Sayantan Dutta

All Publications

• Leveraging polymer modeling to reconstruct chromatin connectivity from live images. Biophysical journal Dutta, S., Ghosh, A., Boettiger, A. N., Spakowitz, A. J. 2023

  Abstract

  Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.

  View details for DOI 10.1016/j.bpj.2023.08.001

  View details for PubMedID 37542372

• Maintaining symmetry during body axis elongation. Current biology : CB Smits, C. M., Dutta, S., Jain-Sharma, V., Streichan, S. J., Shvartsman, S. Y. 2023

  Abstract

  Bilateral symmetry defines much of the animal kingdom and is crucial for numerous functions of bilaterian organisms. Genetic approaches have discovered highly conserved patterning networks that establish bilateral symmetry in early embryos,1 but how this symmetry is maintained throughout subsequent morphogenetic events remains largely unknown.2 Here we show that the terminal patterning system-which relies on Ras/ERK signaling through activation of the Torso receptor by its ligand Trunk3-is critical for preserving bilateral symmetry during Drosophila body axis elongation, a process driven by cell rearrangements in the two identical lateral regions of the embryo and specified by the dorsal-ventral and anterior-posterior patterning systems.4 We demonstrate that fluctuating asymmetries in this rapid convergent-extension process are attenuated in normal embryos over time, possibly through noise-dissipating forces from the posterior midgut invagination and movement. However, when Torso signaling is attenuated via mutation of Trunk or RNAi directed against downstream Ras/ERK pathway components, body axis elongation results in a characteristic corkscrew phenotype,5 which reflects dramatic reorganization of global tissue flow and is incompatible with viability. Our results reveal a new function downstream of the Drosophila terminal patterning system in potentially active control of bilateral symmetry and should motivate systematic search for similar symmetry-preserving regulatory mechanisms in other bilaterians.

  View details for DOI 10.1016/j.cub.2023.07.050

  View details for PubMedID 37562404

• Self-organized intracellular twisters. bioRxiv : the preprint server for biology Dutta, S., Farhadifar, R., Lu, W., KabacaoAYlu, G., Blackwell, R., Stein, D. B., Lakonishok, M., Gelfand, V. I., Shvartsman, S. Y., Shelley, M. J. 2023

  Abstract

  Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, we combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. We use a fast, accurate, and scalable numerical approach to investigate fluid-structure interactions of 1000s of flexible fibers and demonstrate the robust emergence and evolution of cell-spanning vortices, or twisters. Dominated by a rigid body rotation and secondary toroidal components, these flows are likely involved in rapid mixing and transport of ooplasmic components.

  View details for DOI 10.1101/2023.04.04.534476

  View details for PubMedID 37066165

• Spatial organization of transcribing loci early activation in Drosophila CURRENT BIOLOGY Huang, S., Whitney, P. H., Dutta, S., Shvartsman, S. Y., Rushlow, C. A. 2021; 31 (22): 5102-+

  Abstract

  The early Drosophila embryo provides unique experimental advantages for addressing fundamental questions of gene regulation at multiple levels of organization, from individual gene loci to the entire genome. Using 1.5-h-old Drosophila embryos undergoing the first wave of genome activation,1 we detected ∼110 discrete "speckles" of RNA polymerase II (RNA Pol II) per nucleus, two of which were larger and localized to the histone locus bodies (HLBs).2,3 In the absence of the primary driver of Drosophila genome activation, the pioneer factor Zelda (Zld),1,4,5 70% fewer speckles were present; however, the HLBs tended to be larger than wild-type (WT) HLBs, indicating that RNA Pol II accumulates at the HLBs in the absence of robust early-gene transcription. We observed a uniform distribution of distances between active genes in the nuclei of both WT and zld mutant embryos, indicating that early co-regulated genes do not cluster into nuclear sub-domains. However, in instances whereby transcribing genes did come into close 3D proximity (within 400 nm), they were found to have distinct RNA Pol II speckles. In contrast to the emerging model whereby active genes are clustered to facilitate co-regulation and sharing of transcriptional resources, our data support an "individualist" model of gene control at early genome activation in Drosophila. This model is in contrast to a "collectivist" model, where active genes are spatially clustered and share transcriptional resources, motivating rigorous tests of both models in other experimental systems.

  View details for DOI 10.1016/j.cub.2021.09.027

  View details for Web of Science ID 000721720700011

  View details for PubMedID 34614388

  View details for PubMedCentralID PMC8612988

• Temporal integration of inductive cues on the way to gastrulation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA McFann, S., Dutta, S., Toettcher, J. E., Shvartsman, S. Y. 2021; 118 (23)

  Abstract

  Markers for the endoderm and mesoderm germ layers are commonly expressed together in the early embryo, potentially reflecting cells' ability to explore potential fates before fully committing. It remains unclear when commitment to a single-germ layer is reached and how it is impacted by external signals. Here, we address this important question in Drosophila, a convenient model system in which mesodermal and endodermal fates are associated with distinct cellular movements during gastrulation. Systematically applying endoderm-inducing extracellular signal-regulated kinase (ERK) signals to the ventral medial embryo-which normally only receives a mesoderm-inducing cue-reveals a critical time window during which mesodermal cell movements and gene expression are suppressed by proendoderm signaling. We identify the ERK target gene huckebein (hkb) as the main cause of the ventral furrow suppression and use computational modeling to show that Hkb repression of the mesoderm-associated gene snail is sufficient to account for a broad range of transcriptional and morphogenetic effects. Our approach, pairing precise signaling perturbations with observation of transcriptional dynamics and cell movements, provides a general framework for dissecting the complexities of combinatorial tissue patterning.

  View details for DOI 10.1073/pnas.2102691118

  View details for Web of Science ID 000684996500016

  View details for PubMedID 34083443

  View details for PubMedCentralID PMC8201965

• From complex datasets to predictive models of embryonic development NATURE COMPUTATIONAL SCIENCE Dutta, S., Patel, A. L., Keenan, S. E., Shvartsman, S. Y. 2021; 1

  View details for DOI 10.1038/s43588-021-00110-2

• Excess dNTPs Trigger Oscillatory Surface Flow in the Early Drosophila Embryo BIOPHYSICAL JOURNAL Dutta, S., Djabrayan, N., Smits, C. M., Rowley, C. W., Shvartsman, S. Y. 2020; 118 (10): 2349-2353

  Abstract

  During the first 2 hours of Drosophila development, precisely orchestrated nuclear cleavages, cytoskeletal rearrangements, and directed membrane growth lead to the formation of an epithelial sheet around the yolk. The newly formed epithelium remains relatively quiescent during the next hour as it is patterned by maternal inductive signals and zygotic gene products. We discovered that this mechanically quiet period is disrupted in embryos with high levels of dNTPs, which have been recently shown to cause abnormally fast nuclear cleavages and interfere with zygotic transcription. High levels of dNTPs are associated with robust onset of oscillatory two-dimensional flows during the third hour of development. Tissue cartography, particle image velocimetry, and dimensionality reduction techniques reveal that these oscillatory flows are low dimensional and are characterized by the presence of spiral vortices. We speculate that these aberrant flows emerge through an instability triggered by deregulated mechanical coupling between the nascent epithelium and three-dimensional yolk. These results highlight an unexplored connection between a core metabolic process and large-scale mechanics in a rapidly developing embryo.

  View details for DOI 10.1016/j.bpj.2020.03.010

  View details for Web of Science ID 000535494500004

  View details for PubMedID 32247330

  View details for PubMedCentralID PMC7231883

• Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo BIOPHYSICAL JOURNAL Dutta, S., Djabrayan, N., Torquato, S., Shvartsman, S. Y., Krajnc, M. 2019; 117 (4): 743-750

  Abstract

  Embryonic development starts with cleavages, a rapid sequence of reductive divisions that result in an exponential increase of cell number without changing the overall size of the embryo. In Drosophila, the final four rounds of cleavages occur at the surface of the embryo and give rise to ∼6000 nuclei under a common plasma membrane. We use live imaging to study the dynamics of this process and to characterize the emergent nuclear packing in this system. We show that the characteristic length scale of the internuclear interaction scales with the density, which allows the densifying embryo to sustain the level of structural order at progressively smaller length scales. This is different from nonliving materials, which typically undergo disorder-order transition upon compression. To explain this dynamics, we use a particle-based model that accounts for density-dependent nuclear interactions and synchronous divisions. We reproduce the pair statistics of the disordered packings observed in embryos and recover the scaling relation between the characteristic length scale and the density both in real and reciprocal space. This result reveals how the embryo can robustly preserve the nuclear-packing structure while being densified. In addition to providing quantitative description of self-similar dynamics of nuclear packings, this model generates dynamic meshes for the computational analysis of pattern formation and tissue morphogenesis.

  View details for DOI 10.1016/j.bpj.2019.07.009

  View details for Web of Science ID 000482097100012

  View details for PubMedID 31378311

  View details for PubMedCentralID PMC6712419

• Interactions and design rules for assembly of porous colloidal mesophases SOFT MATTER Lindquist, B. A., Dutta, S., Jadrich, R. B., Milliron, D. J., Truskett, T. M. 2017; 13 (7): 1335-1343

  Abstract

  Porous mesophases, where well-defined particle-depleted 'void' spaces are present within a particle-rich background fluid, can be self-assembled from colloidal particles interacting via isotropic pair interactions with competing attractions and repulsions. While such structures could be of wide interest for technological applications (e.g., filtration, catalysis, absorption, etc.), relatively few studies have investigated the interactions that lead to these morphologies and how they compare to those that produce other micro-phase-separated structures, such as clusters. In this work, we use inverse methods of statistical mechanics to design model isotropic pair potentials that form porous mesophases. We characterize the resulting porous structures, correlating features of the pair potential with the targeted pore size and the particle packing fraction. The former is primarily encoded by the amplitude and range of the repulsive barrier of the designed pair potential and the latter by the attractive well depth. We observe a trade-off with respect to the packing fraction of the targeted morphology: greater values support more spherical and monodisperse pores that themselves organize into periodic structures, while lower values yield more mobile pores that do not assemble into ordered structures but remain stable over a larger range of packing fraction. We conclude by commenting on the limitations of targeting a specific pore diameter within the present inverse design approach as well as by describing future directions to overcome these limitations.

  View details for DOI 10.1039/c6sm02718k

  View details for Web of Science ID 000396024800002

  View details for PubMedID 28133680