Biology subjects

Todorov, H.

Publications and source records attributed to Todorov, H..

15 recordsLinked to original sources

bioRxiv2026

Spatially mediated interactions shape founder-cell fitness and community assembly in multi-species soil bacteria

Microbial communities spontaneously colonize pristine environments, yet how species growth kinetics and individual cell variation shape community assembly remains poorly understood. Here, we use time-lapse microscopy imaging to track the division of individual founder cells in communities composed of up to seven soil bacterial isolates grown on nutrient surfaces. With cell lineage tracking, we quantify species-specific absolute biomass formation and growth kinetics from early growth through stationary phase. The reproductive success of individual founder cells depended on the timing of their first cell division, which determined their access to the primary substrate and their maximum growth rates. In mixed-species communities, founder cell success also depended on species-specific, substrate-dependent growth rates and yields. In addition, spatial factors - such as cells positioning, distances to non-kin neighbours, and identities of co-occurring species - further influenced outcomes. In spatially structured communities, interspecific interactions were globally governed by competition for primary substrates. We also observed cross-feeding of leaked metabolites, reflected in fluctuating paired interaction strengths and interaction signs. Species-pair interactions differed locally, with cells within distances of less than 15 {micro}m exhibiting opposite interaction behaviours. Global pairwise interactions predicted from monoculture growth kinetics were observed in approximately half of the measured pairs, whereas measured paired interactions generally weakened in combinations of three or more species. Using a spatially explicit agent-based Monod growth model that includes interspecific interactions, we accurately predicted the compositions of seven-member communities. Overall, our results indicate that emergent, spatially mediated interspecific interactions between cells of different bacterial species primarily drive local and temporal changes in individual cell growth rates, which in turn determine final biomass formation. Because most natural microbial habitats are spatially structured, stochastic founder-cell positioning and fitness differences are key determinants of locally formed interaction patterns and species coexistence.

microbiology↗

bioRxiv2024

Premature upregulation of miR-92a's target RBFOX2 hijacks PTBP splicing and impairs cortical neuronal differentiation.

Alternative splicing is a crucial component of neuronal differentiation, yet the mechanisms that regulate splicing transitions during embryonic brain development remain incompletely understood. Here, we identify a post-transcriptional mechanism that times the expression of the splicing factor Rbfox2 during neurogenesis. RBFOX2 is normally expressed at low levels in neural progenitor cells (NPCs) and becomes upregulated in newborn neurons where it promotes neuronal differentiation. Unexpectedly, premature expression of Rbfox2 in NPCs of the embryonic mouse neocortex blocked their differentiation into neurons rather than promoting it. Genome-wide analysis revealed widespread alternative splicing changes enriched for NDD genes and associated with a hybrid NPC- and neuron-like splicing pattern that significantly deviates from the normal splicing developmental trajectory. Remarkably, premature Rbfox2 expression induced the inclusion of validated target exons that are otherwise repressed by PTBP2 pointing to an antagonistic splicing relationship. Integrative scRNA-seq analysis confirmed a negatively correlated expression between these two RNA-binding proteins (RBP) along differentiation pseudotime. Strikingly, we identified the NPC-specific miRNA 92a-3p as a regulator of the Rbfox2 expression switch: expression of miR-92a reduced RBFOX2 levels and reversed splicing patterns of target genes in vitro, while silencing miR-92a in vivo increased RBFOX2 expression in the embryonic cortex. Together, these findings reveal a previously unrecognized miRNA-RBP regulatory axis that ensures the proper timing of NPC-to-neuron splicing transitions in the developing cortex and provide new insights into splicing dysregulation as a contributing factor to the emergence of neurodevelopmental disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=152 HEIGHT=200 SRC="FIGDIR/small/614071v3_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@16248caorg.highwire.dtl.DTLVardef@198dd0dorg.highwire.dtl.DTLVardef@d8887aorg.highwire.dtl.DTLVardef@1e8419e_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Schematic representation of the proposed splicing regulation for the transition of undifferentiated NPCs to neurons in the developing cerebral cortex.

genomics↗

bioRxiv2024

Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion

Interactions between species are thought to be crucial for modulating their growth and behaviour within communities, and determinant for the emergence of community functions. Several different interaction concepts exist, but there is no consensus on how interactions should be quantified and integrated in community growth theory. Here we expand on existing concepts of real-time measurements of pure culture microcolony growth to develop and benchmark coculture microcolony experiments, and show how these can both parametrize growth kinetic and interspecific interaction effects. We follow surface growth by time-lapse microscopy of fluorescently tagged Pseudomonas putida and Pseudomonas veronii under substrate competition with succinate, or under substrate indifference with D-mannitol and putrescine. Monoculture-grown microcolonies showed substrate concentration dependent expansion rates as expected from Monod relations, whereas individual microcolony yields were strongly dependent on densities and spatial positioning of founder cells. Maximum specific growth rates in cocultures under substrate competition were diminished by ca. 15%, which was seeding-density independent. The collective P. putida population dominated growth over that of P. veronii, but with 27% yield loss under competition compared to monoculture growth; and 90% for that of P. veronii. Incidental local reversal of competition was observed where P. veronii microcolonies profited at the detriment of P. putida, and between 9 and 43% of P. veronii microcolonies grew bigger than expected from bulk competition, depending on seeding density. Simulations with a cell-agent Monod surface growth model suggested that colony expansion rate decrease in competitive coculture is caused by metabolite cross-feeding, which was supported by exometabolite analysis during and after growth of the strains on their individual or swapped supernatant. Coculture microcolony growth experiments thus provide a flexible platform for analysis of kinetic and interspecific interactions, expanding from individual microcolony phenotypic effects to averaged behaviour across all microcolony pairs. The system in theory is scalable to follow real-time growth of multiple species simultaneously into communities.

microbiology↗

bioRxiv2024

Dimalis: A complete standalone pipeline to analyse prokaryotic cell growth from time-lapse imaging

Real-time imaging of bacterial cell division, population growth and behaviour is essential for our understanding of microbial-catalyzed processes at the microscale. However, despite the relative ease by which high resolution imaging data can be acquired, the extraction of relevant cell features from images remains cumbersome. Here we present a versatile pipeline for automated extraction of bacterial cell features from standalone or time-resolved image series, with standardized data output for easy downstream processing. The input consist of phase-contrast images with or without additional fluorescence details, which are denoised to account for potential out-of-focus regions, and segmented to outline the morphologies of individual cells. Cells are then tracked over subsequent time frame images to provide genealogy or microcolony spatial information. We test the pipeline with eight different bacterial strains, cultured in microfluidics systems with or without nutrient flow, or on agarose miniature surfaces to follow microcolony growth. Examples of downstream processing in form of extraction of growth kinetic parameters or bistable cell differentiation are provided. The pipeline is wrapped in a Docker to facilitate installation, consistent processing and avoiding constant software updates.

microbiology↗

bioRxiv2024

Cortexa - a comprehensive resource for studying gene expression and alternative splicing in the murine brain.

MotivationGene expression and alternative splicing are strictly regulated processes that shape brain development and determine the cellular identity of differentiated neural cell populations. Despite the availability of multiple valuable datasets, many functional implications, especially those related to alternative splicing, remain poorly understood. Moreover, neuroscientists working primarily experimentally often lack the bioinformatics expertise required to process alternative splicing data and produce meaningful and interpretable results. Notably, re-analyzing publicly available datasets and integrating them with in-house data can provide substantial novel insights. However, such analyses necessitate devel-oping harmonized data handling and processing pipelines which in turn requires considerable computational resources and in-depth bioinformatics expertise. ResultsHere, we present Cortexa - a comprehensive web-portal that incorporates RNA-sequencing datasets from the mouse cerebral cortex (longitudinal or cell-specific) and the hippocampus. Cortexa facilitates understandable visualization of the expression and alternative splicing patterns of individual genes. Our platform also provides SplicePCA - a tool that allows users to integrate their alternative splicing dataset and compare it to cell-specific or developmental neocortical splicing patterns. All gene expression and alternative splicing data have been processed in a standardized manner and they can also be downloaded for further in-depth down-stream analysis. AvailabilityThe data portal is available at https://cortexa-rna.com/ Contacthristo.todorov@uni-mainz.de.

genomics↗

bioRxiv2024

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often proliferate in highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained to smaller habitats, shared with potentially fewer other species. The effects of microhabitats on the emergence of bacterial interspecific interactions are poorly understood, but potentially important for the maintenance of diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth in picoliter droplets at low population census with that in large (macro) population liquid suspended cultures. Four interaction scenarios were imposed by using different bacterial strain combinations and media: substrate competition, substrate independence, growth inhibition, and cell killing by tailocins. In contrast to macro-level culturing, we observed that fragmented growth in picoliter droplets in all cases yielded more variable outcomes, and even reversing the macro-level assumed interaction type in a small proportion of droplet habitats. Timelapse imaging and mathematical simulations indicated that the variable and alternative interaction outcomes are a consequence of founder cell phenotypic variation and small founder population sizes. Simulations further suggested that increased growth kinetic variation may be a crucial selectable property for slower-growing bacterial species to survive competition. Our results thus demonstrate how microhabitat fragmentation enables the proliferation of alternative interaction trajectories and contributes to the maintenance of higher species diversity under substrate competition.

microbiology↗

bioRxiv2023

Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

microRNAs are particularly important during brain development, however, the composition and temporal dynamics of miRNA regulatory networks are not sufficiently characterized. Here, we performed small RNA sequencing of mouse embryonic cortical samples at E14, E17, and P0 as well as in neural progenitor cells differentiated in vitro into neurons. Using co-expression network analysis, we detected clusters of miRNAs that were co-regulated at distinct developmental stages. miRNAs such as miR-92a/b acted as hubs during early, and miR-124 and miR-137 during late neurogenesis. Notably, validated targets of P0 hub miRNAs were enriched for down-regulated genes related to stem cell proliferation, negative regulation of neuronal differentiation and RNA splicing, among others, suggesting that miRNAs are particularly important for modulating transcriptional programs of crucial factors that guide the switch to neuronal differentiation. As most genes contain binding sites for more than one miRNA, we furthermore constructed a co-targeting network where numerous miRNAs shared more targets than expected by chance. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced transcriptional silencing effect compared to single miRNAs. Taken together, our study provides a comprehensive resource of miRNA longitudinal expression changes during corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can shape embryonic brain development.

developmental biology↗

bioRxiv2023

Freezing responses during prolonged threat memory retrieval reflect trait-like anxiety endophenotypes in female and male inbred mice

Trait anxiety is a major risk factor for stress-induced and anxiety disorders in humans. However, animal models accounting for the inter-individual variability in stress vulnerability are largely lacking. Moreover, the pervasive bias of using mostly male animals in preclinical studies poorly reflects the increased prevalence of psychiatric disorders in women. Using the threat imminence continuum theory, we designed and validated an auditory aversive conditioning-based pipeline in both female and male mice. We operationalized trait anxiety by harnessing the naturally occurring variability of defensive freezing responses combined with a model-based clustering strategy. While sustained freezing during prolonged retrieval sessions was identified as an anxiety-endophenotype biomarker in both sexes, females were consistently associated with an increased freezing response RNA-sequencing of CeA, BLA, ACC and BNST revealed massive differences in phasic and sustained responders transcriptomes, correlating with transcriptomic signatures of psychiatric disorders, particularly PTSD. Moreover, we detected significant alterations in the excitation/inhibition balance of principal neurons in the lateral amygdala. These findings provide compelling evidence that trait anxiety in inbred mice can be leveraged to develop translationally relevant preclinical models to investigate mechanisms of stress susceptibility in a sex-specific manner. We like to think we have constrained an organism to the task we have set. In practice, our paradigms are constrained by the way the organisms respond McNaughton & Corr, 2004

neuroscience↗

bioRxiv2023

Dynamic X-chromosomal reactivation enhances female brain resilience

While random X-chromosome inactivation in female cells of placental mammalians silences one allele of the majority of X-chromosomal genes, a considerable fraction is only incompletely and variably inactivated resulting in a tissue-specific pattern of mono- and biallelic expression. Here we used clonal human female induced pluripotent stem cells (iPSCs) allowing to trace the (in)activation status of the two X-chromosomes individually along neural differentiation trajectories. We discovered X-chromosome-wide locus- and lineage-specific dynamic usage of the two X-chromosomal alleles in female cells induced by differentiation. Leveraging iPSCs derived from patients with an X-linked neurodevelopmental disorder, we demonstrate that activation of alleles on the inactive X-chromosome can exert protective effects on the manifestation of disease phenotypes in female neural cells and tissue. Taken together, our data demonstrate that alleles on the inactive X-chromosome can serve as a critical reservoir reactivated during differentiation, thereby enhancing resilience of female neural tissue.

neuroscience↗

bioRxiv2022

STrack: A tool to Simply Track bacterial cells in microscopy time-lapse images

Bacterial growth can be studied at the single cell-level through time-lapse microscopy imaging. Technical advances in microscopy lead to increasing image quality, which in turn allows to visualize larger areas of growth, containing more and more cells. In this context, the use of automated computational tools becomes essential. In this paper, we present STrack, a tool that allows to track cells in time-lapse images in a fast and efficient way. We compared it to three recently published tracking tools on images ranging over six different bacterial strains, and STrack showed to be the most consistent tracking tool, returning more than 80% of correct cell lineages on average. The python implementation of STrack, a docker structure, and a tutorial on how to download and use the tool can be found on the following github page: https://github.com/Helena-todd/STrack

bioinformatics↗

bioRxiv2022

CD8 memory precursor cells generation is a continuous process

In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that memory precursors are generated continuously with increasing numbers being generated over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence to differentiate into memory cells was confirmed by BrdU pulse-chase experiment in vivo. Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided.

immunology↗

bioRxiv2020

Isolation of nuclei and downstream processing of cell-type-specific nuclei from micro-dissected mouse brain regions - techniques and caveats.

The mammalian brain consists of several structurally and functionally distinct regions equipped with an equally complex cell-type system. Due to its relevance in uncovering disease mechanisms, the study of cell-type-specific molecular signatures of different brain regions has increased. The rapid evolution of newer and cheaper sequencing techniques has also boosted the interest in cell-type-specific epigenetic studies. In fact, the nucleus holds most of the cells epigenetic information and is quite resistant to tissue dissociation processes as compared to cells. As such, nuclei are continually preferred over cells for epigenetic studies. However, the isolation of nuclei from cells is still a biochemically complex process, with every step affecting downstream results. Therefore, it is necessary to use protocols that fit the experimental design to yield nuclei of high quality and quantity. However, the current protocols are not suitable for nuclei isolation of small volumes of micro-dissected brain regions from individual mouse brains. Additionally, the caveats associated with centrifugation steps of nuclei extraction and the effects of different buffers have not been thoroughly investigated. Therefore, in this study, we describe an iodixanol based density gradient ultracentrifugation protocol suitable for micro-dissected brain regions from individual mice using ArccreERT2 (TG/WT).R26CAG-Sun1-sfGFP-Myc (M/WT or M/M). This mouse model shows sfGFP expression (sfGFP+) in the nuclear membrane of specific stimulus activated cells, thereby providing a good basis for the study - nuclei isolation and separation of cell-type-specific nuclei. The study also introduces new tools for rapid visualization and assessment of quality and quantity of nascent extracted nuclei. These tools were then used to examine critical morphological features of nuclei derived from different centrifugation methods and the use of different buffers to uncover underlying effects. Finally, to obtain cell-type-specific nuclei (sfGFP+ nuclei) from the isolated nuclei pool of high viscosity, an optimized protocol for fluorescence activated nuclei sorting (FANS) was established to speed up sorting. Additionally, we present a 1% PFA protocol for fixation of isolated nuclei for long term microscopic visualization.

cell biology↗

bioRxiv2020

Open Source ImmGen: network perspective on metabolic diversity among mononuclear phagocytes

We dissect metabolic variability of mononuclear phagocyte (MNP) subpopulations across different tissues through integrative analysis of three large scale datasets. Specifically, we introduce ImmGen MNP Open Source dataset that profiled 337 samples and extended previous ImmGen effort which included 202 samples of mononuclear phagocytes and their progenitors. Next, we analysed Tabula Muris Senis dataset to extract data for 51,364 myeloid cells from 18 tissues. Taken together, a compendium of data assembled in this work covers phagocytic populations found across 38 different tissues. To analyse common metabolic features, we developed novel network-based computational approach for unbiased identification of key metabolic subnetworks based on cellular transcriptional profiles in large-scale datasets. Using ImmGen MNP Open Source dataset as baseline, we define 9 metabolic subnetworks that encapsulate the metabolic differences within mononuclear phagocytes, and demonstrate that these features are robustly found across all three datasets, including lipid metabolism, cholesterol biosynthesis, glycolysis, and a set of fatty acid related metabolic pathways, as well as nucleotide and folate metabolism. We systematically define major features specific to macrophage and dendritic cell subpopulations. Among other things, we find that cholesterol synthesis appears particularly active within the migratory dendritic cells. We demonstrate that interference with this pathway through statins administration diminishes migratory capacity of the dendritic cells in vivo. This result demonstrates the power of our approach and highlights importance of metabolic diversity among mononuclear phagocytes.

immunology↗

bioRxiv2020

Dynamic longitudinal behavior in animals exposed to chronic social defeat stress

Chronic social defeat (CSD) can lead to impairments in social interaction and other behaviors that are supposed to model features of major depressive disorder (MDD). Not all animals subjected to CSD, however, develop these impairments, and maintained social interaction in some animals is widely used as a model for resilience to stress-induced mental dysfunctions. So far, animals have mainly been studied shortly (24 hours and 7 days) after CSD exposure and longitudinal development of behavioral phenotypes in individual animals has been mostly neglected. We have analyzed social interaction and novel object recognition behavior of stressed mice at different time points after CSD and have found very dynamic courses of behavior of individual animals. Instead of the two groups, resilient or susceptible, that are found at early time points our data suggest four groups with (i, ii) animals behaving resilient or susceptible at early and late time points, respectively (iii) animals that start susceptible and recover with time or (iv) animals that are resilient at early time points but develop vulnerability later on.

animal behavior and cognition↗

bioRxiv2018

A comparison of single-cell trajectory inference methods: towards more accurate and robust tools

Using single-cell-omics data, it is now possible to computationally order cells along trajectories, allowing the unbiased study of cellular dynamic processes. Since 2014, more than 50 trajectory inference methods have been developed, each with its own set of methodological characteristics. As a result, choosing a method to infer trajectories is often challenging, since a comprehensive assessment of the performance and robustness of each method is still lacking. In order to facilitate the comparison of the results of these methods to each other and to a gold standard, we developed a global framework to benchmark trajectory inference tools. Using this framework, we compared the trajectories from a total of 29 trajectory inference methods, on a large collection of real and synthetic datasets. We evaluate methods using several metrics, including accuracy of the inferred ordering, correctness of the network topology, code quality and user friendliness. We found that some methods, including Slingshot, TSCAN and Monocle DDRTree, clearly outperform other methods, although their performance depended on the type of trajectory present in the data. Based on our benchmarking results, we therefore developed a set of guidelines for method users. However, our analysis also indicated that there is still a lot of room for improvement, especially for methods detecting complex trajectory topologies. Our evaluation pipeline can therefore be used to spearhead the development of new scalable and more accurate methods, and is available at github.com/dynverse/dynverse.\n\nTo our knowledge, this is the first comprehensive assessment of trajectory inference methods. For now, we exclusively evaluated the methods on their default parameters, but plan to add a detailed parameter tuning procedure in the future. We gladly welcome any discussion and feedback on key decisions made as part of this study, including the metrics used in the benchmark, the quality control checklist, and the implementation of the method wrappers. These discussions can be held at github.com/dynverse/dynverse/issues.

bioinformatics↗