scholarly journals Towards the rational design of synthetic cells with prescribed population dynamics

2012 ◽  
Vol 9 (76) ◽  
pp. 2883-2898 ◽  
Author(s):  
Neil Dalchau ◽  
Matthew J. Smith ◽  
Samuel Martin ◽  
James R. Brown ◽  
Stephen Emmott ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Design Process ◽  
Rational Design ◽  
Spatial Scales ◽  
Travelling Waves ◽  
Implementation Strategies ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Spatio Temporal ◽  
High Level

The rational design of synthetic cell populations with prescribed behaviours is a long-standing goal of synthetic biology, with the potential to greatly accelerate the development of biotechnological applications in areas ranging from medical research to energy production. Achieving this goal requires well-characterized components, modular implementation strategies, simulation across temporal and spatial scales and automatic compilation of high-level designs to low-level genetic parts that function reliably inside cells. Many of these steps are incomplete or only partially understood, and methods for integrating them within a common design framework have yet to be developed. Here, we address these challenges by developing a prototype framework for designing synthetic cells with prescribed population dynamics. We extend the genetic engineering of cells (GEC) language, originally developed for programming intracellular dynamics, with cell population factors such as cell growth, division and dormancy, together with spatio-temporal simulation methods. As a case study, we use our framework to design synthetic cells with predator–prey interactions that, when simulated, produce complex spatio-temporal behaviours such as travelling waves and spatio-temporal chaos. An analysis of our design reveals that environmental factors such as density-dependent dormancy and reduced extracellular space destabilize the population dynamics and increase the range of genetic variants for which complex spatio-temporal behaviours are possible. Our findings highlight the importance of considering such factors during the design process. We then use our analysis of population dynamics to inform the selection of genetic parts, which could be used to obtain the desired spatio-temporal behaviours. By identifying, integrating and automating key stages of the design process, we provide a computational framework for designing synthetic systems, which could be tested in future laboratory studies.

scholarly journals Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wiggert J. Altenburg ◽  
N. Amy Yewdall ◽  
Daan F. M. Vervoort ◽  
Marleen H. M. E. van Stevendaal ◽  
Alexander F. Mason ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Nitrilotriacetic Acid ◽  
Binding Motif ◽  
Biologically Relevant ◽  
Enzyme Cascade ◽  
Synthetic Cell ◽  
Synthetic Cells ◽  
Membrane Bound ◽  
High Concentrations ◽  
High Level

AbstractThe cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately emulate this environment. Herein, we describe the development of a discrete, membrane-bound coacervate-based protocellular platform that utilizes the well-known binding motif between Ni2+-nitrilotriacetic acid and His-tagged proteins to exercise a high level of control over the loading of biologically relevant macromolecules. This platform can accrete proteins in a controlled, efficient, and benign manner, culminating in the enhancement of an encapsulated two-enzyme cascade and protease-mediated cargo secretion, highlighting the potency of this methodology. This versatile approach for programmed spatial organization of biologically relevant proteins expands the protocellular toolbox, and paves the way for the development of the next generation of complex yet well-regulated synthetic cells.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

scholarly journals Analysis of 220 Years of Floodplain Population Dynamics in the US at Different Spatial Scales

Water ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 141
Author(s):  
Firoza Akhter ◽  
Maurizio Mazzoleni ◽  
Luigia Brandimarte
Keyword(s):  
Population Dynamics ◽  
Large Scale ◽  
Spatial Scales ◽  
National Level ◽  
State Level ◽  
Economic Activities ◽  
Protection Measures ◽  
Management Planning ◽  
The Us ◽  
Over Time

In this study, we explore the long-term trends of floodplain population dynamics at different spatial scales in the contiguous United States (U.S.). We exploit different types of datasets from 1790–2010—i.e., decadal spatial distribution for the population density in the US, global floodplains dataset, large-scale data of flood occurrence and damage, and structural and nonstructural flood protection measures for the US. At the national level, we found that the population initially settled down within the floodplains and then spread across its territory over time. At the state level, we observed that flood damages and national protection measures might have contributed to a learning effect, which in turn, shaped the floodplain population dynamics over time. Finally, at the county level, other socio-economic factors such as local flood insurances, economic activities, and socio-political context may predominantly influence the dynamics. Our study shows that different influencing factors affect floodplain population dynamics at different spatial scales. These facts are crucial for a reliable development and implementation of flood risk management planning.

scholarly journals Increasing frequency of low summer precipitation synchronizes dynamics and compromises metapopulation stability in the Glanville fritillary butterfly

2015 ◽  
Vol 282 (1806) ◽  
pp. 20150173 ◽  
Author(s):  
Ayco J. M. Tack ◽  
Tommi Mononen ◽  
Ilkka Hanski
Keyword(s):  
Population Dynamics ◽  
Population Change ◽  
Temporal Dynamics ◽  
Summer Precipitation ◽  
Life History Stage ◽  
General Effect ◽  
Spatial Synchrony ◽  
Glanville Fritillary Butterfly ◽  
Spatio Temporal

Climate change is known to shift species' geographical ranges, phenologies and abundances, but less is known about other population dynamic consequences. Here, we analyse spatio-temporal dynamics of the Glanville fritillary butterfly ( Melitaea cinxia ) in a network of 4000 dry meadows during 21 years. The results demonstrate two strong, related patterns: the amplitude of year-to-year fluctuations in the size of the metapopulation as a whole has increased, though there is no long-term trend in average abundance; and there is a highly significant increase in the level of spatial synchrony in population dynamics. The increased synchrony cannot be explained by increasing within-year spatial correlation in precipitation, the key environmental driver of population change, or in per capita growth rate. On the other hand, the frequency of drought during a critical life-history stage (early larval instars) has increased over the years, which is sufficient to explain the increasing amplitude and the expanding spatial synchrony in metapopulation dynamics. Increased spatial synchrony has the general effect of reducing long-term metapopulation viability even if there is no change in average metapopulation size. This study demonstrates how temporal changes in weather conditions can lead to striking changes in spatio-temporal population dynamics.

scholarly journals Spatio-Temporal Dynamic Architecture of Living Brush Mattress: Root System and Soil Shear Strength in Riverbanks

Forests ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 493 ◽  
Author(s):  
Dong Zhang ◽  
Jinhua Cheng ◽  
Ying Liu ◽  
Hongjiang Zhang ◽  
Lan Ma ◽  
...  
Keyword(s):  
Shear Strength ◽  
Root Morphology ◽  
Spatial Scales ◽  
Root Diameter ◽  
Slope Position ◽  
Protective Effects ◽  
Salix Alba ◽  
Ecological Protection ◽  
Soil Shear Strength ◽  
Spatio Temporal

As a basal measure of soil bioengineering, the living brush mattress has been widely applied in riparian ecological protection forest construction. The living brush mattress shows favorable protective effects on riverbanks. However, there are few reports on the root structure and the soil strengthening benefit of the living brush mattress. The present work reports a series of experiments on root morphology and soil shear strength enhancement at the temporal and spatial scales. The object of the study is 24 living brush mattress trees constructed with Salix alba L. ‘Tristis’ (LBS hereafter). Traditional root morphology and mechanical measurement methods were used to collect the parameters. The results showed that the root systems of LBS had the characteristics of symmetry and upslope growth. The roots were mainly distributed in a cylindrical region of the soil (radius × thickness: 0.4 m × 0.5 m) and their biomass increased with different growth rates for the periods from 1 to 5 and from 5 to 7 years. Both age and slope position were factors that influence root growth. The root diameter falls within 0–5 mm, has a significant effect on the soil shear strength and provides a conical-shape potentiation zone to ensure the efficient protection of a riverbank. The results of this study demonstrate that LBS is an efficient and feasible engineering measure in the field of riverbank protection.

scholarly journals Population dynamics of two sympatric intertidal fish species (the shanny, Lipophrys pholis and long-spined scorpion fish, Taurulus bubalis) of Great Britain

2016 ◽  
Vol 98 (3) ◽  
pp. 589-595 ◽  
Author(s):  
C.J. Barrett ◽  
M.L. Johnson ◽  
S.L. Hull
Keyword(s):  
Population Dynamics ◽  
Great Britain ◽  
Fish Species ◽  
Gadus Morhua ◽  
Sympatric Species ◽  
Rocky Intertidal ◽  
Melanogrammus Aeglefinus ◽  
Intertidal Zones ◽  
Spatio Temporal ◽  
Scorpion Fish

The shanny/common blenny (Lipophrys pholis) and long-spined scorpionfish/bullhead (Taurulus bubalis) are commonly encountered, sympatric species within much of Great Britain's rocky intertidal zones. Despite being prey items of the cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) respectively, and both contributors to the diet of the near-threatened European otter (Lutra lutra), little is known on the population dynamics of the temperate specimens of Great Britain. It is further less known of the degrees of sympatricity between the two fish species and to what extent they are able to coexist. The current study examines spatio-temporal distributions and abundances at various resolutions: monthly population dynamics of both species along England's Yorkshire coast and seasonal population dynamics along the Yorkshire coast and around the Isle of Anglesey, Wales. Studies of their abundances, sizes, degrees of rock pool co-occurrence and diel activities are further examined, which indicate coexistence is maintained when interspecific co-occurrence takes place only between specimens of similar sizes, thus demoting size-related dominance hierarchies.

scholarly journals Prediction limits of mobile phone activity modelling

2017 ◽  
Vol 4 (2) ◽  
pp. 160900 ◽  
Author(s):  
Dániel Kondor ◽  
Sebastian Grauwin ◽  
Zsófia Kallus ◽  
István Gódor ◽  
Stanislav Sobolevsky ◽  
...  
Keyword(s):  
Mobile Phone ◽  
Spatial Scales ◽  
Urban Environments ◽  
Full Spectrum ◽  
Left Behind ◽  
Social Events ◽  
Prediction Limits ◽  
Spatio Temporal ◽  
City Structure ◽  
The City

Thanks to their widespread usage, mobile devices have become one of the main sensors of human behaviour and digital traces left behind can be used as a proxy to study urban environments. Exploring the nature of the spatio-temporal patterns of mobile phone activity could thus be a crucial step towards understanding the full spectrum of human activities. Using 10 months of mobile phone records from Greater London resolved in both space and time, we investigate the regularity of human telecommunication activity on urban scales. We evaluate several options for decomposing activity timelines into typical and residual patterns, accounting for the strong periodic and seasonal components. We carry out our analysis on various spatial scales, showing that regularity increases as we look at aggregated activity in larger spatial units with more activity in them. We examine the statistical properties of the residuals and show that it can be explained by noise and specific outliers. Also, we look at sources of deviations from the general trends, which we find to be explainable based on knowledge of the city structure and places of attractions. We show examples how some of the outliers can be related to external factors such as specific social events.

Unoccupied aerial vehicle-assisted monitoring of benthic vegetation in the coastal zone enhances the quality of ecological data

2021 ◽  
pp. 030913332110520
Author(s):  
Niels Svane ◽  
Troels Lange ◽  
Sara Egemose ◽  
Oliver Dalby ◽  
Aris Thomasberger ◽  
...  
Keyword(s):  
Zostera Marina ◽  
Spatial Scales ◽  
Fucus Vesiculosus ◽  
Ecosystem Dynamics ◽  
Spatial Extent ◽  
Total Biomass ◽  
Ecological Data ◽  
Error Matrix ◽  
Object Based ◽  
Spatio Temporal

Traditional monitoring (e.g., in-water based surveys) of eelgrass meadows and perennial macroalgae in coastal areas is time and labor intensive, requires extensive equipment, and the collected data has a low temporal resolution. Further, divers and Remotely Operated Vehicles (ROVs) have a low spatial extent that cover small fractions of full systems. The inherent heterogeneity of eelgrass meadows and macroalgae assemblages in these coastal systems makes interpolation and extrapolation of observations complicated and, as such, methods to collect data on larger spatial scales whilst retaining high spatial resolution is required to guide management. Recently, the utilization of Unoccupied Aerial Vehicles (UAVs) has gained popularity in ecological sciences due to their ability to rapidly collect large amounts of area-based and georeferenced data, making it possible to monitor the spatial extent and status of SAV communities with limited equipment requirements compared to ROVs or diver surveys. This paper is focused on the increased value provided by UAV-based, data collection (visual/Red Green Blue imagery) and Object Based Image Analysis for gaining an improved understanding of eelgrass recovery. It is demonstrated that delineation and classification of two species of SAV ( Fucus vesiculosus and Zostera marina) is possible; with an error matrix indicating 86–92% accuracy. Classified maps also highlighted the increasing biomass and areal coverage of F. vesiculosus as a potential stressor to eelgrass meadows. Further, authors derive a statistically significant conversion of percentage cover to biomass ( R2 = 0.96 for Fucus vesiculosus, R2 = 0.89 for Zostera marina total biomass, and R2 = 0.94 for AGB alone, p < 0.001). Results here provide an example of mapping cover and biomass of SAV and provide a tool to undertake spatio-temporal analyses to enhance the understanding of eelgrass ecosystem dynamics.

Automation and Management of Design Process of the Main Drive for an Innovative Fruits and Vegetables Washer

2021 ◽  
Vol 27 (1) ◽  
pp. 9-17
Author(s):  
V. P. Bui ◽  
◽  
S. S. Gavruishin ◽  
V. B. Phung ◽  
H. M. Dang ◽  
...  
Keyword(s):  
Design Process ◽  
Rational Design ◽  
Fruits And Vegetables ◽  
Rational Solution ◽  
Quality Criteria ◽  
Pareto Optimal ◽  
Optimal Domain ◽  
Wide Range ◽  
A New Technique ◽  
New Generation

A new technique is described, used by the authors to automate the design process of the main drive of a new generation machine intended for industrial washing of fruits and vegetables. To solve the problem of multi-criteria design, the original approach is proposed that uses interconnected mathematical models describing the dynamic behavior, strength reliability and functional characteristics of the machine in a unified information space. The generalized mathematical model includes 12 controlled parameters, 16 functional constraints, and 3 quality criteria. A genetic algorithm was used to find the space of Pareto-optimal solutions. The situational approach was used to select the final rational solution from a set of solutions belonging to the Pareto-optimal domain. The rational design of option the washer found using the proposed approach is compared with the existing ones. The proposed design methodology can be recommended for the design of a wide range of similar mechanical structures.

Damage Detection in Flexible Propeller Beam Structures by Exploiting Impact-Induced Coupled Acceleration Signals

2011 ◽  
Author(s):  
Ioannis T. Georgiou
Keyword(s):  
Data Driven ◽  
Distributed Information ◽  
Modal Expansion ◽  
Shape Difference ◽  
Spatio Temporal ◽  
Temporal Sample ◽  
High Level ◽  
Proper Orthogonal ◽  
Acceleration Signals

A local damage at the tip of a composite propeller is diagnosed by properly comparing its impact-induced free coupled dynamics to that of a pristine wooden propeller of the same size and shape. This is accomplished by creating indirectly via collocated measurements distributed information for the coupled acceleration field of the propellers. The powerful data-driven modal expansion analysis delivered by the Proper Orthogonal Decomposition (POD) Transform reveals that ensembles of impact-induced collocated coupled experimental acceleration signals are underlined by a high level of spatio-temporal coherence. Thus they furnish a valuable spatio-temporal sample of coupled response induced by a point impulse. In view of this fact, a tri-axial sensor was placed on the propeller hub to collect collocated coupled acceleration signals induced via modal hammer nondestructive impacts and thus obtained a reduced order characterization of the coupled free dynamics. This experimental data-driven analysis reveals that the in-plane unit components of the POD modes for both propellers have similar shapes-nearly identical. For the damaged propeller this POD shape-difference is quite pronounced. The shapes of the POD modes are used to compute indices of difference reflecting directly damage. At the first POD energy level, the shape-difference indices of the damaged composite propeller are quite larger than those of the pristine wooden propeller.

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