Biology subjects

Swaminathan, V.

Publications and source records attributed to Swaminathan, V..

5 recordsLinked to original sources

bioRxiv2025

Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy

Understanding molecular orientation and density distributions is essential for exploring biological structure and function. Polarized fluorescence microscopy (PFM) provides insights into molecular architecture but struggles to resolve three-dimensional (3D) molecular orientation distributions, particularly in densely labeled or structurally complex specimens. To address this, we introduce the efficient generalized Richardson-Lucy (eGRL) algorithm, a robust framework for reconstructing 3D molecular density and orientation (spatio-angular) distributions from PFM data. By modeling the imaging process in spatio-angular hyperspace, we propose a maximum-likelihood solution enhanced by dimensionality reduction and angular domain transformation to overcome computational challenges. eGRL improves accuracy and efficiency across different PFM implementations, enabling use on standard platforms. We utilize our methods to resolve biological spatio-angular structures and dynamics otherwise impossible to resolve, including the tangential alignment of actin filaments in U2OS cells, nanowire-guided cytoskeletal organization in NIH3T3 cells, rotational actin patterns in live HeLa protrusions, and membrane tension-induced anisotropy in live macrophages.

bioengineering↗

bioRxiv2025

Human mitochondrial transfer modeling reveals biased delivery from mesenchymal-to-hematopoietic stem cells

Within the bone marrow (BM), the intercellular communication between hematopoietic stem and progenitor cells (HSPCs) and mesenchymal stem/stromal cells (MSCs) is critical for the life-long maintenance of functional hematopoiesis. In recent years, the transfer of mitochondria between MSCs and HSPCs has emerged as a key aspect of this communication, occurring both in stress and homeostatic conditions. In human, the mesenchymal-to-hematopoietic transfer process and functional impact remain cryptic, primarily due to a lack of robust models. To this end, we here describe the development and exploitation of iMSOD-mito, an immortalized human MSCs line bearing an inducible mCherry mitochondrial tag. Co-culture with primary healthy HSPCs or a leukemic cell line revealed a high mitochondrial transfer rate (>15%), exclusively relying on cell-to-cell contact. While all CD34+ blood cells received mitochondria, a preferential transfer towards phenotypic hematopoietic stem cells was identified. Similarly, using primary MSCs with genetically labelled mitochondria we confirmed a transfer to all CD34+ populations, albeit occurring at a lower frequency than with the iMSOD-mito (3.38%). By engineering 3D bone marrow niches in perfusion bioreactor, this transfer rate could be significantly increased, while the biased towards HSC as receiver was maintained. Functionally, mitochondria-receiving cells exhibited an increased mitochondria membrane potential and reactive oxygen species (ROS) production, which in HSPCs was associated with retained quiescence in single cell divisional assay. In summary, we propose the iMSOD-mito as a standardized tool to model human mesenchymal-to-hematopoietic mitochondria transfer in 2D or 3D culture systems. Our work prompts the study of mitochondria transfer in both healthy or disease conditions, towards the design of regenerative therapies or identification of new targets in a malignant context.

cell biology↗

bioRxiv2024

Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

biophysics↗

bioRxiv2022

Data-driven microscopy allows for automated targeted acquisition of relevant data withhigher fidelity

Light microscopy is a powerful single-cell technique that allows for quantitative spatial information at subcellular resolution. However, unlike flow cytometry and single-cell sequencing techniques, microscopy has issues achieving high-quality population-wide sample characterization while maintaining high resolution. Here, we present a general framework, data-driven microscopy (DDM), that uses population-wide cell characterization to enable data-driven high-fidelity imaging of relevant phenotypes. DDM combines data-independent and data-dependent steps to synergistically enhance data acquired using different imaging modalities. As proof-of-concept, we apply DDM with plugins for improved high-content screening and live adaptive microscopy. DDM also allows for easy correlative imaging in other systems with a plugin that uses the spatial relationship of the sample population for automated registration. We believe DDM will be a valuable approach for reducing human bias, increasing reproducibility, and placing singlecell characteristics in the context of the sample population when interpreting microscopy data, leading to an overall increase in data fidelity.

systems biology↗

bioRxiv2018

Reversing Glial Scar Back To Neural Tissue Through NeuroD1-Mediated Astrocyte-To-Neuron Conversion

Nerve injury often causes neuronal loss and glial proliferation, disrupting the delicate balance between neurons and glial cells in the brain. Recently, we have developed an innovative technology to convert internal reactive glial cells into functional neurons inside the mouse brain. Here, we further demonstrate that such glia-to-neuron conversion can rebalance neuron-glia ratio and reverse glial scar back to neural tissue. Specifically, using a severe stab injury model in the mouse cortex, we demonstrated that ectopic expression of NeuroD1 in reactive astrocytes significantly reduced glial reactivity and transformed toxic A1 astrocytes into less harmful astrocytes before neuronal conversion. Importantly, astrocytes were not depleted after neuronal conversion but rather repopulated due to its intrinsic proliferation capability. Remarkably, converting reactive astrocytes into neurons also significantly reduced microglia-mediated neuroinflammation. Moreover, accompanying regeneration of new neurons together with repopulation of new astrocytes, blood-brain-barrier was restored and synaptic density was rescued in the injury sites. Together, these results demonstrate that glial scar can be reversed back to neural tissue through rebalancing neuron:glia ratio after glia-to-neuron conversion.

neuroscience↗