Chew M Chai

All Publications

• A genetic and microscopy toolkit for manipulating and monitoring regeneration in Macrostomum lignano. Cell reports Hall, R. N., Li, H., Chai, C., Vermeulen, S., Bigasin, R. R., Song, E. S., Sarkar, S. R., Gibson, J., Prakash, M., Fire, A. Z., Wang, B. 2024; 43 (11): 114892

  Abstract

  Live imaging of regenerative processes can reveal how animals restore their bodies after injury through a cascade of dynamic cellular events. Here, we present a comprehensive toolkit for live imaging of tissue regeneration in the flatworm Macrostomum lignano, including a high-throughput cloning pipeline, targeted cellular ablation, and advanced microscopy solutions. Using tissue-specific reporter expression, we examine how various structures regenerate. Enabled by a custom luminescence/fluorescence microscope, we overcome intense stress-induced autofluorescence to demonstrate genetic cellular ablation and reveal the limited regenerative capacity of neurons and their essential role during wound healing, contrasting muscle cells' rapid regeneration after ablation. Finally, we build an open-source tracking microscope to continuously image freely moving animals throughout the week-long process of regeneration, quantifying kinetics of wound healing, nerve cord repair, body regeneration, growth, and behavioral recovery. Our findings suggest that nerve cord reconnection is highly robust and proceeds independently of regeneration.

  View details for DOI 10.1016/j.celrep.2024.114892

  View details for PubMedID 39427313

• Flexible use of conserved motif vocabularies constrains genome access in cell type evolution. bioRxiv : the preprint server for biology Chai, C., Gibson, J., Li, P., Pampari, A., Patel, A., Kundaje, A., Wang, B. 2024

  Abstract

  Cell types evolve into a hierarchy with related types grouped into families. How cell type diversification is constrained by the stable separation between families over vast evolutionary times remains unknown. Here, integrating single-nucleus multiomic sequencing and deep learning, we show that hundreds of sequence features (motifs) divide into distinct sets associated with accessible genomes of specific cell type families. This division is conserved across highly divergent, early-branching animals including flatworms and cnidarians. While specific interactions between motifs delineate cell type relationships within families, surprisingly, these interactions are not conserved between species. Consistently, while deep learning models trained on one species can predict accessibility of other species' sequences, their predictions frequently rely on distinct, but synonymous, motif combinations. We propose that long-term stability of cell type families is maintained through genome access specified by conserved motif sets, or 'vocabularies', whereas cell types diversify through flexible use of motifs within each set.

  View details for DOI 10.1101/2024.09.03.611027

  View details for PubMedID 39282369

  View details for PubMedCentralID PMC11398382

• Adaptive robustness through incoherent signaling mechanisms in a regenerative brain. Cell reports Bray, S. R., Wyss, L. S., Chai, C., Lozada, M. E., Wang, B. 2024; 43 (8): 114580

  Abstract

  Animal behavior emerges from collective dynamics of neurons, making it vulnerable to damage. Paradoxically, many organisms exhibit a remarkable ability to maintain significant behavior even after large-scale neural injury. Molecular underpinnings of this extreme robustness remain largely unknown. Here, we develop a quantitative pipeline to measure long-lasting latent states in planarian flatworm behaviors during whole-brain regeneration. By combining >20,000 animal trials with neural network modeling, we show that long-range volumetric peptidergic signals allow the planarian to rapidly restore coarse behavior output after large perturbations to the nervous system, while slow restoration of small-molecule neuromodulator functions refines precision. This relies on the different time and length scales of neuropeptide and small-molecule transmission to generate incoherent patterns of neural activity that competitively regulate behavior. Controlling behavior through opposing communication mechanisms creates a more robust system than either alone and may serve as a generalizable approach for constructing robust neural networks.

  View details for DOI 10.1016/j.celrep.2024.114580

  View details for PubMedID 39133614

• Regeneration in the absence of canonical neoblasts in an early branching flatworm. bioRxiv : the preprint server for biology Gąsiorowski, L., Chai, C., Rozanski, A., Purandare, G., Ficze, F., Mizi, A., Wang, B., Rink, J. C. 2024

  Abstract

  The remarkable regenerative abilities of flatworms are closely linked to neoblasts - adult pluripotent stem cells that are the only division-competent cell type outside of the reproductive system. Although the presence of neoblast-like cells and whole-body regeneration in other animals has led to the idea that these features may represent the ancestral metazoan state, the evolutionary origin of both remains unclear. Here we show that the catenulid Stenostomum brevipharyngium, a member of the earliest-branching flatworm lineage, lacks conventional neoblasts despite being capable of whole-body regeneration and asexual reproduction. Using a combination of single-nuclei transcriptomics, in situ gene expression analysis, and functional experiments, we find that cell divisions are not restricted to a single cell type and are associated with multiple fully differentiated somatic tissues. Furthermore, the cohort of germline multipotency genes, which are considered canonical neoblast markers, are not expressed in dividing cells, but in the germline instead, and we experimentally show that they are neither necessary for proliferation nor regeneration. Overall, our results challenge the notion that canonical neoblasts are necessary for flatworm regeneration and open up the possibility that neoblast-like cells may have evolved convergently in different animals, independent of their regenerative capacity.

  View details for DOI 10.1101/2024.05.24.595708

  View details for PubMedID 38853907

  View details for PubMedCentralID PMC11160568

• Ultrafast distant wound response is essential for whole-body regeneration. Cell Fan, Y., Chai, C., Li, P., Zou, X., Ferrell, J. E., Wang, B. 2023

  Abstract

  Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.

  View details for DOI 10.1016/j.cell.2023.06.019

  View details for PubMedID 37480850

• Expansion spatial transcriptomics. Nature methods Fan, Y., Andrusivova, Z., Wu, Y., Chai, C., Larsson, L., He, M., Luo, L., Lundeberg, J., Wang, B. 2023

  Abstract

  Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues; however, their spatial resolution is limited by the density of the array. Here we present expansion spatial transcriptomics to overcome this limitation by clearing and expanding tissue prior to capturing the entire polyadenylated transcriptome with an enhanced protocol. This approach enables us to achieve higher spatial resolution while retaining high library quality, which we demonstrate using mouse brain samples.

  View details for DOI 10.1038/s41592-023-01911-1

  View details for PubMedID 37349575

• Heterologous reporter expression in the planarian Schmidtea mediterranea through somatic mRNA transfection. Cell reports methods Hall, R. N., Weill, U., Drees, L., Leal-Ortiz, S., Li, H., Khariton, M., Chai, C., Xue, Y., Rosental, B., Quake, S. R., Sanchez Alvarado, A., Melosh, N. A., Fire, A. Z., Rink, J. C., Wang, B. 2022; 2 (10): 100298

  Abstract

  Planarians have long been studied for their regenerative abilities. Moving forward, tools for ectopic expression of non-native proteins will be of substantial value. Using a luminescent reporter to overcome the strong autofluorescence of planarian tissues, we demonstrate heterologous protein expression in planarian cells and live animals. Our approach is based on the introduction of mRNA through several nanotechnological and chemical transfection methods. We improve reporter expression by altering untranslated region (UTR) sequences and codon bias, facilitating the measurement of expression kinetics in both isolated cells and whole planarians using luminescence imaging. We also examine protein expression as a function of variations in the UTRs of delivered mRNA, demonstrating a framework to investigate gene regulation at the post-transcriptional level. Together, these advances expand the toolbox for the mechanistic analysis of planarian biology and establish a foundation for the development and expansion of transgenic techniques in this unique model system.

  View details for DOI 10.1016/j.crmeth.2022.100298

  View details for PubMedID 36313809

• Phosphoethanolamine cellulose enhances curli-mediated adhesion of uropathogenic Escherichia coli to bladder epithelial cells. Proceedings of the National Academy of Sciences of the United States of America Hollenbeck, E. C., Antonoplis, A., Chai, C., Thongsomboon, W., Fuller, G. G., Cegelski, L. 2018

  Abstract

  Uropathogenic Escherichia coli (UPEC) are the major causative agents of urinary tract infections, employing numerous molecular strategies to contribute to adhesion, colonization, and persistence in the bladder niche. Identifying strategies to prevent adhesion and colonization is a promising approach to inhibit bacterial pathogenesis and to help preserve the efficacy of available antibiotics. This approach requires an improved understanding of the molecular determinants of adhesion to the bladder urothelium. We designed experiments using a custom-built live cell monolayer rheometer (LCMR) to quantitatively measure individual and combined contributions of bacterial cell surface structures [type 1 pili, curli, and phosphoethanolamine (pEtN) cellulose] to bladder cell adhesion. Using the UPEC strain UTI89, isogenic mutants, and controlled conditions for the differential production of cell surface structures, we discovered that curli can promote stronger adhesive interactions with bladder cells than type 1 pili. Moreover, the coproduction of curli and pEtN cellulose enhanced adhesion. The LCMR enables the evaluation of adhesion under high-shear conditions to reveal this role for pEtN cellulose which escaped detection using conventional tissue culture adhesion assays. Together with complementary biochemical experiments, the results support a model wherein cellulose serves a mortar-like function to promote curli association with and around the bacterial cell surface, resulting in increased bacterial adhesion strength at the bladder cell surface.

  View details for PubMedID 30232265

• Interfacial mechanisms for stability of surfactant-laden films PLOS ONE Bhamla, M. S., Chai, C., Alvarez-Valenzuela, M. A., Tajuelo, J., Fuller, G. G. 2017; 12 (5)

  Abstract

  Thin liquid films are central to everyday life. They are ubiquitous in modern technology (pharmaceuticals, coatings), consumer products (foams, emulsions) and also serve vital biological functions (tear film of the eye, pulmonary surfactants in the lung). A common feature in all these examples is the presence of surface-active molecules at the air-liquid interface. Though they form only molecular-thin layers, these surfactants produce complex surface stresses on the free surface, which have important consequences for the dynamics and stability of the underlying thin liquid film. Here we conduct simple thinning experiments to explore the fundamental mechanisms that allow the surfactant molecules to slow the gravity-driven drainage of the underlying film. We present a simple model that works for both soluble and insoluble surfactant systems in the limit of negligible adsorption-desorption dynamics. We show that surfactants with finite surface rheology influence bulk flow through viscoelastic interfacial stresses, while surfactants with inviscid surfaces achieve stability through opposing surface-tension induced Marangoni flows.

  View details for DOI 10.1371/journal.pone.0175753

  View details for Web of Science ID 000401487700007

  View details for PubMedID 28520734

• Hand-powered ultralow-cost paper centrifuge NATURE BIOMEDICAL ENGINEERING Bhamla, M., Benson, B., Chai, C., Katsikis, G., Johri, A., Prakash, M. 2017; 1 (1)

  View details for DOI 10.1038/s41551-016-0009

  View details for Web of Science ID 000418850600009

• Instability and Breakup of Model Tear Films INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE Bhamla, M. S., Chai, C., Rabiah, N. I., Frostad, J. M., Fuller, G. G. 2016; 57 (3): 949-958

  Abstract

  An experimental platform to replicate the human tear film on a contact lens is presented. The influence of interfacial viscoelasticity in stabilizing in vitro model tear films against breakup and dewetting is investigated using this instrument.Model tear films consisting of bovine meibomian lipids (meibum) spread on either PBS or artificial tear solution (ATS) are created. The interfacial shear rheology of these films is measured as a function of temperature. The dewetting dynamics of these films is then investigated using the Interfacial Dewetting and Drainage Optical Platform (i-DDrOP) on top of silicone hydrogel (SiHy) contact lenses at 23 and 35°C. The film breakup times are evaluated using two parameters: onset of film breakup, Tonset for thick films (∼100 μm), and tear breakup times, TBU for thin films (∼1 μm). Thin film thinning rates as a result of evaporation are also calculated.The ATS/meibum films have the largest surface rheology and correspondingly show the largest Tonset times at both 23 and 35°C. The parameter TBU is also significantly larger for ATS/meibum (TBU ∼ 40 seconds) compared with that of ATS and PBS/meibum films (TBU ∼ 30 seconds) at room temperature. However, at 35°C, all three model tear films exhibit similar TBU ∼ 17 seconds and average rate of thinning of -4 μm/minute.Tear film stability is influenced by both surface rheology and evaporation. The in vitro tear breakup times and thinning rates of model tear films at 35°C are in good agreement with in vivo measurements previously reported, highlighting the utility of the i-DDrOP for in vitro tear film breakup research.

  View details for DOI 10.1167/iovs.15-18064

  View details for Web of Science ID 000374860600026

  View details for PubMedID 26943158