Multi-scaler 3D modelling to reconstruct an experimental landscape: An example from a worker’s cottage at Mount Dutton Bay, South Australia

New advances in 3D GIS provide the opportunity to create and interact with spatial datasets that are both empirical and experiential, thus bridging the historical divide between cartography and phenomenology. Survey and photogrammetry data from the colonial-era woolshed and port of Mount Dutton Bay in South Australia are used to create a visually realistic 3D landscape model. Viewshed analysis provided important information about the use of space and construction techniques for the shearers' cottage on this site. The results demonstrate that rigorous quantitative analysis is not incompatible with understanding the human experience of an archaeological site, and therefore open up exciting new avenues of archaeological enquiry.

Allostery and molecular stripping mechanism in profilin regulated actin filament growth

Profilin is an actin-sequestering protein and plays key role in regulating the polarized growth of actin filament. Binding of profilin to monomeric actin (G-actin) allows continuous elongation at the barbed end, but not the pointed end, of filament. How G-actin exchanges between the profilin-sequestered state and the filament state (F-actin) to support the barbed end elongation is not well understood. Here, we investigate the involved molecular mechanism by constructing a multi-basin energy landscape model and performing molecular simulations. We showed that the actin exchanging occurs by forming a ternary complex. The interactions arising from the barbed end binding drive the conformational change of the attached G-actin in the ternary complex from twist conformation to more flatten conformation without involving the change of nucleotide state, which in turn destabilizes the actin-profilin interface and promotes the profilin stripping event through allosteric coupling. We also showed that attachment of free profilin to the barbed end induces conformational change of the barbed end actin and facilitates its stripping from the filament. These results suggest a molecular stripping mechanism of the polarized actin filament growth dynamics controlled by the concentrations of the actin-profilin dimer and the free profilin, in which the allosteric feature of the monomeric actin plays crucial role.

Prospects of contemplative urban park from expert perspectives

The urban park is part of urban biodiversity that restore the diverse ecosystem to be resilient from rapid urbanisation impact. Also, it is an invented landscape that serves recreational opportunities as well as contemplation. However, significant evidence to measure the contemplativeness of Malaysian urban parks as an eco-psychological restoration resource is indistinct. Previously, the restorative environments have determined by personal opinions and evaluations of researchers without operationalising the empirical study on landscape design quality. This study evaluated Taman Tasik Shah Alam’s contemplativeness via expert evaluation assessed by ten Malaysian Landscape Architects. The assessment involves eight physical attributes using Contemplative Landscape Model criteria on 35 images via an online survey. Eventually, five of the most contemplative scenes are recognised as eco-psychological restoration resources to remedy psychological distress, including landscape composition types. It also highlights the necessary physical attributes of the urban park towards inventing the existing one into a contemplative environment for the betterment of communities. Thus, the contemplative landscape can serve as an antidote for people affected by psychological distress to contemplate themselves by exposing and experiencing well-preserved urban biodiversity.

A Simplified Population-Level Landscape Model Identifying Ecological Risk Drivers of Pesticide Applications, Part One: Case Study for Large Herbivorous Mammals

Environmental risk assessment is a key process for the authorization of pesticides, and is subjected to continuous challenges and updates. Current approaches are based on standard scenarios and independent substance-crop assessments. This arrangement does not address the complexity of agricultural ecosystems with mammals feeding on different crops. This work presents a simplified model for regulatory use addressing landscape variability, co-exposure to several pesticides, and predicting the effect on population abundance. The focus is on terrestrial vertebrates and the aim is the identification of the key risk drivers impacting on mid-term population dynamics. The model is parameterized for EU assessments according to the European Food Safety Authority (EFSA) Guidance Document, but can be adapted to other regulatory schemes. The conceptual approach includes two modules: (a) the species population dynamics, and (b) the population impact of pesticide exposure. Population dynamics is modelled through daily survival and seasonal reproductions rates; which are modified in case of pesticide exposure. All variables, parameters, and functions can be modified. The model has been calibrated with ecological data for wild rabbits and brown hares and tested for two herbicides, glyphosate and bromoxynil, using validated toxicity data extracted from EFSA assessments. Results demonstrate that the information available for a regulatory assessment, according to current EU information requirements, is sufficient for predicting the impact and possible consequences at population dynamic levels. The model confirms that agroecological parameters play a key role when assessing the effect of pesticide exposure on population abundance. The integration of laboratory toxicity studies with this simplified landscape model allows for the identification of conditions leading to population vulnerability or resilience. An Annex includes a detailed assessment of the model characteristics according to the EFSA scheme on Good Modelling Practice.

Propelling and perturbing appendages together facilitate strenuous ground self-righting

Terrestrial animals must self-right when overturned on the ground, but this locomotor task is strenuous. To do so, the discoid cockroach often pushes its wings against the ground to begin a somersault which rarely succeeds. As it repeatedly attempts this, the animal probabilistically rolls to the side to self-right. During winged self-righting, the animal flails its legs vigorously. Here, we studied whether wing opening and leg flailing together facilitate strenuous ground self-righting. Adding mass to increase hind leg flailing kinetic energy increased the animal’s self-righting probability. We then developed a robot with similar strenuous self-righting behavior and used it as a physical model for systematic experiments. The robot’s self-righting probability increased with wing opening and leg flailing amplitudes. A potential energy landscape model revealed that, although wing opening did not generate sufficient kinetic energy to overcome the high pitch potential energy barrier to somersault, it reduced the barrier for rolling, facilitating the small kinetic energy from leg flailing to probabilistically overcome it to self-right. The model also revealed that the stereotyped body motion during self-righting emerged from physical interaction of the body and appendages with the ground. Our work demonstrated the usefulness of potential energy landscape for modeling self-righting transitions.

A landscape model for cell fate decisions during mesoendoderm differentiation in C. elegans based on Wnt dynamics

Geometric models allow us to quantify topography of the Waddington landscape and gain quantitative insights of gene interaction in cell fate differentiation. Often mutant phenotypes show partial penetrance and there is a dearth of quantitative models that can exploit this data and make predictions about new allelic combinations with no additional parameters. C. elegans with its invariant cell lineages has been a key model system for discovering the genes controlling development. Here we focus on the differentiation of the endoderm founder cell named E from its mother, the EMS cell. Mutants that convert E to its sister MS fate have figured prominently in deciphering the Wnt pathway in worm. We construct a bi-valued Waddington landscape model that predicts the effect on POP-1/TCF and SYS-1/beta-catenin levels based on the penetrance of mutant alleles and RNAi, and relates the levels to fate choice decisions. A subset of the available data is used to fit the model and remaining data is then correctly predicted. Simple kinetic arguments show that contrary to current belief the ratio of these two proteins alone is not indicative of fate outcomes. Furthermore, double mutants within a background reduction of POP-1 levels are predicted with no adjustable parameters and their relative penetrance can differ from the same mutants with the wild-type POP-1 level, which calls for further experimental investigations. Our model refines the content of existing gene networks and invites extensions to other manifestations of the Wnt pathway in worm.

A Step-by-Step Guide to Initialize and Calibrate Landscape Models: A Case Study in the Mediterranean Mountains

The use of spatially interactive forest landscape models has increased in recent years. These models are valuable tools to assess our knowledge about the functioning and provisioning of ecosystems as well as essential allies when predicting future changes. However, developing the necessary inputs and preparing them for research studies require substantial initial investments in terms of time. Although model initialization and calibration often take the largest amount of modelers’ efforts, such processes are rarely reported thoroughly in application studies. Our study documents the process of calibrating and setting up an ecophysiologically based forest landscape model (LANDIS-II with PnET-Succession) in a biogeographical region where such a model has never been applied to date (southwestern Mediterranean mountains in Europe). We describe the methodological process necessary to produce the required spatial inputs expressing initial vegetation and site conditions. We test model behaviour on single-cell simulations and calibrate species parameters using local biomass estimations and literature information. Finally, we test how different initialization data—with and without shrub communities—influence the simulation of forest dynamics by applying the calibrated model at landscape level. Combination of plot-level data with vegetation maps allowed us to generate a detailed map of initial tree and shrub communities. Single-cell simulations revealed that the model was able to reproduce realistic biomass estimates and competitive effects for different forest types included in the landscape, as well as plausible monthly growth patterns of species growing in Mediterranean mountains. Our results highlight the importance of considering shrub communities in forest landscape models, as they influence the temporal dynamics of tree species. Besides, our results show that, in the absence of natural disturbances, harvesting or climate change, landscape-level simulations projected a general increase of biomass of several species over the next decades but with distinct spatio-temporal patterns due to competitive effects and landscape heterogeneity. Providing a step-by-step workflow to initialize and calibrate a forest landscape model, our study encourages new users to use such tools in forestry and climate change applications. Thus, we advocate for documenting initialization processes in a transparent and reproducible manner in forest landscape modelling.

Co-opting propelling and perturbing appendages facilitates strenuous ground self-righting

Terrestrial animals must self-right when overturned on the ground. To do so, the discoid cockroach often pushes its wings against the ground to begin a somersault but rarely succeeds in completing it. As it repeatedly attempts this, it probabilistically rolls to the side to self-right. Here, we studied whether seemingly wasteful leg flailing in this process helps. Adding mass to increase hind leg flailing kinetic energy fluctuation increased the animal’s self-righting probability. We then developed a robot with similar, strenuous self-righting behavior and used it as a physical model for systematic experiments. As legs flailed more vigorously and wings opened more, self-righting became more probable. A potential energy landscape model revealed that, although wing opening did not generate sufficient kinetic energy to overcome the high pitch potential energy barrier, it reduced barriers for rolling, facilitating the small kinetic energy fluctuation from leg flailing to probabilistically overcome roll barriers to self-right.Impact statementWhen overturned terrestrial animals self-right on the ground, their seemingly wasteful yet ubiquitous flailing of appendages is crucial in providing kinetic energy fluctuation to probabilistically overcome potential energy barriers.

Global epistasis emerges from a generic model of a complex trait

Epistasis between mutations can make adaptation contingent on evolutionary history. Yet despite widespread ‘microscopic’ epistasis between the mutations involved, microbial evolution experiments show consistent patterns of fitness increase between replicate lines. Recent work shows that this consistency is driven in part by global patterns of diminishing-returns and increasing-costs epistasis, which make mutations systematically less beneficial (or more deleterious) on fitter genetic backgrounds. However, the origin of this ‘global’ epistasis remains unknown. Here, we show that diminishing-returns and increasing-costs epistasis emerge generically as a consequence of pervasive microscopic epistasis. Our model predicts a specific quantitative relationship between the magnitude of global epistasis and the stochastic effects of microscopic epistasis, which we confirm by reanalyzing existing data. We further show that the distribution of fitness effects takes on a universal form when epistasis is widespread and introduce a novel fitness landscape model to show how phenotypic evolution can be repeatable despite sequence-level stochasticity.