Biology subjects

Solecki, D. J.

Publications and source records attributed to Solecki, D. J..

5 recordsLinked to original sources

bioRxiv2026

An Interpretable 3D Bag-Of-Visual-Words Pipeline for Volumetric Microscopy Classification

Fluorescence microscopy increasingly produces complex volumetric datasets whose biologically meaningful differences are difficult to capture with hand-crafted measurements, especially when signal is distributed across three-dimensional space. Here, we present an interpretable 3D Bag-of-Visual-Words (BoVW) pipeline for classification and analysis of volumetric microscopy data. The framework detects multiscale local keypoints, computes rotationally robust 3D gradient-based descriptors, and aggregates them into image-level visual-word representations. These features are then used for low-dimensional visualization and logistic regression classification, while model weights are mapped back to the original volumes to generate attention maps that localize discriminative structures. We applied the pipeline to two cerebellar granule neuron datasets spanning both ideal and non-ideal imaging conditions. In a near-isotropic lattice light-sheet dataset of chromatin organization, the method separated control and NIPBL loss-of-function nuclei and supported accurate classification, with strongest performance in the facultative heterochromatin and H3.3 channels. Attention mapping and downstream connected-component and Haralick analyses revealed that loss-of-function nuclei contained more fragmented high-attention regions and smoother, more homogeneous chromatin-associated textures than controls. We then evaluated the same framework on an anisotropic confocal timelapse dataset of receptor clustering in dense neuronal cultures, where single-cell segmentation was impractical. Despite these challenges, the representation captured the expected ligand-driven clustering response and resolved subtler differences associated with a polarity protein overexpression. Together, these results establish a simple, interpretable, and broadly applicable framework for extracting biologically meaningful structure from volumetric microscopy datasets while preserving native 3D context.

cell biology↗

bioRxiv2024

Junctional Adhesion Molecule (JAM)-C recruitment of Pard3 and drebrin to cell contacts initiates neuron-glia recognition and layer-specific cell sorting in developing cerebella.

Sorting maturing neurons into distinct layers is critical for brain development, with disruptions leading to neurological disorders and pediatric cancers. Lamination coordinates where, when, and how cells interact, facilitating events that direct migrating neurons to their destined positions within emerging neural networks and control the wiring of connections in functional circuits. While the role of adhesion molecule expression and presentation in driving adhesive recognition during neuronal migration along glial fibers is recognized, the mechanisms by which the spatial arrangement of these molecules on the cell surface dictates adhesive specificity and translates contact-based external cues into intracellular responses like polarization and cytoskeletal organization remain largely unexplored. We used the cerebellar granule neuron (CGN) system to demonstrate that JAM-C receptor cis-binding on the same cell and trans-binding to neighboring cells controls the recruitment of the Pard3 polarity protein and drebrin microtubule-actin crosslinker at CGN to glial adhesion sites, complementing previous studies that showed Pard3 controls JAM-C exocytic surface presentation. Leveraging advanced imaging techniques, specific probes for cell recognition, and analytical methods to dissect adhesion dynamics, our findings reveal: 1) JAM-C cis or trans mutants result in reduced adhesion formation between CGNs and cerebellar glia, 2) these mutants exhibit delayed recruitment of Pard3 at the adhesion sites, and 3) CGNs with JAM-C mutations experience postponed sorting and entry into the cerebellar molecular layer (ML). By developing a conditional system to image adhesion components from two different cells simultaneously, we made it possible to investigate the dynamics of cell recognition on both sides of neuron-glial contacts and the subsequent recruitment of proteins required for CGN migration. This system and an approach that calculates local correlation based on convolution kernels at the cell adhesions site revealed that CGN to CGN JAM recognition preferentially recruits higher levels of Pard3 and drebrin than CGN to glia JAM recognition. The long latency time of CGNs in the inner external germinal layer (EGL) can be attributed to the combined strength of CGN-CGN contacts and the less efficient Pard3 recruitment by CGN-BG contacts, acting as gatekeepers to ML entry. As CGNs eventually transition to glia binding for radial migration, our research demonstrates that establishing permissive JAM-recognition sites on glia via cis and trans interactions of CGN JAM-C serves as a critical temporal checkpoint for sorting at the EGL to ML boundary. This mechanism integrates intrinsic and extrinsic cellular signals, facilitating heterotypic cell sorting into the ML and dictating the precise spatial organization within the cerebellar architecture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/586832v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@10f4aa4org.highwire.dtl.DTLVardef@ed5fc9org.highwire.dtl.DTLVardef@2b94fborg.highwire.dtl.DTLVardef@142254c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Antagonistic action of Siah2 and Pard3/JamC to promote germinal zone exit of differentiated cerebellar granule neurons by modulating Ntn1 signaling via Dcc

Germinal zone (GZ) exit is at the top of a cascade of events promoting the maturation of neurons and their assembly into neuronal circuits. Developing neurons and their progenitors must interpret varied niche signals like morphogens, guidance molecules, extracellular matrix, or adhesive cues to navigate GZ occupancy. How newborn neurons integrate multiple cell-extrinsic niche cues with their cell-intrinsic machinery in exiting a GZ is unknown. We establish cooperation between cell polarity-regulated adhesion and Netrin-1 signaling comprises a coincidence detection circuit repelling maturing neurons from their GZ. In this circuit, the Partitioning defective 3 (Pard3) polarity protein and Junctional adhesion molecule-C (JAM-C) adhesion protein promote, while the Seven in absentia 2 (Siah2) ubiquitin ligase inhibits, Deleted in colorectal cancer (DCC) receptor surface recruitment to gate differentiation linked repulsion to GZ Netrin-1. These results demonstrate cell polarity as a central integrator of adhesive- and guidance cues cooperating to spur GZ exit. Highlights-Netrin1 expressed in the cerebellar GZ ranges from an attractive to repulsive cue depending on differentiation status or extracellular matrix context. -Modulation of DCC expression levels impacts the nature of the Netrin1 response and GZ occupancy status. -Siah2, Pard3, and JamC function to modulate responsiveness to purified Netrin1 and cooperate with Dcc to regulate GZ exit. -Pard3 and JamC promote both basal and Netrin1 stimulated DCC surface recruitment to control GZ exit and Netrin1 repulsion

neuroscience↗

bioRxiv2019

Correlative three-dimensional super-resolution and block face electron microscopy of whole vitreously frozen cells

Living cells function through the spatial compartmentalization of thousands of distinct proteins serving a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) has emerged as a pathway to directly view nanoscale protein relationships to the underlying global ultrastructure, but has traditionally suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional correlative cryogenic SR and focused ion beam milled block-face EM across entire vitreously frozen cells that addresses these issues by preserving native ultrastructure and enabling independent SR and EM workflow optimization. Application to a variety of biological systems revealed a number of unexpected protein-ultrastructure relationships and underscored the value of a comprehensive multimodal view of ultrastructural variability across whole cells.

cell biology↗

bioRxiv2019

Siah2 integrates mitogenic and extracellular matrix signalslinking neuronal progenitor ciliogenesis with germinal zoneoccupancy.

Evidence is lacking as to how developing neurons integrate mitogenic signals with microenvironment cues to control proliferation and differentiation. We determined that the Siah2 E3 ubiquitin ligase functions in a coincidence detection circuit linking responses to the Shh mitogen and the extracellular matrix to control cerebellar granule neurons (CGN) germinal zone (GZ) occupancy. We found that Shh maintains Siah2 expression in CGN progenitors (GNPs) in a Ras/Mapk-dependent manner. Siah2 supports ciliogenesis in a feed-forward fashion by restraining ciliogenic targets. Efforts to identify GZ sources of Ras/Mapk signaling led us to discover that GNPs respond to laminin, but not vitronectin, in the microenvironment via integrin {beta}1 receptors, which engages the Ras/Mapk cascade, and that this niche interaction is essential for promoting GNP ciliogenesis. As GNPs leave the GZ, differentiation is seamlessly driven by changing extracellular cues that diminish Siah2-activity leading to primary cilia retraction and attenuation of mitogenic responses.

neuroscience↗