction. Post-translational modifications of the histone tails are intimately associated with regulating chromatin structure: phosphorylation of histone H3 is associated with proper chromosome condensation and dynamics during mitosis, while multiple H2B, H3, and H4 tail acetylations destabilize the chromatin fiber and are sufficient to decondense chromatin fibers in vitro. In this study, we investigate the spatio-temporal dynamics of specific histone H3 phosphorylations and acetylations to better understand the interplay of these post-translational modifications throughout the cell cycle. Using a panel of antibodies that individually, or in combination, recognize phosphorylated serines 10 and 28 and acetylated lysines 9 and 14, we define a series of changes associated with histone H3 that occur as cells progress through the cell cycle. Our results establish that mitosis appears to be a period of the cell cycle when many modifications are highly dynamic. Furthermore, they suggest that the upstream histone acetyltransferases/deacetylases and kinase/phosphatases are temporally regulated to alter their function globally during specific cell cycle time points.

scholarly journals Spontaneous activity emerging from an inferred network model captures complex spatio-temporal dynamics of spike data

2018 ◽  
Author(s):  
Cristiano Capone ◽  
Guido Gigante ◽  
Paolo De Giudice
Keyword(s):  
Spontaneous Activity ◽  
Information Transfer ◽  
Temporal Dynamics ◽  
Model Neuron ◽  
External Noise ◽  
Fine Grained ◽  
Spatio Temporal ◽  
Generative Mechanism ◽  
Effective Models

ABSTRACTInference methods are widely used to recover effective models from observed data. However, few studies attempted to investigate the dynamics of inferred models in neuroscience, and none, to our knowledge, at the network level. We introduce a principled modification of a widely used generalized linear model (GLM), and learn its structural and dynamic parameters from in-vitro spike data. The spontaneous activity of the new model captures prominent features of the non-stationary and non-linear dynamics displayed by the biological network, where the reference GLM largely fails, and also reflects fine-grained spatio-temporal dynamical features. Two ingredients were key for success. The first is a saturating transfer function: beyond its biological plausibility, it limits the neurons information transfer, improving robustness against endogenous and external noise. The second is a super-Poisson spikes generative mechanism; it accounts for the undersampling of the network, and allows the model neuron to flexibly incorporate the observed activity fluctuations.

SPATIO-TEMPORAL DYNAMICS OF BLOOD COAGULATION AND PATTERN FORMATION: AN EXPERIMENTAL STUDY

2002 ◽  
Vol 12 (09) ◽  
pp. 1969-1983 ◽  
Author(s):  
F. I. ATAULLAKHANOV ◽  
YU. V. KRASOTKINA ◽  
V. I. SARBASH ◽  
R. I. VOLKOVA ◽  
E. I. SINAURIDSE ◽  
...  
Keyword(s):  
Experimental Study ◽  
Pattern Formation ◽  
Blood Coagulation ◽  
Temporal Dynamics ◽  
Inhibition Zone ◽  
Excitable Medium ◽  
Experimental Results ◽  
New Type ◽  
Spatio Temporal

We examined the dynamics of clot growth in vitro and found, that initially the clot grows at a constant speed, then abruptly stops and becomes surrounded by an "inhibition zone" in which coagulation is strongly suppressed. We also observed formation of "stratified structures" (target patterns) in which solid layers alternate with liquid blood. The experimental results strongly support a hypothesis that blood is a new type of excitable medium.

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

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