Biology subjects

Kirchner, J.

Publications and source records attributed to Kirchner, J..

5 recordsLinked to original sources

bioRxiv2025

VESNA: An Open-Source Tool for Automated 3D Vessel Segmentation and Network Analysis

BackgroundVasculature is an essential part of all tissues and organs and is involved in a wide range of different diseases. However, available software for blood vessel image analysis is often limited: Some only process two-dimensional data, others lack batch processing, putting a time burden on the user, while still others require tightly defined culturing methods and experimental conditions. This highlights the need for a software that has the ability to batch process three-dimensional image data and requires few and simple experimental preparation steps. ResultsWe present VESNA, a Fiji (ImageJ) macro for automated segmentation and skeletonization of three-dimensional fluorescence images, enabling quantitative vascular network analysis. It requires only basic experimental preparation, making it highly adaptable to a wide range of possible applications across experimental goals and different tissue culturing methods. The macros potential is demonstrated on a range of different image data sets, from organoids with varying sizes, network complexities, and growth conditions to expanding to other 3D tissue culturing methods with an example of hydrogel-based cultures. ConclusionsWith its ability to process large amounts of 3D image data and its flexibility across experimental conditions, VESNA fulfills previously unmet needs in image processing of vascular structures and can be a valuable tool for a variety of experimental setups around three-dimensional vasculature, such as drug screening, research in tissue development and disease mechanisms.

bioinformatics↗

bioRxiv2023

Trade-offs between immunity and competitive ability in fighting ant males

BackgroundFighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colonys worker force. ResultsWe found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on. ConclusionsMales of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk.

evolutionary biology↗

bioRxiv2022

Eyeball translations affect saccadic eye movements beyond brainstem control

Vision requires that we rotate our eyes frequently to look at informative structures in the scene. Eye movements are planned by the brain but their execution depends on the mechanical properties of the oculomotor plant, i.e, the arrangement of eyeball position, muscle insertions and pulley locations. Therefore, the biomechanics of rotations is sensitive to eyeball translation because it changes muscle levers. Eyeball translations are little researched as they are difficult to measure with conventional techniques. Here we study the effects of eyeball translation on the coordination of gaze rotation by high-speed MRI recordings of saccadic eye movements during blinks, which are known to produce strong translations. We found that saccades during blinks massively overshoot their targets, and that these overshoots occur in a transient fashion such that the eye is back on target at the time the blink ends. These dynamic overshoots were tightly coupled to the eyeball translation, both in time and in size. Saccades made without blinks were also accompanied by small amounts of transient eyeball retraction, the size of which scaled with saccade amplitude. These findings demonstrate the complex interaction between rotation and translation movements of the eye. The mechanical consequences of eyeball translation on oculomotor control should be considered along with the neural implementation in the brain to understand the generation of eye movements and their disorders.

neuroscience↗

bioRxiv2022

All the ways your eyes can move if you don't look: Eyeball lifting, retraction and compression during blinks

Blinks occur frequently in normal life and have increasingly been linked to perceptual and cognitive effects. However, the oculomechanics of blink-related eye movements are much less researched than other types of eye movements. While it has been observed that the eye is being pulled back into its socket during a blink, possibly due to co-contraction of extraocular muscles, this elusive eye motion has not been studied in detail due to the technical difficulties that go along with a closed eyelid. Here we use dynamic magnetic resonance imaging (MRI) to obtain videos of this motion and analyse the kinematics with the recently developed MREyeTrack algorithm. We show that the eye is not only retracted but also lifted up during a blink. For some participants we observed eyeball lifting by up to 3 mm, far exceeding the amount of translation believed to occur during natural eye movements. Slow blinks can be accompanied by large tonic rotations of up to 15{degrees}. Furthermore, we collected evidence that the co-contraction of extraocular muscles leads to a slight compression of the eyeball. These findings demonstrate the surprising complexity of ocular motility and offer new opportunities to study orbital mechanics in health and disease.

neuroscience↗

bioRxiv2019

Oxytocin shapes spontaneous activity patterns in the developing visual cortex by activating somatostatin interneurons

Spontaneous network activity shapes emerging neuronal circuits during early brain development, however how neuromodulation influences this activity is not fully understood. Here, we report that the neuromodulator oxytocin powerfully shapes spontaneous activity patterns. In vivo, oxytocin strongly decreased the frequency and pairwise correlations of spontaneous activity events in visual cortex (V1), but not in somatosensory cortex (S1). This differential effect was a consequence of oxytocin only increasing inhibition in V1 and increasing both inhibition and excitation in S1. The increase in inhibition was mediated by the depolarization and increase in excitability of somatostatin+ (SST) interneurons specifically. Accordingly, silencing SST+ neurons pharmacogenetically fully blocked oxytocins effect on inhibition in vitro as well its effect on spontaneous activity patterns in vivo. Thus, oxytocin decreases the excitatory/inhibitory ratio and modulates specific features of V1 spontaneous activity patterns that are crucial for refining developing synaptic connections and sensory processing later in life.

neuroscience↗