Biology subjects

Strobl, F.

Publications and source records attributed to Strobl, F..

5 recordsLinked to original sources

bioRxiv2026

Sixteen isotropic 3D fluorescence live imaging datasets of Tribolium castaneum gastrulation

Gastrulation is a pivotal phase of early embryogenesis during which initially uniform cells undergo coordinated movements and fate specification to establish the basic body plan. Although previous studies have advanced our understanding of gastrulation in the red flour beetle Tribolium castaneum, quantitative morphogenetic data remain limited. Here, we present the second Systematic Live Imaging Collection of Embryogenesis (SLICE-2), consisting of sixteen isotropic 3D fluorescence live imaging datasets that document Tribolium gastrulation and early germband elongation. Imaging was performed using light sheet fluorescence microscopy in conjunction with a homozygous transgenic line that expresses mEmerald-labeled nanobodies against histone H2A/H2B. Embryos were recorded along four orientations, and the resulting axial image stacks were subjected to multiview fusion to obtain isotropic 3D images of entire embryos with reduced shadowing artifacts. Datasets are provided as weighted-average fusion and fusion-deconvolution derivatives, and nuclei segmentation data are available for selected datasets and stages. SLICE-2 expands the resource arsenal for Tribolium, enabling comprehensive analyses of gastrulation dynamics and providing benchmark data for image processing, segmentation, and modeling approaches.

developmental biology↗

bioRxiv2026

Marker-based knockout genotyping in diploid model organisms

Analysis of gene function in diploid organisms typically relies on molecular methods to distinguish wild-type, mono-allelic knockout, and bi-allelic knockout individuals, creating a major practical bottleneck for large-scale developmental studies. Here, we establish a modular visual genotyping approach that enables organism-level discrimination of knockout zygosity by tagging alternative disrupted alleles with spectrally distinct fluorescent markers. Implemented in the red flour beetle Tribolium castaneum, a two-marker strategy permits reliable identification of bi-allelic knockouts within mixed cohorts in a semi-random insertional mutagenesis framework. Further, a four-marker strategy using a targeted CRISPR/Cas9-based gene editing approach enables systematic generation and unambiguous recognition of individuals homozygous for both a disrupted gene of choice and a fluorescent reporter transgene. This design substantially reduces the workload associated with routine molecular genotyping while enabling genotype-resolved long-term live imaging of embryonic morphogenesis. Application to the extra-embryonic specification factor zerknullt 1 reveals haplosufficiency and a semi-lethal phenotype associated with variable morphogenetic outcomes. Together, our approach provides a scalable framework for functional analysis of essential developmental genes. Summary StatementVisual marker-based genotyping enables organism-level discrimination of knockout zygosity, reducing reliance on molecular assays and facilitating scalable, genotype-resolved live imaging of developmental gene function in diploid model organisms.

genetics↗

bioRxiv2024

Spatio-temporal segmentation of contraction waves in the extra-embryonic membranes of the red flour beetle

In this paper, we introduce an image analysis approach for spatio-temporal segmentation, quantification and visualization of movement or contraction patterns in 2D+t or 3D+t microscopy recordings of biological tissues. The imaging pipeline is applied to time lapse images of the embryonic development of the red flour beetle Tribolium castaneum recorded with light-sheet fluorescence microscopy (LSFM). We are particularly interested in the dynamics of extra-embryonic membranes, and provide quantitative evidence of the existence of contraction waves during late stages of development. These contraction waves are a novel observation of which neither origin, nor function are yet known. The proposed pipeline relies on particle image velocimetry (PIV) for quantitative movement analysis, surface detection, tissue cartography, and an algorithmic approach to detect characteristic movement dynamics. This approach locates contraction waves in 2D+t and 3D+t reliably and efficiently and allows the automated quantitative analysis, such as the area involved in the contractile behavior, contraction wave duration and frequency, path of contractile area, or the relation to the spatio-temporal velocity distribution. The pipeline will be used in the future to conduct a large-scale characterization and quantification of contraction wave behavior in Tribolium castaneum development and can be adapted easily to the identification and segmentation of characteristic tissue dynamics in other systems of interest.

bioinformatics↗

bioRxiv2022

How enhancers regulate wavelike gene expression patterns: A novel enhancer prediction and live reporter system identifies an enhancer associated with the arrest of pair-rule waves in Tribolium

A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called enhancers. Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expressions in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here we establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several Tribolium enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expressions (that we call dynamic enhancers) and enhancers that stabilizes gene expressions (that we call static enhancers).

developmental biology↗

bioRxiv2019

An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium castaneum

The genetic control of anterior brain development is highly conserved throughout animals. For instance, a conserved anterior gene regulatory network specifies the ancestral neuroendocrine center of animals and the apical organ of marine organisms. However, its contribution to the brain in non-marine animals has remained elusive. Here, we study the function of the Tc-foxQ2 forkhead transcription factor, a key regulator of the anterior gene regulatory network of insects. We characterized four distinct types of Tc-foxQ2 positive neural progenitor cells based on differential co-expression with Tc-six3/optix, Tc-six4, Tc-chx/vsx, Tc-nkx2.1/scro, Tc-ey, Tc-rx and Tc-fez1. An enhancer trap line built by genome editing marked Tc-foxQ2 positive neurons, which projected through the primary brain commissure and later through a subset of commissural fascicles. Eventually, they contributed to the central complex. Strikingly, in Tc-foxQ2 RNAi knock-down embryos the primary brain commissure did not split and subsequent development of midline brain structures stalled. Our work establishes foxQ2 as a key regulator of brain midline structures, which distinguish the protocerebrum from segmental ganglia. Unexpectedly, our data suggest that the central complex evolved by integrating neural cells from an ancestral anterior neuroendocrine center.\n\nSummary statementAn ancestral neuroendocrine center contributes to the evolution of the central complex. foxQ2 is a gene required for the development of midline structures of the insect brain, which distinguish protocerebrum from segmental ganglia.

developmental biology↗