Professional Education


  • Doctor of Philosophy, Stanford University, BIOPH-PHD (2014)
  • Bachelor of Science, University of British Columbia, Biophysics (2008)

All Publications


  • Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota. Cell Tropini, C., Moss, E. L., Merrill, B. D., Ng, K. M., Higginbottom, S. K., Casavant, E. P., Gonzalez, C. G., Fremin, B., Bouley, D. M., Elias, J. E., Bhatt, A. S., Huang, K. C., Sonnenburg, J. L. 2018; 173 (7): 1742

    Abstract

    Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains invitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.

    View details for DOI 10.1016/j.cell.2018.05.008

    View details for PubMedID 29906449

  • Mechanical Perturbations to the Gut Microbiota Tropini, C., Sonnenburg, J., Huang, K. C., Ng, K. CELL PRESS. 2018: 329A
  • Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 2018; 562 (7727): 367–72

    Abstract

    Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

    View details for DOI 10.1038/s41586-018-0590-4

    View details for PubMedID 30283141

  • Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials ACS CENTRAL SCIENCE Krajina, B. A., Tropini, C., Zhu, A., DiGiacomo, P., Sonnenburg, J. L., Heilshorn, S. C., Spakowitz, A. J. 2017; 3 (12): 1294–1303

    Abstract

    The development of experimental techniques capable of probing the viscoelasticity of soft materials over a broad range of time scales is essential to uncovering the physics that governs their behavior. In this work, we develop a microrheology technique that requires only 12 μL of sample and is capable of resolving dynamic behavior ranging in time scales from 10-6 to 10 s. Our approach, based on dynamic light scattering in the single-scattering limit, enables the study of polymer gels and other soft materials over a vastly larger hierarchy of time scales than macrorheology measurements. Our technique captures the viscoelastic modulus of polymer hydrogels with a broad range of stiffnesses from 10 to 104 Pa. We harness these capabilities to capture hierarchical molecular relaxations in DNA and to study the rheology of precious biological materials that are impractical for macrorheology measurements, including decellularized extracellular matrices and intestinal mucus. The use of a commercially available benchtop setup that is already available to a variety of soft matter researchers renders microrheology measurements accessible to a broader range of users than existing techniques, with the potential to reveal the physics that underlies complex polymer hydrogels and biological materials.

    View details for DOI 10.1021/acscentsci.7b00449

    View details for Web of Science ID 000418706200011

    View details for PubMedID 29296670

    View details for PubMedCentralID PMC5746858

  • Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size CURRENT BIOLOGY Shi, H., Colavin, A., Bigos, M., Tropini, C., Monds, R. D., Huang, K. 2017; 27 (22): 3419-+

    Abstract

    Size is a universally defining characteristic of all living cells and tissues and is intrinsically linked with cell genotype, growth, and physiology. Many mutations have been identified to alter cell size, but pleiotropic effects have largely hampered our ability to probe how cell size specifically affects fundamental cellular properties, such as DNA content and intracellular localization. To systematically interrogate the impact of cell morphology on bacterial physiology, we used fluorescence-activated cell sorting to enrich a library of hundreds of Escherichia coli mutants in the essential cytoskeletal protein MreB for subtle changes in cell shape, cumulatively spanning ∼5-fold variation in average cell volume. Critically, pleiotropic effects in the mutated library are most likely minimized because only one gene was mutated and because growth rate was unaffected, thereby allowing us to query the general effects of morphology on cellular physiology over a large range of cell sizes with high resolution. We discovered linear scaling of the abundance of DNA and the key division protein FtsZ with cell volume, a strong dependency of sensitivity to specific antibiotics on cell width, and a simple correlation between MreB localization pattern and cell width. Our systematic, quantitative approach reveals complex and dynamic links between bacterial morphology and physiology and should be generally applicable for probing size-related genotype-phenotype relationships.

    View details for DOI 10.1016/j.cub.2017.09.065

    View details for Web of Science ID 000415815800020

    View details for PubMedID 29103935

  • The Gut Microbiome: Connecting Spatial Organization to Function CELL HOST & MICROBE Tropini, C., Earle, K. A., Huang, K. C., Sonnenburg, J. L. 2017; 21 (4): 433-442

    Abstract

    The first rudimentary evidence that the human body harbors a microbiota hinted at the complexity of host-associated microbial ecosystems. Now, almost 400 years later, a renaissance in the study of microbiota spatial organization, driven by coincident revolutions in imaging and sequencing technologies, is revealing functional relationships between biogeography and health, particularly in the vertebrate gut. In this Review, we present our current understanding of principles governing the localization of intestinal bacteria, and spatial relationships between bacteria and their hosts. We further discuss important emerging directions that will enable progressing from the inherently descriptive nature of localization and -omics technologies to provide functional, quantitative, and mechanistic insight into this complex ecosystem.

    View details for DOI 10.1016/j.chom.2017.03.010

    View details for Web of Science ID 000398896100005

    View details for PubMedID 28407481

  • Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC biology Ursell, T., Lee, T. K., Shiomi, D., Shi, H., Tropini, C., Monds, R. D., Colavin, A., Billings, G., Bhaya-Grossman, I., Broxton, M., Huang, B. E., Niki, H., Huang, K. C. 2017; 15 (1): 17-?

    Abstract

    The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features.Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features. We applied these tools to bacterial cells because the small size of these cells and the subtlety of certain morphological changes have thus far obscured correlations between bacterial morphology and genotype. We used an online resource of images of the Keio knockout library of nonessential genes in the Gram-negative bacterium Escherichia coli to demonstrate that cell width, width variability, and length significantly correlate with each other and with drug treatments, nutrient changes, and environmental conditions. Further, we combined morphological classification of genetic variants with genetic meta-analysis to reveal novel connections among gene function, fitness, and cell morphology, thus suggesting potential functions for unknown genes and differences in modes of action of antibiotics.Morphometrics and BlurLab set the stage for future quantitative studies of bacterial cell shape and intracellular localization. The previously unappreciated connections between morphological parameters measured with these software packages and the cellular environment point toward novel mechanistic connections among physiological perturbations, cell fitness, and growth.

    View details for DOI 10.1186/s12915-017-0348-8

    View details for PubMedID 28222723

    View details for PubMedCentralID PMC5320674

  • High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography JOURNAL OF BIOLOGICAL CHEMISTRY Desmarais, S. M., Tropini, C., Miguel, A., Cava, F., Monds, R. D., de Pedro, M. A., Huang, K. C. 2015; 290 (52): 31090-31100

    View details for DOI 10.1074/jbc.M115.661660

    View details for Web of Science ID 000367199000037

    View details for PubMedID 26468288

  • Principles of Bacterial Cell-Size Determination Revealed by Cell-Wall Synthesis Perturbations CELL REPORTS Tropini, C., Lee, T. K., Hsin, J., Desmarais, S. M., Ursell, T., Monds, R. D., Huang, K. C. 2014; 9 (4): 1520-1527

    Abstract

    Although bacterial cell morphology is tightly controlled, the principles of size regulation remain elusive. In Escherichia coli, perturbation of cell-wall synthesis often results in similar morphologies, making it difficult to deconvolve the complex genotype-phenotype relationships underlying morphogenesis. Here we modulated cell width through heterologous expression of sequences encoding the essential enzyme PBP2 and through sublethal treatments with drugs that inhibit PBP2 and the MreB cytoskeleton. We quantified the biochemical and biophysical properties of the cell wall across a wide range of cell sizes. We find that, although cell-wall chemical composition is unaltered, MreB dynamics, cell twisting, and cellular mechanics exhibit systematic large-scale changes consistent with altered chirality and a more isotropic cell wall. This multiscale analysis enabled identification of distinct roles for MreB and PBP2, despite having similar morphological effects when depleted. Altogether, our results highlight the robustness of cell-wall synthesis and physical principles dictating cell-size control.

    View details for DOI 10.1016/j.celrep.2014.10.027

    View details for Web of Science ID 000345529600031

    View details for PubMedCentralID PMC4254626

  • Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations. Cell reports Tropini, C., Lee, T. K., Hsin, J., Desmarais, S. M., Ursell, T., Monds, R. D., Huang, K. C. 2014; 9 (4): 1520-1527

    Abstract

    Although bacterial cell morphology is tightly controlled, the principles of size regulation remain elusive. In Escherichia coli, perturbation of cell-wall synthesis often results in similar morphologies, making it difficult to deconvolve the complex genotype-phenotype relationships underlying morphogenesis. Here we modulated cell width through heterologous expression of sequences encoding the essential enzyme PBP2 and through sublethal treatments with drugs that inhibit PBP2 and the MreB cytoskeleton. We quantified the biochemical and biophysical properties of the cell wall across a wide range of cell sizes. We find that, although cell-wall chemical composition is unaltered, MreB dynamics, cell twisting, and cellular mechanics exhibit systematic large-scale changes consistent with altered chirality and a more isotropic cell wall. This multiscale analysis enabled identification of distinct roles for MreB and PBP2, despite having similar morphological effects when depleted. Altogether, our results highlight the robustness of cell-wall synthesis and physical principles dictating cell-size control.

    View details for DOI 10.1016/j.celrep.2014.10.027

    View details for PubMedID 25456140

  • A dynamically assembled cell wall synthesis machinery buffers cell growth. Proceedings of the National Academy of Sciences of the United States of America Lee, T. K., Tropini, C., Hsin, J., Desmarais, S. M., Ursell, T. S., Gong, E., Gitai, Z., Monds, R. D., Huang, K. C. 2014; 111 (12): 4554-4559

    Abstract

    Assembly of protein complexes is a key mechanism for achieving spatial and temporal coordination in processes involving many enzymes. Growth of rod-shaped bacteria is a well-studied example requiring such coordination; expansion of the cell wall is thought to involve coordination of the activity of synthetic enzymes with the cytoskeleton via a stable complex. Here, we use single-molecule tracking to demonstrate that the bacterial actin homolog MreB and the essential cell wall enzyme PBP2 move on timescales orders of magnitude apart, with drastically different characteristic motions. Our observations suggest that PBP2 interacts with the rest of the synthesis machinery through a dynamic cycle of transient association. Consistent with this model, growth is robust to large fluctuations in PBP2 abundance. In contrast to stable complex formation, dynamic association of PBP2 is less dependent on the function of other components of the synthesis machinery, and buffers spatially distributed growth against fluctuations in pathway component concentrations and the presence of defective components. Dynamic association could generally represent an efficient strategy for spatiotemporal coordination of protein activities, especially when excess concentrations of system components are inhibitory to the overall process or deleterious to the cell.

    View details for DOI 10.1073/pnas.1313826111

    View details for PubMedID 24550500

  • Physical constraints on the establishment of intracellular spatial gradients in bacteria BMC BIOPHYSICS Tropini, C., Rabbani, N., Huang, K. C. 2012; 5

    Abstract

    Bacteria dynamically regulate their intricate intracellular organization involving proteins that facilitate cell division, motility, and numerous other processes. Consistent with this sophisticated organization, bacteria are able to create asymmetries and spatial gradients of proteins by localizing signaling pathway components. We use mathematical modeling to investigate the biochemical and physical constraints on the generation of intracellular gradients by the asymmetric localization of a source and a sink.We present a systematic computational analysis of the effects of other regulatory mechanisms, such as synthesis, degradation, saturation, and cell growth. We also demonstrate that gradients can be established in a variety of bacterial morphologies such as rods, crescents, spheres, branched and constricted cells.Taken together, these results suggest that gradients are a robust and potentially common mechanism for providing intracellular spatial cues.

    View details for DOI 10.1186/2046-1682-5-17

    View details for Web of Science ID 000311052500001

    View details for PubMedID 22931750

  • Interplay between the Localization and Kinetics of Phosphorylation in Flagellar Pole Development of the Bacterium Caulobacter crescentus PLOS COMPUTATIONAL BIOLOGY Tropini, C., Huang, K. C. 2012; 8 (8)

    Abstract

    Bacterial cells maintain sophisticated levels of intracellular organization that allow for signal amplification, response to stimuli, cell division, and many other critical processes. The mechanisms underlying localization and their contribution to fitness have been difficult to uncover, due to the often challenging task of creating mutants with systematically perturbed localization but normal enzymatic activity, and the lack of quantitative models through which to interpret subtle phenotypic changes. Focusing on the model bacterium Caulobacter crescentus, which generates two different types of daughter cells from an underlying asymmetric distribution of protein phosphorylation, we use mathematical modeling to investigate the contribution of the localization of histidine kinases to the establishment of cellular asymmetry and subsequent developmental outcomes. We use existing mutant phenotypes and fluorescence data to parameterize a reaction-diffusion model of the kinases PleC and DivJ and their cognate response regulator DivK. We then present a systematic computational analysis of the effects of changes in protein localization and abundance to determine whether PleC localization is required for correct developmental timing in Caulobacter. Our model predicts the developmental phenotypes of several localization mutants, and suggests that a novel strain with co-localization of PleC and DivJ could provide quantitative insight into the signaling threshold required for flagellar pole development. Our analysis indicates that normal development can be maintained through a wide range of localization phenotypes, and that developmental defects due to changes in PleC localization can be rescued by increased PleC expression. We also show that the system is remarkably robust to perturbation of the kinetic parameters, and while the localization of either PleC or DivJ is required for asymmetric development, the delocalization of one of these two components does not prevent flagellar pole development. We further find that allosteric regulation of PleC observed in vitro does not affect the predicted in vivo developmental phenotypes. Taken together, our model suggests that cells can tolerate perturbations to localization phenotypes, whose evolutionary origins may be connected with reducing protein expression or with decoupling pre- and post-division phenotypes.

    View details for DOI 10.1371/journal.pcbi.1002602

    View details for Web of Science ID 000308553500004

    View details for PubMedID 22876167

  • Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity MOLECULAR MICROBIOLOGY Tuson, H. H., Auer, G. K., Renner, L. D., Hasebe, M., Tropini, C., Salick, M., Crone, W. C., Gopinathan, A., Huang, K. C., Weibel, D. B. 2012; 84 (5): 874-891

    Abstract

    Although bacterial cells are known to experience large forces from osmotic pressure differences and their local microenvironment, quantitative measurements of the mechanical properties of growing bacterial cells have been limited. We provide an experimental approach and theoretical framework for measuring the mechanical properties of live bacteria. We encapsulated bacteria in agarose with a user-defined stiffness, measured the growth rate of individual cells and fit data to a thin-shell mechanical model to extract the effective longitudinal Young's modulus of the cell envelope of Escherichia coli (50-150 MPa), Bacillus subtilis (100-200 MPa) and Pseudomonas aeruginosa (100-200 MPa). Our data provide estimates of cell wall stiffness similar to values obtained via the more labour-intensive technique of atomic force microscopy. To address physiological perturbations that produce changes in cellular mechanical properties, we tested the effect of A22-induced MreB depolymerization on the stiffness of E. coli. The effective longitudinal Young's modulus was not significantly affected by A22 treatment at short time scales, supporting a model in which the interactions between MreB and the cell wall persist on the same time scale as growth. Our technique therefore enables the rapid determination of how changes in genotype and biochemistry affect the mechanical properties of the bacterial envelope.

    View details for DOI 10.1111/j.1365-2958.2012.08063.x

    View details for Web of Science ID 000304301500007

    View details for PubMedID 22548341

  • Islands Containing Slowly Hydrolyzable GTP Analogs Promote Microtubule Rescues PLOS ONE Tropini, C., Roth, E. A., Zanic, M., Gardner, M. K., Howard, J. 2012; 7 (1)

    Abstract

    Microtubules are dynamic polymers of GTP- and GDP-tubulin that undergo stochastic transitions between growing and shrinking phases. Rescues, the conversion from shrinking to growing, have recently been proposed to be to the result of regrowth at GTP-tubulin islands within the lattice of growing microtubules. By introducing mixed GTP/GDP/GMPCPP (GXP) regions within the lattice of dynamic microtubules, we reconstituted GXP islands in vitro (GMPCPP is the slowly hydrolyzable GTP analog guanosine-5'-[(α,β)-methyleno]triphosphate). We found that such islands could reproducibly induce rescues and that the probability of rescue correlated with both the size of the island and the percentage of GMPCPP-tubulin within the island. The islands slowed the depolymerization rate of shortening microtubules and promoted regrowth more readily than GMPCPP seeds. Together, these findings provide new mechanistic insights supporting the possibility that rescues could be triggered by enriched GTP-tubulin regions and present a new tool for studying such rescue events in vitro.

    View details for DOI 10.1371/journal.pone.0030103

    View details for Web of Science ID 000301454400059

    View details for PubMedID 22272281

  • Megapixel digital PCR NATURE METHODS Heyries, K. A., Tropini, C., Vaninsberghe, M., Doolin, C., Petriv, O. I., Singhal, A., Leung, K., Hughesman, C. B., Hansen, C. L. 2011; 8 (8): 649-U64

    Abstract

    We present a microfluidic 'megapixel' digital PCR device that uses surface tension-based sample partitioning and dehydration control to enable high-fidelity single DNA molecule amplification in 1,000,000 reactors of picoliter volume with densities up to 440,000 reactors cm(-2). This device achieves a dynamic range of 10(7), single-nucleotide-variant detection below one copy per 100,000 wild-type sequences and the discrimination of a 1% difference in chromosome copy number.

    View details for DOI 10.1038/NMETH.1640

    View details for Web of Science ID 000293220600018

    View details for PubMedID 21725299

  • Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chen, Y. E., Tropini, C., Jonas, K., Tsokos, C. G., Huang, K. C., Laub, M. T. 2011; 108 (3): 1052-1057

    Abstract

    Spatial asymmetry is crucial to development. One mechanism for generating asymmetry involves the localized synthesis of a key regulatory protein that diffuses away from its source, forming a spatial gradient. Although gradients are prevalent in eukaryotes, at both the tissue and intracellular levels, it is unclear whether gradients of freely diffusible proteins can form within bacterial cells given their small size and the speed of diffusion. Here, we show that the bacterium Caulobacter crescentus generates a gradient of the active, phosphorylated form of the master regulator CtrA, which directly regulates DNA replication. Using a combination of mathematical modeling, single-cell microscopy, and genetic manipulation, we demonstrate that this gradient is produced by the polarly localized phosphorylation and dephosphorylation of CtrA. Our data indicate that cells robustly establish the asymmetric fates of daughter cells before cell division causes physical compartmentalization. More generally, our results demonstrate that uniform protein abundance may belie gradients and other sophisticated spatial patterns of protein activity in bacterial cells.

    View details for DOI 10.1073/pnas.1015397108

    View details for Web of Science ID 000286310300033

    View details for PubMedID 21191097

  • Nonexponential Kinetics of DNA Escape from alpha-Hemolysin Nanopores BIOPHYSICAL JOURNAL Wiggin, M., Tropini, C., Tabard-Cossa, V., Jetha, N. N., Marziali, A. 2008; 95 (11): 5317-5323

    Abstract

    Throughput and resolution of DNA sequence detection technologies employing nanometer scale pores hinge on accurate kinetic descriptions of DNA motion in nanopores. We present the first detailed experimental study of DNA escape kinetics from alpha-hemolysin nanopores and show that anomalously long escape times for some events result in nonexponential kinetics. From the distribution of first-passage times, we determine that the energy barrier to escape follows a Poisson-like distribution, most likely due to stochastic weak binding events between the DNA and amino acid residues in the pore.

    View details for DOI 10.1529/biophysj.108.137760

    View details for Web of Science ID 000260999500031

    View details for PubMedID 18775965

  • Multi-nanopore force Spectroscopy for DNA analysis BIOPHYSICAL JOURNAL Tropini, C., Marziali, A. 2007; 92 (5): 1632-1637

    Abstract

    The need for low-cost DNA sequence detection in clinical applications is driving development of new technologies. We demonstrate a method for detection of mutations in a DNA sequence purely by electronic means, and without need for fluorescent labeling. Our method uses an array of nanopores to perform synchronized single-molecule force spectroscopy measurements over many molecules in parallel, yielding detailed information on the kinetics of hundreds of molecule dissociations in a single measurement.

    View details for DOI 10.1529/biophysj.106.094060

    View details for Web of Science ID 000244373800018

    View details for PubMedID 17158571