Optogenetics enables real-time spatiotemporal control over spiral wave dynamics in an excitable cardiac system

Propagation of non-linear waves is key to the functioning of diverse biological systems. Such waves can organize into spirals, rotating around a core, whose properties determine the overall wave dynamics. Theoretically, manipulation of a spiral wave core should lead to full spatiotemporal control over its dynamics. However, this theory lacks supportive evidence (even at a conceptual level), making it thus a long-standing hypothesis. Here, we propose a new phenomenological concept that involves artificially dragging spiral waves by their cores, to prove the aforementioned hypothesis in silico, with subsequent in vitro validation in optogenetically modified monolayers of rat atrial cardiomyocytes. We thereby connect previously established, but unrelated concepts of spiral wave attraction, anchoring and unpinning to demonstrate that core manipulation, through controlled displacement of heterogeneities in excitable media, allows forced movement of spiral waves along pre-defined trajectories. Consequently, we impose real-time spatiotemporal control over spiral wave dynamics in a biological system.

From a spinning galaxy to a swarm of honeybees, rotating spirals are widespread in nature. Even within the muscles of the heart, waves of electrical activity sometimes rotate spirally, leading to irregular heart rhythms or arrhythmia – a condition that can be fatal.

Irrespective of where they occur, spiral waves organize around a center or core with different biophysical properties compared to the rest of the medium. The properties of the core determine the overall dynamics of the spiral. This means that, theoretically, it should be possibly to completely control a spiral wave just by manipulating its core.

Now, Majumder, Feola et al. have tested this long-standing hypothesis using a combination of computer modeling and experiments with single layers of rat heart cells grown in a laboratory. First, the heart cells were genetically modified so that their electrical properties could be altered with light; in other words, the cells were put under optical control. Next, by using of a narrow beam of light, Majumder, Feola et al. precisely controlled the electrical properties of a small number of cells, which then attracted and supported a rotating spiral wave by acting as its new core. Moving the light beam allowed the core of the spiral wave to be shifted too, meaning the spiral wave could now be steered along any desired path in the cell layer.

Majumder, Feola et al. hope that these underlying principles may one day provide the basis of new treatments for irregular heartbeats that are more effective and less damaging to the heart than existing options. Yet first, more work is needed to translate these findings from single layers of cells to actual hearts.

A perspective on using experiment and theory to identify design principles in dye-sensitized solar cells

Dye-sensitized solar cells (DSCs) have been the subject of wide-ranging studies for many years because of their potential for large-scale manufacturing using roll-to-roll processing allied to their use of earth abundant raw materials. Two main challenges exist for DSC devices to achieve this goal; uplifting device efficiency from the 12 to 14% currently achieved for laboratory-scale 'hero' cells and replacement of the widely-used liquid electrolytes which can limit device lifetimes. To increase device efficiency requires optimized dye injection and regeneration, most likely from multiple dyes while replacement of liquid electrolytes requires solid charge transporters (most likely hole transport materials - HTMs). While theoretical and experimental work have both been widely applied to different aspects of DSC research, these approaches are most effective when working in tandem. In this context, this perspective paper considers the key parameters which influence electron transfer processes in DSC devices using one or more dye molecules and how modelling and experimental approaches can work together to optimize electron injection and dye regeneration.

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease

Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual differences between patients contributes to the difficulty to define a standardized treatment. Computational modeling can systematically investigate metabolic interactions between gut microbes to unravel mechanistic insights. In this study, we integrated metagenomic data of CD patients and healthy controls with genome-scale metabolic models into personalized in silico microbiotas. We predicted short chain fatty acid (SFCA) levels for patients and controls, which were overall congruent with experimental findings. As an emergent property, low concentrations of SCFA were predicted for CD patients and the SCFA signatures were unique to each patient. Consequently, we suggest personalized dietary treatments that could improve each patient's SCFA levels. The underlying modeling approach could aid clinical practice to find dietary treatment and guide recovery by rationally proposing food aliments.

Intrinsic and extrinsic regulation of human skin melanogenesis and pigmentation

In human skin, melanogenesis is a tightly regulated process. Indeed, several extracellular signals are transduced via dedicated signalling pathways and mostly converge to MITF, a transcription factor integrating upstream signalling and regulating downstream genes involved in the various inherent mechanisms modulating melanogenesis. The synthesis of melanin pigments occurs in melanocytes inside melanosomes where melanogenic enzymes (tyrosinase and related proteins) are addressed with the help of specific protein complexes. The melanosomes loaded with melanin are then transferred to keratinocytes. A more elaborate level of melanogenesis regulation comes into play via the action of non-coding RNAs (microRNAs, lncRNAs). Besides this canonical regulation, melanogenesis can also be modulated by other non-specific intrinsic pathways (hormonal environment, inflammation) and by extrinsic factors (solar irradiation such as ultraviolet irradiation, environmental pollution). We developed a bioinformatic interaction network gathering the multiple aspects of melanogenesis and skin pigmentation as a resource to better understand and study skin pigmentation biology.

Collaborative Working Architecture for IoT-Based Applications

The new sensing applications need enhanced computing capabilities to handle the requirements of complex and huge data processing. The Internet of Things (IoT) concept brings processing and communication features to devices. In addition, the Cloud Computing paradigm provides resources and infrastructures for performing the computations and outsourcing the work from the IoT devices. This scenario opens new opportunities for designing advanced IoT-based applications, however, there is still much research to be done to properly gear all the systems for working together. This work proposes a collaborative model and an architecture to take advantage of the available computing resources. The resulting architecture involves a novel network design with different levels which combines sensing and processing capabilities based on the Mobile Cloud Computing (MCC) paradigm. An experiment is included to demonstrate that this approach can be used in diverse real applications. The results show the flexibility of the architecture to perform complex computational tasks of advanced applications.

Commentary on Apostolopoulos et al. (2018): Systems and complex systems approaches for public health planning-back to the future?

If complex systems modeling and analysis of the drinking environment are important, then why do researchers not build such models and policymakers not commission such analyses? Previous efforts have been hampered by disincentives, credibility concerns and technological limitations, but now may be the time for a quantitative complex systems revival.

Distribution of cardiac sodium channels in clusters potentiates ephaptic interactions in the intercalated disc

KEY POINTS

It has been proposed that ephaptic conduction, relying on interactions between the sodium (Na⁺ ) current and the extracellular potential in intercalated discs, might contribute to cardiac conduction when gap junctional coupling is reduced, but this mechanism is still controversial. In intercalated discs, Na⁺ channels form clusters near gap junction plaques, but the functional significance of these clusters has never been evaluated. In HEK cells expressing cardiac Na⁺ channels, we show that restricting the extracellular space modulates the Na⁺ current, as predicted by corresponding simulations accounting for ephaptic effects. In a high-resolution model of the intercalated disc, clusters of Na⁺ channels that face each other across the intercellular cleft facilitate ephaptic impulse transmission when gap junctional coupling is reduced. Thus, our simulations reveal a functional role for the clustering of Na⁺ channels in intercalated discs, and suggest that rearrangement of these clusters in disease may influence cardiac conduction.

ABSTRACT

It has been proposed that ephaptic interactions in intercalated discs, mediated by extracellular potentials, contribute to cardiac impulse propagation when gap junctional coupling is reduced. However, experiments demonstrating ephaptic effects on the cardiac Na⁺ current (I_Na ) are scarce. Furthermore, Na⁺ channels form clusters around gap junction plaques, but the electrophysiological significance of these clusters has never been investigated. In patch clamp experiments with HEK cells stably expressing human Na_v 1.5 channels, we examined how restricting the extracellular space modulates I_Na elicited by an activation protocol. In parallel, we developed a high-resolution computer model of the intercalated disc to investigate how the distribution of Na⁺ channels influences ephaptic interactions. Approaching the HEK cells to a non-conducting obstacle always increased peak I_Na at step potentials near the threshold of I_Na activation and decreased peak I_Na at step potentials far above threshold (7 cells, P = 0.0156, Wilcoxon signed rank test). These effects were consistent with corresponding control simulations with a uniform Na⁺ channel distribution. In the intercalated disc computer model, redistributing the Na⁺ channels into a central cluster of the disc potentiated ephaptic effects. Moreover, ephaptic impulse transmission from one cell to another was facilitated by clusters of Na⁺ channels facing each other across the intercellular cleft when gap junctional coupling was reduced. In conclusion, our proof-of-principle experiments demonstrate that confining the extracellular space modulates cardiac I_Na , and our simulations reveal the functional role of the aggregation of Na⁺ channels in the perinexus. These findings highlight novel concepts in the physiology of cardiac excitation.

Twists and turns

Computational modelling of the heart tube during development reveals the interplay between tissue asymmetry and growth that helps our hearts take shape.

A predictive model of asymmetric morphogenesis from 3D reconstructions of mouse heart looping dynamics

How left-right patterning drives asymmetric morphogenesis is unclear. Here, we have quantified shape changes during mouse heart looping, from 3D reconstructions by HREM. In combination with cell labelling and computer simulations, we propose a novel model of heart looping. Buckling, when the cardiac tube grows between fixed poles, is modulated by the progressive breakdown of the dorsal mesocardium. We have identified sequential left-right asymmetries at the poles, which bias the buckling in opposite directions, thus leading to a helical shape. Our predictive model is useful to explore the parameter space generating shape variations. The role of the dorsal mesocardium was validated in Shh^-/- mutants, which recapitulate heart shape changes expected from a persistent dorsal mesocardium. Our computer and quantitative tools provide novel insight into the mechanism of heart looping and the contribution of different factors, beyond the simple description of looping direction. This is relevant to congenital heart defects.

Modelling the effects of chloroquine on KCNJ2-linked short QT syndrome

A gain-of-function KCNJ2 D172N mutation in KCNJ2-encoded Kir2.1 channels underlies one form of short QT syndrome (SQT3), which is associated with increased susceptibility to arrhythmias and sudden death. Anti-malarial drug chloroquine was reported as an effective inhibitor of Kir2.1 channels. Using biophysically-detailed human ventricle computer models, this study assessed the effects of chloroquine on SQT3. The ten Tusscher et al. model of human ventricular cell action potential was modified to recapitulate functional changes in the inward rectifier K⁺ current (I_K1) due to heterozygous and homozygous forms of the D172N mutation. Mutant formulations were incorporated into multi-scale models. The blocking effects of chloroquine on ionic currents were modelled using IC₅₀ and Hill coefficient values from literatures. Effects of chloroquine on action potential duration (APD), effective refractory period (ERP) and pseudo-ECGs were quantified. It was shown that chloroquine caused a dose-dependent reduction in I_K1, prolonged APD, and decreased the maximum voltage heterogeneity. Chloroquine prolonged QT interval and declined the T-wave amplitude. Although chloroquine reduced tissue’s temporal vulnerability, it increased the minimum substrate size necessary for sustaining re-entry. The actions of chloroquine decreased arrhythmia risk, due to the reduced tissue vulnerability, prolonged ERP and wavelength of re-entrant excitation waves, which in combination prevented and terminated re-entry in the tissue models. In conclusion, the results of this study provide new evidence that the anti-arrhythmic effects of chloroquine on SQT3 and, by extension, to the possibility that chloroquine may be a potential therapeutic agent for SQT3 treatment.

δ-cells and β-cells are electrically coupled and regulate α-cell activity via somatostatin

Key points

We used a mouse expressing a light‐sensitive ion channel in β‐cells to understand how α‐cell activity is regulated by β‐cells.

Light activation of β‐cells triggered a suppression of α‐cell activity via gap junction‐dependent activation of δ‐cells.

Mathematical modelling of human islets suggests that 23% of the inhibitory effect of glucose on glucagon secretion is mediated by β‐cells via gap junction‐dependent activation of δ‐cells/somatostatin secretion.

Abstract

Glucagon, the body's principal hyperglycaemic hormone, is released from α‐cells of the pancreatic islet. Secretion of this hormone is dysregulated in type 2 diabetes mellitus but the mechanisms controlling secretion are not well understood. Regulation of glucagon secretion by factors secreted by neighbouring β‐ and δ‐cells (paracrine regulation) have been proposed to be important. In this study, we explored the importance of paracrine regulation by using an optogenetic strategy. Specific light‐induced activation of β‐cells in mouse islets expressing the light‐gated channelrhodopsin‐2 resulted in stimulation of electrical activity in δ‐cells but suppression of α‐cell activity. Activation of the δ‐cells was rapid and sensitive to the gap junction inhibitor carbenoxolone, whereas the effect on electrical activity in α‐cells was blocked by CYN 154806, an antagonist of the somatostatin‐2 receptor. These observations indicate that optogenetic activation of the β‐cells propagates to the δ‐cells via gap junctions, and the consequential stimulation of somatostatin secretion inhibits α‐cell electrical activity by a paracrine mechanism. To explore whether this pathway is important for regulating α‐cell activity and glucagon secretion in human islets, we constructed computational models of human islets. These models had detailed architectures based on human islets and consisted of a collection of >500 α‐, β‐ and δ‐cells. Simulations of these models revealed that this gap junctional/paracrine mechanism accounts for up to 23% of the suppression of glucagon secretion by high glucose.

We used a mouse expressing a light‐sensitive ion channel in β‐cells to understand how α‐cell activity is regulated by β‐cells.

Light activation of β‐cells triggered a suppression of α‐cell activity via gap junction‐dependent activation of δ‐cells.

Mathematical modelling of human islets suggests that 23% of the inhibitory effect of glucose on glucagon secretion is mediated by β‐cells via gap junction‐dependent activation of δ‐cells/somatostatin secretion.

Comparing the Nutritional Impact of Dietary Strategies to Reduce Discretionary Choice Intake in the Australian Adult Population: A Simulation Modelling Study

Dietary strategies to reduce discretionary choice intake are commonly utilized in practice, but evidence on their relative efficacy is lacking. The aim was to compare the potential impact on nutritional intake of three strategies to reducing discretionary choices intake in the Australian adult (19-90 years) population. Dietary simulation modelling using data from the National Nutrition and Physical Activity Survey 2011-2012 was conducted (n = 9341; one 24 h dietary recall). Strategies modelled were: moderation (reduce discretionary choices by 50%, with 0%, 25% or 75% energy compensation); substitution (replace 50% of discretionary choices with core choices); reformulation (replace 50% SFA with unsaturated fats, reduce added sugars by 25%, and reduce sodium by 20%). Compared to the base case (observed) intake, modelled intakes in the moderation scenario showed: -17.3% lower energy (sensitivity analyses, 25% energy compensation -14.2%; 75% energy compensation -8.0%), -20.9% lower SFA (-17.4%; -10.5%), -43.3% lower added sugars (-41.1%; -36.7%) and 17.7% lower sodium (-14.3%; -7.5%). Substitution with a range of core items, or with fruits, vegetables and core beverages only, resulted in similar changes in energy intake (-13.5% and -15.4%), SFA (-17.7% and -20.1%), added sugars (-42.6% and -43%) and sodium (-13.7% and -16.5%), respectively. Reformulating discretionary choices had minimal impact on reducing energy intake but reduced SFA (-10.3% to -30.9%), added sugars (-9.3% to -52.9%), and alcohol (-25.0% to -49.9%) and sodium (-3.3% to -13.2%). The substitution and reformulation scenarios minimized negative changes in fiber, protein and micronutrient intakes. While each strategy has strengths and limitations, substitution of discretionary choices with core foods and beverages may optimize the nutritional impact.

Central control of interlimb coordination and speed-dependent gait expression in quadrupeds

KEY POINTS

Quadrupeds express different gaits depending on speed of locomotion. Central pattern generators (one per limb) within the spinal cord generate locomotor oscillations and control limb movements. Neural interactions between these generators define interlimb coordination and gait. We present a computational model of spinal circuits representing four rhythm generators with left-right excitatory and inhibitory commissural and fore-hind inhibitory interactions within the cord. Increasing brainstem drive to all rhythm generators and excitatory commissural interneurons induces an increasing frequency of locomotor oscillations accompanied by speed-dependent gait changes from walk to trot and to gallop and bound. The model closely reproduces and suggests explanations for multiple experimental data, including speed-dependent gait transitions in intact mice and changes in gait expression in mutants lacking certain types of commissural interneurons. The model suggests the possible circuit organization in the spinal cord and proposes predictions that can be tested experimentally.

ABSTRACT

As speed of locomotion is increasing, most quadrupeds, including mice, demonstrate sequential gait transitions from walk to trot and to gallop and bound. The neural mechanisms underlying these transitions are poorly understood. We propose that the speed-dependent expression of different gaits results from speed-dependent changes in the interactions between spinal circuits controlling different limbs and interlimb coordination. As a result, the expression of each gait depends on (1) left-right interactions within the spinal cord mediated by different commissural interneurons (CINs), (2) fore-hind interactions on each side of the spinal cord and (3) brainstem drives to rhythm-generating circuits and CIN pathways. We developed a computational model of spinal circuits consisting of four rhythm generators (RGs) with bilateral left-right interactions mediated by V0 CINs (V0_D and V0_V sub-types) providing left-right alternation, and conditional V3 CINs promoting left-right synchronization. Fore and hind RGs mutually inhibited each other. We demonstrate that linearly increasing excitatory drives to the RGs and V3 CINs can produce a progressive increase in the locomotor speed accompanied by sequential changes of gaits from walk to trot and to gallop and bound. The model closely reproduces and suggests explanations for the speed-dependent gait expression observed in vivo in intact mice and in mutants lacking V0_V or all V0 CINs. Specifically, trot is not expressed after removal of V0_V CINs, and only bound is expressed after removal of all V0 CINs. The model provides important insights into the organization of spinal circuits and neural control of locomotion.

The arrangement of Brachypodium distachyon chromosomes in interphase nuclei

The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus.

The effects of benzylsulfonyl-D-Ser-homoPhe-(4-amidino-benzylamide), a dual plasmin and urokinase inhibitor, on facial skin barrier function in subjects with sensitive skin

OBJECTIVE

The aim of this study was to optimize the synthesis of the plasmin and urokinase (uPA) inhibitor benzylsulfonyl-D-Ser-homoPhe-(4-amidino-benzylamide) (BSFAB), to characterize its activity and mechanism of action and to assess its use to improve stratum corneum (SC) barrier function.

METHODS

Peptide coupling methods were used to synthesize BSFAB, and high-performance liquid chromatography-mass spectrometry (HPLC-MS) together with ¹ H- and ¹³ C-nuclear magnetic resonance spectroscopy (NMR) were applied to clarify its structure and determine its purity. Its binding mode was determined by docking studies to the catalytic domains of plasmin and uPA. Inhibition constants (K_i ) were determined by enzyme kinetic studies, and the effect of BSFAB on plasmin, uPA and transglutaminase 1 expression was evaluated in non-cytokine and cytokine-stimulated keratinocytes. A vehicle-controlled clinical study on SC barrier function was conducted on facial skin of subjects with self-perceived sensitive skin.

RESULTS

BSFAB was synthesized with high purity (97.3%). In silico studies indicated that the amidine moiety of BSFAB was anchored in the S1 pocket of both enzymes by binding to Asp189, Ser190 and Gly219, whereas the backbone of the D-Ser residue makes an anti-parallel β-sheet interaction with Gly216. BSFAB was shown to be an effective inhibitor of plasmin and uPA with K_i values of 29 and 25 nM, respectively. BSFAB also inhibited keratinocyte-secreted protease activities in basal (plasmin inhibition 37.7%, P < 0.05 and uPA inhibition 96.6%, P < 0.01) and cytokine-induced conditions (plasmin inhibition 41.1%, P < 0.05 and uPA inhibition 97.0%, P < 0.001) and stimulated the gene expression of transglutaminase 1 in cytokine-stimulated keratinocytes (approximately 4.5 times increased expression, P < 0.01). Clinically, BSFAB was shown to improve SC barrier integrity (P < 0.02 on day 29) and subjective improvements in the perception of healthy skin (P < 0.05 on day 28).

CONCLUSION

BSFAB binds as a reversible competitive inhibitor to the active sites of plasmin and uPA. Additionally, BSFAB positively improved keratinocyte differentiation gene expression (transglutaminase 1). These effects were translated into improvements in SC barrier integrity clinically in subjects with dry and sensitive skin and improved their perception of having a healthy skin condition.

How common standards can diminish collective intelligence: a computational study

Making good decisions depends on having accurate information - quickly, and in a form in which it can be readily communicated and acted upon. Two features of medical practice can help: deliberation in groups and the use of scores and grades in evaluation. We study the contributions of these features using a multi-agent computer simulation of groups of physicians. One might expect individual differences in members' grading standards to reduce the capacity of the group to discover the facts on which well-informed decisions depend. Observations of the simulated groups suggest on the contrary that this kind of diversity can in fact be conducive to epistemic performance. Sometimes, it is adopting common standards that may be expected to result in poor decisions.

Organization of flexor-extensor interactions in the mammalian spinal cord: insights from computational modelling

KEY POINTS

Alternation of flexor and extensor activity in the mammalian spinal cord is mediated by two classes of genetically identified inhibitory interneurons, V1 and V2b. The V1 interneurons are essential for high-speed locomotor activity. They secure flexor-extensor alternations in the intact cord but lose this function after hemisection, suggesting that they are activated by inputs from the contralateral side of the cord. The V2b interneurons are involved in flexor-extensor alternations in both intact cord and hemicords. We used a computational model of the spinal network, simulating the left and right rhythm-generating circuits interacting via several commissural pathways, and extended this model by incorporating V1 and V2b neuron populations involved in flexor-extensor interactions on each cord side. The model reproduces multiple experimental data on selective silencing and activation of V1 and/or V2b neurons and proposes the organization of their connectivity providing flexor-extensor alternation in the spinal cord.

ABSTRACT

Alternating flexor and extensor activity represents the fundamental property underlying many motor behaviours including locomotion. During locomotion this alternation appears to arise in rhythm-generating circuits and transpires at all levels of the spinal cord including motoneurons. Recent studies in vitro and in vivo have shown that flexor-extensor alternation during locomotion involves two classes of genetically identified, inhibitory interneurons: V1 and V2b. Particularly, in the isolated mouse spinal cord, abrogation of neurotransmission derived by both V1 and V2b interneurons resulted in flexor-extensor synchronization, whereas selective inactivation of only one of these neuron types did not abolish flexor-extensor alternation. After hemisection, inactivation of only V2b interneurons led to the flexor-extensor synchronization, while inactivation of V1 interneurons did not affect flexor-extensor alternation. Moreover, optogenetic activation of V2b interneurons suppressed extensor-related activity, while similar activation of V1 interneurons suppressed both flexor and extensor oscillations. Here, we address these issues using the previously published computational model of spinal circuitry simulating bilateral interactions between left and right rhythm-generating circuits. In the present study, we incorporate V1 and V2b neuron populations on both sides of the cord to make them critically involved in flexor-extensor interactions. The model reproduces multiple experimental data on the effects of hemisection and selective silencing or activation of V1 and V2b neurons and suggests connectivity profiles of these neurons and their specific roles in left-right (V1) and flexor-extensor (both V2b and V1) interactions in the spinal cord that can be tested experimentally.

Temporal and phylogenetic evolution of the sauropod dinosaur body plan

The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic-Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous.

[Computer modelling of monoaminoxidases]

The article summarized results of studies on active site structures of monoamine oxidases (MAO) performed in the Institute of Biomedical Chemistry (Russia) by computer modelling approaches. MAO, catalyzing the reaction of oxidative deamination of major neurotransmitter monoamines, exists in two highly homologous forms, MAO A and MAO B, distinguished by substrate specificity and inhibitor selectivity. The development of approaches for active site modelling of these enzymes (with unknown three-dimensional structures) started from analysis of relationship between the geometrical sizes of rigid indole and isatin derivatives and their inhibitory activity. These studies resulted in molding of the active site structures of MAO A and MAO B. These molds reflect the sizes and shapes of active sites of these enzymes. These mold models have been used for virtual screening of molecular databases for new inhibitors. The models obtained at different stages of MAO investigations have been compared with recently appeared three-dimensional structures of MAO A and MAO B.

Validation of a non-linear model of health

PURPOSE

The purpose of this study was to evaluate the veracity of a theoretically derived model of health that describes a non-linear trajectory of health from birth to death with available population data sets.

METHODS

The distribution of mortality by age is directly related to health at that age, thus health approximates 1/mortality. The inverse of available all-cause mortality data from various time periods and populations was used as proxy data to compare with the theoretically derived non-linear health model predictions, using both qualitative approaches and quantitative one-sample Kolmogorov-Smirnov analysis with Monte Carlo simulation.

RESULTS

The mortality data's inverse resembles a log-normal distribution as predicted by the proposed health model. The curves have identical slopes from birth and follow a logarithmic decline from peak health in young adulthood. A majority of the sampled populations had a good to excellent quantitative fit to a log-normal distribution, supporting the underlying model assumptions. Post hoc manipulation showed the model predictions to be stable.

CONCLUSIONS

This is a first theory of health to be validated by proxy data, namely the inverse of all-cause mortality. This non-linear model, derived from the notion of the interaction of physical, environmental, mental, emotional, social and sense-making domains of health, gives physicians a more rigorous basis to direct health care services and resources away from disease-focused elder care towards broad-based biopsychosocial interventions earlier in life.

Gating function of isoleucine-116 in TM-3 (position III:16/3.40) for the activity state of the CC-chemokine receptor 5 (CCR5)

BACKGROUND AND PURPOSE

A conserved amino acid within a protein family indicates a significance of the residue. In the centre of transmembrane helix (TM)-5, position V:13/5.47, an aromatic amino acid is conserved among class A 7TM receptors. However, in 37% of chemokine receptors - a subgroup of 7TM receptors - it is a leucine indicating an altered function. Here, we describe the significance of this position and its possible interaction with TM-3 for CCR5 activity.

EXPERIMENTAL APPROACH

The effects of [L203F]-CCR5 in TM-5 (position V:13/5.47), [I116A]-CCR5 in TM-3 (III:16/3.40) and [L203F;G286F]-CCR5 (V:13/5.47;VII:09/7.42) were determined in G-protein- and β-arrestin-coupled signalling. Computational modelling monitored changes in amino acid conformation.

KEY RESULTS

[L203F]-CCR5 increased the basal level of G-protein coupling (20-70% of Emax ) and β-arrestin recruitment (50% of Emax ) with a threefold increase in agonist potency. In silico, [I116A]-CCR5 switched χ1-angle in [L203F]-CCR5. Furthermore, [I116A]-CCR5 was constitutively active to a similar degree as [L203F]-CCR5. Tyr(244) in TM-6 (VI:09/6.44) moved towards TM-5 in silico, consistent with its previously shown function for CCR5 activation. On [L203F;G286F]-CCR5 the antagonist aplaviroc was converted to a superagonist.

CONCLUSIONS AND IMPLICATIONS

The results imply that an aromatic amino acid in the centre of TM-5 controls the level of receptor activity. Furthermore, Ile(116) acts as a gate for the movement of Tyr(244) towards TM-5 in the active state, a mechanism proposed previously for the β2 -adrenoceptor. The results provide an understanding of chemokine receptor function and thereby information for the development of biased and non-biased antagonists and inverse agonists.

Perforin-dependent direct cytotoxicity in natural killer cells induces considerable knockdown of spontaneous lung metastases and computer modelling-proven tumor cell dormancy in a HT29 human colon cancer xenograft mouse model

BACKGROUND

For long, natural killer (NK) cells have been suspected to play a critical role in suppressing the development of spontaneous metastases in cancer patients. Despite a wide range of studies it remains unclear so far to what extent primary tumor growth together with formation of distant metastases and NK cell activity influence each other.

METHODS

To precisely investigate the role of NK cells with a perforin-deficiency in cancer growth and metastasis formation, human HT29 colon cancer cells were subcutaneously grafted into pore forming protein and recombination activating gene 2 double knock out (pfp/rag2) mice and in recombination activating gene 2 only knock out (rag2) mice both with black six background. Both mice lack B and T cell functions due to the absence of rag2.

RESULTS

Primary tumors developed in 16/16 in pfp/rag2 and 20/20 rag2 mice. At sacrifice primary tumor weight did not differ significantly. However, tumors grew faster in pfp/rag2 mice (50 days) than in pfp/rag2 mice (70 days). Circulating tumor cells (CTC) in murine blood were nearly three times higher in pfp/rag2 (68 cells/ml) than in rag2 mice (24 cells/ml). Lung metastases occurred frequently in pfp/rag2 mice (13/16) and infrequently in rag2 mice (5/20). The mean number of metastases was 789 in pfp/rag2 mice compared to 210 in rag2 mice. Lung metastases in pfp/rag2 mice consisted of 10-100 tumor cells while those in rag2 mice were generally disseminated tumor cells (DTCs).Computer modelling showed that perforin-dependent killing of NK cells decelerates the growth of the primary tumour and kills 80% of CTCs. Furthermore, perforin-mediated cytotoxicity hampers the proliferation of the malignant cells in host tissue forcing them to stay dormant for at least 30 days.

CONCLUSION

The results exactly quantified the effect of perforin-dependent direct cytotoxicity of NK cells on HT29 on primary tumor growth, number of CTCs in the blood and the number of metastases. The largest effects were seen in the number of mice developing spontaneous lung metastases and the mean number of lung metastases. Hence, perforin-mediated cytotoxicity used for direct killing by NK cells is more important than indirect killing by secretion of death-inducing ligands by NK cells.

Analysing the movement of a hair swatch using video and image analysis: a promising technique for exploring the dynamic properties of hair

OBJECTIVE

The aim of this paper is to present a new instrumental evaluation method of hair movement in order to propose new criteria in the performances of hair products. The in vitro evaluation of hair swatches movement allows us to better understand the phenomena that appear when various hair care and styling technologies are applied upon the mechanisms of hair movements.

METHODS

The method consists of a video acquisition system with fast cameras (100 frames/second). The swatch is placed on a motor drive and moved with a back and forth movement. The frequency and amplitude are set by the operator. Facing each camera, a backlight provides high contrast to capture all the fibres of the swatch. A software was specifically developed to analyse the video recordings and provide the physical parameters that characterize the movement. Accordingly, it is possible to follow the surface and shape of the swatch during movement from the 'skeleton' of the swatch and to study the contraction and expansion phases of the swatch(es) during the movement together with 'the envelope' of the swatch.

RESULTS

Results show that applying various hair treatments modifies the behaviour of the swatch through the hair shapes contraction or expansion induced by the oscillating movement. Expansion of the swatch suggests that the interactions between hair fibres (adhesions or frictions) play an important role, leading to an 'individualization' of hair swatch (more 'space' between fibres) or to a 'wider' movement related to the increase of the total surface developed by the swatch. As an example, the application of a highly conditioning formula on a hair swatch largely decreases its expansion by a two-fold factor during movements and increases the horizontal amplitude by a two-fold factor, as compared to a commercial bland shampoo.

CONCLUSION

In conclusion, this method is complementary to the ones used generally to characterize global visual perceptions (colour, styling, shine). This dynamic component not only opens doors to new qualitative evaluations, linked with sensorial experts and consumers perceptions, but also to new quantitative parameters.

Fibrillar adhesion with no clusterisation: Functional significance of material gradient along adhesive setae of insects

It has been recently demonstrated that adhesive tarsal setae of beetles possess material gradients along their length. These gradients presumably represent an evolutionary optimization enhancing the adaptation to rough surfaces while simultaneously preventing clusterisation of the setae by lateral collapse. The numerical experiment of the present study has clearly demonstrated that gradient-bearing fibers with short soft tips and stiff bases have greater advantage in maximizing adhesion and minimizing clusterisation in multiple attachment-detachment cycles, if compared to the fibers with longer soft tips on the stiff bases and fibers with stiff tips on the soft bases. This study not only manifests the crucial role of gradients in material properties along the setae in beetle fibrillar adhesive system, but predicts that similar gradients must have been convergently evolved in various lineages of arthropods.

Sun protection and hydration of stratum corneum: a study by 2-D differential method

OBJECTIVE

The stratum corneum is the outermost layer of the skin. Its components and its morphology (such as the size of its cells) play a role in sun protection, and it has been noted that the stratum corneum hydration can change these properties. Sunscreens, applied on the skin, can be more or less effective depending on the stratum corneum characteristics. We therefore propose to simulate the quality of the sun protection and the effect of the stratum corneum hydration on the sun protection.

METHODS

We first determined the sunscreen distribution on a plastic substrate using an optical coherence tomography device. We were then able to calculate, by 2-D differential method, the extinction of several sunscreens. We modelled the hydration of the stratum corneum, by changing the substrate with corneocytes of different thicknesses.

RESULTS

Our results showed that hydrated stratum corneum protects more against the UV. The benefit from changing the substrate varies depending on the sunscreen applied.

CONCLUSION

We modelled sunscreens on different substrates using electromagnetic simulations. To compare these results with measurements, we have to carefully hydrate or dehydrate the SC: the simulations did not take into account modifications of the surface (water on the surface for example) or any change in the characteristics of the stratum corneum other than the modification of the corneocytes thickness.

Coracoclavicular ligaments anatomical reconstruction: a feasibility study

BACKGROUND

This study assessed the feasibility of anatomical coracoclavicular (CC) ligaments reconstruction, using three-dimensional (3D) measurement and virtual drilling.

METHODS

One-hundred-and-five 3D shoulder models were constructed using SuperImage software, based on computed tomography (CT) scan data. For each model the attachment sites and footprint dimensions of the CC ligaments were defined and adjusted according to constant anatomical ratios and individual measurement results. Different drilling techniques and 3D measurements were carried out separately on each model.

RESULTS

The collinear drilling technique with one bundle was used to breach the clavicle and/or coracoid process bone cortex in 38 of 105 models (36.2%); the percentage with two bundles was 90.5% (95/105). No cortical breach was observed using the non-collinear drilling technique.

CONCLUSIONS

The non-collinear drilling technique provides the capability to prepare bony tunnels without any risk of cortical breach.

Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: comparing histology with in silico modelling

Re-establishing a functional endothelium following endovascular treatment is an important factor in arresting neointimal proliferation. In this study, both histology (in vivo) and computational simulations (in silico) are used to evaluate neointimal growth patterns within coronary arteries along the axial direction of the stent. Comparison of the growth configurations in vivo and in silico was undertaken to identify candidate mechanisms for endothelial repair. Stent, lumen and neointimal areas were measured from histological sections obtained from eight right coronary stented porcine arteries. Two re-endothelialization scenarios (endothelial cell (EC) random seeding and EC growth from proximal and distal ends) were implemented in silico to evaluate their influence on the morphology of the simulated lesions. Subject to the assumptions made in the current simulations, comparison between in vivo and in silico results suggests that endothelial growth does not occur from the proximal and distal ends alone, but is more consistent with the assumption of a random seeding process. This may occur either from the patches of endothelium which survive following stent implantation or from attachment of circulating endothelial progenitor cells.

Edentulism, beaks, and biomechanical innovations in the evolution of theropod dinosaurs

Maniraptoriformes, the speciose group of derived theropod dinosaurs that ultimately gave rise to modern birds, display a diverse and remarkable suite of skeletal adaptations. Apart from the evolution of flight, a large-scale change in dietary behavior appears to have been one of the main triggers for specializations in the bauplan of these derived theropods. Among the different skeletal specializations, partial or even complete edentulism and the development of keratinous beaks form a recurring and persistent trend in from the evolution of derived nonavian dinosaurs. Therizinosauria is an enigmatic maniraptoriform clade, whose members display these and other osteological characters thought to be correlated with the shift from carnivory to herbivory. This makes therizinosaurians prime candidates to assess the functional significance of these morphological characters. Based on a highly detailed biomechanical model of Erlikosaurus andrewsi, a therizinosaurid from the Upper Cretaceous of Mongolia, different morphological configurations incorporating soft-tissue structures, such as a keratinous rhamphotheca, are evaluated for their biomechanical performance. Our results indicate that the development of beaks and the presence of a keratinous rhamphotheca would have helped to dissipate stress and strain, making the rostral part of the skull less susceptible to bending and displacement, and this benefit may extend to other vertebrate clades that possess rhamphothecae. Keratinous beaks, paralleled by edentulism, thus represent an evolutionary innovation developed early in derived theropods to enhance cranial stability, distinct to postulated mass-saving benefits associated with the origin of flight.

Application of D-optimal experimental design method to optimize the formulation of O/W cosmetic emulsions

OBJECTIVE

This study investigates the application of D-optimal mixture experimental design in optimization of O/W cosmetic emulsions. Cetearyl glucoside was used as a natural, biodegradable non-ionic emulsifier in the relatively low concentration (1%), and the mixture of co-emulsifiers (stearic acid, cetyl alcohol, stearyl alcohol and glyceryl stearate) was used to stabilize the formulations.

METHODS

To determine the optimal composition of co-emulsifiers mixture, D-optimal mixture experimental design was used. Prepared emulsions were characterized with rheological measurements, centrifugation test, specific conductivity and pH value measurements.

RESULTS

All prepared samples appeared as white and homogenous creams, except for one homogenous and viscous lotion co-stabilized by stearic acid alone. Centrifugation testing revealed some phase separation only in the case of sample co-stabilized using glyceryl stearate alone. The obtained pH values indicated that all samples expressed mild acid value acceptable for cosmetic preparations. Specific conductivity values are attributed to the multiple phases O/W emulsions with high percentages of fixed water. Results of the rheological measurements have shown that the investigated samples exhibited non-Newtonian thixotropic behaviour. To determine the influence of each of the co-emulsifiers on emulsions properties, the obtained results were evaluated by the means of statistical analysis (ANOVA test). On the basis of comparison of statistical parameters for each of the studied responses, mixture reduced quadratic model was selected over the linear model implying that interactions between co-emulsifiers play the significant role in overall influence of co-emulsifiers on emulsions properties.

CONCLUSION

Glyceryl stearate was found to be the dominant co-emulsifier affecting emulsions properties. Interactions between the glyceryl stearate and other co-emulsifiers were also found to significantly influence emulsions properties. These findings are especially important as they can be used for development of the product that meets users' requirements, as represented in the study.

Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk

AIMS

The level of inhibition of the human Ether-à-go-go-related gene (hERG) channel is one of the earliest preclinical markers used to predict the risk of a compound causing Torsade-de-Pointes (TdP) arrhythmias. While avoiding the use of drugs with maximum therapeutic concentrations within 30-fold of their hERG inhibitory concentration 50% (IC(50)) values has been suggested, there are drugs that are exceptions to this rule: hERG inhibitors that do not cause TdP, and drugs that can cause TdP but are not strong hERG inhibitors. In this study, we investigate whether a simulated evaluation of multi-channel effects could be used to improve this early prediction of TdP risk.

METHODS AND RESULTS

We collected multiple ion channel data (hERG, Na, L-type Ca) on 31 drugs associated with varied risks of TdP. To integrate the information on multi-channel block, we have performed simulations with a variety of mathematical models of cardiac cells (for rabbit, dog, and human ventricular myocyte models). Drug action is modelled using IC(50) values, and therapeutic drug concentrations to calculate the proportion of blocked channels and the channel conductances are modified accordingly. Various pacing protocols are simulated, and classification analysis is performed to evaluate the predictive power of the models for TdP risk. We find that simulation of action potential duration prolongation, at therapeutic concentrations, provides improved prediction of the TdP risk associated with a compound, above that provided by existing markers.

CONCLUSION

The suggested calculations improve the reliability of early cardiac safety assessments, beyond those based solely on a hERG block effect.

A computational model of quantitative chromatin immunoprecipitation (ChIP) analysis

Chromatin immunoprecipitation (ChIP) analysis is widely used to identify the locations in genomes occupied by transcription factors (TFs). The approach involves chemical cross-linking of DNA with associated proteins, fragmentation of chromatin by sonication or enzymatic digestion, immunoprecipitation of the fragments containing the protein of interest, and then PCR or hybridization analysis to characterize and quantify the genomic sequences enriched. We developed a computational model of quantitative ChIP analysis to elucidate the factors contributing to the method’s resolution. The most important variables identified by the model were, in order of importance, the spacing of the PCR primers, the mean length of the chromatin fragments, and, unexpectedly, the type of fragment width distribution, with very small DNA fragments and smaller amplicons providing the best resolution of TF binding. One of the major predictions of the model was also validated experimentally.

Computer simulation in conjunction with medical thermography as an adjunct tool for early detection of breast cancer

BACKGROUND

Mathematical modelling and analysis is now accepted in the engineering design on par with experimental approaches. Computer simulations enable one to perform several 'what-if' analyses cost effectively. High speed computers and low cost of memory has helped in simulating large-scale models in a relatively shorter time frame. The possibility of extending numerical modelling in the area of breast cancer detection in conjunction with medical thermography is considered in this work.

METHODS

Thermography enables one to see the temperature pattern and look for abnormality. In a thermogram there is no radiation risk as it only captures the infrared radiation from the skin and is totally painless. But, a thermogram is only a test of physiology, whereas a mammogram is a test of anatomy. It is hoped that a thermogram along with numerical modelling will serve as an adjunct tool. Presently mammogram is the 'gold-standard' in breast cancer detection. But the interpretation of a mammogram is largely dependent on the radiologist. Therefore, a thermogram that looks into the physiological changes in combination with numerical simulation performing 'what-if' analysis could act as an adjunct tool to mammography.

RESULTS

The proposed framework suggested that it could reduce the occurrence of false-negative/positive cases.

CONCLUSION

A numerical bioheat model of a female breast is developed and simulated. The results are compared with experimental results. The possibility of this method as an early detection tool is discussed.