Biology subjects

Loewe, A.

Publications and source records attributed to Loewe, A..

6 recordsLinked to original sources

bioRxiv2026

Label-free detection of individual virus-infected cells using deep learning

Numerous applications in research and medicine rely on reliable identification and quantification of virus-infected cells. Current methods either apply reporter viruses, that often differ from clinical isolates (e. g. cell tropism, immune evasion) or staining approaches, that prevent live-cell experiments and may introduce biases through manual counting. We present a deep learning model for the label-free identification of virus-infected cells on light microscopy images (VAIruScope). To overcome limitations, our pipeline enables an automated quantification of virus-infected cells based on the recognition of cytopathic effects. The method was applied to different cell models and four clinically relevant prototype viruses representing RNA- (influenza A virus), DNA- (human cytomegalovirus, herpes simplex virus-1) and retroviruses (human immunodeficiency virus-1). VAIruScope identified infected cells achieving classification accuracies of up to 96 %. As proof-of-concept, the method was validated using electron microscopy for a wild-type HSV-1. VAIruScope may be applicable to live-cell imaging to investigate infection dynamics.

bioinformatics↗

bioRxiv2026

Cardiomyocyte mechanical activity counteracts intraluminal calcium depletion in the transverse-axial tubular system during fast electrical stimulation

The transverse-axial tubular system (TATS) enables close structural and functional coupling between plasma membrane and sarcoplasmic reticulum of cardiomyocytes. It supports fast and efficient Ca2+-induced Ca2+ release upon cell depolarisation, crucial for excitation-contraction coupling in the heart. Due to the small diameter and tortuosity of individual tubules, the TATS forms a domain of restricted diffusive transport. It has previously been suggested that, as a consequence of an uneven distribution of Ca2+ influx and efflux pathways in TATS compared to outer surface plasma membrane domains of cardiomyocytes, cyclic electrical activity may lead to a gradual depletion of Ca2+ in the TATS. Here, we show experimentally that in mechanically uncoupled rabbit ventricular cardiomyocytes, electrical stimulation does indeed lead to an L-type Ca2+ channel-dependent gradual depletion of Ca2+ inside TATS, an effect that scales with pacing frequency. Ca2+ depletion was absent in freely contracting cardiomyocytes, presumably as a result of cyclic TATS deformation during cell shortening. This squeezes transverse TATS tubules and adds an advective contribution to, and thereby accelerates the, intra-TATS content exchange with bulk extracellular fluid. Our results reveal a novel mechanism of cardiac mechano-dependent auto-regulation, where the increased propensity for development of intra-TATS Ca2+ gradients at high electrical stimulation rates is mitigated by the coinciding mechanically induced TATS deformation, twice on each cycle in the heart (during diastolic stretch and systolic shortening), which accelerates luminal content exchange. Our study provides first insight into a novel facet of cardiac mechano-biology, whose auto-regulatory benefit may be reduced by TATS remodelling in disease.

cell biology↗

bioRxiv2024

Sympathetic Stimulation Can Compensate for Hypocalcaemia-Induced Bradycardia in Human and Rabbit Sinoatrial Node Cells

Regular activation of the heart originates from cyclic spontaneous depolarisations of sinoatrial node cells (SANC). Variations in electrolyte levels, commonly observed in haemodialysis (HD) patients, and the autonomic nervous system (ANS) profoundly affect the SANC function. Thus, we investigated the effects of hypocalcaemia and sympathetic stimulation on SANC beating rate (BR). The {beta}-adrenergic ({beta}-AR) signalling cascade, as described by Behar et al., was incorporated into the SANC models of Severi et al. (rabbit) and Fabbri et al. (human). Simulations were conducted across various extracellular calcium ([Ca2+]o) (0.6 to 1.8 mM) and isoprenaline concentrations [ISO] (0 to 1000 nM) for a sufficient time to allow transient oscillations to equilibrate and reach a limit cycle. The {beta}-AR cell response of the extended models was validated against new Langendorff-perfused rabbit heart experiments and literature data. The extended models revealed that decreased [Ca2+]o necessitated an exponential-like increase in [ISO] to restore the basal BR. Specifically, at 1.2 mM [Ca2+]o, the Severi and Fabbri model required 15.5 and 7.3 nM [ISO], respectively, to restore the initial BR. Further reduction of [Ca2+]o to 0.6 mM required 60.0 and 41.7 nM [ISO] to compensate for hypocalcaemia. A sudden loss of sympathetic tone at low [Ca2+]o resulted in extreme bradycardia or even loss of automaticity within seconds. These findings suggest that hypocalcaemic bradycardia can be compensated for by an elevated sympathetic tone. The integration of the {beta}-AR pathways led to a logarithmic BR increase and offers insights into potential pathomechanisms underlying sudden cardiac death (SCD) in HD patients. Key Points- We extended the sinoatrial node cell (SANC) models of Severi et al. (rabbit) and Fabbri et al. (human) with the {beta}-adrenergic ({beta}-AR) signalling cascade Behar et al. described. - Simulations were conducted across various extracellular calcium ([Ca2+]o) (0.6 to 1.8 mM) and isoprenaline concentrations [ISO] (0 to 1000 nM) to mimic conditions in haemodialysis patients. - An exponential-like increase in [ISO] compensated for hypocalcaemia-induced bradycardia in both models, while inter-species differences lead to more sensitivity of the extended Fabbri model towards hypocalcaemia and increased sympathetic tone. - The extended models may help to further understand the pathomechanisms of several cardiovascular diseases affecting pacemaking, such as the high occurrence of sudden cardiac death (SCD) in chronic kidney disease (CKD) patients.

cell biology↗

bioRxiv2022

Characterization of the Pace-and-Drive Capacity of the Human Sinoatrial Node: a 3D in silico Study

The sinoatrial node (SAN) is a complex structure that spontaneously depolarizes rhythmically ("pacing") and excites the surrounding non-automatic cardiac cells ("drive") to initiate each heart beat. However, the mechanisms by which the SAN cells can activate the large and hyperpolarized surrounding cardiac tissue are incompletely understood. Experimental studies demonstrated the presence of an insulating border that separates the SAN from the hyperpolarizing influence of the surrounding myocardium, except at a discrete number of sinoatrial exit pathways (SEP). We propose a highly detailed 3D model of the human SAN, including 3D SEPs to study the requirements for successful electrical activation of the primary pacemaking structure of the human heart. A total of 788 simulations investigate the ability of the SAN to pace and drive with different heterogeneous characteristics of the nodal tissue (gradient and mosaic models) and myocyte orientation. A sigmoidal distribution of the tissue conductivity combined with a mosaic model of SAN and atrial cells in the SEP was able to drive the right atrium (RA). Additionally, we investigated the influence of the SEPs by varying their number, length and width. SEPs created a transition zone of transmembrane voltage (TMV) and ionic currents to enable successful pace and drive. Unsuccessful simulations showed a hyperpolarized TMV (-66 mV), which blocked the L-type channels and attenuated the sodium-calcium exchanger. The fiber direction influenced the SEPs that preferentially activated the crista terminalis (CT). The location of the leading pacemaker site (LPS) shifted towards the SEP-free areas. LPSs were located closer to the SEP-free areas (3.46{+/-}1.42 mm), where the hyperpolarizing influence of the CT was reduced, compared to a larger distance from the LPS to the areas where SEPs were located (7.17{+/-}0.98 mm). This study identified the geometrical and electrophysiological aspects of the 3D SAN-SEP-CT structure required for successful pace-and-drive in silico. SIGNIFICANCEThe human sinoatrial node (SAN) is the intrinsic natural pacemaker of the heart. Despite its remarkable robustness to failure, the electrophysiological properties, and mechanisms by which the SAN overcomes the source-sink mismatch towards the hyperpolarized surrounding cardiac tissue remains a mystery. The SAN is electrically isolated from the hyperpolarized cardiac tissue, except at a discrete number of sinoatrial exit pathways (SEP). Using in silico experiments, we explore the influence of the fiber orientation, the SEPs number, geometry and location on the activation of the SAN and the surrounding atrial tissue. We provide the mechanisms in a first 3D model of the human SAN-SEP structure that can successfully drive the working myocardium.

physiology↗

bioRxiv2021

The openCARP Simulation Environment for Cardiac Electrophysiology

Background and ObjectiveCardiac electrophysiology is a medical specialty with a long and rich tradition of computational modeling. Nevertheless, no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could foster the needs of large parts of this community. Methods and ResultsopenCARP and the Python-based carputils framework allow developing and sharing simulation pipelines which automate in silico experiments including all modeling and simulation steps to increase reproducibility and productivity. The continuously expanding openCARP user community is supported by tailored infrastructure. Documentation and training material facilitate access to this complementary research tool for new users. After a brief historic review, this paper summarizes requirements for a high-usability electrophysiology simulator and describes how openCARP fulfills them. We introduce the openCARP modeling workflow in a multi-scale example of atrial fibrillation simulations on single cell, tissue, organ and body level and finally outline future development potential. ConclusionAs an open simulator, openCARP can advance the computational cardiac electrophysiology field by making state-of-the-art simulations accessible. In combination with the carputils framework, it offers a tailored software solution for the scientific community and contributes towards increasing use, transparency, standardization and reproducibility of in silico experiments.

bioinformatics↗

bioRxiv2019

Inter-Species Differences in the Response of Sinus Node Cellular Pacemaking to Changes of Extracellular Calcium

Changes of serum and extracellular ion concentrations occur regularly in patients with chronic kidney disease (CKD). Recently, hypocalcemia, i.e. a decrease of the extra-cellular calcium concentration [Ca2+]o, has been suggested as potential pathomechanism contributing to the unexplained high rate of sudden cardiac death (SCD) in CKD patients. In particular, there is a hypothesis that hypocalcaemia could slow down natural pacemaking in the human sinus node to fatal degrees. Here, we address the question whether there are inter-species differences in the response of cellular sinus node pacemaking to changes of [Ca2+]o. Towards this end, we employ computational models of mouse, rabbit and human sinus node cells. The Fabbri et al. human model was updated to consider changes of intracellular ion concentrations. We identified crucial inter-species differences in the response of cellular pacemaking in the sinus node to changes of [Ca2+]o with little changes of cycle length in mouse and rabbit models (<83 ms) in contrast to a pronounced bradycardic effect in the human model (up to > 1000 ms). Our results suggest that experiments with human sinus node cells are required to investigate the potential mechanism of hypocalcaemia-induced bradycardic SCD in CKD patients and small animal models are not well suited.

cell biology↗