Biology subjects

Kamenz, J.

Publications and source records attributed to Kamenz, J..

6 recordsLinked to original sources

bioRxiv2026

XIBBIT: A biometric recognition tool for efficient Xenopus laevis identification and colony management

The African clawed frog Xenopus laevis is a widely utilized model organism in biomedical research; however, significant challenges in experimental reproducibility and colony management remain. A major obstacle lies in the reliable identification of individual animals, since frogs are generally housed in large groups and are difficult to distinguish due to their high morphological similarity. Conventional methods, including toe clipping and microchipping, are invasive and cause distress, emphasizing the need for non-invasive methods for accurate documentation and welfare monitoring. In this study, we introduce XIBBIT (Xenopus Image-Based Biometric-pattern Identification Tool), a web-based application integrating computer vision and machine learning to identify individual Xenopus laevis based on their dorsal patterning. By exploiting these natural biometric signatures, the platform achieves reliable identification with up to 95.7% accuracy within three image captures under real life conditions. In addition to identification, XIBBIT provides a centralized colony management system. It archives individual data, including health records and experimental histories, with customizable fields. To demonstrate XIBBITs capabilities, we used the application to track egg quality across repeated egg-laying events, revealing that egg quality is a repeatable, individual-specific trait in Xenopus laevis. Furthermore, we find seasonal effects on egg laying performance with the lowest performance during late-spring and summer months. Ultimately, XIBBIT provides an effective, time-efficient, and non-invasive solution to the problem of individual Xenopus laevis identification, facilitating both experimental reproducibility and high animal welfare standards.

developmental biology↗

bioRxiv2026

Chromosome segregation synchrony in S. pombe is noise-limited and arises without positive feedback

Anaphase is a key cell cycle transition that ensures faithful genome inheritance. At anaphase onset, sister chromatids separate abruptly and synchronously upon activation of the protease separase. Major cell cycle transitions often involve positive feedback, which contributes to their abruptness and irreversibility; however, whether such feedback is required for anaphase remains unclear. Here, we analyze sister chromatid separation dynamics in fission yeast using high-resolution live-cell imaging and computational modeling. We find that anaphase synchrony relies on fast degradation of the separase inhibitor securin, but does not require separase-mediated positive feedback. Hence, sister chromatid separation, being inherently irreversible, may be one of the few major cell cycle transitions that can proceed without positive feedback. A stochastic model fitted to the data revealed that separation synchrony is limited by stochasticity resulting from small-number effects. Together, these results support a feedback-independent mechanism for anaphase onset and identify molecular noise as a fundamental constraint on its temporal precision.

cell biology↗

bioRxiv2026

Cell cycle dynamics of redox state and lipid metabolism in S. cerevisiae, S. pombe and murine leukaemia cells

Coordination of metabolism, cell growth and cell division is essential to life. Recent single-cell measurements in S. cerevisiae have shown that metabolic processes and the cellular redox state are dynamic along the cell cycle. However, it is unknown whether similar metabolic oscillations also occur in other organisms. Until now, the dynamics of metabolism in other eukaryotes have predominantly been studied in cell cycle synchronised populations. Since cell cycle synchronisation methods can perturb metabolism, they may also introduce artefacts in the recorded dynamics. Here, we performed time-lapse microscopy analyses of exponentially growing single cells of the budding yeast S. cerevisiae, the fission yeast S. pombe and murine leukaemia L1210 cells. Measuring the NAD(P)H autofluorescence and the cell surface area growth rate in unsynchronised cells, we discovered oscillations along the cell cycle of the cellular redox state and lipid metabolism, respectively. Thus, our work shows that metabolism is dynamic along the cell cycle of these three evolutionarily distant eukaryotic organisms. This finding suggests that such metabolic oscillations could be a conserved characteristic among eukaryotes.

cell biology↗

bioRxiv2024

Imaging-Based Quantitative Assessment of Biomolecular Condensates in vitro and in Cells

The formation of biomolecular condensates contributes to intracellular compartmentalization, and plays an important role in many cellular processes. The characterization of condensates is however challenging, requiring advanced biophysical or biochemical methods that are often less suitable for in vivo studies. A particular need for easily accessible yet thorough methods that enable the characterization of condensates across different experimental systems thus remains. To address this, we present PhaseMetrics, a semi-automated FIJI-based image analysis pipeline tailored for quantifying particle properties from microscopy data. Tested using the FG-domain of yeast nucleoporin Nup100, PhaseMetrics accurately assesses particle properties across diverse experimental setups, including in vitro, Xenopus egg extracts, and cellular systems. It reliably detects changes induced by various conditions such as the presence of polyethylene glycol, 1,6-hexanediol, a salt gradient, and the molecular chaperone DNAJB6b. By enabling the accurate representation of the variability within the population and the detection of subtle changes at the single particle level, the method complements conventional biochemical assays. Combined, PhaseMetrics is an easily accessible, customizable pipeline that enables imaging-based quantitative assessment of biomolecular condensates in vitro and in cells, providing a valuable addition to the current toolbox.

biochemistry↗

bioRxiv2020

Bistable, biphasic regulation of PP2A-B55 accounts for the dynamics of mitotic substrate phosphorylation

The phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activation of the cyclin-dependent kinase Cdk1. However, more recently it has been suggested that bistability also arises from positive feedback in the regulation of the Cdk1-counteracting phosphatase, PP2A-B55. Here, we demonstrate biochemically using Xenopus laevis egg extracts that the Cdk1-counteracting phosphatase PP2A-B55 functions as a bistable switch, even when the bistability of Cdk1 activation is suppressed. In addition, Cdk1 regulates PP2A-B55 in a biphasic manner; low concentrations of Cdk1 activate PP2A-B55 and high concentrations inactivate it. As a consequence of this incoherent feedforward regulation, PP2A-B55 activity rises concurrently with Cdk1 activity during interphase and suppresses substrate phosphorylation. PP2A-B55 activity is then sharply downregulated at the onset of mitosis. During mitotic exit Cdk1 activity initially falls with no obvious change in substrate phosphorylation; dephosphorylation then commences once PP2A-B55 spikes in activity. These findings suggest that changes in Cdk1 activity are permissive for mitotic entry and exit, but the changes in PP2A-B55 activity are the ultimate trigger.

cell biology↗

bioRxiv2019

The apparent requirement for protein synthesis during G2 phase is due to checkpoint activation

Protein synthesis inhibitors (e.g. cycloheximide) prevent cells from entering mitosis, suggesting that cell cycle progression requires protein synthesis until right before mitotic entry. However, cycloheximide is also known to activate p38 MAPK, which can delay mitotic entry through a G2/M checkpoint. Here we asked whether checkpoint activation or a requirement for protein synthesis is responsible for the cycloheximide effect. We found that p38 inhibitors prevent cycloheximide-treated cells from arresting in G2 phase, and that G2 duration is normal in about half of these cells. The Wee1/Myt1 inhibitor PD0166285 also prevents cycloheximide from blocking mitotic entry, raising the possibility that Wee1 and/or Myt1 mediate the cycloheximide-induced G2 arrest. Thus, the ultimate trigger for mitotic entry appears not to be the continued synthesis of mitotic cyclins or other proteins. However, M-phase progression was delayed in cycloheximide-plus-kinase-inhibitor-treated cells, emphasizing the different requirements of protein synthesis for timely entry and completion of mitosis. Impact statementCycloheximide arrests cells in G2 phase due to activation of p38 MAPK, not inhibition of protein synthesis, arguing that protein synthesis in G2 phase is not required for mitotic entry.

cell biology↗