Biology subjects

Baer, M.

Publications and source records attributed to Baer, M..

9 recordsLinked to original sources

bioRxiv2025

Ethylene signal-driven plant-multitrophic synergy boosts crop performance

Efficient nutrient use in agriculture depends on the dynamic interplay between plant roots, soil, and microbial communities. The root-rhizosphere interface is central to nutrient uptake and serves as a key hub for interactions with beneficial microbes. Arbuscular mycorrhizal (AM) fungi, positioned at the nexus between plant roots and soil microbiota, play a critical role in enhancing crop performance under nutrient-limited conditions. In this study, we dissected the genetic and molecular basis of AM fungi-induced lateral root development in maize (Zea mays), focusing on the role of ethylene-responsive transcription factors (ERFs). We identified ERF genes as essential regulators of pericycle cell division, acting downstream of ethylene biosynthesis genes (ACS6 and ACS7) and AM fungal signaling. Our findings reveal that AM fungi promote lateral root initiation by activating ERF expression and reprogramming flavonoid metabolism, particularly reducing the accumulation of flavonols such as kaempferol and quercetin, which otherwise inhibit root development when over-accumulated. Furthermore, we demonstrated that Massilia, a beneficial rhizobacterium, synergizes with AM fungi to enhance lateral root formation by colonizing fungal hyphae, degrading flavonoids, and contributing to auxin production. Together, our results uncover a tripartite signaling network linking ethylene signaling, flavonoid-mediated microbial recruitment, and AM symbiosis. This study highlights ERFs as central integrators of plant-microbe interactions and provides a molecular framework for engineering root architecture and microbiome assembly to improve nutrient acquisition and support sustainable crop productivity.

plant biology↗

bioRxiv2025

Forecasting bryozoan assemblage dynamics under simulated climate change

The shallow Antarctic continental shelf experiences strong physical disturbances in the form of ice-scour which play a key role in maintaining biodiversity. Due to climate change, both the extent and duration of sea ice cover is expected to rapidly decline, leading to complex shifts in disturbance regimes with unknown impacts on successional dynamics and biodiversity in benthic communities. We introduce a simulation model to study the assemblage dynamics of Bryozoa, which are sessile, suspension feeding animals and key pioneers in the shallows. The model captures colonisation events, colony growth as well as intra- and interspecific overgrowth competition for space between colonies. Mortality due to predation is modelled as the removal of zooids within small areas of the model world. Using the model, we simulate various disturbance regimes, e.g. by varying the timing of ice-scour events, the length of the growing season and the spatial distribution of predation events. We find that the timing of ice-scour events throughout the growing season has only minor short-term effects on successional dynamics in bryozoan assemblages, while an extended growing season substantially accelerates succession in the long term. We furthermore find that relatively rare but large predation events lead to a slower recovery, whereas relatively frequent but small events result in a faster succession with higher overall abundances. These results highlight that in order to understand how benthic biodiversity will be impacted by climate change, it is necessary to consider the interplay between biotic interactions and complex changes in physical disturbance regimes. HighlightsO_LIWe use an individual-based model to simulate climate change impacts on bryozoan assemblages. C_LIO_LIWarming leads to complex shifts in timing and spatial distribution of disturbances. C_LIO_LISuccessional dynamics are affected by changes in growing season and predation events. C_LIO_LIInterplay of biotic interactions and physical disturbances drives benthic biodiversity. C_LI

ecology↗

bioRxiv2024

Synchronization and metachronal waves of elastic cilia caused by transient viscous flow

Hydrodynamic coordination of cilia is ubiquitous in biology. It is commonly modeled using the steady Stokes equations. The flow around ciliated cells, however, exhibits finite time vorticity diffusion, requiring a dynamical description. We present a model of elastic cilia coupled by transient viscous flow in the bulk fluid. Therein, vorticity diffusion impacts cilia coordination qualitatively and quantitatively. In particular, pairs of cilia synchronize in antiphase for long diffusion times. Moreover, metachronal waves occur in cilia chains larger than the viscous penetration depth, whereas global synchronization occurs in Stokes flow.

biophysics↗

bioRxiv2023

Hydrodynamic synchronization of elastic cilia: How flow confinement determines the characteristics of metachronal waves

Cilia are hair-like micro-actuators whose cyclic motion is specialized to propel extracellular fluids at low Reynolds numbers. Clusters of these organelles can form synchronized beating patterns, called metachronal waves, which presumably arise from hydrodynamic interactions. We model hydrodynamically interacting cilia by microspheres elastically bound to circular orbits, whose inclinations with respect to the cellular wall model the ciliary power and recovery stroke, resulting in an anisotropy of the viscous flow. We derive a coupled phase oscillator description by reducing the microsphere dynamics to the slow time scale of synchronization and determine analytical metachronal wave solutions and their stability in a periodic chain setting. In this framework, a simple intuition for the hydrodynamic coupling between phase oscillators is established by relating the geometry of near-wall flow to the directionality of the hydrodynamic coupling functions. This intuition naturally explains the properties of the linear stability of metachronal waves. The flow confinement at the wall stabilizes metachronal waves with long wavelengths propagating in the direction of the power stroke and, moreover, metachronal waves with short wave lengths propagating perpendicularly to the power stroke. Performing simulations of phase oscillator chains with periodic boundary conditions, we indeed find that both wave types emerge with a variety of linearly stable wave numbers. In open chains of phase oscillators, the dynamics of metachronal waves is fundamentally different. Here, the elasticity of the model cilia controls the wave direction and selects a particular wave number: At large elasticity, waves traveling in the direction of the power stroke are stable, whereas at smaller elasticity waves in the opposite direction are stable. For intermediate elasticity both wave directions coexist. In this regime, waves propagating towards both ends of the chain form, but only one wave direction prevails, depending on the elasticity and initial conditions.

biophysics↗

bioRxiv2023

Mechanism of defibrillation of cardiac tissue by periodic low-energy pacing

Rotating excitation waves and electrical turbulence in excitable cardiac tissue are associated with arrhythmias such as life-threatening ventricular fibrillation. Experimental studies (S. Luther et al., Nature 475, 235-239 (2011)). have shown that a time-periodic sequence of low-energy electrical far-field pulses is able to terminate fibrillation more gently than a single high-energy pulse. During this so called low-energy antifibrillation pacing (LEAP), only tissue near sufficiently large conduction heterogeneities, such as large coronary arteries, is activated. Based on extensive simulations and simple theoretical reasoning, we present a comprehensive unified mechanism for successful LEAP in two spatial dimensional systems, which is able to explain both the termination of stable spirals and of spatiotemporal chaos. We carried out extensive simulations (more than 500000 runs for each considered model) varying pacing periods, pacing field strength and initial conditions using a model of cardiac tissue perforated by blood vessels, which was found earlier to reproduce the behavior seen in the LEAP experiments for different dynamical regimes and different cellular models (P. Buran et al., Chaos 27, 113110 (2017) and New J. Phys. 24 083024 (2022)). We studied altogether three different cellular models to capture qualitatively different kinds of fibrillatory states like stable spirals and spatiotemporal chaos. To achieve a mechanistic understanding of the simulation results, we have investigated a variety of macroscopic observables characterizing an excitable medium with respect to their correlation with the success of an individual low-energy pulse during LEAP. We found in all considered cases that the refractory boundary length LRB, the total length of the borders between refractory and excitable parts of the tissue, displays the strongest correlation with the success of the pacing and thus predicts best the success of an individual LEAP pulse. Furthermore, we found the success probability PL decays exponentially with this length according to PL = exp(- k(E)LRB), where E is the strength of the electrical field in pacing and k(E) is a monotonically decreasing function of E. A closer look at the spatiotemporal dynamics in the simulations reveals that actually each pulse during LEAP annihilates practically all defects and excitation fronts, however, also induces new pairs of defects and associated excitation fronts at the refractory boundaries. The success probability of each individual pulse can thus be simply interpreted as the probability that no new rotor pair gets created by the shock, while all existing defects get annihilated. This assumption allows to derive the observed exponential dependence of the success probability on the refractory boundary length, where the prefactor k(E) in the exponent is equal (for stable spirals) or proportional (for spatiotemporal chaos) to the probability{lambda} (E) that a new rotor pairs is created by the shock along a segment of unit length along the refractory boundary. Our findings are in conformity with the upper limit of vulnerability (ULV) hypothesis, which states that the single pulse defibrillation threshold is simply given by the lowest field strength, where no new rotor pairs arise as a result of the shock. LEAP operates at field strengths (and energies) below this ULV limit. Successful LEAP protocols are characterized by a coordinated interplay between the pulses, that gradually decreases the refractory boundary length and therefore simultaneously increases the success probability until complete defibrillation is achieved.

biophysics↗

bioRxiv2023

Heritable maize microbiomes contribute to local adaptation and host stress resilience

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adapted Zea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbe Massilia and source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

genetics↗

bioRxiv2022

ENHANCED GRAVITROPISM 2 coordinates molecular adaptations to gravistimulation in the elongation zone of barley roots

O_LIRoot gravitropism includes gravity perception in the root cap, signal transduction between root cap and elongation zone, and curvature response in the elongation zone. The barley (Hordeum vulgare) mutant enhanced gravitropism 2 (egt2) displays a hypergravitropic root phenotype. C_LIO_LIWe compared the transcriptomic reprogramming of the root cap, the meristem and the elongation zone of wild type and egt2 seminal roots upon gravistimulation in a time-course experiment and identified direct interaction partners of EGT2 by yeast-two-hybrid screening and bimolecular fluorescence complementation (BiFC) validation. C_LIO_LIWe demonstrated that the elongation zone is subjected to most transcriptomic changes after gravistimulation. Here, 35% of graviregulated genes are also transcriptionally controlled by EGT2, suggesting a central role of this gene in controlling the molecular networks associated with gravitropic bending. Gene co-expression analyses suggested a role of EGT2 in cell wall and reactive oxygen species (ROS)-related processes, in which direct interaction partners of EGT2 regulated by EGT2 and gravity might be involved. C_LIO_LITaken together, this study demonstrated the central role of EGT2 and its interaction partners in the networks controlling root zone-specific transcriptomic reprogramming of barley roots upon gravistimulation. These findings can contribute to the development of novel root idiotypes leading to improved crop performance. C_LI

plant biology↗

bioRxiv2021

Suppression of fibrillation consisting of stable rotors by periodic pacing

Recent experimental studies have shown that a sequence of low-energy electrical far-field pulses is able to terminate fibrillation with substantially lower per-pulse energy than a single high-energy electric shock (see S. Luther et al. Nature 475 (7355), 235-239). During this low-energy antifibrillation pacing (LEAP) procedure only tissue near sufficiently large conduction heterogeneities, such as large coronary arteries, is activated. In order to understand the mechanism behind LEAP, We have carried out a statistical study of resetting a medium filled by one or more stable spirals ("rotors") in a two-dimensional electrophysiological model of cardiac tissue perforated by blood vessels to the resting state ("defibrillation"). We found the highest success probabilities for this defibrillation for underdrive pacing with periods 10 - 20 percent larger than the dominant period of the stable rotors in the unperturbed dynamics. If a sufficiently large number pulses is applied and an optimal pacing period chosen, the energy per pulse required for successful defibrillation is about 75 - 80 percent lower than the energy needed for single-shock defibrillation. Optimal conditions to control and suppress fibrillation based on stable rotors, hence, are similar to the ones in found for the case of an electrophysiological model displaying spatiotemporal chaos ("electrical turbulence") in an earlier study (see P. Buran et al. Chaos 27, 113110 (2017)). The optimal pacing period is found to increase with increasing strength of the electrical field strength used in the model. The success probability also increases strongly until the fourth or fifth pulse administered, which is strongly correlated to an observed increase of the fraction of re-excitable tissue with each subsequent pulse. Monitoring the fraction of excitable tissue in the model as key quantity of the excitable medium, moreover, enabled us to successfully predict the optimal pacing period for defibrillation.

biophysics↗

bioRxiv2017

Dual Function For Tango1 In Secretion Of Bulky Cargo And In ER-Golgi Morphology

Tango1 helps the efficient delivery of large proteins to the cell surface. We show here that loss of Tango1, in addition to interfering with protein secretion, causes ER stress and defects in cell and ER/Golgi morphology. We find that the previously observed dependence of smaller cargos on Tango1 is a secondary effect, due to an indirect requirement: if large cargos like Dumpy, which we identify here as a new Tango1 cargo, are removed from the cell, non-bulky proteins re-enter the secretory pathway. Removal of the blocking cargo also attenuates the ER-stress response, and cell morphology is restored. Thus, failures in the secretion of non-bulky proteins, ER stress and defective cell morphology are secondary consequences of the retention of cargo. By contrast, the ERES defects in Tango1-depleted cells persist in the absence of bulky cargo, showing that they are due to a secretion-independent function of Tango1. Therefore, the maintenance of proper ERES architecture may be a primary function for Tango1.

cell biology↗