Biology subjects

Rode, J.

Publications and source records attributed to Rode, J..

8 recordsLinked to original sources

bioRxiv2026

The expression of colonic keratins is elevated in IBD, reduced in microscopic colitis, and unchanged in IBS : a retrospective study

BackgroundKeratins, a major subgroup of intermediate filament proteins, play a critical role in maintaining epithelial barrier and intracellular epithelial integrity. Studies have demonstrated possible links between inflammatory signaling and colonic keratins type II K8, and type I K18, K19 and K20, in animal models of colitis, and in patients with Inflammatory Bowel Disease (IBD). K7 is de novo expressed in patients with the IBD subtypes Ulcerative Colitis (UC) and Crohns Disease (CD). However, the histopathological roles of colonocyte keratins across IBD, microscopic colitis (MC), and Irritable Bowel Syndrome (IBS) remain poorly understood. Given the established utility as biomarkers in cancer diagnostics, we investigated whether keratin expression patterns could be used to distinguish inflammatory and functional colonic disorders. MethodsBiobank samples from patients with IBD (n=27), MC (n=18), IBS (n=32) and healthy controls (n=31), were collected and immunohistochemically stained for K7, K8, K18, K19, and K20. Digital image analysis quantified staining intensities, which were correlated with histopathological severity scores and clinical parameters. ResultsColonic keratin expression was significantly elevated in IBD, particularly in UC, while they were decreased in MC, and unaltered in IBS. Notably, K8 and K19 expression were strongly associated with areas of severe epithelial damage in IBD. Keratin expression was most pronounced in patients who had undergone colectomy due to treatment-resistant IBD. DiscussionKeratin changes in IBD and MC but not in IBS highlight their importance in maintaining barrier homeostasis. Whether these changes are causes or consequences for these diseases will warrant further research.

cell biology↗

bioRxiv2023

Chemotactic agents combining spatial and temporal gradient-sensing boost spatial comparison if they are large, slow, and less persistent

Biological cells and small organisms navigate in concentration fields of signaling molecules using two fundamental gradient-sensing strategies: spatial comparison of concentrations measured at different positions on their surface, or temporal comparison of concentrations measured at different locations visited along their motion path. It is believed that size and speed dictate which gradient-sensing strategy cells choose, yet this has never been formally proven. Using information theory, we investigate the optimal gradient-sensing mechanism for an ideal chemotactic agent that combines spatial and temporal comparison. We account for physical limits of chemo-sensation: molecule counting noise at physiological concentrations, and motility noise inevitable at the micro-scale. Our simulation data collapses onto an empirical power-law that predicts an optimal weighting of information as function of motility and sensing noise, demonstrating how spatial comparison becomes more beneficial for agents that are large, slow and less persistent. This refines and quantifies the previous heuristic notion. Our idealized model assuming unlimited information processing capabilities serves as a benchmark for the chemotaxis of biological cells.

biophysics↗

bioRxiv2023

A latent cardiomyocyte regeneration potential in the human heart

Cardiomyocytes in the adult human heart show a regenerative capacity, with an annual renewal rate around 0.5%. Whether this regenerative capacity of human cardiomyocytes is employed in heart failure has been controversial. Using retrospective 14C birth dating we analyzed cardiomyocyte renewal in patients with end-stage heart failure. We show that cardiomyocyte generation is minimal in end-stage heart failure patients at rates 18-50 times lower compared to the healthy heart. However, patients receiving left ventricle support device therapy, who showed significant functional and structural cardiac improvement, had a >6-fold increase in cardiomyocyte renewal relative to the healthy heart. Our findings reveal a substantial cardiomyocyte regeneration potential in human heart disease, which could be exploited therapeutically.

cell biology↗

bioRxiv2022

Genetic identification and reiterated captures suggests that the Astyanax mexicanus El Pachon cavefish population is closed and declining

The size of Astyanax mexicanus blind cavefish populations of North-East Mexico is a demographic parameter of great importance for investigating a variety of ecological, evolutionary and conservation issues. However, very few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but the feasibility of such approach and the interpretation of the results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals can give insights on cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachon cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachon cave since the last census in 1971 raises serious conservation issues.

zoology↗

bioRxiv2021

Population monitoring of snow leopards using camera trapping in Naryn State Reserve, Kyrgyzstan, between 2016 and 2019

Four field seasons of snow leopard (Panthera uncia) camera trapping inside Naryn State Reserve, performed thanks to citizen science expeditions, allowed detecting a minimal population of five adults, caught every year with an equilibrated sex ratio (1.5:1), and reproduction: five cubs or subadults have been identified from three litters of two different females. Crossings were observed one to three times a year, in front of most camera traps, and several times a month in front of one of them. Overlap of adults territories was observed in front of several camera traps regardless of their sex. Significant snow leopard presence was detected in the buffer area and at Ulan, situated at the reserve border. To avoid poaching on this umbrella species and its preys, extending the more stringent protection measures of the core zone to both the Southern buffer area and land adjacent to Ulan is necessary.

ecology↗

bioRxiv2020

Diploid hepatocytes drive physiological liver renewal in adult humans

Physiological liver cell replacement is central to maintaining the organs high metabolic activity, although its characteristics are difficult to study in humans. Using retrospective 14C birth dating of cells, we report that human hepatocytes show continuous and lifelong turnover, maintaining the liver a young organ (average age < 3 years). Hepatocyte renewal is highly dependent on the ploidy level. Diploid hepatocytes show an seven-fold higher annual exchange rate than polyploid hepatocytes. These observations support the view that physiological liver cell renewal in humans is mainly dependent on diploid hepatocytes, whereas polyploid cells are compromised in their ability to divide. Moreover, cellular transitions between these two subpopulations are limited, with minimal contribution to the respective other ploidy class under homeostatic conditions. With these findings, we present a new integrated model of homeostatic liver cell generation in humans that provides fundamental insights into liver cell turnover dynamics.

cell biology↗

bioRxiv2019

Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

Snow leopards (Panthera uncia) are a keystone species of Central Asias high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.

genetics↗

bioRxiv2019

How fast are cells dividing: Probabilistic model of continuous labeling assays

Correct estimates of cell proliferation rates are crucial for quantitative models of the development, maintenance and regeneration of tissues. Continuous labeling assays are used to infer proliferation rates in vivo. So far, the experimental and theoretical study of continuous labeling assays focused on the dynamics of the mean labeling-fraction but neglected stochastic effects. To study the dynamics of the labeling-fraction in detail and fully exploit the information hidden in fluctuations, we developed a probabilistic model of continuous labeling assays which incorporates biological variability at different levels, between cells within a tissue sample but also between multiple tissue samples. Using stochastic simulations, we find systematic shifts of the mean-labeling fraction due to variability in cell cycle lengths. Using simulated data as ground truth, we show that current inference methods can give biased proliferation rate estimates with an error of up to 40 %. We derive the analytical solution for the Likelihood of our probabilistic model. We use this solution to infer unbiased proliferation rate estimates in a parameter recovery study. Furthermore, we show that the biological variability on different levels can be disentangled from the fluctuations in the labeling data. We implemented our model and the unbiased parameter estimation method as an open source Python tool and provide an easy to use web service for cell cycle length estimation from continuous labeling assays (https://imc.zih.tu-dresden.de/cellcycle).

biophysics↗