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In the last 30 years, the field of cyclic adenosine 3′,5′-monophosphate (cAMP) signalling has witnessed a transformative development with the realization that cAMP is compartmentalized and that spatial regulation of cAMP is critical for faithful signal propagation and hormonal specificity. This recognition has changed our understanding of cAMP signalling from the canonical model, where a linear pathway connects a plasma membrane receptor to intracellular effectors and their targets, to a model where signal transduction occurs within a complex network of alternative branches and where an individual receptor leads to activation of a limited fraction of the network, enabled by local regulation of independent signalling units, resulting in a specific functional outcome. The cardiac myocyte has served as the cell model for many of the original findings leading to this paradigm. In this review, we cover some of the evidence supporting this new perspective and discuss how this model is providing novel mechanistic insight into cardiac myocyte physiology. With a focus on the regulation of cardiac rhythm, we consider how this model can provide an original framework for the identification of disease mechanisms. This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.

Coupled electro-mechanical waves define heart’s function in health and disease. Genetic abnormalities, drug-triggered or acquired pathologies can disrupt and uncouple these waves with potentially lethal consequences. Optical mapping of electrical waves using fluorescent dyes or genetically-encoded sensors in human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) offers mechanistic insights into cardiac conduction abnormalities. Interferometric dye-free/label-free wave mapping (without specific sensors) presents an alternative, likely capturing the mechanical aspects of cardiac conduction. Because of its non-invasive nature and spectral flexibility (not restricted to a specific excitation wavelength), it is an attractive chronic imaging tool in iPSC-CMs, as part of all-optical high-throughput platforms. In this study, we developed simultaneous widefield voltage and interferometric dye-free optical imaging methodology that was used: 1) to validate dye-free optical mapping for quantification of cardiac wave properties in human iPSC-CMs; 2) to demonstrate low-cost optical mapping of electromechanical waves in hiPSC-CMs using recent near-infrared (NIR) voltage sensors and orders of magnitude cheaper miniature CMOS cameras; 3) to uncover previously underexplored frequency- and space-varying parameters of cardiac electromechanical waves in hiPSC-CMs. We find similarity in the frequency-dependent responses of electrical (NIR fluorescence imaged) and mechanical (dye-free imaged) waves, with the latter being more sensitive to faster rates and showing steeper restitution and earlier appearance of wave-front tortuosity. During regular pacing, the dye-free imaged conduction velocity and the electrical wave velocity are correlated; both modalities being sensitive to pharmacological uncoupling and both dependent on gap-junctional protein (connexins) determinants of wave propagation. We uncover strong frequency-dependence of the electromechanical delay (EMD) locally and globally in hiPSC-CMs on a rigid substrate. The presented framework and results offer new means to track the functional responses of hiPSC-CM inexpensively and non-invasively for counteracting heart disease and aiding cardiotoxicity testing and drug development.

AimsSudden death after myocardial infarction (MI) is associated with electrophysiological heterogeneities and ionic remodelling, which are reflected as variable phenotypes. Low ejection fraction (EF) is used in risk stratification, but its mechanistic links with the post-MI electrophysiological heterogeneities are unknown. We aim to unravel how phenotypic ECG and EF variability in post-MI may be explained by the impact of ionic remodelling on spatio-temporal dispersion of repolarization using human biventricular electromechanical modelling and simulation.Methods and ResultsMultiple post-MI ECG phenotypes observed clinically were investigated using multi-scale modelling and simulation, calibrated and evaluated using experimental and clinical data. Acute stage T-wave inversion was caused by delayed repolarization in the epicardial border zone (BZ), and Brugada phenocopy was generated by repolarization delay and activation failure in the BZ. Upright tall T-waves in chronic MI represented large repolarisation dispersion between BZ and surrounding tissue, which promoted ectopic propagation at fast pacing. T-wave morphology alternans were present at fast-pacing due to prolonged refractoriness in the mid-myocardium. Post-MI ionic remodelling reduced EF through inhibition of calcium transient amplitude, but the EF at resting heart rate was not sensitive to the extent of repolarisation heterogeneity and the risk of repolarisation abnormalities at fast pacing.ConclusionsIn acute post-MI, ionic remodelling and its effect on refractoriness and propagation failure in the BZ have a strong impact on phenotypic ECG variability, whereas in chronic post-MI, the repolarisation dispersion across the BZ is crucial. T-wave and QT abnormalities are better indicators of repolarisation heterogeneities than EF in post-MI.

Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Wellcome Trust Background Sudden cardiac death (SCD) occurs in both acute and chronic stages post myocardial infarction (MI), and the left ventricular ejection fraction (LVEF) and electrocardiogram (ECG) characteristics are important biomarkers for clinical decision making. While various ionic remodelling has been reported in literature at various stages post-MI, the effect of them on clinical biomarkers have not been fully explored. Purpose Evaluate the effects of cellular ionic remodelling in acute and chronic post myocardial infarction on ECG and LVEF biomarkers through computational modelling and simulations of human biventricular electromechanics. Methods An electromechanical coupled biventricular model with ToR-ORd (Tomek 2019) human electrophysiology coupled with human excitation-contraction machinery (Land 2017) and orthotropic passive mechanics (Holzapfel 2009) was used as baseline model. The 12-lead ECG were simulated at standard body-surface electrode locations, and the biventricular pressure volume loop was simulated to quantify the simulated LVEF. A cardiac magnetic resonance (CMR) derived human biventricular geometry (Strocchi 2020) was used in combination with rigidly aligned torso geometry (Minchole 2019). An anterior sub-endocardial infarction was delineated with infarct, border zone (BZ) and remote zone (RZ) regions. For acute infarction, three types of BZ ionic remodelling from literature, and their effects on simulated LVEF and ECG characteristics were quantified. For chronic infarction, a single chronic BZ ionic remodelling was combine with two different models of RZ ionic remodelling from literature, and the effects of these remodelling on the simulated LVEF and ECG were quantified. The electromechanical properties of the sub-endocardial infarct region did not significantly affect simulated ECG or LVEF biomarkers. Results For the acute phase, simulations showed pre-cordial ECG abnormalities for all three BZ models, with T-wave inversion and QT prolongation (80 ms) in BZ1, ST-segment elevation with T-wave inversion in BZ2, and decreased T-wave amplitude in BZ3. Activation maps showed conduction block in BZ2 simulations, leading to ST-segment elevation. Repolarisation maps showed high dispersion in BZ1 simulations, leading to T-wave inversion. LVEF for BZ2 decreased by 4% (from 57% in control) due to conduction block in BZ and lack of contraction in that region, LVEF remained constant for BZ1 and BZ3 simulations. For the chronic phase, there was QT prolongation in both RZ1 (80 ms) and RZ2 (170 ms) as well as decreased T-wave amplitude, reflected by elevated repolarisation dispersion. LVEF was not significantly altered for either simulations. Conclusions Post-MI ionic remodelling at the acute and chronic stages cause varying degrees of dispersion of repolarisation and T-wave and ST-segment abnormalities, with minimal effect on mechanical function, except in the case of severe conduction abnormality. Abstract Figure.

Repolarization alternans, a periodic oscillation of long-short action potential duration, is an important source of arrhythmogenic substrate, although the mechanisms driving it are insufficiently understood. Despite its relevance as an arrhythmia precursor, there are no successful therapies able to target it specifically. We hypothesized that blockade of the sodium‑calcium exchanger (NCX) could inhibit alternans. The effects of the selective NCX blocker ORM-10962 were evaluated on action potentials measured with microelectrodes from canine papillary muscle preparations, and calcium transients measured using Fluo4-AM from isolated ventricular myocytes paced to evoke alternans. Computer simulations were used to obtain insight into the drug's mechanisms of action. ORM-10962 attenuated cardiac alternans, both in action potential duration and calcium transient amplitude. Three morphological types of alternans were observed, with differential response to ORM-10962 with regards to APD alternans attenuation. Analysis of APD restitution indicates that calcium oscillations underlie alternans formation. Furthermore, ORM-10962 did not markedly alter APD restitution, but increased post-repolarization refractoriness, which may be mediated by indirectly reduced L-type calcium current. Computer simulations reproduced alternans attenuation via ORM-10962, suggesting that it is acts by reducing sarcoplasmic reticulum release refractoriness. This results from the ORM-10962-induced sodium‑calcium exchanger block accompanied by an indirect reduction in L-type calcium current. Using a computer model of a heart failure cell, we furthermore demonstrate that the anti-alternans effect holds also for this disease, in which the risk of alternans is elevated. Targeting NCX may therefore be a useful anti-arrhythmic strategy to specifically prevent calcium driven alternans., Graphical abstract Unlabelled Image, Highlights • Cardiac alternans is a major proarrhythmic phenomenon with no specific treatment. • We demonstrate that NCX blockade via ORM-10962 attenuates alternans. • Three distinct morphological types of APD alternans observed. • Human cardiac simulations provide a mechanism of alternans attenuation by ORM-10962. • This is mainly due to reduced refractoriness of calcium cycling in the SR.

Cardiac arrhythmias are among the leading causes of mortality. They often arise from alterations in the electrophysiological properties of cardiac cells and their underlying ionic mechanisms. It is therefore critical to further unravel the pathophysiology of the ionic basis of human cardiac electrophysiology in health and disease. In the first part of this review, current knowledge on the differences in ion channel expression and properties of the ionic processes that determine the morphology and properties of cardiac action potentials and calcium dynamics from cardiomyocytes in different regions of the heart are described. Then the cellular mechanisms promoting arrhythmias in congenital or acquired conditions of ion channel function (electrical remodeling) are discussed. The focus is on human-relevant findings obtained with clinical, experimental, and computational studies, given that interspecies differences make the extrapolation from animal experiments to human clinical settings difficult. Deepening the understanding of the diverse pathophysiology of human cellular electrophysiology will help in developing novel and effective antiarrhythmic strategies for specific subpopulations and disease conditions.

Duchenne muscular dystrophy (DMD) is the most frequent and severe form of muscular dystrophy. The disease presents with progressive body-wide muscle deterioration and, with recent advances in respiratory care, cardiac involvement is an important cause of morbidity and mortality. DMD is caused by mutations in the dystrophin gene resulting in the absence of dystrophin and, consequently, disturbance of other proteins that form the dystrophin-associated protein complex (DAPC), including neuronal nitric oxide synthase (nNOS). The molecular mechanisms that link the absence of dystrophin with the alteration of cardiac function remain poorly understood but disruption of NO-cGMP signalling, mishandling of calcium and mitochondrial disturbances have been hypothesized to play a role. cGMP and cAMP are second messengers that are key in the regulation of cardiac myocyte function and disruption of cyclic nucleotide signalling leads to cardiomyopathy. cGMP and cAMP signals are compartmentalised and local regulation relies on the activity of phosphodiesterases (PDEs). Here, using genetically encoded FRET reporters targeted to distinct subcellular compartments of neonatal cardiac myocytes from the DMD mouse model mdx, we investigate whether lack of dystrophin disrupts local cyclic nucleotide signalling, thus potentially providing an early trigger for the development of cardiomyopathy. Our data show a significant alteration of both basal and stimulated cyclic nucleotide levels in all compartments investigated, as well as a complex reorganization of local PDE activities.

Recently, our group published a new model of human ventricular cardiomyocyte named ToR-ORd (Tomek et al., 2019). Its development, calibration, and validation, were performed using a broad range of human experimental data and brought general insights into modelling of ionic channels. Model calibration ensured the reproduction of key physiological cellular features, with independent multiscale validation demonstrating a correct response to channel blocking drugs and pathophysiological remodelling.However, for very long simulations (several hours rather than minutes), the ToR-ORd simulations display a drift in its behaviour, caused by modelling chloride concentrations as constant values. This may be a limitation for simulations considering extremely long protocols, or for studies on model stability. To remedy this, we present here an updated version, termed ToR-ORd-dynCl, with dynamic representation of intracellular chloride. This model behaves very similarly to the original ToR-ORd, but with stable properties over long simulations and only a small increase in model complexity.

OBJECTIVE The patients after Mustard and Senning corrections of transposition of the great arteries (TGA) are at an increased risk of unexpected death. The aim of this study was to identify markers allowing risk stratification of patients after atrial switch correction of TGA to provide them with optimum care. METHODS AND RESULTS In this study, 87 patients were retrospectively evaluated after atrial switch correction of TGA followed-up between 2005 and 2015. The mortality during the follow-up was 9% (8 cardiac deaths). Markers significantly predictive of death using univariable Cox proportional hazard ratio survival analysis were: N-terminal pro-B-type natriuretic peptide (NT-proBNP), ejection fraction and end-diastolic dimension of the systemic right ventricle, mitral E, e', and s'. Surprisingly, the Doppler parameters of mitral valve in subpulmonary ventricle were more important for prognosis than those of systemic tricuspid valve. In multivariable analysis, the only independent predictors of mortality were NT-proBNP (P = .00048; AUC 0.97) and the velocity of early diastolic filling (mitral E) in subpulmonary ventricle (P = .01815; AUC 0.81). According to Kaplan-Meier survival analysis, patients with NT-proBNP > 1000 pg/ml are at high risk of death. Patients with mitral E

Cardiac imaging and electrophysiological measurements yield vast amounts of data that typically need to be processed automatically. However, the detection and segmentation of calcium transients or action potentials is complicated by signal noise or signal drift, which may cause both false positive and negative segmentation. This article presents a simple but accurate ‘comb’ algorithm for detection of calcium transients and action potentials in such data where the pattern of activation is regular and its frequency is known. This corresponds either to cases where the cardiac preparation is paced externally, or where the preparation is beating in a stable rhythm. The prior knowledge of the heart rate is leveraged to overcome a broad range of artefacts and complications which arise in experimental data, such as different types of noise, signal drift, or alternans. The algorithm is simple to implement and has only a single free parameter, which is furthermore simple to set. A Matlab/Octave implementation of the comb algorithm is provided.

Alterations in autonomic function are known to occur in cardiac conditions including sudden cardiac death. Cardiac stimulation via sympathetic neurons can potentially trigger arrhythmias. Dissecting direct neural-cardiac interactions at the cellular level is technically challenging and understudied due to the lack of experimental model systems and methodologies. Here we demonstrate the utility of optical interrogation of sympathetic neurons and their effects on macroscopic cardiac monolayer dynamics to address research targets such as the effects of adrenergic stimulation via the release of neurotransmitters, the effect of neuronal numbers on cardiac wave behaviour and the applicability of optogenetics in mechanisticin vitrostudies. We combine photo-uncaging or optogenetic neural stimulation with imaging of cardiac monolayers to measure electrical activity in an automated fashion, illustrating the power and high throughput capability of such interrogations. The methods described highlight the challenges and benefits of co-cultures as experimental model systems.

Uvod: Zajistěni dobre kvality života je důležitý cil lecby pacientů s komplexni cyanotickou vrozenou srdecni vadou (VSV). V literatuře vsak neexistuje shoda o kvalitě života těchto pacientů. Cilem nasi studie bylo zhodnoceni kvality života a výskytu depresi u dospělých s původně komplexni cyanotickou VSV v dlouhodobem odstupu od operace. Metody: Vysetřili jsme celkem 212 dospělých po operaci komplexni cyanoticke VSV a 86 zdravých kontrol pomoci dotazniku hodnoceni kvality života SF-36 a Zungova dotazniku hodnoceni deprese. Vsichni pacienti byli dale dotazani na subjektivni hodnoceni vlivu VSV na jejich život, na fyzicke aktivity, funkcni třidu NYHA, vzdělani, zaměstnani, pocet děti a vsichni podstoupili echokardiograficke vysetřeni. Výsledky byly srovnany se skupinou 32 neoperovaných pacientů s komplexni cyanotickou VSV, jejichž výsledky jsme publikovali v minulosti. Výsledky: Výskyt deprese se významně nelisil mezi skupinou operovaných s VSV a zdravými kontrolami. Těžka deprese byla u 8,5 % pacientů s operovanou komplexni cyanotickou VSV a u 7 % zdravých kontrol (p = 0,816). Mezi neoperovanými pacienty s perzistujici cyanozou byl výskyt těžke deprese významně vyssi (28,1 %) oproti operovaným (p = 0,003). Kvalita života hodnocena pomoci dotazniku SF-36 se významně nelisila mezi pacienty s operovanými komplexnimi VSV a kontrolami, kromě horsiho vnimani obecneho zdravi, hodnoceni fyzických funkci a fyzickeho omezeni cinnosti. Zavěr: Pacienti s operovanou komplexni cyanotickou VSV maji v dospělosti dobrou kvalitu života, srovnatelnou s kontrolni skupinou zdravých jedinců, zatimco neoperovani pacienti s perzistujici cyanozou u komplexni VSV maji významně vyssi pocet depresi. © 2019, CKS.

Aims ST-elevation myocardial infarction is associated with high levels of cardiac sympathetic drive and release of the co-transmitter neuropeptide Y (NPY). We hypothesized that despite beta-blockade, NPY promotes arrhythmogenesis via ventricular myocyte receptors. Methods and results In 78 patients treated with primary percutaneous coronary intervention, sustained ventricular tachycardia (VT) or fibrillation (VF) occurred in 6 (7.7%) within 48 h. These patients had significantly (P Conclusions The co-transmitter NPY is released during sympathetic stimulation and acts as a novel arrhythmic trigger. Drugs inhibiting the Y1 receptor work synergistically with beta-blockade as a new anti-arrhythmic therapy.

V poslednich deseti letech bylo na Kardiochirurgickem odděleni v Nemocnici Na Homolce (NNH) provedeno celkem 844 operaci u 805 dospělých s vrozenou srdecni vadou (VSV). Median věku operovaných byl 37 let (mezikvartilove rozpěti 25-49, celkove rozpěti 16-81 let). Operace komplexnich a vzacných VSV tvořily 47 %. Ve 44 % (u 354 pacientů) se jednalo o reoperaci po předchozi operaci v dětstvi ci dospělosti, ve 14 % (113 pacientů) se jednalo o opakovanou reoperaci. Kombinovane výkony byly provedeny v 70 % připadů.Celkova 30denni mortalita cinila v celem souboru 1,36 %; hospitalizacni mortalita 1,7 %. Průměrne pětilete přeživani po operaci VSV v NNH cinilo 97 %.Mezi významne rizikove faktory casneho i pozdniho umrti po operaci VSV patřily symptomy ve třidě NYHA III-IV (p < 0,0001; OR 30,8), anamneza městnaveho srdecni selhani (p = 0,001; OR 6,7), cyanoza (p < 0,0001; OR 60,5), pocet předchozich operaci (p = 0,00033), přitomnost mechanicke chlopenni protezy (p = 0,0032; OR 3,7) a univentrikularni cirkulace (p = 0,0276; OR 5,4). Statisticke významnosti pro riziko umrti nedosahly arytmie (p = 0,078), plicni hypertenze (p = 0,072), věk v době operace (p = 0,372) a pohlavi (p = 0,48).Centralizace pece o dospěle s VSV do center s vysokým poctem výkonů a zkusenostmi přinasi velmi dobre chirurgicke výsledky s nizkou casnou i pozdni mortalitou.Důležita je vcasna indikace operace a odstraněni vsech rezidualnich nalezů kombinovaným výkonem. Přitomnost dětskeho kardiochirurga je nezbytna u operaci komplexnich VSV.

Human-based modelling and simulations are becoming ubiquitous in biomedical science due to their ability to augment experimental and clinical investigations. Cardiac electrophysiology is one of the most advanced areas, with cardiac modelling and simulation being considered for virtual testing of pharmacological therapies and medical devices. Current models present inconsistencies with experimental data, which limit further progress. In this study, we present the design, development, calibration and independent validation of a human-based ventricular model (ToR-ORd) for simulations of electrophysiology and excitation-contraction coupling, from ionic to whole-organ dynamics, including the electrocardiogram. Validation based on substantial multiscale simulations supports the credibility of the ToR-ORd model under healthy and key disease conditions, as well as drug blockade. In addition, the process uncovers new theoretical insights into the biophysical properties of the L-type calcium current, which are critical for sodium and calcium dynamics. These insights enable the reformulation of L-type calcium current, as well as replacement of the hERG current model., eLife digest Decades of intensive experimental and clinical research have revealed much about how the human heart works. Though incomplete, this knowledge has been used to construct computer models that represent the activity of this organ as a whole, and of its individual chambers (the atria and ventricles), tissues and cells. Such models have been used to better understand life-threatening irregular heartbeats; they are also beginning to be used to guide decisions about the treatment of patients and the development of new drugs by the pharmaceutical industry. Yet existing computer models of the electrical activity of the human heart are sometimes inconsistent with experimental data. This problem led Tomek et al. to try to create a new model that was consistent with established biophysical knowledge and experimental data for a wide range of conditions including disease and drug action. Tomek et al. designed a strategy that explicitly separated the construction and validation of a model that could recreate the electrical activity of the ventricles in a human heart. This model was able to integrate and explain a wide range of properties of both healthy and diseased hearts, including their response to different drugs. The development of the model also uncovered and resolved theoretical inconsistencies that have been present in almost all models of the heart from the last 25 years. Tomek et al. hope that their new human heart model will enable more basic, translational and clinical research into a range of heart diseases and accelerate the development of new therapies.

Alterations in autonomic function are known to occur in cardiac conditions including sudden cardiac death. Cardiac stimulation via sympathetic neurons can potentially trigger arrhythmias. Dissecting direct neural-cardiac interactions at the cellular level is technically challenging and understudied due to the lack of experimental model systems and methodologies. Here we demonstrate the utility of optical interrogation of sympathetic neurons and their effects on macroscopic cardiomyocyte network dynamics to address research targets such as the effects of adrenergic stimulation via the release of neurotransmitters, the effect of neuronal numbers on cardiac wave behaviour and the applicability of optogenetics in mechanistic in vitro studies. We combine photo-uncaging or optogenetic neural stimulation with imaging of cardiac monolayers to measure electrical activity in an automated fashion, illustrating the power and high throughput capability of such interrogations. The methods described highlight the challenges and benefits of co-cultures as experimental model systems.

Background DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures—each representing a mutagenic process—derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. Results We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. Conclusions Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes. Electronic supplementary material The online version of this article (10.1186/s13059-018-1509-y) contains supplementary material, which is available to authorized users.

In nature, macroscopic excitation waves1,2 are found in a diverse range of settings including chemical reactions, metal rust, yeast, amoeba and the heart and brain. In the case of living biological tissue, the spatiotemporal patterns formed by these excitation waves are different in healthy and diseased states2,3. Current electrical and pharmacological methods for wave modulation lack the spatiotemporal precision needed to control these patterns. Optical methods have the potential to overcome these limitations, but to date have only been demonstrated in simple systems, such as the Belousov–Zhabotinsky chemical reaction4. Here, we combine dye-free optical imaging with optogenetic actuation to achieve dynamic control of cardiac excitation waves. Illumination with patterned light is demonstrated to optically control the direction, speed and spiral chirality of such waves in cardiac tissue. This all-optical approach offers a new experimental platform for the study and control of pattern formation in complex biological excitable systems.

Plants engineer the rhizosphere to their advantage by secreting various nutrients and secondary metabolites. Coupling transcriptomic and metabolomic analyses of the pea (Pisum sativum) rhizosphere, a suite of bioreporters has been developed in Rhizobium leguminosarum bv viciae strain 3841, and these detect metabolites secreted by roots in space and time. Fourteen bacterial lux fusion bioreporters, specific for sugars, polyols, amino acids, organic acids, or flavonoids, have been validated in vitro and in vivo. Using different bacterial mutants (nodC and nifH), the process of colonization and symbiosis has been analyzed, revealing compounds important in the different steps of the rhizobium-legume association. Dicarboxylates and sucrose are the main carbon sources within the nodules; in ineffective (nifH) nodules, particularly low levels of sucrose were observed, suggesting that plant sanctions affect carbon supply to nodules. In contrast, high myo-inositol levels were observed prior to nodule formation and also in nifH senescent nodules. Amino acid biosensors showed different patterns: a γ-aminobutyrate biosensor was active only inside nodules, whereas the phenylalanine bioreporter showed a high signal also in the rhizosphere. The bioreporters were further validated in vetch (Vicia hirsuta), producing similar results. In addition, vetch exhibited a local increase of nod gene-inducing flavonoids at sites where nodules developed subsequently. These bioreporters will be particularly helpful in understanding the dynamics of root exudation and the role of different molecules secreted into the rhizosphere.

Two-Photon Processor (TPP) is a versatile, ready-to-use, and freely available software package in MATLAB to process data from in vivo two-photon calcium imaging. TPP includes routines to search for cell bodies in full-frame (Search for Neural Cells Accelerated; SeNeCA) and line-scan acquisition, routines for calcium signal calculations, filtering, spike-mining, and routines to construct parametric fields. Searching for somata in artificial in vivo data, our algorithm achieved better performance than human annotators. SeNeCA copes well with uneven background brightness and in-plane motion artifacts, the major problems in simple segmentation methods. In the fast mode, artificial in vivo images with a resolution of 256 × 256 pixels containing ∼100 neurons can be processed at a rate up to 175 frames per second (tested on Intel i7, 8 threads, magnetic hard disk drive). This speed of a segmentation algorithm could bring new possibilities into the field of in vivo optophysiology. With such a short latency (down to 5–6 ms on an ordinary personal computer) and using some contemporary optogenetic tools, it will allow experiments in which a control program can continuously evaluate the occurrence of a particular spatial pattern of activity (a possible correlate of memory or cognition) and subsequently inhibit/stimulate the entire area of the circuit or inhibit/stimulate a different part of the neuronal system. TPP will be freely available on our public web site. Similar all-in-one and freely available software has not yet been published.

DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures – each representing a mutagenic process – derived from 3056 patients spanning 19 cancer types to quantify the asymmetry of mutational signatures around replication origins and between early and late replicating regions. We observe that 22 out of 29 mutational signatures are significantly impacted by DNA replication. The distinct associations of different signatures with replication timing and direction around origins shed new light on several mutagenic processes, for example suggesting that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. Together, our results indicate an involvement of DNA replication and associated damage repair in most mutagenic processes.

Hypertension induces considerable cardiac remodelling, such as hypertrophy, interstitial fibrosis, and abnormal activity of the cardiac sympathetic nervous system, which are established risk factors in several highly dangerous heart diseases, such as ventricular fibrillation and congestive heart failure. All these risk factors and heart diseases are studied extensively in isolation, but to our knowledge, there is no comprehensive review of their interactions. At the same time, there is growing evidence suggesting that such interactions are numerous and that a successful therapy against a particular condition may have unexpectedly weak effects on mortality, as treated patients may die of a different cause exacerbated by the therapy. In this article, we present a multiscale review of the literature focusing on the relationships between the above‐mentioned risk factors and heart diseases, and introduce a framework that gives insight into their possible interactions. We use this framework to demonstrate that conditions such as fibrosis and elevated activity of the sympathetic nervous system may be compensatory, rather than purely pathological, mechanisms in certain contexts. Finally, we show why the described mechanisms are relevant not only in hypertension, but also in the case of healed myocardial infarction.