Evolution of anthocyanidin synthase in Hawaiian silverswords and California tarweeds

Includes bibliographical references (leaves 25-30)One of the most spectacular examples of insular adaptive radiation can be found among the Hawaiian silverswords (Asteraceae-Madiinae). This monophyletic group was transported to the Hawaiian archipelago about five million years ago, and today comprises 32 species in three genera. Having to adapt to very varied and dynamic environments, the plants display stunning morphological and physiological diversity. However, their genotypic diversity is low, as evidenced by the ease with which species of different genera form hybrids in nature and in the lab. This discrepancy can be explained by differences in just a few key loci, which could modify entire pathways. The closest relatives of the silverswords are thought to be the tarweeds (Asteraceae-Madiinae) on the west coast ofNorth America. Two tarweed ancestors hybridized to form the allotetraploid ancestor of all known silverswords, which was then transported to the Hawaiian islands, most likely by a bird. The pathway I am concemed with is the anthocyanin-producing pathway, in particular anthocyanidin synthase (ANS), a late gene in the pathway. Anthocyanins are pigments responsible for blue, red and purple color in flowers. However, due to their many other functions, such as light attenuation in chloroplasts, I expect the genes of this pathway, including ANS, to be intact in most silverswords, even though only one species has red flowers. I also expect to find two copies in silverswords due to tetraploidy. Degenerate primers were designed in conserved regions of ANS and PCR was done to obtain the gene from two tarweeds (Madia elegans, Madia gracilis) and two silverswords (Dubautia linearis, Wilkesia gymnoxiphium). Gene sequences were spliced and edited with BioEdit, and were aligned with ClustalW 1.8. A maximum likelihood tree was made with MEGA 5, and a bayesian tree was made with MrBayes 3 .1.2. A Z-test of selection and a Ka/Ks test were done using MEGA 5. A RACE reaction wasperfonned on mRNA from the flowers of M elegans. The entire gene (except 20bp of primers in the flanking regions) of two exons and one intron was sequenced from all species studied. The RACE in M elegans produced the entire gene, and showed there was some expression in the floral tissues of this plant. As expected, two copies were found in the silverswords and only one in each of the tarweeds. No premature stop codons were found within coding sequences. Phylogenetic analysis groups the Madiinae separately from other Asteraceae, and the tarweeds separately from the silverswords. Within the siverswords, copy 1 from both species is separate from copy 2 from both species. Interestingly, intron size seems to be conserved within the tarweeds and copy 2 (547bp), and also within copy 1 (485bp). Purifying selection was detected in the silversword copies, while no positive selection was found in any copy. The positions of all copies studied and their relative position to other Asteraceae support the allopolyploid origin of the silverswords. Each copy in the silverswords most likely came from each of the two mainland ancestors. Given the overall similarity of the sequences within all Madiinae, it is reasonable to conclude that the gene starts and ends in the same position in all Madiinae. The lack of premature stop codons indicates that the gene may be at the very least functional, although we have no knowledge of its level of expression within the floral or other tissues. The flower color of all plants in this study is yellow, indicating no accumulation of anthocyanins, although they may be found in other tissues. The lab is cunently investigating the sequences of other genes in the pathway, and future studies will focus on sequencing the promoter region and known regulators of ANS expression. This will give us a more complete picture of the evolution of the pathway, helping us understand the genetic mechanisms behind adaptive radiations

Influence of geometrical properties for the calculation of a pressure-free whole heart geometry

Individualized computer models of the geometry of the human heart are often based on magnetic resonance images (MRI) or computed tomography (CT) scans. The stress distribution in the imaged state cannot be measured but needs to be estimated from the segmented geometry, e.g. by an iterative algorithm. As the convergence of this algorithm depends on different geometrical conditions, we systematically studied their influence. Beside various shape alterations, we investigated the chamber volume, as well as the effect of material parameters. We found a marked influence of passive material parameters: increasing the model stiffness by a factor of ten halved the residual norm in the first iteration. Flat and concave areas led to a reduced robustness and convergence rate of the unloading algorithm. With this study, the geometric effects and modeling aspects governing the unloading algorithm\u27s convergence are identified and can be used as a basis for further improvement

Causes of altered ventricular mechanics in hypertrophic cardiomyopathy: an in-silico study

Hypertrophic cardiomyopathy (HCM) is typically caused by mutations in sarcomeric genes leading to cardiomyocyte disarray, replacement fibrosis, impaired contractility, and elevated filling pressures. These varying tissue properties are associated with certain strain patterns that may allow to establish a diagnosis by means of non-invasive imaging without the necessity of harmful myocardial biopsies or contrast agent application. With a numerical study, we aim to answer: how the variability in each of these mechanisms contributes to altered mechanics of the left ventricle (LV) and if the deformation obtained in in-silico experiments is comparable to values reported from clinical measurements

Estimating cardiac active tension from wall motion—An inverse problem of cardiac biomechanics

The contraction of the human heart is a complex process as a consequence of the interaction of internal and external forces. In current clinical routine, the resulting deformation can be imaged during an entire heart beat. However, the active tension development cannot be measured in vivo but may provide valuable diagnostic information. In this work, we present a novel numerical method for solving an inverse problem of cardiac biomechanics—estimating the dynamic active tension field, provided the motion of the myocardial wall is known. This ill‐posed non‐linear problem is solved using second order Tikhonov regularization in space and time. We conducted a sensitivity analysis by varying the fiber orientation in the range of measurement accuracy. To achieve RMSE 0.95). The results obtained with non‐matching input data are promising and indicate directions for further improvement of the method. In future, this method will be extended to estimate the active tension field based on motion data from clinical images, which could provide important insights in terms of a new diagnostic tool for the identification and treatment of diseased heart tissue

Sequential Coupling Shows Minor Effects of Fluid Dynamics on Myocardial Deformation in a Realistic Whole-Heart Model

Background: The human heart is a masterpiece of the highest complexity coordinating multi-physics aspects on a multi-scale range. Thus, modeling the cardiac function in silico to reproduce physiological characteristics and diseases remains challenging. Especially the complex simulation of the blood's hemodynamics and its interaction with the myocardial tissue requires a high accuracy of the underlying computational models and solvers. These demanding aspects make whole-heart fully-coupled simulations computationally highly expensive and call for simpler but still accurate models. While the mechanical deformation during the heart cycle drives the blood flow, less is known about the feedback of the blood flow onto the myocardial tissue. Methods and Results: To solve the fluid-structure interaction problem, we suggest a cycle-to-cycle coupling of the structural deformation and the fluid dynamics. In a first step, the displacement of the endocardial wall in the mechanical simulation serves as a unidirectional boundary condition for the fluid simulation. After a complete heart cycle of fluid simulation, a spatially resolved pressure factor (PF) is extracted and returned to the next iteration of the solid mechanical simulation, closing the loop of the iterative coupling procedure. All simulations were performed on an individualized whole heart geometry. The effect of the sequential coupling was assessed by global measures such as the change in deformation and—as an example of diagnostically relevant information—the particle residence time. The mechanical displacement was up to 2 mm after the first iteration. In the second iteration, the deviation was in the sub-millimeter range, implying that already one iteration of the proposed cycle-to-cycle coupling is sufficient to converge to a coupled limit cycle. Conclusion: Cycle-to-cycle coupling between cardiac mechanics and fluid dynamics can be a promising approach to account for fluid-structure interaction with low computational effort. In an individualized healthy whole-heart model, one iteration sufficed to obtain converged and physiologically plausible results

Electro-mechanical whole-heart digital twins: A fully coupled multi-physics approach

Mathematical models of the human heart are evolving to become a cornerstone of precision medicine and support clinical decision making by providing a powerful tool to understand the mechanisms underlying pathophysiological conditions. In this study, we present a detailed mathematical description of a fully coupled multi-scale model of the human heart, including electrophysiology, mechanics, and a closed-loop model of circulation. State-of-the-art models based on human physiology are used to describe membrane kinetics, excitation-contraction coupling and active tension generation in the atria and the ventricles. Furthermore, we highlight ways to adapt this framework to patient specific measurements to build digital twins. The validity of the model is demonstrated through simulations on a personalized whole heart geometry based on magnetic resonance imaging data of a healthy volunteer. Additionally, the fully coupled model was employed to evaluate the effects of a typical atrial ablation scar on the cardiovascular system. With this work, we provide an adaptable multi-scale model that allows a comprehensive personalization from ion channels to the organ level enabling digital twin modeling

Model Based Estimation of the Elastomechanical Properties of the Human Heart

Das menschliche Herz ist ein komplexes Organ, in dem verschiedene Phänomene zusammenwirken. Einerseits fließt das Blut durch die Herzkammern und übt Druck auf die Innenflächen aus. Andererseits ist das Herz von einem Herzbeutel umgeben, der die Bewegung der Kammern beeinflusst. Darüber hinaus breiten sich elektrische Wellen durch das Herzgewebe aus und initiieren die Kontraktion des Herzmuskels, welche, addiert zu der passiven Kraft, dem Kammerdruck entgegenwirkt und zur Deformation des Myokards führt. In den letzten Jahren wurden fortschrittliche Computermodelle des Herzens entwickelt und in Simulationsumgebungen integriert, um den menschlichen Herzschlag zu untersuchen. Zusätzlich ermöglicht die rasante Weiterentwicklung der bildgebenden Verfahren in den letzten Jahren die Gewinnung patientenspezifischer Informationen, die auf ein valides Herzmodell übertragen werden können, um Rückschlüsse auf Eigenschaften des Gewebes zu ermöglichen. Informationen über Gewebeeigenschaften können neue Erkenntnisse über die Physiologie und Pathophysiologie des Herzens liefern. Sie können neue Wege zur Diagnose von Krankheiten eröffnen und detaillierte Informationen über Mechanismen des Herzschlages liefern, die auf andere Weise nicht zu erhalten sind. Insbesondere können Computermodelle eingesetzt werden, um elastomechanische Eigenschaften des Herzgewebes zu bestimmen: die passive Kraft, die sich aus den intrinsischen elastischen Materialeigenschaften des Gewebes ergibt und die aktive Kraft (Spannung), die zur Kontraktion des Herzgewebes führt. In dieser Arbeit werden Schritte zur Abschätzung der elastomechanischen Eigenschaften des Herzgewebes vorgestellt und diskutiert. Ein menschliches Ganzherzmodell wurde basierend auf in vivo MRT-Bildern erstellt. Die Deformation des Gewebes wurde mit der Simulationsumgebung \textit{CardioMechanics} simuliert und mit Hilfe von Volumenkurven, regionalen Wanddicken und Deformationsgeschwindigkeiten aus klinischen Daten validiert. Weitere Deformationsmessungen (regionale Dehnungen, Dehnungsraten und Geschwindigkeiten) wurden mit Literaturwerten verglichen, um die Validität des entwickelten gesunden Herzmodells zu demonstrieren. Nachdem ein gültiges Modell erstellt wurde, ist eine Sensitivitätsstudie durchgeführt worden, um den Einfluss der elastomechanischen Eigenschaften auf die Deformationsmessungen zu quantifizieren. Dies war eine Voraussetzung für die modellbasierte Schätzung der elastomechanischen Eigenschaften. In einer weiteren Studie wurde das geometrische Herzmodell modifiziert, um Pathologien zu simulieren, die bei der hypertrophen Kardiomyopathie auftreten. Es wurde gezeigt, welche pathologischen Mechanismen die ventrikuläre Verformung beeinflussen. Nachdem gezeigt wurde, dass die passiven elastomechanischen Eigenschaften des Herzgewebes die Deformationsmessungen des linken Ventrikels beeinflussen, wurden diese Eigenschaften mit Hilfe eines Optimierungsverfahrens geschätzt. Die Parameter des Modells, das die passive Kraft beschreibt, wurden basierend auf einer Druck-Volumen-Relation aus der Literatur unter Anwendung einfacher und robuster Optimierungsmethoden ermittelt. In dieser Arbeit wird gezeigt, dass eine Zielfunktion, die nur auf dieser Relation basiert, keinen eindeutigen Parametersatz liefern konnte und daher wurde sie um einen zusätzlichen Term erweitert, der ein absolutes Volumenverhältnis beinhaltet. Weiterhin wurde ein dynamisches aktives Kraftfeld aus Bewegungsdaten des linken Ventrikels mit Hilfe eines inversen Lösers rekonstruiert, um eine Sensitivitätsanalyse mit synthetischen Daten durchzuführen. Mit Hilfe einer zusätzlichen räumlichen Regularisierung stimmte die Morphologie der rekonstruierten aktiven Kraftkurve mit der Grundwahrheit überein, während die Amplitude der rekonstruierten Kraft unterschiedlich war. Trotz der Rekonstruktionsfehler in der aktiven Kraft konnten unterschiedlich große Infarktgebiete in der inversen Lösung genau identifiziert werden. Unter Verwendung von endokardialen Bewegungsdaten, die aus klinisch gemessenen Bildern abgeleitet wurden, rekonstruierte die Methode einen aktiven Kraftverlauf. Allerdings sind weitere Untersuchungen erforderlich, um die Methode direkt auf klinische Daten anzuwenden. Insgesamt wurde die Konstruktion eines Herzmodells und die Validierung eines simulierten Herzschlags vorgestellt und Schritte zur Abschätzung der elastomechanischen Eigenschaften des Herzgewebes geliefert. Die beschriebenen Ergebnisse weisen Richtungen für zukünftige Verbesserungen auf und zeigen insbesondere, dass mehr Eingabedaten benötigt werden, um realistische Ergebnisse zu erzielen

Effects of local activation times on the tension development of human cardiomyocytes in a computational model

The human heart is an organ of high complexity and hence, very challenging to simulate. To calculate the force developed by the human heart and therefore the tension of the muscle fibers, accurate models are necessary. The force generated by the cardiac muscle has physiologically imposed limits and depends on various characteristics such as the length, strain and the contraction velocity of the cardiomyocytes. Another characteristic is the activation time of each cardiomyocyte, which is a wave and not a static value for all cardiomyocytes. To simulate a physiologically correct excitation, the functionality of the cardiac simulation framework CardioMechanics was extended to incorporate inhomogeneous activation times. The functionality was then used to evaluate the effects of local activation times with two different tension models. The active stress generated by the cardiomyocytes was calculated by (i) an explicit function and (ii) an ode-based model. The results of the simulations showed that the maximum pressure in the left ventricle dropped by 2.3% for the DoubleHill model and by 5.3% for the Lumens model. In the right ventricle the simulations showed similar results. The maximum pressure in both the left and the right atrium increased using both models. Given that the simulation of the inhomogeneously activated cardiomyocytes increases the simulation time when used with the more precise Lumens model, the small drop in maximum pressure seems to be negligible in favor of a simpler simulation mode

Effects of local activation times on the tension development of human cardiomyocytes in a computational model

The human heart is an organ of high complexity and hence, very challenging to simulate. To calculate the force developed by the human heart and therefore the tension of the muscle fibers, accurate models are necessary. The force generated by the cardiac muscle has physiologically imposed limits and depends on various characteristics such as the length, strain and the contraction velocity of the cardiomyocytes. Another characteristic is the activation time of each cardiomyocyte, which is a wave and not a static value for all cardiomyocytes. To simulate a physiologically correct excitation, the functionality of the cardiac simulation framework CardioMechanics was extended to incorporate inhomogeneous activation times. The functionality was then used to evaluate the effects of local activation times with two different tension models. The active stress generated by the cardiomyocytes was calculated by (i) an explicit function and (ii) an ode-based model. The results of the simulations showed that the maximum pressure in the left ventricle dropped by 2.3% for the DoubleHill model and by 5.3% for the Lumens model. In the right ventricle the simulations showed similar results. The maximum pressure in both the left and the right atrium increased using both models. Given that the simulation of the inhomogeneously activated cardiomyocytes increases the simulation time when used with the more precise Lumens model, the small drop in maximum pressure seems to be negligible in favor of a simpler simulation model

Validating a Numerical Simulation of Human Heart Motion Using Clinical Data

Numerical simulations are increasingly often involved in developing new and improving existing medical therapies. While the models involved in those simulations are designed to resemble a specific phenomenon realistically, the results of the interplay of those models are often not sufficiently validated. We created a plugin for a cardiac simulation framework to validate the simulation results using clinical MRI data. The MRI data were used to create a static wholeheart mesh as well as slices from the left ventricular short axis, providing the motion over time. The static heart was a starting point for a simulation of the heart’s motion. From the simulation result, we created slices and compared them to the clinical MRI slices using two different metrics: the area of the slices and the point distances. The comparison showed global similarities in the deformation of simulated and clinical data, but also indicated points for potential improvements. Performing this comparison with more clinical data could lead to personalized modeling of elastomechanics of the heart