Biology subjects

Sokol, S.

Publications and source records attributed to Sokol, S..

12 recordsLinked to original sources

bioRxiv2026

Axin2L regulates planar cell polarity in Xenopus embryos

Axin proteins function as central scaffolds of the {beta}-catenin destruction complex in the Wnt/{beta}-catenin pathway that has been considered distinct from the planar cell polarity (PCP) pathway. Here, we show that dorsal expression of mutated Axin2L, a predominant Axin homolog in Xenopus early embryos, disrupts convergent extension movements and neural tube closure in a manner reminiscent of the mutations in vertebrate PCP genes. GFP-Axin2L becomes planar polarized in the epidermal cells adjacent to the folding neural plate and those surrounding a wound. Axin2L associated and colocalized with ADIP, a similarly polarized protein that is essential for neural tube morphogenesis and embryonic wound healing. Interference with Axin2L function abrogated Vangl2 accumulation at the anterior sides of neuroepithelial cells and impaired ciliogenesis in the gastrocoel roof plate. We propose that, in addition to the canonical Wnt pathway, Axin2L controls PCP signaling during vertebrate morphogenesis.

cell biology↗

bioRxiv2026

R-spondin2 regulates planar cell polarity in the vertebrate neural plate

Vertebrate neural tube closure requires planar cell polarity (PCP) signaling to coordinate cell behaviors in the neuroepithelium. In the Xenopus neural plate, PCP is marked by enrichment of the core PCP protein Vangl2 at the anterior edge of every cell, but the distribution of the extracellular factors modulating this asymmetry remains largely unknown. Here, we identify the secreted protein R-spondin2 (Rspo2) as a modulator of neural plate PCP. Rspo2 exhibits predominantly anterior localization in neuroepithelial cells. Morpholino-mediated knockdown of Rspo2 causes neural tube closure defects and disrupts the anterior enrichment of Vangl2. Rspo2 associates with Vangl2 and inhibits FGF receptor-dependent Vangl2 tyrosine phosphorylation in vivo, as shown by both depletion and overexpression experiments. Rspo2 domain analysis shows that the thrombospondin domain contributes to both anterior Rspo2 membrane enrichment and inhibition of Vangl2 phosphorylation. Together, these findings identify a role of Rspo2 in PCP signaling in the Xenopus neural plate and support a model in which anteriorly localized Rspo2 helps maintain Vangl2 asymmetry while limiting Vangl2 tyrosine phosphorylation during neural plate morphogenesis.

developmental biology↗

bioRxiv2026

Force-dependent stabilization of apical actomyosin by Lmo7 during vertebrate neurulation

Coordinated control of actomyosin contractility is essential for epithelial morphogenesis, including vertebrate neural tube closure. Lim domain only 7 (Lmo7) is a force-sensitive regulator of contractility that binds non-muscle myosin II (NMII) heavy chain to initiate apical constriction (AC) during Xenopus neural tube closure. Lmo7 is not required for actomyosin pulsatile activity or changes in the junction length in the intercalating cells during anteroposterior axis elongation. However, Lmo7 knockdown fails to stabilize actomyosin at the apical cortex at the onset of neural tube folding. Gain-of-function approach in gastrula ectoderm confirms a role for Lmo7 in actomyosin stabilization. Mechanistically, force-dependent dephosphorylation of Ser355 in the Lmo7 myosin binding domain enhances Lmo7 binding to NMII and increases NMII abundance at the apical cortex. Notably, initially homogeneous expression of Lmo7 in ectoderm cells progressively leads to apical domain heterogeneity that tightly correlates with Lmo7 levels, arguing for a positive feedback regulation between mechanical forces and Lmo7 activity. We propose that the force-dependent binding of Lmo7 to NMII stabilizes both proteins at the apical cortex, triggering enhanced apical constriction.

developmental biology↗

bioRxiv2026

Planar polarization of endogenous ADIP during Xenopus neurulation

Coordinated cell polarity and force-responsive protein localization are essential for tissue morphogenesis, yet how embryonic cells sense forces and respond to mechanical cues remains a challenging question. Afadin- and alpha-actinin-binding protein (ADIP) has been implicated in microtubule minus-end anchoring, centrosome maturation and ciliogenesis. ADIP is also proposed to associate with the actomyosin cortex and regulate collective cell migration. ADIP behaves as a mechanosensitive planar cell polarity (PCP) protein when overexpressed in Xenopus embryos, but the distribution and regulation of endogenous ADIP has been unknown. Here we show that ADIP is present in early ectoderm as randomly distributed puncta that rapidly reorganize and polarize during epithelial wound repair. Endogenous ADIP also becomes enriched and planar polarized in the anterior neural plate towards the midline, consistent with its regulation by mechanical forces that operate during neural tube closure. ADIP polarization is attenuated by depletion of the core PCP component Diversin/Ankrd6, in agreement with the proposed interaction between the two proteins during PCP establishment. Finally, pharmacological disruption of microtubules, F-actin, and nonmuscle myosin II eliminates ADIP polarization in the neuroectoderm, indicating roles for microtubules and actomyosin networks in PCP. Together, these findings suggest that endogenous ADIP senses mechanical cues via the cytoskeletal machinery and functions in the context-dependent manner to control collective cell behaviors during vertebrate morphogenesis.

developmental biology↗

bioRxiv2025

Estimating flux dynamics from metabolite concentration time courses with dynafluxr

MotivationQuantifying metabolic fluxes and their dynamics is crucial for addressing fundamental and applied questions in systems and synthetic biology, health, and biotechnology. Since metabolic fluxes are not directly observable, they must be estimated using model-based approaches. While several methods are available to quantify steady-state fluxes, approaches for quantifying flux dynamics remain limited. ResultsWe present a method to quantify flux dynamics from metabolite concentration time courses. Our approach employs constrained B-splines to solve mass balance equations without requiring prior knowledge of catalytic or regulatory mechanisms, or enzymatic parameters. We provide a comprehensive mathematical framework for dynamic flux calculation and demonstrate that our method enables accurate and robust quantification of flux dynamics for both simulated and experimental datasets. Availability and implementationdynafluxr is implemented in R and available on Windows, Unix, and MacOS platforms. The source code and the documentation are freely distributed under GPL-3 license at https://github.com/MetaSys-LISBP/dynafluxr/. A companion notebook producing figures similar to those of this article is available at https://github.com/MetaSys-LISBP/DynafluxR_notebook.

systems biology↗

bioRxiv2025

Mechanosensitive localization of Diversin highlights its function in vertebrate morphogenesis and planar cell polarity

Diversin is a vertebrate homolog of the core planar cell polarity (PCP) protein Diego. Here we studied the function of Diversin in Xenopus embryo morphogenesis and its subcellular localization at different locations in superficial ectoderm cells. Depletion of Diversin in the neuroectoderm inhibited apical domain size and neural tube closure and disrupted the polarized localization of endogenous Vangl2, another PCP protein. Whereas Diversin puncta were randomly distributed in early ectoderm, they acquired planar polarity in the neuroectoderm in a stage- and position-specific manner. We find that Diversin is accumulated at the cell junctions adjacent to apically constricting cells at the Xenopus neural plate border and the gastrula blastopore lip. Moreover, Diversin cytoplasmic puncta redistributed in the direction of the pulling forces from the cells with constricting apical domains, suggesting a mechanosensitive process. PCP complexes of Dishevelled (Dvl2) and Diversin or the mechanosensitive adaptor ADIP exhibited planar polarity in the neural plate and the wound edge and promoted wound healing. We propose that Diversin- and Dvl2-containing PCP complexes control morphogenesis in a tension-dependent manner.

cell biology↗

bioRxiv2025

FGF receptor modulates planar cell polarity in the neuroectoderm via Vangl2 tyrosine phosphorylation

FGF receptors (FGFR) play pivotal roles in morphogenetic processes including vertebrate neurulation. Planar cell polarity (PCP) signaling coordinates cell polarization in tissue plane and also plays an essential role in neural tube closure. Here we demonstrate abnormal PCP in Xenopus neuroectoderm depleted of FGFR1, suggesting a mechanistic connection between FGFR signaling and morphogenesis. FGFR1 associated with the core PCP protein Vangl2 leading to its phosphorylation at N-terminal tyrosine residues. This phosphorylation required FGFR1 activity in frog embryos and mouse embryonic stem cells, extending our observations to mammals. Mutagenesis indicated that the phosphorylation inhibits the interaction of Vangl2 with Prickle and the receptor tyrosine kinase PTK7, leading to the disruption of neuroectodermal PCP. This study identifies a cross-talk between the FGFR and PCP pathways mediated by Vangl2 tyrosine phosphorylation.

developmental biology↗

bioRxiv2024

An inferotemporal coding strategy robust to partial object occlusion

Object coding in primate ventral pathway cortex progresses in sparseness/compression/efficiency, from many orientation signals in V1, to fewer 2D/3D part signals in V4, to still fewer multi-part configuration signals in AIT (anterior inferotemporal cortex).1-11 This progression could lead to individual neurons exclusively selective for unique objects, the sparsest code for identity, especially for highly familiar, important objects.12-18 To test this, we trained macaque monkeys to discriminate 8 simple letter-like shapes in a match-to-sample task, a design in which one-to-one coding of letters by neurons could streamline behavior. Performance increased from chance to >80% correct over a period of weeks, after which AIT neurons showed clear learning effects, with increased selectivity for multi-part configurations within the trained alphabet shapes. But these neurons were not exclusively tuned for unique letters based on training, since their responsiveness generalized to different, non-trained shapes containing the same configurations. This multi-part configuration coding limit in AIT is not maximally sparse, but it could explain the robustness of primate vision to partial object occlusion, which is common in the natural world and problematic for computer vision. Multi-part configurations are highly diagnostic of identity, and neural signals for various partial object structures can provide different but equally sufficient evidence for whole object identity across most occlusion conditions.

neuroscience↗

bioRxiv2021

Frizzled3 inhibits Vangl2-Prickle3 association to establish planar cell polarity in the vertebrate neural plate

The orientation of epithelial cells in the plane of the tissue, known as planar cell polarity (PCP), is regulated by interactions of asymmetrically localized PCP protein complexes. In the Xenopus neural plate, Van Gogh-like2 (Vangl2) and Prickle3 (Pk3) proteins form a complex at the anterior cell boundaries, but how this complex is regulated in vivo remains largely unknown. Here we show that Vangl2-Pk3 association is inhibited by Frizzled3 (Fz3), a core PCP protein that is specifically expressed in the neuroectoderm and is essential for the establishment of PCP in this tissue. Proximity biotinylation and crosslinking studies revealed that the Vangl2-Pk3 interaction is suppressed by overexpressed Fz3, but enhanced in Fz3 morphants. In addition, Fz3 induced Vangl2 phosphorylation on T76 and T78, and this phosphorylation was required for Fz3-mediated inhibition of Vangl2-Pk3 complex formation. Consistent with this observation, the complex of Pk3 with nonphosphorylatable Vangl2 was not polarized in the neural plate. These findings provide evidence for in vivo regulation of the Vangl2-Pk3 complex formation and localization by a Frizzled receptor.

developmental biology↗

bioRxiv2021

The dorsal blastopore lip is a source of signals inducing PCP in the Xenopus neural plate

Coordinated polarization of cells in the tissue plane, known as planar cell polarity (PCP), is associated with a signaling pathway critical for the control of morphogenetic processes. Although the segregation of PCP components to opposite cell borders is believed to play a critical role in this pathway, whether PCP derives from egg polarity or preexistent long-range gradient, or forms in response to a localized cue remains a challenging question. Here we investigate the Xenopus neural plate, a tissue that has been previously shown to exhibit PCP. By imaging Vangl2 and Prickle3, we show that PCP is progressively acquired in the neural plate and requires a signal from the posterior region of the embryo. Tissue transplantations indicated that PCP is triggered in the neural plate by a planar cue from the dorsal blastopore lip. The PCP cue did not depend on the orientation of the graft and was distinct from neural inducers. These observations suggest that neuroectodermal PCP is not instructed by a preexisting molecular gradient, but induced by a signal from the dorsal blastopore lip. HighlightsO_LIThe Xenopus neural plate progressively acquires PCP in a posterior-to-anterior direction. C_LIO_LIThe dorsal blastopore lip is likely the source of the PCP-instructing signal for the Xenopus neural plate. C_LIO_LIThe PCP cue is distinct from neural inducers and has a planar mode of transmission. C_LI

developmental biology↗

bioRxiv2021

Pinhead antagonizes Admp to promote notochord formation

Dorsoventral patterning of a vertebrate embryo critically depends on the activity of Smad1 that mediates signaling by several BMP proteins, anti-dorsalizing morphogenetic protein (Admp), and their antagonists. Pinhead (Pnhd), a cystine-knot-containing secreted protein, is expressed in the ventrolateral marginal zone during Xenopus gastrulation, however, its molecular targets and signaling mechanisms have not been fully elucidated. An unbiased mass spectrometry-based screen of the gastrula secretome identified Admp as a primary Pnhd-associated protein. We show that Pnhd binds Admp and inhibits its ventralizing activity by reducing Smad1 phosphorylation and suppressing its transcriptional targets. By contrast, Pnhd did not affect the signaling activity of BMP4. Importantly, the Admp gain-of-function phenotype and phospho-Smad1 levels have been enhanced after Pnhd depletion. Furthermore, Pnhd strongly synergized with Chordin and a truncated BMP4 receptor in the induction of notochord markers in ectoderm cells, and Pnhd-depleted embryos displayed notochord defects. Our findings suggest that Pnhd binds and inactivates Admp to promote notochord development. We propose that the interaction between Admp and Pnhd refines Smad1 activity gradients during vertebrate gastrulation.

developmental biology↗

bioRxiv2021

IsoSolve: an integrative framework to improve isotopic coverage and consolidate isotopic measurements by MS and/or NMR

Stable-isotope labeling experiments are widely used to investigate the topology and functioning of metabolic networks. Label incorporation into metabolites can be quantified using a broad range of mass spectrometry (MS)and nuclear magnetic resonance (NMR)spectroscopy methods, but in general, no single approach can completely cover isotopic space, even for small metabolites. The number of quantifiable isotopic species could be increased, and the coverage of isotopic space improved, by integrating measurements obtained by different methods; however, this approach has remained largely unexplored because no framework able to deal with partial, heterogeneous isotopic measurements has yet been developed. Here, we present a generic computational framework based on symbolic calculus that can integrate any isotopic dataset by connecting measurements to the chemical structure of the molecules. As a test case, we apply this framework to isotopic analyses of amino acids, which are ubiquitous to life, central to many biological questions, and can be analyzed by a broad range of MS and NMR methods. We demonstrate how this integrative framework helps to i) clarify and improve the coverage of isotopic space, ii) evaluate the complementarity and redundancy of different techniques, iii) consolidate isotopic datasets, iv) design experiments, and v) guide future analytical developments. This framework, which can be applied to any labeled element, isotopic tracer, metabolite, and analytical platform, has been implemented in IsoSolve (available at https://github.com/MetaSysLISBP/IsoSolve and https://pypi.org/project/IsoSolve), an open source software that can be readily integrated into data analysis pipelines.

systems biology↗