Biology subjects

Koenig, L.

Publications and source records attributed to Koenig, L..

10 recordsLinked to original sources

bioRxiv2026

Probing the neural geometry of conscious object perception in time

Conscious object recognition is a critical brain function, key to making sense of the plethora of visual inputs and guiding adaptive behavior. Yet, the sequence of neural processing underlying conscious object recognition remains unclear. Existing proposals alternatively suggest that conscious object recognition proceeds in a "coarse-to-fine" sequence or a "fine-to-coarse" sequence. Here, we recorded high-density EEG while participants of both sexes performed a threshold-level object recognition task under different viewing conditions. Both superordinate and basic-level category information emerged early in neural activity, followed by a late superordinate category representation in an abstract format that is disentangled from low-level object features. Strikingly, in the early period, while basic-level category information positively correlated with perceptual awareness, superordinate category information negatively predicted perceptual awareness. By contrast, both superordinate and basic-level category information positively correlated with objective categorization accuracy in the early period. In the late period, both levels of category information positively correlated with awareness. These results suggest that neural processing underlying conscious object perception proceeds from the basic to the superordinate category level.

neuroscience↗

bioRxiv2026

Electric signal polymorphism predicts dietary niche partitioning in a weakly electric fish

Electric organ discharge (EOD) waveform diversity in African elephantfish is often attributed to sexual selection, yet EODs also mediate active electrolocation during prey detection, raising the possibility that natural selection on foraging ecology contributes to waveform divergence. Paramormyrops kingsleyae exhibits an intraspecific polymorphism where certain populations emit biphasic EODs whereas other populations emit triphasic waveforms. The genes underlying this polymorphism show signatures of selection; the polymorphism persists despite gene flow and is behaviorally discriminable by the fish themselves. If waveform differences influence prey detection during active electrolocation, biphasic and triphasic fish should consume systematically different prey. We tested this prediction using DNA metabarcoding of gut contents from 186 mormyrids representing 16 species across eight sites in Gabon, employing two independent COI primer sets for cross-validation and pairing dietary data with environmental invertebrate sampling to distinguish active prey preference from passive availability. At the community level in the diverse Bale Creek mormyrid assemblage, species identity was the dominant predictor of diet composition (R{superscript 2} {approx} 24%), consistent with phylogenetic signal in foraging ecology. Within P. kingsleyae, waveform type was the strongest independent predictor of dietary composition (R{superscript 2} = 5-6%), explaining variance independently of geographic region, sex, body size, and parasitism status -- a result concordant across both primer sets. Dietary differences were driven by prey species turnover rather than differential abundance of shared prey, and prey selectivity analyses confirmed that waveform types differ in which prey they actively prefer, not merely in what is locally available. These findings are consistent with natural selection on foraging ecology contributing to the maintenance of EOD waveform polymorphism, though the sensory mechanisms linking subtle waveform differences to prey detection remain an open question.

ecology↗

bioRxiv2026

The Genomic Basis of Electric Signal Diversity

Behavioral diversity is a striking result of species diversity, shaped by intertwined mechanisms, developmental pathways, and evolutionary histories. Yet the genetic underpinnings of behavioral evolution remain obscure, even though they are key to understanding how organisms adapt and diversify. Weakly electric African elephantfishes provide a rare opportunity to dissect the genetics of behavior because their electric communication signals are quantifiable, stereotyped, and directly tied to identifiable cellular mechanisms. Among elephantfishes, electric organ discharges (EODs) vary widely across species and populations, shaping mate choice, social interactions, and reproductive isolation. A key axis of this diversity is the presence or absence of an initial phase in the EOD waveform--a discrete, repeated evolutionary transition whose genetic basis has remained unresolved. Here we show, using whole-genome resequencing, population-genomic analyses, transcriptomics, and histology from 306 specimens, that biphasic EODs in Paramormyrops kingsleyae have evolved repeatedly through independent de novo regulatory mutations at distinct genomic loci. These population-specific mutations occur exclusively in noncoding regions, show localized signatures of selection, and are associated with differences in gene expression and protein localization in the electric organ, indicating that they act through cis-regulatory mechanisms affecting electrocyte development. These findings challenge the expectation that repeated within-species adaptations primarily draw from standing ancestral variation, revealing instead that the developmental program underlying electric signaling contains multiple points of regulatory sensitivity. Distinct genetic changes can therefore produce the same behavioral phenotype, enabling repeated evolutionary transitions even within a single species. More broadly, our results show how developmental architecture shapes the evolutionary pathways available to behavior, helping explain why communication signals in elephantfishes--and in other radiations--diversify so rapidly.

evolutionary biology↗

bioRxiv2025

Re-enacting steps supports human path integration consistent with motor-corrected grid cell drift

Efficient navigation, especially in the absence of vision, requires path integration -- the continuous updating of spatial position from self-motion cues. However, path integration is prone to cumulative error, which can be amplified when body-derived information is inconsistent between encoding and retrieval paths. Drawing on evidence from sensorimotor reactivation during memory retrieval, we hypothesized that re-enacting encoding-related movement patterns could serve as a body-derived mechanism to counteract such errors. In a novel virtual reality task with motion tracking, participants learned unique, irregular step sequences linked to specific target distances during an encoding phase. They later reproduced these distances in complete darkness under three conditions: self-paced free retrieval, retrieval with encoding-congruent movements, and retrieval with encoding-incongruent, regular gait. During free retrieval, participants naturally re-enacted encoding-related movements associated with improved distance reproduction. As predicted, distance estimation was significantly more accurate during congruent retrieval than during incongruent retrieval. These behavioral findings are consistent with a neural network model in which retrieved encoding-related motor patterns correct path integration errors in grid cells. Together, these results provide converging behavioral and computational evidence that body-derived, encoding-related motor patterns can enhance distance estimation, possibly by filtering grid cell error accumulation, offering new insights into embodied mechanisms of path integration.

neuroscience↗

bioRxiv2025

Locomotion-dependent use of geometric and body cues in humans mapping 3D space

The ability to represent locations across multiple dimensions of space is a core function of cognitive maps. While the influence of boundary-dependent environmental geometry on spatial representations has been extensively studied in 2D spaces, less is known about the role of boundaries for volumetric spatial memory. Research in humans and other animals has demonstrated distinct processing of the vertical and horizontal spatial dimensions, likely related to species-specific modes of locomotion. Here, we investigate whether different locomotion modes, flying and walking, affect the use of vertical boundaries, leading to possibly distinct volumetric representations. In a Virtual Reality experiment, human participants memorized objects within a symmetric 3D enclosure, and then were asked to replace them in either the familiar or geometrically deformed environments. We found that the flying group exhibited lower vertical than horizontal spatial memory precision, whereas the walking group showed the opposite pattern, an effect related to using their body axis as a vertical "ruler". Within deformed environments, object replacements in the flying group followed the predictions from a 3D-extended boundary-vector-cell-like computational model of spatial mapping that treated all boundaries equally, whereas those in the walking condition favored a modified model that prioritized the ground boundary. Our findings suggest that gravity-related movement constraints promote different utilization of geometric and body-related cues, resulting in flexible representations of volumetric space.

neuroscience↗

bioRxiv2022

Patterns of NFkB activation resulting from damage, reactive microglia, cytokines, and growth factors in the mouse retina

Muller glia are a cellular source for neuronal regeneration in vertebrate retinas. However, the capacity for retinal regeneration varies widely across species. Understanding the mechanisms that regulate the reprogramming of Muller glia into progenitor cells is key to reversing the loss of vision that occurs with retinal diseases. In the mammalian retina, NF{kappa}B signaling promotes glial reactivity and represses the reprogramming of Muller glia into progenitor cells. Here we investigate different cytokines, growth factors, cell signaling pathways, and damage paradigms that influence NF{kappa}B-signaling in the mouse retina. We find that exogenous TNF and IL1{beta} potently activate NF{kappa}B-signaling in Muller glia in undamaged retinas, and this activation is independent of microglia. By comparison, TLR1/2 agonist indirectly activates NF{kappa}B-signaling in Muller glia, and this activation depends on the presence of microglia as Tlr2 is predominantly expressed by microglia, but not other types of retinal cells. Exogenous FGF2 did not activate NF{kappa}B-signaling, whereas CNTF, Osteopontin, WNT4, or inhibition of GSK3{beta} activated NF{kappa}B in Muller glia in the absence of neuronal damage. By comparison, dexamethasone, a glucocorticoid agonist, suppressed NF{kappa}B-signaling in Muller glia in damaged retinas, in addition to reducing numbers of dying cells and the accumulation of reactive microglia. Although NMDA-induced retinal damage activated NF{kappa}B in Muller glia, optic nerve crush had no effect on NF{kappa}B activation within the retina, whereas glial cells within the optic nerve were responsive. We conclude that the NF{kappa}B pathway is activated in retinal Muller glia in response to many different cell signaling pathways, and activation often depends on signals produced by reactive microglia.

neuroscience↗

bioRxiv2022

Sound Frequency Predicts the Bodily Location of Auditory-Induced Tactile Sensations in Synesthetic and Ordinary Perception

For individuals who experience sound-touch synesthesia, sounds consistently evoke strong, localized sensations on the body. Interestingly, visual and auditory information can also evoke bodily sensations in ordinary perception, such as the sight or sound of a mosquito producing phantom sensations of touch. We systematically investigated the functional relationship between sound frequency and several characteristics of induced tactile experiences in synesthetes and controls. Sound frequency strongly predicted the location of tactile sensations on the body in both synesthetes and controls. Synesthetes felt sound-induced touch more frequently and in significantly more concentrated locations on their bodies compared to sound-induced touch perceptions in controls. This spatial distribution of touch reflects a behavioral mapping between tonotopy and somatotopy that suggests the involvement of early, tonotopically- and somatotopically-organized brain areas. Sound frequency also predicted the hardness, roughness, and sharpness of tactile sensations in both groups. Together, these findings highlight a strong similarity between auditory-tactile mappings in synesthetic and ordinary perception, suggesting that synesthesia only differs in the strength of the mappings and therefore is on a spectrum with ordinary perception. Furthermore, these findings offer insights into the possible underlying neural mechanisms of sound-touch mappings, suggesting that they rely on cross-modal neural pathways already in use in ordinary perception.

neuroscience↗

bioRxiv2021

Differential regulation of degradation and immune pathways underlies adaptation of the symbiotic nematode Laxus oneistus to oxic-anoxic interfaces

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also upregulated when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worms Toll- like innate immunity pathway and several immune effectors (e.g., Bacterial Permeability Increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires oxidative phosphorylation and by reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.

genomics↗

bioRxiv2020

Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology or metabolism. Here, by applying omics, Raman microspectroscopy and stable isotope labelling, we investigated the effect of oxygen on Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated in oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that Ca. T. oneisti may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation by the ectosymbiont. IMPORTANCEChemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One long standing hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of Candidatus Thiosymbion oneisti, a Gammaproteobacterium which lives attached to marine nematodes inhabiting shallow water sand. Surprisingly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

microbiology↗

bioRxiv2018

Towards an autologous iPSC-derived patient-on-a-chip

Microphysiological systems are fundamental for progressing towards a global paradigm shift in drug development through the generation of patient-on-a-chip models. An increasing number of single- and multi-organ systems have been adopted by the pharmaceutical and cosmetic industries for predictive substance testing. These models run on heterogeneous tissues and cell types from different donors. However, a patient is an individual. Therefore, patient-on-a-chip systems need to be built from tissues from one autologous source. Individual on-chip organ differentiation from a single induced pluripotent stem cell source could provide a solution to this challenge.\n\nWe designed a four-organ chip based on human physiology. It enables the interconnection of miniaturized human intestine, liver, brain and kidney equivalents. All four organ models were predifferentiated from induced pluripotent stem cells from the same healthy donor and integrated into the microphysiological system. The cross talk led to further differentiation over a 14-day cultivation period under pulsatile blood flow conditions in one common medium deprived of growth factors. This model platform will pave the way for disease induction and subsequent drug testing.

bioengineering↗