Biology subjects

Koenig, P.

Publications and source records attributed to Koenig, P..

12 recordsLinked to original sources

bioRxiv2026

Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function

Structural variants (SVs) are abundant in plant genomes and influence agronomic traits, yet their regulatory interpretation remains challenging. Here, we combine pangenome-wide profiling of DNA methylation and chromatin accessibility across 20 barley genotypes, complemented by histone modification and chromatin interaction data in a subset of 10 genotypes. Comparative analysis of genotype-specific epigenomes reveals a globally conserved DNA methylation landscape across the barley pangenome alongside extensive regulatory variability at orthologous genes. We show that SVs do not broadly remodel global chromatin landscapes but instead act through context-dependent rewiring of local regulatory interactions. Despite this epigenomic stability, SVs may contribute to gene expression changes via chromatin contacts. Tissue-specific chromatin accessibility demonstrates that SV effects depend on developmental context. Integrating chromatin state variation with SVs at key vernalization genes explains epigenetic contributions to growth habit diversity. Together, these results provide a framework for interpreting the regulatory consequences of structural variation in crop genomes.

plant biology↗

bioRxiv2026

Infection Tunes the Dynamics of Adenoviral E1A Disordered Regions

Intrinsically Disordered Proteins and protein regions (IDPs) are abundant in many viral proteomes and play diverse roles in the viral infectious cycles. The adenovirus Early Protein 1A (E1A) is one such viral IDP. E1A acts as a molecular hub that regulates viral infection by mediating interactions between viral and multiple host proteins. Like other IDPs, E1A exists in a flexible ensemble of conformations. Despite a demonstrated link between ensemble structure and function in E1A, no real-time measurement of its ensemble has been performed. Here, we use live cell FRET microscopy to measure the local ensemble structure of E1A in human cells, both in healthy cells and in cells infected with adenovirus. We found specific disordered regions undergo significant changes to their ensemble in infected cells. Furthermore, infection also alters the propensity of these regions to partition between the cytoplasm and nucleus, a hallmark of E1A function during infection. Our results showcase that the structural ensembles of viral IDPs are responsive to infection, and suggest that these may play a role in regulating infection progression. SignificanceIntegral to many viral proteomes are intrinsically disordered proteins and protein regions (IDPs), which target and rewire cellular pathways to ensure infection progression. During this process, the physical and chemical composition of the cell changes dramatically: metabolism is rewired, viral proteins are produced en masse, and as a result, the chemical composition of the host proteome is significantly altered. IDPs are known to be structurally sensitive to even mild changes in their environment, and their structural changes can result in a change to function. Here, using live cell FRET microscopy, we show that the structure and spatial localization of an adenovirus IDP, E1A, is altered in cells infected by the virus. Beyond a possible functional role for structural sensitivity in viral IDP function, our findings suggest that host IDPs may also be structurally altered by infection, with downstream functional consequences.

biophysics↗

bioRxiv2025

Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells

While extracellular vesicles (EVs) are established mediators of intra-species signaling, their role as active participants in cross-kingdom communication remains incompletely understood. Here, we reveal that human colon cells and both Gram-positive and Gram-negative gut bacteria engage in species-specific, EV-mediated molecular dialogue, driven in part by RNA cargo. We show that bacterial EVs (BEVs) induce distinct transcriptomic responses in human cells, and that BEV-RNA independently causes similar effects. Conversely, we demonstrate that human EVs and highly abundant miR-192-5p are differentially internalized by bacteria, affecting their physiology. Our findings support a conceptual model in which EVs function as directional messengers that shape host-microbiome interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease. Highlights[1] L. casei, E. faecalis and P. mirabilis produce BEVs that are internalized by Caco-2 cells at different rates. BEVs produced by L. casei have a positive influence on the viability of Caco-2 cells. Incubation of Caco-2 cells with BEVs leads to changes in the gene expression of immune-response-related genes. [2] BEVs carry RNAs and the type of RNA cargo varies significantly between the BEVs from the different bacteria. Comparison of Caco-2 gene deregulation between BEVs and transfection of RNA isolated from BEV highlights component-specific effects. [3] Caco-2 EVs are taken up by E. faecalis and influence their growth. MiRNA-192-5p can be frequently detected in EVs from Caco-2 cells. Synthetic miR-192-5p is internalized by P. mirabilis and the ability to take up human miRNAs by L. casei and E. faecalis can be increased by packaging of the miRNA in artificial liposomes.

molecular biology↗

bioRxiv2024

Saccade onset, not fixation onset, best explains early sensory responses across the human visual cortex during naturalistic vision

Visual processing is traditionally studied using static viewing paradigms in which researchers analyse brain responses to the onsets of a sequence of randomly selected stimuli. Translating this "stimulus onset" approach to active vision paradigms that allow for free eye-movements, researchers often consider fixation onsets as the events that trigger visual activity across the visual system. Here, we test this assumption by analysing a large-scale magnetoencephalography (MEG) dataset with simultaneously recorded eye movements of 5 participants who freely explored thousands of natural images, yielding approximately 200,000 gaze events. We show that saccade-related events, particularly peak saccade curvature, rather than fixation onsets, explain most variance in latency of the early sensory component M100. Further, comparing the classic M100 elicited by stimulus onsets with the M100s elicited during active vision revealed stark differences, both in response to saccade-related and fixation-onset events. This indicates that phenomena discovered using gold standard stimulus onset paradigms do not necessarily translate to natural vision. Our findings challenge the prevailing approach to studying vision in static paradigms and highlight the importance of internally generated and action-driven signals in the dynamics of natural sensory processing.

neuroscience↗

bioRxiv2024

The Three Stages of Learning to Master a Sensory Augmentation Device: Activation - Acquisition - Integration

By augmenting sensory perception through technology, researchers study how humans use and perceive the novel sensory input provided. Nevertheless, little is known about how learning unfolds over time. To this end, 27 participants trained with an augmentation device (feelSpace belt), which provides tactile feedback about the direction of the cardinal north, over the course of six weeks. During the training phase, we tracked participants progress using two different self-report questionnaires containing Likert-scale and open questions. Experts quantified responses to open questions using a previously established category system. As human raters are known to be susceptible to biases, we later reproduced the expert categorization using ChatGPT-4, finding a high congruence between the two classification approaches. The results suggest a three-stage model that best describes the process of acquiring an augmented sense. During the early activation stage, processing the augmented signal requires effort, induces fatigue, and a heightened awareness of the environment. In the knowledge acquisition phase, participants develop a more detailed cognitive spatial representation containing information about objects and places in relation to their current location. The deep integration stage is marked by participants seamlessly integrating the augmented information into existing perceptual processes and automatic use. The results support the supervised use of large language models (LLMs) for the analysis of qualitative data.

neuroscience↗

bioRxiv2024

Low-Dimensional Representations of Visuomotor Coordination for Natural Behavior

Understanding how the eyes, head, and hands coordinate in natural contexts is a critical challenge in visuomotor coordination research, often constrained by sedentary tasks, cued actions, or restricted settings. To address this gap, we conducted an experiment where participants could self-generate pick-and-place actions on a life-size shelf in a virtual environment, recording concurrent gaze and body movements. Subjects exhibited intricate translation and rotation movements of the eyes, head, and hands during the task. We employed a time-dependent principal component analysis to study the relationship between the movements of the eyes, head, and hands relative to the onset of the action. We reduced the overall dimensionality into 2D representations, capturing up to 65% of the movement variance just in time with the actions. Our analysis revealed a synergistic coupling of the eye-head and eye-hand systems, as well as a strong coupling within the head-hand system. The eyes synchronized with the head and hands close to the action onset, with variations in coupling observed in horizontal and vertical planes, indicating distinct mechanisms for coordination in the brain. Crucially, the head and hands remained tightly coupled throughout the observation period, suggesting a shared neural code driving these effectors. Notably, the low-dimensional representations of the eye-head-hand movement vectors showed maximum predictive accuracy of the actions location ~200ms before the action onset, highlighting just-in-time coordination among the three effectors. Furthermore, the predictive accuracy was significantly influenced by the location of the upcoming action. Our study emphasizes the differential visuomotor control subject to the task structure, providing insights into the dynamic interplay of eye, head, and hand movements during natural behavior. NEW & NOTEWORTHYStudying natural, self-initiated, complex visuomotor coordination, we observe low-dimensional dynamics with distinct patterns along horizontal and vertical axes. The eyes horizontal movement showed notable independence, aligning with head and hand movements just in time for action. Notably, around critical events, the dimensionality of the complex movements is further reduced, indicating dynamic correspondence of eye-head-hand coordination.

neuroscience↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2023

InCellCryst - A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins

With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by conventional methods extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely unmodified proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, new strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.

biophysics↗

bioRxiv2021

Realism Matters. Eye movements in VR reveal prior tool knowledge, intended interaction, and end-state comfort planning

AO_SCPLOWBSTRACTC_SCPLOWSeminal studies on human cognitive behavior have been conducted in controlled laboratory settings, demonstrating that visual attention is mainly goal-directed and allocated based on the action performed. However, it is unclear how far these results generalize to cognition in more naturalistic settings. The present study investigates active inference processes revealed by eye movements during interaction with familiar and novel tools with two levels of realism of the action affordance. We presented participants with 3D tool models that were either familiar or unfamiliar, oriented congruent or incongruent to their handedness, and asked participants to interact with them by lifting or using. Importantly, we used the same experimental design in two setups. In the first experiment, participants interacted with a VR controller in a low realism environment; in the second, they performed the task with an interaction setup that allowed differentiated hand and finger movements in a high realism environment. We investigated the differences in odds of fixations and their eccentricity towards the tool parts before action initiation. The results show that participants fixate more on the tools effector part before action initiation for the use task for unfamiliar tools. Furthermore, with more realistic action affordances, subjects fixate more on the tools handle as a function of the tools orientation, well before the action was executed. Secondly, the spatial viewing bias on the tool reveals early fixations are influenced by the task and the familiarity of the tools. In contrast, later fixations are associated with the manual planning of the interaction. In sum, the findings from the experiments suggest that fixations are made in a task-oriented way to plan the intended action well before action initiation. Further, with more realistic action affordances, fixations are made towards the proximal goal of optimally planning the grasp even though the perceived action on the tools is identical for both experimental setups. Taken together, proximal and distal goal-oriented planning is contextualized to the realism of action/interaction afforded by an environment.

neuroscience↗

bioRxiv2021

Wild lab: A naturalistic free viewing experiment reveals previously unknown EEG signatures of face processing.

Neural mechanisms of face perception are predominantly studied in well-controlled experimental settings that involve random stimulus sequences and fixed eye positions. While powerful, the employed paradigms are far from what constitutes natural vision. Here, we demonstrate the feasibility of ecologically more valid experimental paradigms using natural viewing behavior, by combining a free viewing paradigm on natural scenes, free of photographer bias, with advanced data processing techniques that correct for overlap effects and co-varying nonlinear dependencies of multiple eye movement parameters. We validate this approach by replicating classic N170 effects in neural responses, triggered by fixation onsets (fERPs). Importantly, our more natural stimulus paradigm yielded smaller variability between subjects than the classic setup. Moving beyond classic temporal and spatial effect locations, our experiment furthermore revealed previously unknown signatures of face processing. This includes modulation of early fERP components, as well as category-specific adaptation effects across subsequent fixations that emerge even before fixation onset.

neuroscience↗

bioRxiv2021

Just-in-time: gaze guidance behavior while action planning and execution in VR

Natural eye movements have primarily been studied for over-learned activities such as tea-making, sandwich-making, and hand-washing, which have a fixed sequence of associated actions. These studies indicate a sequential activation of low-level cognitive schemas facilitating task completion. However, it is unclear if these action schemas are activated in the same pattern when a task is novel and a sequence of actions must be planned in the moment. Here, we recorded gaze and body movements in a naturalistic task to study action-oriented gaze behavior. In a virtual environment, subjects moved objects on a life-size shelf to achieve a given order. In order to compel cognitive planning, we added complexity to the sorting tasks. Fixations aligned with the action onset showed gaze as tightly coupled with the action sequence, and task complexity moderately affected the proportion of fixations on the task-relevant regions. Our analysis further revealed that the gaze was allocated to action-relevant targets just in time. Planning behavior predominantly corresponded to a greater visual search for task-relevant objects before the action onset. The results support the idea that natural behavior relies very little on working memory, and humans refrain from encoding objects in the environment to plan long-term actions. Instead, they prefer just-in-time planning by searching for action-relevant items in the moment, directing their body and hand to it, monitoring the action until it is terminated, and moving on to the next action. Author SummaryEye movements in the natural environment have primarily been studied for over-learned and habitual everyday activities (tea-making, sandwich-making, hand-washing) with a fixed sequence of associated actions. These studies show eye movements correspond to a specific order of actions learned over time. In this study, we were interested in how humans plan and execute actions for tasks that do not have an inherent action sequence. To that end, we asked subjects to sort objects based on object features on a life-size shelf in a virtual environment as we recorded their eye and body movements. We investigated the general characteristics of gaze behavior while acting under natural conditions. Our paper provides a comprehensive approach to preprocess naturalistic gaze data in virtual reality. Furthermore, we provide a data-driven method of analyzing the different action-oriented functions of gaze. The results show that bereft of a predefined action sequence, humans prefer to plan only their immediate actions where eye movements are used to search for the target object to immediately act on, then to guide the hand towards it, and to monitor the action until it is terminated. Such a simplistic approach ensures that humans choose sub-optimal behavior over planning under sustained cognitive load.

neuroscience↗

bioRxiv2019

A new comprehensive Eye-Tracking Test Battery concurrently evaluating the Pupil Labs Glasses and the EyeLink 1000

Eye-tracking experiments rely heavily on good data quality of eye-trackers. Unfortunately, it is often that only the spatial accuracy and precision values are available from the manufacturers. These two values alone are not sufficient enough to serve as a benchmark for an eye-tracker: Eye-tracking quality deteriorates during an experimental session due to head movements, changing illumination or calibration decay. Additionally, different experimental paradigms require the analysis of different types of eye movements, for instance smooth pursuit movements, blinks or microsaccades, which themselves cannot readily be evaluated by using spatial accuracy or precision alone. To obtain a more comprehensive description of properties, we developed an extensive eye-tracking test battery. In 10 different tasks, we evaluated eye-tracking related measures such as: the decay of accuracy, fixation durations, pupil dilation, smooth pursuit movement, microsaccade detection, blink detection, or the influence of head motion. For some measures, true theoretical values exist. For others, a relative comparison to a gold standard eye-tracker is needed. Therefore, we collected our gaze data simultaneously from a gold standard remote EyeLink 1000 eye-tracker and compared it with the mobile Pupil Labs glasses. As expected, the average spatial accuracy of 0.57{degrees} for the EyeLink 1000 eye-tracker was better than the 0.82{degrees} for the Pupil Labs glasses (N=15). Furthermore, we detected less fixations and shorter saccade durations for the Pupil Labs glasses. Similarly, we found fewer microsaccades using the Pupil Labs glasses. The accuracy over time decayed only slightly for the EyeLink 1000, but strongly for the Pupil Labs glasses. Finally we observed that the measured pupil diameters differed between eye-trackers on the individual subject level but not the group level. To conclude, our eye-tracking test battery offers 10 tasks that allow us to benchmark the many parameters of interest in stereotypical eye-tracking situations, or addresses a common source of confounds in measurement errors (e.g. yaw and roll head movements). All recorded eye-tracking data (including Pupil Labs eye video files), the stimulus code for the test battery and the modular analysis pipeline are available (https://github.com/behinger/etcomp). BVE, KG, II and PK conceived the experiment. II and BVE created the experiment and recorded the gaze data. BVE and KG performed the analysis. BVE, KG and PK reviewed the manuscript critically.

neuroscience↗