383 Publications

Sequence-structure-function relationships in the microbial protein universe

J. Koehler, Pawel Szczerbiak, D. Renfrew, N. Carriero, I. Fisk, R. Bonneau, et al.

For the past half-century, structural biologists relied on the notion that similar protein sequences give rise to similar structures and functions. While this assumption has driven research to explore certain parts of the protein universe, it disregards spaces that don’t rely on this assumption. Here we explore areas of the protein universe where similar protein functions can be achieved by different sequences and different structures. We predict ∼200,000 structures for diverse protein sequences from 1,003 representative genomes1 across the microbial tree of life, and annotate them functionally on a per-residue basis. Structure prediction is accomplished using the World Community Grid, a large-scale citizen science initiative. The resulting database of structural models is complementary to the AlphaFold database, with regards to domains of life as well as sequence diversity and sequence length. We identify 161 novel folds and describe examples where we map specific functions to structural motifs. We also show that the structural space is continuous and largely saturated, highlighting the need for shifting the focus from obtaining structures to putting them into context, to transform all branches of biology, including a shift from sequence-based to sequence-structure-function based meta-omics analyses.

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March 20, 2022

Deconstructing gastrulation at single-cell resolution

T. Stern, S. Shvartsman, E. F. Wieschaus

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets, which are driven by cell divisions, cell shape changes, and cell intercalations. Each of these behaviors has been associated with distinct aspects of gastrulation and has been a subject of intense research using genetic, cell biological, and more recently, biophysical approaches. Most of these studies, however, focus either on cellular processes driving gastrulation or on large-scale tissue deformations. Recent advances in microscopy and image processing create a unique opportunity for integrating these complementary viewpoints. Here, we take a step toward bridging these complementary strategies and deconstruct the early stages of gastrulation in the entire Drosophila embryo. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. The detected events are then mapped back onto the blastoderm shell, providing an intuitive visual means to examine complex cellular activity patterns within the context of their initial anatomic domains. By analyzing these maps, we identified that the loss of nearly half of surface cells to invaginations is compensated primarily by transient mitotic rounding. In addition, by analyzing mapped cell intercalation events, we derived direct quantitative relations between intercalation frequency and the rate of axis elongation. This work is setting the stage for systems-level dissection of a pivotal step in animal development.

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March 14, 2022

Thermodynamically consistent coarse-graining of polar active fluids

Scott Weady, D. Stein, M. Shelley

We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a thermodynamically consistent, quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the kinetic theory, including its linear stability and the balance of entropy production and dissipation. Nonlinear simulations show the model reproduces the qualitative behavior and nonequilibrium statistics of the kinetic theory, unlike commonly used closure models. We use the closure model to simulate highly turbulent suspensions in both two and three dimensions in which we observe complex multiscale dynamics, including large concentration fluctuations and a proliferation of polar and nematic defects.

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March 11, 2022

Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms

Zidong Zhang, Michel Zamojski, O. Troyanskaya, et al

Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource from pediatric, adult, and aged postmortem pituitaries (snpituitaryatlas.princeton.edu) and characterize cell-type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early-life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors that are significantly associated with gene expression in PSCs compared with other cell types and within PSCs. We identify distinct deterministic mechanisms that contribute to heterogeneous marker expression within PSCs. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes and cell type identity.

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Enhanced clamshell swimming with asymmetric beating at low Reynolds number

Shiyuan Hu, Jun Zhang, M. Shelley

A single flexible filament can be actuated to escape from the scallop theorem and generate net propulsion at low Reynolds number. In this work, we study the dynamics of a simple boundary-driven multi-filament swimmer, a two-arm clamshell actuated at the hinged point, using a nonlocal slender body approximation with full hydrodynamic interactions. We first consider an elastic clamshell consisted of flexible filaments with intrinsic curvature, and then build segmental models consisted of rigid segments connected by different mechanical joints with different forms of response torques. The simplicity of the system allows us to fully explore the effect of various parameters on the swimming performance. Optimal included angles and elastoviscous numbers are identified. The segmental models capture the characteristic dynamics of the elastic clamshell. We further demonstrate how the swimming performance can be significantly enhanced by the asymmetric beating patterns induced by biased torques.

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March 4, 2022

Incompressible active phases at an interface. I. Formulation and axisymmetric odd flows

L. Jia, William T. M. Irvine, M. Shelley

Inspired by the recent realization of a 2D chiral fluid as an active monolayer droplet moving atop a 3D Stokesian fluid, we formulate mathematically its free-boundary dynamics. The surface droplet is described as a general 2D linear, incompressible, and isotropic fluid, having a viscous shear stress, an active chiral driving stress, and a Hall stress allowed by the lack of time-reversal symmetry. The droplet interacts with itself through its driven internal mechanics and by driving flows in the underlying 3D Stokes phase. We pose the dynamics as the solution to a singular integral-differential equation, over the droplet surface, using the mapping from surface stress to surface velocity for the 3D Stokes equations. Specializing to the case of axisymmetric droplets, exact representations for the chiral surface flow are given in terms of solutions to a singular integral equation, solved using both analytical and numerical techniques. For a disc-shaped monolayer, we additionally employ a semi-analytical solution that hinges on an orthogonal basis of Bessel functions and allows for efficient computation of the monolayer velocity field, which ranges from a nearly solid-body rotation to a unidirectional edge current depending on the subphase depth and the Saffman-Delbruck length. Except in the near-wall limit, these solutions have divergent surface shear stresses at droplet boundaries, a signature of systems with codimension one domains embedded in a three-dimensional medium. We further investigate the effect of a Hall viscosity, which couples radial and transverse surface velocity components, on the dynamics of a closing cavity

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February 28, 2022

Multi-omic analysis along the gut-brain axis points to a functional architecture of autism

J. Morton, Dong-Min Jin, R. Bonneau

Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens of cross-sectional microbiome and other omic studies revealing autism-specific profiles along the GBA albeit with little agreement in composition or magnitude. To explore the functional architecture of autism, we developed an age and sex-matched Bayesian differential ranking algorithm that identified autism-specific profiles across 10 cross-sectional microbiome datasets and 15 other omic datasets, including dietary patterns, metabolomics, cytokine profiles, and human brain expression profiles. The analysis uncovered a highly significant, functional architecture along the GBA that encapsulated the overall heterogeneity of autism phenotypes. This architecture was determined by autism-specific amino acid, carbohydrate and lipid metabolism profiles predominantly encoded by microbial species in the genera Prevotella, Enterococcus, Bifidobacterium, and Desulfovibrio, and was mirrored in brain-associated gene expression profiles and restrictive dietary patterns in individuals with autism. Pro-inflammatory cytokine profiling and virome association analysis further supported the existence of an autism-specific architecture associated with particular microbial genera. Re-analysis of a longitudinal intervention study in autism recapitulated the cross-sectional profiles, and showed a strong association between temporal changes in microbiome composition and autism symptoms. Further elucidation of the functional architecture of autism, including of the role the microbiome plays in it, will require deep, multi-omic longitudinal intervention studies on well-defined stratified cohorts to support causal and mechanistic inference.

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February 26, 2022

Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus

Achal Mahajan, W. Yan, Alexandra Zidovska, D. Saintillan, M. Shelley

The large-scale organization of the genome inside the cell nucleus is critical for the cell’s function. Chromatin – the functional form of DNA in cells – serves as a substrate for active nuclear processes such as transcription, replication and DNA repair. Chromatin’s spatial organization directly affects its accessibility by ATP-powered enzymes, e.g., RNA polymerase II in the case of transcription. In differentiated cells, chromatin is spatially segregated into compartments – euchromatin and heterochromatin – the former being largely transcriptionally active and loosely packed, the latter containing mostly silent genes and densely compacted. The euchromatin/heterochromatin segregation is crucial for proper genomic function, yet the physical principles behind it are far from understood. Here, we model the nucleus as filled with hydrodynamically interacting active Zimm chains – chromosomes – and investigate how large heterochromatic regions form and segregate from euchromatin through their complex interactions. Each chromosome presents a block copolymer composed of heterochromatic blocks, capable of crosslinking that increases chromatin’s local compaction, and euchromatic blocks, subjected to stochastic force dipoles that capture the microscopic stresses exerted by nuclear ATPases. These active stresses lead to a dynamic self-organization of the genome, with its coherent motions driving the mixing of chromosome territories as well as large-scale heterochromatic segregation through crosslinking of distant genomic regions. We study the stresses and flows that arise in the nucleus during the heterochromatic segregation, and identify their signatures in Hi-C proximity maps. Our results reveal the fundamental role of active mechanical processes and hydrodynamic interactions in the kinetics of chromatin compartmentalization and in the emergent large-scale organization of the nucleus.

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February 22, 2022

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

Fuqing Wu, Amy Xiao, R. Bonneau, et al.

Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4–10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations.

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A multiscale biophysical model gives quantized metachronal waves in a lattice of beating cilia

B. Chakrabarti, S. Fürthauer, M. Shelley

Motile cilia are slender, hair-like cellular appendages that spontaneously oscillate under the action of internal molecular motors and are typically found in dense arrays. These active filaments coordinate their beating to generate metachronal waves that drive long-range fluid transport and locomotion. Until now, our understanding of their collective behavior largely comes from the study of minimal models that coarse grain the relevant biophysics and the hydrodynamics of slender structures. Here we build on a detailed biophysical model to elucidate the emergence of metachronal waves on millimeter scales from nanometer-scale motor activity inside individual cilia. Our study of a one-dimensional lattice of cilia in the presence of hydrodynamic and steric interactions reveals how metachronal waves are formed and maintained. We find that, in homogeneous beds of cilia, these interactions lead to multiple attracting states, all of which are characterized by an integer charge that is conserved. This even allows us to design initial conditions that lead to predictable emergent states. Finally, and very importantly, we show that, in nonuniform ciliary tissues, boundaries and inhomogeneities provide a robust route to metachronal waves.

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