The evolutionary dynamics of within-generation immune priming in invertebrate hosts

While invertebrates lack the machinery necessary for ‘acquired immunity’, there is increasing empirical evidence that exposure to low levels of disease may ‘prime’ an invertebrate''s immune response, increasing its defence to subsequent exposure. Despite this increasing empirical data, there has been little theoretical attention paid to immune priming. Here, we investigate the evolution of immune priming, focusing on the role of the unique feedbacks generated by a newly developed susceptible–primed–infected epidemiological model. Contrasting our results with previous models on the evolution of acquired immunity, we highlight that there are important implications to the evolution of immunity through priming owing to these different epidemiological feedbacks. In particular, we find that in contrast to acquired immunity, priming is strongly selected for at high as well as intermediate pathogen virulence. We also find that priming may be greatest at either intermediate or high host lifespans depending on the severity of disease. Furthermore, hosts faced with more severe pathogens are more likely to evolve diversity in priming. Finally, we show when the evolution of priming leads to the exclusion of the pathogens or hosts experiencing population cycles. Overall the model acts as a baseline for understanding the evolution of priming in host–pathogen systems.     

Structural performance of a climbing cactus: making the most of softness

Climbing plants must reach supports and navigate gaps to colonize trees. This requires a structural organization ensuring the rigidity of so-called ‘searcher’ stems. Cacti have succulent stems adapted for water storage in dry habitats. We investigate how a climbing cactus Selenicereus setaceus develops its stem structure and succulent tissues for climbing. We applied a ‘wide scale’ approach combining field-based bending, tensile and swellability tests with fine-scale rheological, compression and anatomical analyses in laboratory conditions. Gap-spanning ‘searcher’ stems rely significantly on the soft cortex and outer skin of the stem for rigidity in bending (60–94%). A woody core contributes significantly to axial and radial compressive strength (80%). Rheological tests indicated that storage moduli were consistently higher than loss moduli indicating that the mucilaginous cortical tissue behaved like a viscoelastic solid with properties similar to physical or chemical hydrogels. Rheological and compression properties of the soft tissue changed from young to old stages. The hydrogel–skin composite is a multi-functional structure contributing to rigidity in searcher stems but also imparting compliance and benign failure in environmental situations when stems must fail. Soft tissue composites changing in function via changes in development and turgescence have a great potential for exploring candidate materials for technical applications.     

An analytical approach to bistable biological circuit discrimination using real algebraic geometry

Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm''s theorem—a tool from nineteenth-century real algebraic geometry—to comparing ‘functionally equivalent’ bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh–Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm''s theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.     

Mathematical model and nanoindentation properties of the claws of Cyrtotrachelus buqueti Guer (Coleoptera: Curculionidae)

Scanning electron microscopy (SEM) was used to observe the macroscopic, microscopic, and cross‐sectional structures of the claws of Cyrtotrachelus buqueti Guer (Coleoptera: Curculionidae), and a mathematical model of a claw was used to investigate the structure–function relationships. To improve the quality of the SEM images, a non‐local means (NLM) algorithm and an improved NLM algorithm were applied. After comparison and analysis of five classical edge‐detection algorithms, the boundaries of the structural features of the claw were extracted based on a B‐spline wavelet algorithm, and the results showed that the variable curvature of the beetle claw enhances its adhesion force and improves its strength. Adhesion models of the claw were established, and the mechanical properties of its biomaterials were measured using nanoindentation. Considering that the presence of water can affect the hardness and Young''s modulus, both ‘dry’ and ‘wet’ samples were examined. For the dry samples, the hardness and Young''s modulus were 0.197 ± 0.074 GPa and 1.105 ± 0.197 GPa, respectively, whereas the respective values for the wet samples were both lower at 0.071 ± 0.030 GPa and 0.693 ± 0.163 GPa. This study provides data that can inform the design of climbing robots.     

Electronic transport properties of electrically doped cytosine‐based optical molecular switch with single‐wall carbon nanotube electrodes

This study represents an empirical model of cytosine‐based optical molecular switch. This possible biomolecular switch has been designed using the first principle approach which is based on density functional theory and non‐equilibrium Green''s function. The quantum‐ballistic transport property and current–voltage (I–V) characteristics of cytosine‐based optomolecular switch have been investigated at 25 THz operating frequency. The influence of highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gaps on the electronic transmission and I–V characteristics has been discussed in detail. The aim of this study is to highlight the minimum conformational change during a single ON–OFF switching cycle. The biomolecule comprises switching behaviour when converts from straightened to twisted form during photo‐excitement. The straightened and twisted forms of the molecule are represented as logic ‘0’ and logic ‘1’, respectively. This p and n regions of this switch has been made using electrical doping process. The current through the twisted form of the cytosine biomolecule is ∼1000 times higher than the straightened form. The maximum switching ratio 62.1 is obtained at 1 V bias. The origin of the switching behaviour of the biomolecule can be interpreted by quantum–ballistic transport model along with HOMO–LUMO gaps.Inspec keywords: ballistic transport, organic compounds, Green''s function methods, ab initio calculations, density functional theory, molecular biophysics, optical switches, single‐wall carbon nanotubes, electrochemical electrodesOther keywords: electrical doping process, cytosine biomolecule, electronic transport properties, single‐wall carbon nanotube electrodes, cytosine‐based optical molecular switch, density functional theory, electronic transmission, HOMO‐LUMO gaps, current–voltage characteristics, biomolecular switching behaviour, quantum–ballistic transport property model, electrically doped cytosine‐based optical molecular switch, first principle approach, nonequilibrium Green''s function, I‐V characteristics, highest occupied molecular orbital–lowest unoccupied molecular orbital gaps, single ON–OFF switching cycle, photoexcitement, frequency 25.0 THz, voltage 1.0 V, C     

The entropic basis of collective behaviour

We identify a unique viewpoint on the collective behaviour of intelligent agents. We first develop a highly general abstract model for the possible future lives these agents may encounter as a result of their decisions. In the context of these possibilities, we show that the causal entropic principle, whereby agents follow behavioural rules that maximize their entropy over all paths through the future, predicts many of the observed features of social interactions among both human and animal groups. Our results indicate that agents are often able to maximize their future path entropy by remaining cohesive as a group and that this cohesion leads to collectively intelligent outcomes that depend strongly on the distribution of the number of possible future paths. We derive social interaction rules that are consistent with maximum entropy group behaviour for both discrete and continuous decision spaces. Our analysis further predicts that social interactions are likely to be fundamentally based on Weber''s law of response to proportional stimuli, supporting many studies that find a neurological basis for this stimulus–response mechanism and providing a novel basis for the common assumption of linearly additive ‘social forces’ in simulation studies of collective behaviour.     

Informatics derived materials databases for multifunctional properties

In this review, we provide an overview of the development of quantitative structure–property relationships incorporating the impact of data uncertainty from small, limited knowledge data sets from which we rapidly develop new and larger databases. Unlike traditional database development, this informatics based approach is concurrent with the identification and discovery of the key metrics controlling structure–property relationships; and even more importantly we are now in a position to build materials databases based on design ‘intent’ and not just design parameters. This permits for example to establish materials databases that can be used for targeted multifunctional properties and not just one characteristic at a time as is presently done. This review provides a summary of the computational logic of building such virtual databases and gives some examples in the field of complex inorganic solids for scintillator applications.     

Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study

This paper presents new computational and modelling tools for studying the dynamics of an epidemic in its initial stages that use both available incidence time series and data describing the population''s infection network structure. The work is motivated by data collected at the beginning of the H1N1 pandemic outbreak in Israel in the summer of 2009. We formulated a new discrete-time stochastic epidemic SIR (susceptible-infected-recovered) model that explicitly takes into account the disease''s specific generation-time distribution and the intrinsic demographic stochasticity inherent to the infection process. Moreover, in contrast with many other modelling approaches, the model allows direct analytical derivation of estimates for the effective reproductive number (R_e) and of their credible intervals, by maximum likelihood and Bayesian methods. The basic model can be extended to include age–class structure, and a maximum likelihood methodology allows us to estimate the model''s next-generation matrix by combining two types of data: (i) the incidence series of each age group, and (ii) infection network data that provide partial information of ‘who-infected-who’. Unlike other approaches for estimating the next-generation matrix, the method developed here does not require making a priori assumptions about the structure of the next-generation matrix. We show, using a simulation study, that even a relatively small amount of information about the infection network greatly improves the accuracy of estimation of the next-generation matrix. The method is applied in practice to estimate the next-generation matrix from the Israeli H1N1 pandemic data. The tools developed here should be of practical importance for future investigations of epidemics during their initial stages. However, they require the availability of data which represent a random sample of the real epidemic process. We discuss the conditions under which reporting rates may or may not influence our estimated quantities and the effects of bias.     

First principle approach towards logic design using hydrogen‐doped single‐strand DNA

Molecular logic gate has been proposed using single‐strand DNA (ssDNA) consisting of basic four nucleobases. In this study, density functional theory and non‐equilibrium Green''s function based first principle approach is applied to investigate the electronic transmission characteristics of ssDNA chain. The heavily hydrogen‐doped‐ssDNA (H‐ssDNA) chain is connected with gold electrode to achieve enhanced quantum‐ballistic transmission along 〈1 1 1〉 direction. Logic gates OR, Ex‐OR, NXOR have been implemented using this analytical model of H‐ssDNA device. Enhanced logic properties have been observed for ssDNA after H adsorption due to improved electronic transmission. Dense electron cloud is considered as logic ‘high’ (1) output in presence of hydrogen molecule and on the contrary sparse cloud indicate logic ‘low’ (0) in the absence of hydrogen molecule. Device current is significantly increased from 0.2 nA to 2.4 µA (approx.) when ssDNA chain is heavily doped with hydrogen molecule. The current–voltage characteristics confirm the formation of various Boolean logic gate operations.Inspec keywords: molecular electronics, Green''s function methods, hydrogen, logic gates, density functional theory, adsorption, DNA, logic design, logic circuitsOther keywords: hydrogen molecule, contrary sparse cloud, current–voltage characteristics, Boolean logic gate operations, first principle approach, logic design, hydrogen‐doped single‐strand DNA, molecular logic gate, density functional theory, electronic transmission characteristics, H, analytical model, NXOR logic gates, Ex‐OR logic gates, OR logic gates, hydrogen‐doped‐ssDNA chain, nonequilibrium Green''s function, nucleobases, dense electron cloud, improved electronic transmission, enhanced logic properties, H‐ssDNA device, enhanced quantum‐ballistic transmission, gold electrode     

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials'' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials'' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed.     

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained'' and ‘unconstrained'' sequences, in the broadest possible sense. As ‘constrained'' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained'' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding'' and ‘non-coding'' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.     

Viscoelastic incremental formulation using creep and relaxation differential approaches

A new incremental formulation in the time domain for linear, non-ageing viscoelastic materials undergoing mechanical deformation is presented in this work. The formulation is derived from linear differential equations based on a discrete spectrum representation for the creep and relaxation tensors. The incremental constitutive equations are then obtained by finite difference integration. Thus the difficulty of retaining the stress and strain history in computer solutions is avoided. A complete general formulation of linear viscoelastic stress analysis is developed in terms of increments of strains and stresses in order to establish the constitutive stress–strain relationship. The presented method is validated using numerical simulations and reliable results are obtained.     

Photosymbiotic giant clams are transformers of solar flux

‘Giant’ tridacnid clams have evolved a three-dimensional, spatially efficient, photodamage-preventing system for photosymbiosis. We discovered that the mantle tissue of giant clams, which harbours symbiotic nutrition-providing microalgae, contains a layer of iridescent cells called iridocytes that serve to distribute photosynthetically productive wavelengths by lateral and forward-scattering of light into the tissue while back-reflecting non-productive wavelengths with a Bragg mirror. The wavelength- and angle-dependent scattering from the iridocytes is geometrically coupled to the vertically pillared microalgae, resulting in an even re-distribution of the incoming light along the sides of the pillars, thus enabling photosynthesis deep in the tissue. There is a physical analogy between the evolved function of the clam system and an electric transformer, which changes energy flux per area in a system while conserving total energy. At incident light levels found on shallow coral reefs, this arrangement may allow algae within the clam system to both efficiently use all incident solar energy and avoid the photodamage and efficiency losses due to non-photochemical quenching that occur in the reef-building coral photosymbiosis. Both intra-tissue radiometry and multiscale optical modelling support our interpretation of the system''s photophysics. This highly evolved ‘three-dimensional’ biophotonic system suggests a strategy for more efficient, damage-resistant photovoltaic materials and more spatially efficient solar production of algal biofuels, foods and chemicals.     

Three-dimensional tracking and behaviour monitoring of multiple fruit flies

The increasing interest in the investigation of social behaviours of a group of animals has heightened the need for developing tools that provide robust quantitative data. Drosophila melanogaster has emerged as an attractive model for behavioural analysis; however, there are still limited ways to monitor fly behaviour in a quantitative manner. To study social behaviour of a group of flies, acquiring the position of each individual over time is crucial. There are several studies that have tried to solve this problem and make this data acquisition automated. However, none of these studies has addressed the problem of keeping track of flies for a long period of time in three-dimensional space. Recently, we have developed an approach that enables us to detect and keep track of multiple flies in a three-dimensional arena for a long period of time, using multiple synchronized and calibrated cameras. After detecting flies in each view, correspondence between views is established using a novel approach we call the ‘sequential Hungarian algorithm’. Subsequently, the three-dimensional positions of flies in space are reconstructed. We use the Hungarian algorithm and Kalman filter together for data association and tracking. We evaluated rigorously the system''s performance for tracking and behaviour detection in multiple experiments, using from one to seven flies. Overall, this system presents a powerful new method for studying complex social interactions in a three-dimensional environment.     

Atomic force microscopy of the morphology and mechanical behaviour of barnacle cyprid footprint proteins at the nanoscale

Barnacles are a major biofouler of man-made underwater structures. Prior to settlement, cypris larvae explore surfaces by reversible attachment effected by a ‘temporary adhesive’. During this exploratory behaviour, cyprids deposit proteinaceous ‘footprints’ of a putatively adhesive material. In this study, footprints deposited by Balanus amphitrite cyprids were probed by atomic force microscopy (AFM) in artificial sea water (ASW) on silane-modified glass surfaces. AFM images obtained in air yielded better resolution than in ASW and revealed the fibrillar nature of the secretion, suggesting that the deposits were composed of single proteinaceous nanofibrils, or bundles of fibrils. The force curves generated in pull-off force experiments in sea water consisted of regions of gradually increasing force, separated by sharp drops in extension force manifesting a characteristic saw-tooth appearance. Following the relaxation of fibrils stretched to high strains, force–distance curves in reverse stretching experiments could be described by the entropic elasticity model of a polymer chain. When subjected to relaxation exceeding 500 ms, extended footprint proteins refolded, and again showed saw-tooth unfolding peaks in subsequent force cycles. Observed rupture and hysteresis behaviour were explained by the ‘sacrificial bond’ model. Longer durations of relaxation (>5 s) allowed more sacrificial bond reformation and contributed to enhanced energy dissipation (higher toughness). The persistence length for the protein chains (L_P) was obtained. At high elongation, following repeated stretching up to increasing upper strain limits, footprint proteins detached at total stretched length of 10 µm.     

Asymptotic burnout and homeostatic awakening: a possible solution to the Fermi paradox?

Previous studies show that city metrics having to do with growth, productivity and overall energy consumption scale superlinearly, attributing this to the social nature of cities. Superlinear scaling results in crises called ‘singularities’, where population and energy demand tend to infinity in a finite amount of time, which must be avoided by ever more frequent ‘resets’ or innovations that postpone the system''s collapse. Here, we place the emergence of cities and planetary civilizations in the context of major evolutionary transitions. With this perspective, we hypothesize that once a planetary civilization transitions into a state that can be described as one virtually connected global city, it will face an ‘asymptotic burnout’, an ultimate crisis where the singularity-interval time scale becomes smaller than the time scale of innovation. If a civilization develops the capability to understand its own trajectory, it will have a window of time to affect a fundamental change to prioritize long-term homeostasis and well-being over unyielding growth—a consciously induced trajectory change or ‘homeostatic awakening’. We propose a new resolution to the Fermi paradox: civilizations either collapse from burnout or redirect themselves to prioritizing homeostasis, a state where cosmic expansion is no longer a goal, making them difficult to detect remotely.     

Fish and robots swimming together: attraction towards the robot demands biomimetic locomotion

The integration of biomimetic robots in a fish school may enable a better understanding of collective behaviour, offering a new experimental method to test group feedback in response to behavioural modulations of its ‘engineered’ member. Here, we analyse a robotic fish and individual golden shiners (Notemigonus crysoleucas) swimming together in a water tunnel at different flow velocities. We determine the positional preference of fish with respect to the robot, and we study the flow structure using a digital particle image velocimetry system. We find that biomimetic locomotion is a determinant of fish preference as fish are more attracted towards the robot when its tail is beating rather than when it is statically immersed in the water as a ‘dummy’. At specific conditions, the fish hold station behind the robot, which may be due to the hydrodynamic advantage obtained by swimming in the robot''s wake. This work makes a compelling case for the need of biomimetic locomotion in promoting robot–animal interactions and it strengthens the hypothesis that biomimetic robots can be used to study and modulate collective animal behaviour.     

Exploration–exploitation trade-off features a saltatory search behaviour

Searching experiments conducted in different virtual environments over a gender-balanced group of people revealed a gender irrelevant scale-free spread of searching activity on large spatio-temporal scales. We have suggested and solved analytically a simple statistical model of the coherent-noise type describing the exploration–exploitation trade-off in humans (‘should I stay’ or ‘should I go’). The model exhibits a variety of saltatory behaviours, ranging from Lévy flights occurring under uncertainty to Brownian walks performed by a treasure hunter confident of the eventual success.