arXiv subjects

Marcelo Nollmann

Publications and source records attributed to Marcelo Nollmann.

5 recordsLinked to original sources

arXiv2026

Hi-M imaging of chromatin architecture in adult Drosophila brain cryosections

Hi-M combines fluorescence in situ hybridization (FISH), automated microfluidics, sequential imaging, and computational chromatin tracing to measure the three-dimensional organization of selected genomic regions in single cells. This chapter describes a Hi-M workflow adapted for cryosections of adult Drosophila melanogaster brains, enabling chromatin tracing while preserving tissue architecture and cell identity. The protocol covers Oligopaint library design and amplification, fixation, brain dissection, cryoprotection, cryosectioning, sequential RNA-FISH for cell-type identification, sequential DNA-FISH labeling, automated acquisition, and chromatin trace reconstruction. We also provide practical guidance for experimental design, sample preparation, tissue handling, image acquisition, and data analysis, highlighting critical steps that influence tissue integrity, hybridization efficiency, image registration, barcode detection, and chromatin trace reconstruction. The workflow is readily adaptable to different genomic loci and cell types, providing a robust approach for studying 3D genome organization in intact adult tissues.

q-bio.NC↗

arXiv2026

Enhancer-promoter proximity predicts transcriptional competence but not transcriptional output in the Drosophila brain

How 3D genome architecture contributes to transcriptional specificity across neuronal cell types remains unclear. Here, we used multiplexed chromatin tracing to map chromatin architecture and cell identity at single-cell resolution in the adult Drosophila brain. We found that enhancer-promoter (E-P) proximity was increased in transcriptionally active compared with inactive neurons. Analysis of single traces revealed the existence of distinct proximal and distal E-P states, with active neurons enriched in the proximal state. However, this relationship broke down across active neuronal subtypes, where neither E-P proximity nor chromatin accessibility predicted transcriptional output. Thus, 3D genome organization distinguishes transcriptionally competent from inactive neuronal states without quantitatively specifying transcriptional output. Our findings support a model in which E-P proximity establishes a permissive structural state, while additional cell-type-specific regulatory mechanisms tune transcriptional output.

q-bio.GN↗

arXiv2026

Bacterial Motility Across Scales: Mechanisms, Live Imaging, and Quantitative Analysis

Bacteria live in environments that are constantly changing. To survive, they rely on different motility systems that let them move, explore, and interact with their surroundings. These motility systems not only control the movement of individual cells but also give rise to collective behaviors such as coordinated spreading, cooperative predation, and multicellular development. Understanding these processes requires not only a description of the underlying molecular machines, but also quantitative observations spanning single-cell behavior and collective dynamics. Imaging approaches now make it possible to follow motility across scales, from molecular machines to bacterial communities, while computational analyses extract principles that link mechanisms to emergent dynamics. By combining molecular, behavioral, imaging, and analytical perspectives, this review provides an integrated view of bacterial motility that links single-cell behavior to community-level dynamics across scales.

physics.bio-ph↗

arXiv2025

FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format

In recent years, multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods have rapidly expanded, enabling the quantification of chromatin organization in single cells, often in conjunction with measurements of RNA and protein. These approaches have deepened our understanding of how 3D chromosome architecture relates to transcriptional activity and cell states in health and disease. Despite these advances, results from Chromatin Tracing FISH-omics experiments remain challenging to share, reuse, and analyze due to the absence of standardized data exchange specifications. Building on the release of microscopy metadata standards, we introduce the FISH Omics Format-Chromatin Tracing (FOF-CT), a community-developed standard for processed results from diverse imaging modalities. We describe the FOF-CT file format and present a curated collection of datasets deposited in the 4DN Data Portal and the OME Image Data Resource (IDR). We also highlight their potential for reuse, integration, and modeling by outlining example analysis pipelines and illustrating biological insights enabled by standardized, FAIR-compliant Chromatin Tracing datasets. While this manuscript focuses on the representation of ball-and-stick Chromatin Tracing, the format is designed to be extensible to volumetric Chromatin Tracing.

q-bio.OT↗

arXiv2017

Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or "volumetric" chemophoresis, force field. This minimal description, in the sense of Occam's Razor principle, captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insights into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes.

q-bio.SC↗