Biology subjects

Klimovich, A.

Publications and source records attributed to Klimovich, A..

11 recordsLinked to original sources

bioRxiv2026

Optogenetic perturbations reveal temporal integration of Wnt signaling during pattern formation

The Wnt signaling pathway is a conserved regulator of tissue patterning and regeneration, yet how cells interpret dynamic Wnt inputs to generate robust developmental outcomes remains poorly understood. Here, we establish the first optogenetically activatable Hydra line, enabling precise temporal control of canonical Wnt signaling in vivo. Optogenetic stimulation induced dose-dependent patterning phenotypes whose rate of progression scaled with stimulation intensity. Transcriptomic analysis revealed that distinct combinations of signal intensity and duration converged onto shared transcriptional trajectories and could be described by an effective exposure metric that represents the cumulative signaling input. Functionally, Wnt activation rescued head regeneration under conditions that normally prevent organizer formation, and equivalent regenerative outcomes could be achieved through either strong, short-lived stimulation or weaker, prolonged activation. Together, our results indicate that Hydra tissues decode Wnt signaling through temporal integration of cumulative pathway activity, progressively accumulating transcriptional responses until patterning thresholds are reached. These findings establish a quantitative framework for understanding how dynamic morphogen signaling is translated into stable developmental decisions during regeneration.

developmental biology↗

bioRxiv2026

Single-cell, clonal and spatial atlases of cranial placodes illuminate their specification and evolution

The vertebrate head is defined by complex sensory structures derived from cranial placodes. Placodes arise alongside the neural crest at the neural plate border, yet the mechanisms governing their identity, diversification, and evolutionary origins are unclear. We present an integrated single-cell, spatial, and clonal atlas of placode development to resolve the dynamics of their lineage segregation. Combining single-cell RNA-sequencing, spatial transcriptomics, and high-resolution clonal tracing, we show that placodal and neighboring progenitors form a continuous transcriptional landscape with gradual transitions between domains. Domain boundary cells co-express markers of adjacent territories, suggesting transient bipotent states. Consistent with this, clonal analysis reveals sharing of progenitors between neighboring placodes, supporting a model of competitive segregation. Comparisons with amphioxus suggests that vertebrate olfactory placodes emerged from an ancestral neuroectoderm that later partitioned into distinct neural and olfactory domains. Our findings provide a unified framework for understanding the developmental and evolutionary origins of vertebrate sensory organs.

developmental biology↗

bioRxiv2024

Evolutionary trends in the emergence of skeletal cell types.

The emergence of novel cell types fuels evolutionary innovations and contributes to the diversity of life forms and their morphological and functional traits. Cell types are fundamental functional units of multicellular organisms defined by their specific gene expression programs. The evolution of these transcriptional programs is driven by genetic changes, such as gene co-option and cis- regulatory evolution, known to facilitate the assembly or rewiring of molecular networks and give rise to new cell types with specialized functions. However, the role of novel genes in this complex evolutionary process is underexplored. Here, we examine the trends in skeletal cell type evolution with a focus on lineage-specific genes. We find that immature chondrocytes express the oldest transcriptome and resemble ancestral skeletogenic cell type, supporting the existence of a conserved genetic program for cartilage development in bilaterians. The subsequent acquisition of lineage-restricted genes led to the individuation of the ancient gene expression program and powered the emergence of osteoblasts and hypertrophic chondrocytes. We found a significant enrichment of Vertebrate-specific genes in osteoblasts and Gnathostome-specific genes in hypertrophic chondrocytes. By identifying the functional properties of the recruited genes, coupled with the recently discovered fossil evidence, our findings challenge the long-standing view on the evolution of vertebrate skeletal structures and suggest that endochondral ossification and chondrocyte hypertrophy evolved already in the last common ancestors of gnathostomes. Finally, our findings highlight the critical role of novel genes in shaping cellular diversity.

evolutionary biology↗

bioRxiv2024

The microbiota affects stem cell decision making in Hydra

Research on microbial communities colonizing animals has revealed that the microbiota, despite its typical containment to surfaces, influences virtually all organ systems of the host. In absence of a natural microbiota, the hosts development can be disturbed, but how developmental programs are affected by the microbiota is still poorly understood. Removing the microbiota from Hydra, a classic model animal in developmental biology, causes drastic developmental malformations and leads to polyps that temporarily lack the ability to bud. Recolonizing non-budding germfree Hydra with bacteria reverses this budding inhibition. Single-nucleus ATAC-seq detected a unique chromatin landscape associated with the non-budding phenotype. Single-cell RNA-seq and trajectory-based differential expression analysis showed that epithelial stem cell decision making is disturbed in non-budding polyps, whereby key developmental regulators are not expressed. This process is reversible by adding back bacteria. Transcriptionally silencing of one of the genes that failed to be activated in non-budding animals, GAPR1, led to polyps that have a significantly reduced budding capacity. The results show that maintaining a species-specific microbiota may enable the animal host to maintain its developmental program. Significance StatementAnimal developmental programs work within the context of coevolved associations with microbes. Here, we provide mechanistic evidence of the involvement of the microbiota in maintaining the pattern formation program of Hydra with the asexual formation of buds in the lower part of the body column. We demonstrate that in the absence of bacteria both the epigenetic and transcriptomic landscape is changed and that key regulatory factors are not expressed, causing changes in stem cell trajectories that result in loss of budding capacity. This study provides a new perspective on the role that microbiota plays during animal development and evolution. One Sentence SummaryMicrobiota interfere with Hydras asexual reproduction via modulating its stem cell differentiation programs.

developmental biology↗

bioRxiv2024

A functional network model for body column neural connectivity in Hydra

Hydra is a non-senescent animal with a relatively small number of cell types and overall low structural complexity, but a surprisingly rich behavioral repertoire. The main drivers of Hydra s behavior are neurons that are arranged in two nerve nets comprising several distinct neuronal populations. Among these populations is the ectodermal nerve net N3 which is located throughout the animal. It has been shown that N3 is necessary and sufficient for the complex behavior of somersaulting and is also involved in Hydra feeding behavior. Despite being a behavioral jack-of-all-trades, there is insufficient knowledge on the coupling structure of neurons in N3, its connectome, and its role in activity propagation and function. We construct a model connectome for the part of N3 located on the body column. Using experimental data on the placement of neuronal somata and the spatial dimensions of the body column, we show that a generative network model combining non-random placement of neuronal somata and the preferred orientation of primary neurites yields good agreement with experimentally observed distributions of connection distances, connection angles, and the number of primary neurites per neuron. Having validated the N3 connectome model in this fashion, we place a simple excitable dynamical model on each node of the body column network and show that it generates directed, short-lived, fast propagating patterns of activity. In addition, by slightly changing the parameters of the dynamical model, the same structural network can also generate persistent activity. Finally, we use a neuromorphic circuit based on the Morris-Lecar model to show that the same structural connectome can, in addition to through-conductance with biologically plausible time scales, also host a dynamical pattern related to the complex behavioral pattern of somersaulting. We speculate that such different dynamical regimes act as dynamical substrates for the different functional roles of N3, allowing Hydra to exhibit behavioral complexity with a relatively simple nervous system that does not possess modules or hubs.

neuroscience↗

bioRxiv2024

Genetic interference with HvNotch provides new insights into the role of the Notch-signalling pathway for developmental pattern formation in Hydra

The Notch-signalling pathway plays an important role in pattern formation in Hydra. Using pharmacological Notch inhibitors (DAPT and SAHM1), it has been demonstrated that HvNotch is required for head regeneration and tentacle patterning in Hydra. HvNotch is also involved in establishing the parent-bud boundary and instructing buds to develop feet and detach from the parent. To further investigate the functions of HvNotch, we successfully constructed NICD (HvNotch intracellular domain)-overexpressing and HvNotch-knockdown transgenic Hydra strains. NICD-overexpressing transgenic Hydra showed a pronounced inhibition on the expression of predicted HvNotch-target genes, suggesting a dominant negative effect of ectopic NICD. This resulted in a "Y-shaped" phenotype, which arises from the parent-bud boundary defect seen in polyps treated with DAPT. Additionally, "multiple heads", "two-headed" and "ectopic tentacles" phenotypes were observed. The HvNotch-knockdown transgenic Hydra with reduced expression of HvNotch exhibited similar, but not identical phenotypes, with the addition of a "two feet" phenotype. Furthermore, approximately 20% of the HvNotch-knockdown polyps were unable to regenerate a new head after decapitation. We integrated these findings into a mathematical model based on long-range gradients of signalling molecules underlying sharply defined positions of HvNotch-signalling cells at the Hydra tentacle and bud boundaries.

developmental biology↗

bioRxiv2023

Microbes as part of ancestral neuronal circuits: Bacterial produced signals affect neurons controlling eating behavior in Hydra

Although recent studies indicate the impact of microbes on the central nervous systems and behavior, it remains unclear how the relationship between the functionality of the nervous system, behavior and the microbiota arise. We studied the eating behavior of Hydra, a host that has a simple nervous system and a low-complexity microbiota. To identify the neuronal subpopulations involved, we used a subpopulation specific cell ablation system and calcium imaging. The role of the microbiota was uncovered by reducing the diversity of the natural microbiota. Here, we demonstrate that different neuronal subpopulations are functioning together to control the eating behavior. The microbiota participates in control of the eating behavior since germ-free or mono-colonized animals have drastic difficulties in mouth opening. This was restored by adding a full complement of the microbiota. In summary, we provide a mechanistic explanation of how the eating behavior is controlled in Hydra and how microbes can affect the neuronal circuit. Highlights- Multiple neuronal modules and their networks control complex behavior in an animal lacking a central nervous system. - Its associated microbes participate in these neuronal circuits and influence the eating behavior. - Disorganization of the microbiota negatively impacts this eating behavior. - Glutamate participates in an evolutionary ancient interkingdom language.

animal behavior and cognition↗

bioRxiv2022

Spontaneous body wall contractions stabilize the fluid microenvironment that shapes host-microbe associations

The freshwater polyp Hydra is a popular biological model system; however, we still do not understand one of its most salient behaviours, the generation of spontaneous body wall contractions. Here, by applying experimental fluid dynamics analysis and mathematical modelling, we provide functional evidence that spontaneous contractions of body walls enhance the transport of chemical compounds from and to the tissue surface where symbiotic bacteria reside. Experimentally, a reduction in the frequency of spontaneous body wall contractions is associated with a changed composition of the colonizing microbiota. Together, our findings suggest that spontaneous body wall contractions create an important fluid transport mechanism that (1) may shape and stabilize specific host-microbe associations and (2) create fluid microhabitats that may modulate the spatial distribution of the colonizing microbes. This mechanism may be more broadly applicable to animal-microbe interactions since research has shown that rhythmic spontaneous contractions in the gastrointestinal tracts are essential for maintaining normal microbiota.

biophysics↗

bioRxiv2019

Prototypical pacemaker neurons are immunocompetent cells

Pacemaker neurons exert control over neuronal circuit function by their intrinsic ability to generate rhythmic bursts of action potential. Recent work has identified rhythmic gut contractions in human, mice and hydra to be dependent on both neurons and the resident microbiota. However, little is known about the evolutionary origin of these neurons and their interaction with microbes. In this study, we identified and functionally characterized prototypical ANO/SCN/TRPM ion channel expressing pacemaker cells in the basal metazoan Hydra by using a combination of single-cell transcriptomics, immunochemistry, and functional experiments. Unexpectedly, these prototypical pacemaker neurons express a rich set of immune-related genes mediating their interaction with the microbial environment. Functional experiments validated a model of the evolutionary emergence of pacemaker cells as neurons using components of innate immunity to interact with the microbial environment and ion channels to generate rhythmic contractions.

developmental biology↗

bioRxiv2019

Ancestral role of Fat-like cadherins in planar cell polarity

Fat family cadherins are enormous proteins that regulate planar cell polarity (PCP) and cell adhesion in bilaterian animals. Their evolutionary origin can be traced back to prebilaterian species, but their ancestral function(s) are unknown. We identified Fat-like and Dachsous cadherins in Hydra, a member of the early-diverging metazoan phylum Cnidaria. Hydra has a simple body plan with only two epithelial layers and radial symmetry. We find that Hydra homologues of Fat-like (HyFat) and Dachsous (HyDs) co-localize at the apico-lateral membrane of ectodermal epithelial cells. Remarkably, HyFat is planar polarized perpendicular to the oral-aboral axis of the animal. Using knockdown approaches we found that HyFat is involved in the regulation of local cell alignment, but is dispensable for the global alignment of ectodermal myonemes along the oral-aboral axis. The intracellular domain (ICD) of HyFat is involved in the morphogenesis of ectodermal myonemes. Thus, Fat family cadherins have ancient, prebilaterian functions in cell adhesion, tissue organization and planar polarity.

developmental biology↗

bioRxiv2018

Hydra Bcl-2 and TMBIMP family proteins display anti-apoptotic functions

BackgroundMechanisms of programmed cell death differ considerably between animals, plants and fungi. In animals they depend on caspases and Bcl-2 family proteins and this kind of cell death is called apoptosis. Most gene families encoding proteins involved in apoptosis are found in multicellular animals already in the eldest phyla but their functional conservation is still being studied. Much older protein families have cytoprotective functions across all kingdoms of life. This includes the TMBIMP-family, the presence and function of which in early metazoans has not been investigated yet.\n\nMethodsWe quantified apoptosis in transgenic Hydra overexpressing HyBcl-2-like 4. Moreover, we investigated putative TMBIMP-family members in Hydra by sequence comparison. By overexpression of TMBIMP-family members in Hydra and human HEK cells we analysed their subcellular localisation and in one case their capacity to protect cells from camptothecin induced apoptosis.\n\nResultsHyBcl-2-like 4, as previously shown in a heterologous system, was localised to mitochondria and able to protect Hydra epithelial cells from apoptosis. The TMBIMP-family in Hydra includes HyBax-Inhibitor-1, HyLifeguard-1a and -1b and HyLifeguard 4 proteins. HyBax-inhibitor-1 protein was found localised to ER-membranes, HyLifeguard-family members were found at the plasma membrane and in Golgi-vesicles. Moreover, HyBax-inhibitor-1 protected human cells from apoptosis.\n\nConclusionThis work provides the first functional study to support an anti-apoptotic function of Bcl-2 like proteins in pre-bilaterians within a physiological context. Furthermore it illustrates that genes that were \"inherited\" from non-animal ancestors, like the TMBIMP-family, were recruited to carry out cell protective anti-apoptotic functions already in early metazoans.

developmental biology↗