Biology subjects

Brambach, M.

Publications and source records attributed to Brambach, M..

5 recordsLinked to original sources

bioRxiv2026

Whole-Embryo 3D Quantification Reveals Conserved Topological Design and Scaling of Germ Layers in Xenopus

How embryos with markedly different absolute sizes and cell numbers establish comparable tissue organization during development remains a fundamental question in developmental biology. To address this question, we compared two closely related Xenopus species that differ substantially in embryonic size, Xenopus laevis and Xenopus tropicalis. We generated a whole-embryo quantitative 3D atlas of cell allocation, spatial organization, and mitotic dynamics at key time points between gastrulation to tailbud stages. Using tissue clearing, and 3D imaging we tracked single-nucleus coordinates across developmental milestones to resolve how body plans adapt to organismal scale. We show that embryonic scaling is not achieved through simple proportional changes in cell number. Instead, the smaller X. tropicalis embryo is characterized by a distinct high-density tissue organization associated with a persistently higher mitotic index (~1.4-fold higher than in X. laevis at both gastrula and tailbud stages). Across development, this is accompanied by a near-doubling of cell number in X. tropicalis without a proportional increase in embryo volume. We quantify tissue organization and find species-specific cellular architectures during gastrulation that largely converge by the tailbud stage. At this stage, homologous tissues display broadly similar structural profiles despite persistent differences in embryo size, cell number, and density. Together, our findings reveal that closely related vertebrate embryos can follow distinct cellular organization trajectories while converging toward comparable tissue architecture, providing a quantitative framework for understanding robust body plan formation across divergent physical scales.

Developmental Biology↗

bioRxiv2024

In toto analysis of multicellular arrangement reduces embryonic tissue diversity to two archetypes that require specific cadherin expression

Breakthroughs in transcriptomics are providing exciting new ways to characterise cellular diversity within organisms1-3. Yet, organisms are more than the sum of their differentiated cells, as the biological function of most cell types only emerges when they are organised into tissues with characteristic architectures4. The mechanisms that drive architectural diversification at the tissue level remain poorly understood, in part due to a general lack of methods for directly comparing different organisational patterns. Here we establish nuQLOUD, an efficient imaging and computational framework that reduces complex tissues to clouds of nuclear positions, enabling the extraction of cell-type agnostic architectural features. Applying nuQLOUD to whole developing zebrafish embryos reveals that global tissue diversity can be efficiently reduced to two primary archetypes, termed amorphous and crystalline. We investigate the molecular drivers of tissue archetypes by focussing on cadherin cell adhesion molecules and demonstrate that the expression domains of major cadherins segregate along tissue-archetypal lines. Further spatiotemporal analysis and targeted perturbation of cadherin expression in different organs identifies N-Cadherin as a general driver of the amorphous archetype. Thus, this systematic investigation of architectural diversity provides a new way to conceptualise embryonic organisation and understand drivers of tissue diversification within a standardised framework.

developmental biology↗

bioRxiv2024

Synergy Between TNFα and Proteostatic Stress Drives Cell Death and Guard Immunity

The production and sensing of type I interferons (IFN-I) are critical for antiviral defense, yet most virus-infected cells do not produce IFN-I or upregulate IFN-stimulated genes. Using quantitative proteomics and global protein synthesis measurements, we show that productive viral infection globally down-regulates protein synthesis, restricting the IFN response. Guard immunity, which responds to disruptions in essential cellular processes, might compensate for the lack of IFN-I response by rapidly killing infected cells. However, non-pathological stressors can also disrupt proteostasis, making it unclear how cells decide to trigger guard immunity. We hypothesized that TNF, produced by macrophages, provides a contextual signal allowing specificity. Using live-cell fluorescence microscopy and mathematical modeling, we showed that TNF synergizes with the rapid decay of the anti-apoptotic protein c-FLIP to induce cell death and prevent viral spread. Our findings demonstrate that TNF contextualizes proteostasis loss as non-sterile, enabling the activation of guard immunity to counteract viral infection.

immunology↗

bioRxiv2022

A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo

During brain development, many newborn neurons undergo apoptosis and are engulfed by microglia, the tissue-resident phagocytes of the brain, in a process known as efferocytosis. A hallmark of microglia is their highly branched morphology characterised by the presence of numerous dynamic extensions that these cells use for scanning the brain parenchyma and engulfing unwanted material. The mechanisms driving branch formation and apoptotic cell engulfment in microglia are unclear. By taking a live imaging approach in zebrafish, we show that while microglia generate multiple microtubule-based branches, they only successfully engulf one apoptotic neuron at a time. Further investigation into the mechanism underlying this sequential engulfment revealed that targeted migration of the centrosome into one branch is predictive of phagosome formation and polarised vesicular trafficking. Moreover, experimentally doubling centrosomal numbers in microglia increases the rate of engulfment and even allows microglia to remove two neurons simultaneously, providing direct supporting evidence for a model where centrosomal migration is a rate-limiting step in branch-mediated efferocytosis. Conversely, light-mediated depolymerization of microtubules causes microglia to lose their typical branched morphology and switch to an alternative mode of engulfment, characterised by directed migration towards target neurons, revealing unexpected plasticity in their phagocytic ability. Finally, building on work focusing on the establishment of the immunological synapse, we identified a conserved signalling pathway underlying centrosomal movement in engulfing microglia.

cell biology↗

bioRxiv2020

Neural tube patterning: from a minimal model for rostrocaudal patterning towards an integrated 3D model

The rostrocaudal patterning of the neural tube is a key event in early brain development. This process is mainly driven by a gradient of WNT, which defines the fate of the present neural progenitor cells in a dose dependent matter and leads to a subdivision of the tube into forebrain, midbrain and hindbrain. Although this process is extensively studied experimentally both in vivo and in vitro, an integrated view of the responsible genetic circuitry is currently lacking. In this work, we present a minimal gene regulatory model for rostrocaudal neural tube patterning. The model's nodes and architecture are determined in a data driven way, leading to a tristable configuration of mutually repressing brain regions. Analysis of the parameter sensitivity and simulations of knockdown and overexpression cases show that repression of hindbrain fate is a promising strategy for the improvement of current protocols for the generation of dopaminergic neurons in vitro. Furthermore, we combine the model with an existing model for dorsoventral neural tube patterning, to test its capabilities in an in vivo setting, by predicting the steady state pattern of a realistic three-dimensional neural tube. This reveals that the rostrocaudal pattern stacks dorsoventrally in the caudal half of the neural tube. Finally, we simulate morphogen secretion overexpression, which highlights the sensitivity of neural tube patterning to the morphogen levels.

systems biology↗