Biology subjects

Schulz, R.

Publications and source records attributed to Schulz, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Matrix metalloproteinases proteolyze RAB proteins and contribute to cisplatin-induced ototoxicity

Matrix metalloproteinases (MMPs) are rapidly expressed and activated in response to oxidative stress and contribute to various pathological conditions. Cisplatin is a highly effective chemotherapeutic agent; however, its clinical use is limited by its associated permanent hearing loss (ototoxicity). While cispwlatin-induced oxidative stress and inner ear cell death are well-established, the contribution of MMPs remains unclear. In this study, we demonstrate that cisplatin exposure triggers activation of MMP-2 and MMP-9 and expression of an intracellular N-terminal-truncated isoform of MMP-2 in mouse inner ear hair cells. Pharmacological inhibition of MMP-2 and genetic knockdown of Mmp-9 enhanced hair cell survival and attenuated cisplatin-induced inflammation and cytotoxicity. Furthermore, proteomic analysis revealed that proteins involved in intracellular trafficking, including RAB proteins, may serve as potential substrates of intracellular MMP-2 upon cisplatin exposure, pointing to a previously unrecognized mechanism of cisplatin-induced hair cell injury. In vitro analysis confirmed that MMP-2 cleaves RAB9A in response to cisplatin, and in silico analyses predicted MMP-2-preferred cleavage sites on RAB9A. Collectively, our findings identify MMP-2 as a promising therapeutic target for mitigating cisplatin-induced ototoxicity.

pharmacology and toxicology↗

bioRxiv2025

Infarctsize-AI: an efficient infarct size image analysis tool for small rodent myocardial infarction studies

BackgroundMyocardial infarct size (IS) is the gold standard end-point in shorth-term studies on cardioprotection. However, IS quantification in rodent models with standard Evans Blue and 2,3,5-triphenyltetrazolium chloride (TTC) staining is time-consuming and prone to inter-observer variance. Therefore, we aimed to develop an artificial intelligence (AI)-based application to reduce time and inter-observer variability of IS analysis in rodent acute myocardial infarction (MI) models. MethodsWe used TTC/Evans blue-stained heart slice images of independent laboratories from previously published projects. Rat (n = 325 and 248 slices) and mouse (n = 77 slices) datasets were used to train deep learning segmentation models with three different neural network architectures, which were combined into a single AI analysis. AI analysis was compared with manual analysis on rat data from a training laboratory (internal data, n = 496 slices, n = 41 whole-hearts) and data from independent laboratories (external data, n = 60 and 62 slices). Additionally, two independent evaluators performed manual and AI-assisted analysis, consisting of AI-analysis and its manual correction, on internal (n = 36 slices) and external data (n = 37 slices). ResultsLins concordance correlation coefficient (CCC) between IS/AAR values from manual and AI analysis was 0.844 with 95% CI of [0.814; 0.869] for images of internal data heart slices. On external data heart slices, AI accurately annotated slice area and AAR but failed to annotate infarcted area. On internal whole-heart data, CCC between AI and AI-assisted IS/AAR was 0.894 with 95% CI of [0.812; 0.942]. AI-assisted analysis reduced evaluation time on both internal and external datasets and increased region overlap for AAR between the two independent evaluators on dependent data. ConclusionsAI-assisted analysis significantly reduced analysis time and inter-observer variability. For optimal performance, lab-specific AI training is recommended. Infarctsize-AI is available at https://infarctsize.com. Translational perspectiveMyocardial infarct size (IS) is the gold-standard end-point in shorth-term studies to assess potential cardioprotective therapies against acute myocardial infarction (AMI). However, IS quantification in rodent AMI models is time-consuming and prone to inter-observer variance. Therefore, we developed an AI-based software that can reduce analysis time and inter-observer variability and facilitate documentation, which facilitates the clinical translation of potential cardioprotective therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=34 SRC="FIGDIR/small/688527v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@187c938org.highwire.dtl.DTLVardef@1ab8bb4org.highwire.dtl.DTLVardef@160dc68org.highwire.dtl.DTLVardef@264617_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Overexpression of the MADS-box gene CRM3 in the fern Ceratopteris richardii affects sporophyte development

MADS-box genes encode MADS-domain transcription factors that play important roles in the development and evolution of land plants. Especially well-characterized is their role as organ identity genes during flower development of angiosperms. Even though the first MADS-box genes have been molecularly cloned from ferns almost 30 years ago, little is known about their function, mainly due to a lack of mutants. Also their quite broad expression domain, often comprising both the gametophytic and the sporophytic phase of the life cycle of ferns, provide few specific clues concerning gene function. However, as sister group of seed plants monilophytes (ferns and their allies such as horsetails) are of great interest in many attempts to understand both MADS-box gene and land plant evolution. Here we report, to the best of our knowledge, the first mutant phenotype based on transgenic overexpression of a fern MADS-box gene. Transgenic plants of the fern model system Ceratopteris richardii overexpressing the MIKCC-type MADS-box gene CRM3 under control of the Cauliflower Mosaic Virus (CaMV) 35S promoter show a significant reduction of the length of sporophylls. This finding reveals that overexpression of CRM3 affects sporophyll development in C. richardii, possibly by inhibiting cell proliferation or elongation.

plant biology↗

bioRxiv2025

Ceratopteris richardii U6 promoters and plants expressing Cas9 endonuclease as tools for efficient genome editing in a fern

Ferns and their allies (monilophytes) represent the second most species-rich group of land plants and are of considerable ecological importance. As a sister group of seed plants (including flowering plants) they are also of great evolutionary interest. Compared to flowering plants, however, much less is known about the developmental and molecular biology of ferns. Among the most important reasons have been the huge genome sizes of ferns and technical obstacles such as the lack of an efficient transformation system. In recent years the situation has improved considerably, however. For the fern model system Ceratopteris richardii a whole genome sequence has been published, and an efficient transformation system has been developed. To further facilitate studies on fern biology we aim at simplifying genome engineering of C. richardii with the CRISPR-Cas9 system. We report C. richardii plants that express Cas9 nuclease under control of the strong CaMV 35S promoter. For efficient expression of single guide RNA (sgRNA) by RNA polymerase III we identified C. richardii U6 promoters. These technical improvements may foster many fields of fern physiology, development and evolution.

plant biology↗

bioRxiv2024

Identification of a novel myosin antigen activating CD8+ T cells in C57BL/6 mice

Heart-specific T cells play important roles in myocardial diseases, including myocarditis, myocardial infarction, and heart failure. However, only few cardiac antigens and their respective specific T cell receptors (TCRs) have been validated so far. Therefore, we sought to identify new cardiac T cell epitopes in C57BL/6 mice and to characterize the specific TCRs. Antigen mapping of myosin heavy chain alpha (MYHCA) led to the identification of a 9-mer epitope (MYHCA724-732) recognized by CD8+ T cells. Single-cell TCR sequencing (scTCR-seq) analysis of MYHCA-stimulated CD8+ T cells enabled the identification of distinct TCRs enriched on specific T cells. Selected TCRs inferred from scTCR-seq data were then expressed on reporter cell lines and functionally validated. Our study expands the toolkit required to study heart-directed immune responses by revealing a new cardiac antigen and specific TCRs. These tools will enable in vivo characterization of myosin-specific CD8+ T cells in murine models of myocardial diseases.

immunology↗

bioRxiv2023

Cortical high gamma power relates to movement speed and is disproportionately reduced after stroke

Motor cortical high-gamma oscillations (60 to 90 Hz) occur at the onset of movement and are spatially focused over the contralateral primary motor cortex. Although high-gamma oscillations are widely recognized for their significance in human motor control, their precise function on a cortical level remains elusive. Importantly, their relevance in human stroke pathophysiology is unknown. Understanding the neurophysiological processes of motor coding could be an important step in improving motor recovery after stroke. We recorded magnetoencephalography data during a thumb movement speed task in 14 chronic stroke survivors, 15 age-matched control participants and 29 healthy young participants. Motor cortical high-gamma oscillations showed a strong relation with movement speed as trials with higher movement speed were associated with greater high-gamma power. Stroke survivors showed reduced cortical high-gamma power, surpassing the effect attributable to decreased movement speed in these participants. Even though motor skill acquisition was evident in all groups, it was not linked to high-gamma power. Our study is, to our knowledge, the first to quantify high-gamma oscillations after stroke, revealing a reduction in movement-related high-gamma power. Moreover, we provide strong evidence for a pivotal role of motor cortical high-gamma oscillations in encoding movement speed.

neuroscience↗

bioRxiv2023

Meta-analysis on the effects of chemical stressors on five ecosystem functions: are there generalizable relationships?

Despite considerable progress in our predictive capacity for the response of different trophic levels to chemical stressors, generalizable relations between chemical stressors and ecosystem functions are lacking. We addressed this knowledge gap by conducting a meta-analysis (153 studies; 350 observations) on the responses of freshwater ecosystem functions (community respiration, organic matter decomposition, nutrient cycling, photosynthesis, and primary production) under controlled conditions (laboratory or outdoor mesocosms) to pesticides, pharmaceuticals, and metals. We identified monotonic dose-response relationships between standardized chemical concentrations, in terms of toxic units, for selected chemical use groups and organic matter decomposition by decomposer-detritivore-systems as well as photosynthesis by algae and macrophytes. By contrast, consistent relationships were not found for other ecosystem functions, such as organic matter decomposition by microbial decomposers alone and primary production under the conditions studied. Importantly, the shape and direction of the relationships identified here match those reported in field-based studies, indicating a decrease in functioning as chemical stress increases, strengthening the ecological relevance of our findings. Finally, we found a disconnect between regulatory ecological quality targets and ecological outcomes, highlighting a need to re-evaluate risk assessment approaches if they are supposed to be ecologically meaningful and protective of ecosystem functions.

ecology↗

bioRxiv2023

Lesion aware automated processing pipeline for multimodal neuroimaging stroke data and The Virtual Brain (TVB)

BackgroundProcessing stroke magnetic resonance imaging (MRI) brain data can be susceptible to lesion-based abnormalities. In this study we developed and validated the Lesion Aware automated Processing Pipeline (LeAPP) that incorporates mitigation measures, improving volumetric and connectomics outputs compared to current standards in automated MRI processing pipelines. MethodsBuilding upon the Human Connectome Project (HCP) minimal processing pipeline, we introduced correction measures, such as cost-function masking and virtual brain transplant, and extended functional and diffusion processing to match acquisition protocols often found in a clinical context. A total of 51 participants (36 stroke patients (65.7{+/-}12.96 years, 18 female) and 15 healthy controls (69.2{+/-}7.4 years, 7 female)) were processed across four time points for patients (3-5, 30-40, 85-95, 340-380 days after stroke onset) and one time point for controls. Artificially lesioned brains (N=82), derived from healthy brains and informed by real stroke lesions were created, thus generating ground-truth data for validation. The processing pipeline and validation framework are available as containerized open-source software. Reconstruction quality has been quantified on whole brain level and for lesion affected and unaffected regions-of-interest (ROIs) using metrics like dice score, volume difference and center-of-gravity distance. Global and local level connectome reconstruction was assessed using node strength, node centrality and clustering coefficient. ResultsThe new pipeline LeAPP provides close reconstructions of the ground truth. Deviations in reconstructed averaged whole brain node strength and all ROI based volume and connectome metrics were significantly reduced compared to the HCP pipeline without stroke specific mitigation measures. ConclusionsLeAPP improves reconstruction quality of multimodal MRI processing for brain parcellation and structural connectome estimation significantly over the non-adapted HCP in the presence of lesions and provides a robust framework for diffusion and functional image processing of clinical stroke data. This novel open-source automated processing pipeline contributes to a development towards reproducible research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/555078v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@ca58aborg.highwire.dtl.DTLVardef@8342f4org.highwire.dtl.DTLVardef@1a0d4b9org.highwire.dtl.DTLVardef@1edf1cf_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Dispersal in Kentish plovers (Charadrius alexandrinus): Adult females perform furthest movements

Dispersal is an important behavioural process that plays a significant role in, among others, speciation, population viability, and individual fitness. Despite progress in avian dispersal research, there are still many knowledge gaps. For example, it is of interest to study how movement propensity (i.e., nomadic vs. philopatric) relates to age- and/or sex-specific patterns of dispersal. Here, we investigated the role of sex and life-stage on natal (i.e., displacement between birth site and first breeding site) and breeding dispersal (i.e., displacement between sequential breeding sites) in the Kentish plover (Charadrius alexandrinus). This small and inconspicuous wader is characterised by flexible mating behaviour that includes monogamy, and serial polygyandry. Using a continent-wide dataset of ringing and re-encounter data throughout the species range in Europe, we found that adult females generally dispersed further than adult males between seasons, but we detected no sex-difference in natal dispersal distances and no general difference between natal and breeding dispersal distances. Furthermore, females were the main group exhibiting long-distance breeding dispersal, which we defined as breeding movements greater than [≥]108 km (i.e., upper 10% percentile of our dataset). Our work detected two females breeding in the Mediterranean before dispersing and breeding at the North Sea in the subsequent year, distances of 1,290 and 1,704 km, respectively - this represents the longest known breeding dispersal within the genus Charadrius. The long-distance dispersal records we identified are consistent with low genetic differentiation between mainland populations shown in previous work. The dispersive nature of the Kentish plover is likely attributed to its breeding behaviour: polyandrous females exhibit extensive mate searching and habitat prospecting. We recommend that the dispersal traits of Kentish plover be incorporated into the species conservation and management planning to more accurately inform models of population connectivity and metapopulation dynamics.

animal behavior and cognition↗

bioRxiv2023

Early functional connectivity alterations in contralesional motor networks influence outcome after severe stroke

Connectivity studies have significantly extended the knowledge on motor network alterations after stroke. Compared to interhemispheric or ipsilesional networks, changes in the contralesional hemisphere are poorly understood. Data obtained in the acute stage after stroke and in severely impaired patients are remarkably limited. This study aimed to investigate early functional connectivity changes of the contralesional parieto-frontal motor network and their relevance for the functional outcome after severe motor stroke. Resting-state functional imaging data were acquired in 19 patients within the first two weeks after severe stroke. Nineteen healthy participants served as a control group. Functional connectivity was calculated from five key motor areas of the parieto-frontal network on the contralesional hemisphere as seed regions and compared between the groups. Connections exhibiting stroke-related alterations were correlated with clinical follow-up data obtained after 3 to 6 months. The main finding was an increase in coupling strength between the contralesional supplementary motor area and the sensorimotor cortex. This increase was linked to persistent clinical deficits at follow-up. Thus, an upregulation in contralesional motor network connectivity might be an early pattern in severely impaired stroke patients. It might carry relevant information regarding the outcome which adds to the current concepts of brain network alterations and recovery processes after severe stroke.

neuroscience↗

bioRxiv2023

Ventral premotor cortex influences spinal cord activation during force generation

Force generation is a crucial element of dexterity and a highly relevant skill of the human motor system. How cerebral and spinal components interact and how spinal activation is influenced by cerebral primary motor and premotor areas is poorly understood. Here we conducted combined cortico-spinal functional MRI during a simple visually guided isometric force generation task in a group of 20 healthy young subjects. Activation was localized in the ipsilateral cervical spinal cord and contralateral primary motor and premotor areas. The main finding is that spinal activation was influenced by ventral premotor cortex activation. Spinal activation was furthermore significantly correlated with primary motor cortex activation while increasing target forces led to an increase in the amount of activation. These data indicate that human premotor areas such as the ventral premotor cortex might be functionally connected to the lower cervical spinal cord contributing to distal upper limb functions, a finding which extends our understanding about human motor function beyond the animal literature.

neuroscience↗

bioRxiv2022

Replacing bar graphs of continuous data with more informative graphics: Are we making progress?

Recent work has raised awareness about the need to replace bar graphs of continuous data with informative graphs showing the data distribution. The impact of these efforts is not known. This observational meta-research study examined how often scientists in different fields use various graph types, and assessed whether visualization practices have changed between 2010 and 2020. We developed and validated an automated screening tool, designed to identify bar graphs of counts or proportions, bar graphs of continuous data, bar graphs with dot plots, dot plots, box plots, violin plots, histograms, pie charts, and flow charts. Papers from 23 fields (approximately 1,000 papers/field/year) were randomly selected from PubMed Central and screened (n=227,998). F1 scores for different graphs ranged between 0.83 and 0.95 in the internal validation set. While the tool also performed well in external validation sets, F1 scores were lower for uncommon graphs. Bar graphs are more often used incorrectly to display continuous data than they are used correctly to display counts or proportions. The proportion of papers that use bar graphs of continuous data varies markedly across fields (range in 2020: 4%-58%), with high rates in biochemistry and cell biology, complementary and alternative medicine, physiology, genetics, oncology and carcinogenesis, pharmacology, microbiology and immunology. Visualization practices have improved in some fields in recent years. Fewer than 25% of papers use flow charts, which provide information about attrition and the risk of bias. This study highlights the need for continued interventions to improve visualization and identifies fields that would benefit most.

scientific communication and education↗

bioRxiv2021

Microglial MorphOMICs unravel region- and sex-dependent morphological phenotypes from postnatal development to degeneration

Microglia contribute to tissue homeostasis in physiological conditions with environmental cues influencing their ever-changing morphology. Strategies to identify these changes usually involve user-selected morphometric features, which, however, have proved ineffective in establishing a spectrum of context-dependent morphological phenotypes. Here, we have developed MorphOMICs, a topological data analysis approach to overcome feature-selection-based biases and biological variability. We extracted a spatially heterogeneous and sexually-dimorphic morphological phenotype for seven adult brain regions, with ovariectomized females forming their own distinct cluster. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration models, 5xFAD and CK-p25. Females show an earlier morphological shift in the immediately-affected brain regions. Finally, we demonstrate that both the primary- and the short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs maps microglial morphology into a spectrum of cue-dependent phenotypes in a minimally-biased and semi-automatic way.

neuroscience↗

bioRxiv2021

Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus spp.) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

plant biology↗

bioRxiv2021

Linking rhizosphere processes across scales: Opinion

PurposeSimultaneously interacting small-scale rhizosphere processes determine emergent plant-scale behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. Current advances in modelling and experimental methods open the path to unravel and link those processes. MethodsWe present a series of examples of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. ResultsEach example includes a model that links scales and experimental data to set-up simulations that explain and predict spatial and temporal distribution of rhizodeposition as driven by root architecture development, soil structure, presence of root hairs, soil water content and distribution of soil water. Furthermore, two models explicitly simulate the impact of the rhizodeposits on plant nutrient uptake and soil microbial activity, respectively. This exemplifies the currently available state of the art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling and functional-structural plant modelling. We further show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. ConclusionModelling allows to integrate and make use of new experimental data across different rhizosphere processes (and thus across different disciplines) and scales. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes is the logical next step for future research.

bioengineering↗

bioRxiv2021

Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses

G protein-coupled receptors (GPCRs) regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell type-specific responses when the same GPCR is expressed on different cells within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest. We show that the chimeric DREADD-{beta}2-adrenergic receptor ({beta}2AR/ADRB2) triggers comparable responses to levalbuterol on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate {beta}2AR-mediated filopodia formation in microglia, a {beta}2AR-expressing immune cell that can drive inflammation in the nervous system. To further dissect microglial inflammation, we compared DREADD-{beta}2AR with two additionally designed DREADD-based chimeras mimicking GPR65 and GPR109A/HCAR2, both enriched in microglia. DREADD-{beta}2AR and DREADD-GPR65 modulate the inflammatory response with a similar profile as endogenously expressed {beta}2AR, while DREADD-GPR109A had no impact. Our DREADD-based approach allows investigation of cell type-dependent signaling pathways and function without known endogenous ligands.

synthetic biology↗

bioRxiv2021

Mating Strategies Of Invasive Versus Indigenous Crayfish: Multiple Paternity As Driver For Invasion Success?

The invasive spiny-cheek crayfish (Faxonius limosus) has been able to colonize many European waterbodies since its first introduction into Europe, threatening the indigenous crayfish fauna. Faxonius limosus remarkable reproductive plasticity has been suggested as an important factor contributing to this species alarming invasiveness. This is the first study comparing the reproductive strategies of an invasive (F. limosus) and a sympatric indigenous crayfish (Pontastacus leptodactylus). We investigated if and how parthenogenesis and multiple paternity contribute to the invasion process in the River Danube. Using microsatellites, we genotyped the offspring and their mothers of 11 clutches of F. limosus and 18 clutches of P. leptodactylus. While no parthenogenesis has been found in F. limosus populations, multiple paternity has been detected for the first time in both species, with comparable incidence. The results of the study indicate that multiple paternity does not play a dominant role in F. limosus successful colonization of the Danube. However, the presented results have to be regarded as pilot study, with a limited number of samples and loci investigated. Given the relevance of mating system knowledge for management measures, future studies with larger sample number could provide precious contributions to the conservation actions.

ecology↗

bioRxiv2020

EntireAxon: Deep learning deciphers four distinct patterns of axonal degeneration

BackgroundAxonal degeneration (AxD) is a pathological hallmark of many neurodegenerative diseases. Deciphering the morphological patterns of AxD will help to understand the underlying mechanisms and to develop effective therapeutic interventions. Here, we evaluated the progression of AxD in cortical neurons using a novel microfluidic device in combination with a deep learning tool, the EntireAxon, that we developed for the enhanced-throughput analysis of AxD on microscopic images. ResultsThe EntireAxon convolutional neural network sensitively and specifically segmented the features of AxD, including axons, axonal swellings, and axonal fragments, and its performance exceeded that of human expert raters. In an in vitro model of AxD in hemorrhagic stroke induced by the hemolysis product hemin, we detected the concentration- and time-dependent degeneration of axons leading to a decrease in axon area, while the axonal swelling and axonal fragment area increased. Time course analysis revealed that axonal swellings preceded axon fragmentation, suggesting that swellings may be reliable predictors of AxD. Using a recurrent neural network, we further identified four morphological patterns of AxD (granular, retraction, swelling, and transport degeneration) in cortical axons subjected to hemin. ConclusionsThese findings indicate a morphological heterogeneity of AxD under pathophysiologic conditions. The combination of the microfluidic device with the EntireAxon deep learning tool enable the systematic analysis of AxD but also unravel a so far unknown intricacy in which AxD can occur in a disease context.

neuroscience↗