372 Publications

Evaluating the Arrhenius equation for developmental processes

Joseph Crapse, Nishant Pappireddi, S. Shvartsman, et al.

The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi-step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi-step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and β-galactosidase show non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non-uniform developmental scaling and propose that the observed departure from this law likely results more from non-idealized individual steps rather than from the complexity of the system.

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From complex datasets to predictive models of embryonic development

Sayantan Dutta , Aleena L. Patel, Shannon E. Keenan, S. Shvartsman

Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here, we use data from our work on signal-dependent gene repression in the Drosophila embryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.

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Lévy Walks and Path Chaos in the Dispersal of Elongated Structures Moving across Cellular Vortical Flows

Shi-Yuan Hu, Jun-Jun Chu, M. Shelley, Jun Zhang

In cellular vortical flows, namely arrays of counterrotating vortices, short but flexible filaments can show simple random walks through their stretch-coil interactions with flow stagnation points. Here, we study the dynamics of semirigid filaments long enough to broadly sample the vortical field. Using simulation, we find a surprising variety of long-time transport behavior—random walks, ballistic transport, and trapping—depending upon the filament’s relative length and effective flexibility. Moreover, we find that filaments execute Lévy walks whose diffusion exponents generally decrease with increasing filament length, until transitioning to Brownian walks. Lyapunov exponents likewise increase with length. Even completely rigid filaments, whose dynamics is finite dimensional, show a surprising variety of transport states and chaos. Fast filament dispersal is related to an underlying geometry of “conveyor belts.” Evidence for these various transport states is found in experiments using arrays of counterrotating rollers, immersed in a fluid and transporting a flexible ribbon.

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

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 1D 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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August 3, 2021

Decoding disease: from genomes to networks to phenotypes

A. Wong, R. Sealfon, Chandra L. Theesfeld, O. Troyanskaya

Interpreting the effects of genetic variants is key to understanding individual susceptibility to disease and designing personalized therapeutic approaches. Modern experimental technologies are enabling the generation of massive compendia of human genome sequence data and associated molecular and phenotypic traits, together with genome-scale expression, epigenomics and other functional genomic data. Integrative computational models can leverage these data to understand variant impact, elucidate the effect of dysregulated genes on biological pathways in specific disease and tissue contexts, and interpret disease risk beyond what is feasible with experiments alone. In this Review, we discuss recent developments in machine learning algorithms for genome interpretation and for integrative molecular-level modelling of cells, tissues and organs relevant to disease. More specifically, we highlight existing methods and key challenges and opportunities in identifying specific disease-causing genetic variants and linking them to molecular pathways and, ultimately, to disease phenotypes.

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Signatures of elastoviscous buckling in the dilute rheology of stiff polymers

B. Chakrabarti, Y. Liu, O. du Roure, A. Linder, D. Saintillan

As a stiff polymer tumbles in shear flow, it experiences compressive viscous forces that can cause it to buckle and undergo a sequence of morphological transitions with increasing flow strength. We use numerical simulations to uncover the effects of these transitions on the steady shear rheology of a dilute suspension of stiff polymers. Our results agree with classic scalings for Brownian rods in relatively weak flows but depart from them above the buckling threshold. Signatures of elastoviscous buckling include enhanced shear thinning and an increase in the magnitude of normal stress differences. We discuss our findings in the light of past work on rigid Brownian rods and non-Brownian elastic fibres and highlight the subtle role of thermal fluctuations in triggering instabilities.

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ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements

X. Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan

Transcription factors (TFs) often function as a module including both master factors and mediators binding at cis-regulatory regions to modulate nearby gene transcription. ChIP-seq profiling of multiple TFs makes it feasible to infer functional TF modules. However, when inferring TF modules based on co-localization of ChIP-seq peaks, often many weak binding events are missed, especially for mediators, resulting in incomplete identification of modules. To address this problem, we develop a ChIP-seq data-driven Gibbs Sampler to infer Modules (ChIP-GSM) using a Bayesian framework that integrates ChIP-seq profiles of multiple TFs. ChIP-GSM samples read counts of module TFs iteratively to estimate the binding potential of a module to each region and, across all regions, estimates the module abundance. Using inferred module-region probabilistic bindings as feature units, ChIP-GSM then employs logistic regression to predict active regulatory elements. Validation of ChIP-GSM predicted regulatory regions on multiple independent datasets sharing the same context confirms the advantage of using TF modules for predicting regulatory activity. In a case study of K562 cells, we demonstrate that the ChIP-GSM inferred modules form as groups, activate gene expression at different time points, and mediate diverse functional cellular processes. Hence, ChIP-GSM infers biologically meaningful TF modules and improves the prediction accuracy of regulatory region activities.

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Machine learning methods to model multicellular complexity and tissue specificity

Experimental approaches to study tissue specificity enable insight into the nature and organization of the cell types and tissues that constitute complex multicellular organisms. Machine learning provides a powerful tool to investigate and interpret tissue-specific experimental data. In this Review, we first provide a brief introduction to key single-cell and whole-tissue approaches that allow investigation of tissue specificity and then highlight two classes of machine-learning-based methods, which can be applied to analyse, model and interpret these experimental data. Deep learning methods can predict tissue-dependent effects of individual mutations on gene expression, alternative splicing and disease phenotypes. Network-based approaches can capture relationships between biomolecules, integrate large heterogeneous data compendia to model molecular circuits and identify tissue-specific functional relationships and regulatory connections. We conclude with an outlook to future possibilities in examining multicellular complexity by combining high-resolution, large-scale multiomics data sets and interpretable machine learning models.

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CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes

Victoria R Li, O. Troyanskaya, Z. Zhang

CRISPR/Cas9 is a revolutionary gene-editing technology that has been widely utilized in biology, biotechnology and medicine. CRISPR/Cas9 editing outcomes depend on local DNA sequences at the target site and are thus predictable. However, existing prediction methods are dependent on both feature and model engineering, which restricts their performance to existing knowledge about CRISPR/Cas9 editing

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July 12, 2021

A fast Chebyshev method for the Bingham closure with application to active nematic suspensions

Scott Weady, D. Stein, M. Shelley

Continuum kinetic theories provide an important tool for the analysis and simulation of particle suspensions. When those particles are anisotropic, the addition of a particle orientation vector to the kinetic description yields a 2d−1 dimensional theory which becomes intractable to simulate, especially in three dimensions or near states where the particles are highly aligned. Coarse-grained theories that track only moments of the particle distribution functions provide a more efficient simulation framework, but require closure assumptions. For the particular case where the particles are apolar, the Bingham closure has been found to agree well with the underlying kinetic theory; yet the closure is non-trivial to compute, requiring the solution of an often nearly-singular nonlinear equation at every spatial discretization point at every timestep. In this paper, we present a robust, accurate, and efficient numerical scheme for evaluating the Bingham closure, with a controllable error/efficiency tradeoff. To demonstrate the utility of the method, we carry out high-resolution simulations of a coarse-grained continuum model for a suspension of active particles in parameter regimes inaccessible to kinetic theories. Analysis of these simulations reveals that inaccurately computing the closure can act to effectively limit spatial resolution in the coarse-grained fields. Pushing these simulations to the high spatial resolutions enabled by our method reveals a coupling between vorticity and topological defects in the suspension director field, as well as signatures of energy transfer between scales in this active fluid model.

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arXiv e-prints
June 28, 2021
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