Bo Wang

All Publications

• Coordinated wound responses in a regenerative animal-algal holobiont. Nature communications Nanes Sarfati, D., Xue, Y., Song, E. S., Byrne, A., Le, D., Darmanis, S., Quake, S. R., Burlacot, A., Sikes, J., Wang, B. 2024; 15 (1): 4032

  Abstract

  Animal regeneration involves coordinated responses across cell types throughout the animal body. In endosymbiotic animals, whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis sp. green algae and can regenerate entire bodies from tissue fragments. We show that animal injury causes a decline in the photosynthetic efficiency of the symbiotic algae, alongside two distinct, sequential waves of transcriptional responses in acoel and algal cells. The initial algal response is characterized by the upregulation of a cohort of photosynthesis-related genes, though photosynthesis is not necessary for regeneration. A conserved animal transcription factor, runt, is induced after injury and required for acoel regeneration. Knockdown of Cl-runt dampens transcriptional responses in both species and further reduces algal photosynthetic efficiency post-injury. Our results suggest that the holobiont functions as an integrated unit of biological organization by coordinating molecular networks across species through the runt-dependent animal regeneration program.

  View details for DOI 10.1038/s41467-024-48366-2

  View details for PubMedID 38740753

  View details for PubMedCentralID 4540581

• 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

• Mapping single-cell atlases throughout Metazoa unravels cell type evolution. eLife Tarashansky, A. J., Musser, J. M., Khariton, M., Li, P., Arendt, D., Quake, S. R., Wang, B. 2021; 10

  Abstract

  Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.

  View details for DOI 10.7554/eLife.66747

  View details for PubMedID 33944782

• Single-cell deconstruction of stem-cell-driven schistosome development. Trends in parasitology Nanes Sarfati, D., Li, P., Tarashansky, A. J., Wang, B. 2021

  Abstract

  Schistosomes cause one of the most devastating neglected tropical diseases, schistosomiasis. Their transmission is accomplished through a complex life cycle with two obligate hosts and requires multiple radically different body plans specialized for infecting and reproducing in each host. Recent single-cell transcriptomic studies on several schistosome body plans provide a comprehensive map of their cell types, which include stem cells and their differentiated progeny along an intricate developmental hierarchy. This progress not only extends our understanding of the basic biology of the schistosome life cycle but can also inform new therapeutic and preventive strategies against the disease, as blocking the development of specific cell types through genetic manipulations has shown promise in inhibiting parasite survival, growth, and reproduction.

  View details for DOI 10.1016/j.pt.2021.03.005

  View details for PubMedID 33893056

• Single-cell analysis of Schistosoma mansoni identifies a conserved genetic program controlling germline stem cell fate. Nature communications Li, P., Nanes Sarfati, D., Xue, Y., Yu, X., Tarashansky, A. J., Quake, S. R., Wang, B. 2021; 12 (1): 485

  Abstract

  Schistosomes are parasitic flatworms causing one of the most prevalent infectious diseases from which millions of people are currently suffering. These parasites have high fecundity and their eggs are both the transmissible agents and the cause of the infection-associated pathology. Given its biomedical significance, the schistosome germline has been a research focus for more than a century. Nonetheless, molecular mechanisms that regulate its development are only now being understood. In particular, it is unknown what balances the fate of germline stem cells (GSCs) in producing daughter stem cells through mitotic divisions versus gametes through meiosis. Here, we perform single-cell RNA sequencing on juvenile schistosomes and capture GSCs during de novo gonadal development. We identify a genetic program that controls the proliferation and differentiation of GSCs. This program centers around onecut, a homeobox transcription factor, and boule, an mRNA binding protein. Their expressions are mutually dependent in the schistosome male germline, and knocking down either of them causes over-proliferation of GSCs and blocks germ cell differentiation. We further show that this germline-specific regulatory program is conserved in the planarian, schistosome's free-living evolutionary cousin, but the function of onecut has changed during evolution to support GSC maintenance.

  View details for DOI 10.1038/s41467-020-20794-w

  View details for PubMedID 33473133

• Chromatic neuronal jamming in a primitive brain. NATURE PHYSICS Khariton, M., Kong, X., Qin, J., Wang, B. 2020; 16 (5): 553-557

  View details for DOI 10.1038/s41567-020-0809-9

• Mechanically resolved imaging of bacteria using expansion microscopy. PLoS biology Lim, Y., Shiver, A. L., Khariton, M., Lane, K. M., Ng, K. M., Bray, S. R., Qin, J., Huang, K. C., Wang, B. 2019; 17 (10): e3000268

  Abstract

  Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (muExM) in which bacterial cells are physically expanded prior to imaging. We find that expansion patterns depend on the structural and mechanical properties of the cell wall, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of muExM to distinguish species through an in vitro defined community of human gut commensals and in vivo imaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.

  View details for DOI 10.1371/journal.pbio.3000268

  View details for PubMedID 31622337

• Self-assembling manifolds in single-cell RNA sequencing data. ELIFE Tarashansky, A. J., Xue, Y., Li, P., Quake, S. R., Wang, B. 2019; 8: e48994

  View details for DOI 10.7554/eLife.48994

• Stem cell heterogeneity drives the parasitic life cycle of Schistosoma mansoni ELIFE Wang, B., Lee, J., Li, P., Section, A., Yang, H., Liu, C., Zhao, M., Newmark, P. A. 2018; 7

  View details for DOI 10.7554/eLife.35449

  View details for Web of Science ID 000438149300001

• Memoryless self-reinforcing directionality in endosomal active transport within living cells NATURE MATERIALS Chen, K., Wang, B., Granick, S. 2015; 14 (6): 589-593

  Abstract

  In contrast to Brownian transport, the active motility of microbes, cells, animals and even humans often follows another random process known as truncated Lévy walk. These stochastic motions are characterized by clustered small steps and intermittent longer jumps that often extend towards the size of the entire system. As there are repeated suggestions, although disagreement, that Lévy walks have functional advantages over Brownian motion in random searching and transport kinetics, their intentional engineering into active materials could be useful. Here, we show experimentally in the classic active matter system of intracellular trafficking that Brownian-like steps self-organize into truncated Lévy walks through an apparent time-independent positive feedback such that directional persistence increases with the distance travelled persistently. A molecular model that allows the maximum output of the active propelling forces to fluctuate slowly fits the experiments quantitatively. Our findings offer design principles for programming efficient transport in active materials.

  View details for DOI 10.1038/NMAT4239

  View details for Web of Science ID 000354801500021

  View details for PubMedID 25822692

• Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni ELIFE Wang, B., Collins, J. J., Newmark, P. A. 2013; 2

  Abstract

  Schistosomes infect hundreds of millions of people in the developing world. Transmission of these parasites relies on a stem cell-driven, clonal expansion of larvae inside a molluscan intermediate host. How this novel asexual reproductive strategy relates to current models of stem cell maintenance and germline specification is unclear. Here, we demonstrate that this proliferative larval cell population (germinal cells) shares some molecular signatures with stem cells from diverse organisms, in particular neoblasts of planarians (free-living relatives of schistosomes). We identify two distinct germinal cell lineages that differ in their proliferation kinetics and expression of a nanos ortholog. We show that a vasa/PL10 homolog is required for proliferation and maintenance of both populations, whereas argonaute2 and a fibroblast growth factor receptor-encoding gene are required only for nanos-negative cells. Our results suggest that an ancient stem cell-based developmental program may have enabled the evolution of the complex life cycle of parasitic flatworms. DOI:http://dx.doi.org/10.7554/eLife.00768.001.

  View details for DOI 10.7554/eLife.00768

  View details for Web of Science ID 000328622300001

  View details for PubMedID 23908765

• When Brownian diffusion is not Gaussian NATURE MATERIALS Wang, B., Kuo, J., Bae, S. C., Granick, S. 2012; 11 (6): 481-485

  View details for DOI 10.1038/nmat3308

  View details for Web of Science ID 000304320300003

  View details for PubMedID 22614505

• Anomalous yet Brownian PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wang, B., Anthony, S. M., Bae, S. C., Granick, S. 2009; 106 (36): 15160-15164

  Abstract

  We describe experiments using single-particle tracking in which mean-square displacement is simply proportional to time (Fickian), yet the distribution of displacement probability is not Gaussian as should be expected of a classical random walk but, instead, is decidedly exponential for large displacements, the decay length of the exponential being proportional to the square root of time. The first example is when colloidal beads diffuse along linear phospholipid bilayer tubes whose radius is the same as that of the beads. The second is when beads diffuse through entangled F-actin networks, bead radius being less than one-fifth of the actin network mesh size. We explore the relevance to dynamic heterogeneity in trajectory space, which has been extensively discussed regarding glassy systems. Data for the second system might suggest activated diffusion between pores in the entangled F-actin networks, in the same spirit as activated diffusion and exponential tails observed in glassy systems. But the first system shows exceptionally rapid diffusion, nearly as rapid as for identical colloids in free suspension, yet still displaying an exponential probability distribution as in the second system. Thus, although the exponential tail is reminiscent of glassy systems, in fact, these dynamics are exceptionally rapid. We also compare with particle trajectories that are at first subdiffusive but Fickian at the longest measurement times, finding that displacement probability distributions fall onto the same master curve in both regimes. The need is emphasized for experiments, theory, and computer simulation to allow definitive interpretation of this simple and clean exponential probability distribution.

  View details for DOI 10.1073/pnas.0903554106

  View details for Web of Science ID 000269632400015

  View details for PubMedID 19666495

• Nanoparticle-induced surface reconstruction of phospholipid membranes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wang, B., Zhang, L., Bae, S. C., Granick, S. 2008; 105 (47): 18171-18175

  Abstract

  The nonspecific adsorption of charged nanoparticles onto single-component phospholipid bilayers bearing phosphocholine headgroups is shown, from fluorescence and calorimetry experiments, to cause surface reconstruction at the points where nanoparticles adsorb. Nanoparticles of negative charge induce local gelation in otherwise fluid bilayers; nanoparticles of positive charge induce otherwise gelled membranes to fluidize locally. Through this mechanism, the phase state deviates from the nominal phase transition temperature by tens of degrees. This work generalizes the notions of environmentally induced surface reconstruction, prominent in metals and semiconductors. Bearing in mind that chemical composition in these single-component lipid bilayers is the same everywhere, this offers a mechanism to generate patchy functional properties in phospholipid membranes.

  View details for DOI 10.1073/pnas.0807296105

  View details for Web of Science ID 000261489300026

  View details for PubMedID 19011086

• Alleviating Cell Lysate-Induced Inhibition to Enable RT-PCR from Single Cells in Picoliter-Volume Double Emulsion Droplets. Analytical chemistry Khariton, M., McClune, C. J., Brower, K. K., Klemm, S., Sattely, E. S., Fordyce, P. M., Wang, B. 2023

  Abstract

  Microfluidic droplet assays enable single-cell polymerase chain reaction (PCR) and sequencing analyses at unprecedented scales, with most methods encapsulating cells within nanoliter-sized single emulsion droplets (water-in-oil). Encapsulating cells within picoliter double emulsion (DE) (water-in-oil-in-water) allows sorting droplets with commercially available fluorescence-activated cell sorter (FACS) machines, making it possible to isolate single cells based on phenotypes of interest for downstream analyses. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. This poses challenges for molecular biology, as prior reports suggest that reverse transcription (RT) and PCR amplification cannot proceed efficiently at volumes below 1 nL due to cell lysate-induced inhibition. To overcome this limitation, we used a plate-based RT-PCR assay designed to mimic reactions in picoliter droplets to systematically quantify and ameliorate the inhibition. We find that RT-PCR is blocked by lysate-induced cleavage of nucleic acid probes and primers, which can be efficiently alleviated through heat lysis. We further show that the magnitude of inhibition depends on the cell type, but that RT-PCR can proceed in low-picoscale reaction volumes for most mouse and human cell lines tested. Finally, we demonstrate one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS. These results open up new avenues for improving picoscale droplet RT-PCR reactions and expanding microfluidic droplet-based single-cell analysis technologies.

  View details for DOI 10.1021/acs.analchem.2c03475

  View details for PubMedID 36598332

• mRNA Transfection ofS. mediterraneafor Luminescence Analysis. Methods in molecular biology (Clifton, N.J.) Weill, U., Hall, R. N., Drees, L., Wang, B., Rink, J. C. 2023; 2680: 263-275

  Abstract

  Planarians have become a powerful model system for stem cell research and regeneration. While the tool kit for mechanistic investigations has been steadily expanding over the last decade, robust genetic tools for transgene expression are still lacking. We describe here methods for in vivo and in vitro mRNA transfection of the planarian species Schmidtea mediterranea. These methods utilize the commercially available TransIT-mRNA transfection reagent to efficiently deliver mRNA encoding a synthetic nanoluciferase reporter. Using a luminescent reporter overcomes the bright autofluorescent background of planarian tissues and allows quantitative measurements of protein expression levels. Collectively, our methods provide the means for heterologous reporter expression in planarian cells and the basis for future development of transgenic techniques.

  View details for DOI 10.1007/978-1-0716-3275-8_17

  View details for PubMedID 37428384

• Multicellularity in animals: The potential for within-organism conflict. Proceedings of the National Academy of Sciences of the United States of America Howe, J., Rink, J. C., Wang, B., Griffin, A. S. 2022; 119 (32): e2120457119

  Abstract

  Metazoans function as individual organisms but also as "colonies" of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicellularity focus on two aspects of development which promote cooperation and limit conflict among cells: a single-cell bottleneck, which creates organisms composed of clones, and a separation of somatic and germ cell lineages, which reduces the selective advantage of cheating. However, many obligately multicellular organisms thrive with neither, creating the potential for within-organism conflict. Here, we argue that the prevalence of such organisms throughout the Metazoa requires us to refine our preconceptions of conflict-free multicellularity. Evolutionary theory must incorporate developmental mechanisms across a broad range of organisms-such as unusual reproductive strategies, totipotency, and cell competition-while developmental biology must incorporate evolutionary principles. To facilitate this cross-disciplinary approach, we provide a conceptual overview from evolutionary biology for developmental biologists, using analogous examples in the well-studied social insects.

  View details for DOI 10.1073/pnas.2120457119

  View details for PubMedID 35862435

• Cellular diversity and developmental hierarchy in the planarian nervous system. Current opinion in genetics & development Wyss, L. S., Bray, S. R., Wang, B. 2022; 76: 101960

  Abstract

  Our ability to dissect celltype diversity, development, and plasticity in the nervous system has been transformed by the recent surge of massive sequencing studies at thesingle-cell level. A large body of this work has focused primarily on organisms with nervous systems established early in development. Using planarian flatworms in which neurons are constantly respecified, replenished, and regenerated, we analyze several existing single-cell transcriptomic datasets and observe features in neuron identity, differentiation, maturation, and function that may provide the planarian nervous system with high levels of adaptability required to respond to various cues including injury. This analysis allows us to place many prior observations made by functional characterizations in a general framework and provide additional hypothesis and predictions to test in future investigations.

  View details for DOI 10.1016/j.gde.2022.101960

  View details for PubMedID 35878572

• Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America Xu, J., Liu, Y., Li, H., Tarashansky, A. J., Kalicki, C. H., Hung, R., Hu, Y., Comjean, A., Kolluru, S. S., Wang, B., Quake, S. R., Luo, L., McMahon, A. P., Dow, J. A., Perrimon, N. 2022; 119 (25): e2203179119

  Abstract

  Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult Drosophila renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified fruitless (fru) as playing a role in stem cell regeneration and Hepatocyte nuclear factor 4 (Hnf4) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including Rho guanine nucleotide exchange factor at 64C (RhoGEF64c), Frequenin 2 (Frq2), Prip, and CG1093 that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus datasetallows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney.

  View details for DOI 10.1073/pnas.2203179119

  View details for PubMedID 35696569

• Comparisons of cell proliferation and cell death from tornaria larva to juvenile worm in the hemichordate Schizocardium californicum. EvoDevo Bump, P., Khariton, M., Stubbert, C., Moyen, N. E., Yan, J., Wang, B., Lowe, C. J. 2022; 13 (1): 13

  Abstract

  BACKGROUND: There are a wide range of developmental strategies in animal phyla, but most insights into adult body plan formation come from direct-developing species. For indirect-developing species, there are distinct larval and adult body plans that are linked together by metamorphosis. Some outstanding questions in the development of indirect-developing organisms include the extent to which larval tissue undergoes cell death during the process of metamorphosis and when and where the tissue that will give rise to the adult originates. How do the processes of cell division and cell death redesign the body plans of indirect developers? In this study, we present patterns of cell proliferation and cell death during larval body plan development, metamorphosis, and adult body plan formation, in the hemichordate Schizocardium californium (Cameron and Perez in Zootaxa 3569:79-88, 2012) to answer these questions.RESULTS: We identified distinct patterns of cell proliferation between larval and adult body plan formation of S. californicum. We found that some adult tissues proliferate during the late larval phase prior to the start of overt metamorphosis. In addition, using an irradiation and transcriptomic approach, we describe a genetic signature of proliferative cells that is shared across the life history states, as well as markers that are unique to larval or juvenile states. Finally, we observed that cell death is minimal in larval stages but begins with the onset of metamorphosis.CONCLUSIONS: Cell proliferation during the development of S. californicum has distinct patterns in the formation of larval and adult body plans. However, cell death is very limited in larvae and begins during the onset of metamorphosis and into early juvenile development in specific domains. The populations of cells that proliferated and gave rise to the larvae and juveniles have a genetic signature that suggested a heterogeneous pool of proliferative progenitors, rather than a set-aside population of pluripotent cells. Taken together, we propose that the gradual morphologicaltransformation of S. californicum is mirrored at the cellular level and may be more representative of the development strategies that characterize metamorphosis in many metazoan animals.

  View details for DOI 10.1186/s13227-022-00198-1

  View details for PubMedID 35668535

• Single cell biology-a Keystone Symposia report. Annals of the New York Academy of Sciences Cable, J., Elowitz, M. B., Domingos, A. I., Habib, N., Itzkovitz, S., Hamidzada, H., Balzer, M. S., Yanai, I., Liberali, P., Whited, J., Streets, A., Cai, L., Stergachis, A. B., Hong, C. K., Keren, L., Guilliams, M., Alon, U., Shalek, A. K., Hamel, R., Pfau, S. J., Raj, A., Quake, S. R., Zhang, N. R., Fan, J., Trapnell, C., Wang, B., Greenwald, N. F., Vento-Tormo, R., Santos, S. D., Spencer, S. L., Garcia, H. G., Arekatla, G., Gaiti, F., Arbel-Goren, R., Rulands, S., Junker, J. P., Klein, A. M., Morris, S. A., Murray, J. I., Galloway, K. E., Ratz, M., Romeike, M. 2021

  Abstract

  Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.

  View details for DOI 10.1111/nyas.14692

  View details for PubMedID 34605044

• Mechanical expansion microscopy. Methods in cell biology Fan, Y. n., Lim, Y. n., Wyss, L. S., Park, S. n., Xu, C. n., Fu, H. n., Fei, J. n., Hong, Y. n., Wang, B. n. 2021; 161: 125–46

  Abstract

  This chapter describes two mechanical expansion microscopy methods with accompanying step-by-step protocols. The first method, mechanically resolved expansion microscopy, uses non-uniform expansion of partially digested samples to provide the imaging contrast that resolves local mechanical properties. Examining bacterial cell wall with this method, we are able to distinguish bacterial species in mixed populations based on their distinct cell wall rigidity and detect cell wall damage caused by various physiological and chemical perturbations. The second method is mechanically locked expansion microscopy, in which we use a mechanically stable gel network to prevent the original polyacrylate network from shrinking in ionic buffers. This method allows us to use anti-photobleaching buffers in expansion microscopy, enabling detection of novel ultra-structures under the optical diffraction limit through super-resolution single molecule localization microscopy on bacterial cells and whole-mount immunofluorescence imaging in thick animal tissues. We also discuss potential applications and assess future directions.

  View details for DOI 10.1016/bs.mcb.2020.04.013

  View details for PubMedID 33478686

• Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science (New York, N.Y.) Musser, J. M., Schippers, K. J., Nickel, M., Mizzon, G., Kohn, A. B., Pape, C., Ronchi, P., Papadopoulos, N., Tarashansky, A. J., Hammel, J. U., Wolf, F., Liang, C., Hernández-Plaza, A., Cantalapiedra, C. P., Achim, K., Schieber, N. L., Pan, L., Ruperti, F., Francis, W. R., Vargas, S., Kling, S., Renkert, M., Polikarpov, M., Bourenkov, G., Feuda, R., Gaspar, I., Burkhardt, P., Wang, B., Bork, P., Beck, M., Schneider, T. R., Kreshuk, A., Wörheide, G., Huerta-Cepas, J., Schwab, Y., Moroz, L. L., Arendt, D. 2021; 374 (6568): 717-723

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/science.abj2949

  View details for PubMedID 34735222

• Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS. Analytical chemistry Brower, K. K., Khariton, M., Suzuki, P. H., Still, C. 2., Kim, G., Calhoun, S. G., Qi, L. S., Wang, B., Fordyce, P. M. 2020

  Abstract

  In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput screening via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying sizes and morphologies as well as a heterogeneous cell mixture of a whole dissociated flatworm (5-25 mum in diameter) within highly monodisperse double emulsions (35 mum in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS screening of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional phenotyping.

  View details for DOI 10.1021/acs.analchem.0c02499

  View details for PubMedID 32900183

• Forecasting unprecedented ecological fluctuations. PLoS computational biology Bray, S. R., Wang, B. 2020; 16 (6): e1008021

  Abstract

  Forecasting 'Black Swan' events in ecosystems is an important but challenging task. Many ecosystems display aperiodic fluctuations in species abundance spanning orders of magnitude in scale, which have vast environmental and economic impact. Empirical evidence and theoretical analyses suggest that these dynamics are in a regime where system nonlinearities limit accurate forecasting of unprecedented events due to poor extrapolation of historical data to unsampled states. Leveraging increasingly available long-term high-frequency ecological tracking data, we analyze multiple natural and experimental ecosystems (marine plankton, intertidal mollusks, and deciduous forest), and recover hidden linearity embedded in universal 'scaling laws' of species dynamics. We then develop a method using these scaling laws to reduce data dependence in ecological forecasting and accurately predict extreme events beyond the span of historical observations in diverse ecosystems.

  View details for DOI 10.1371/journal.pcbi.1008021

  View details for PubMedID 32598364

• Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity. PLoS neglected tropical diseases Ehrenkaufer, G. n., Li, P. n., Stebbins, E. E., Kangussu-Marcolino, M. M., Debnath, A. n., White, C. V., Moser, M. S., DeRisi, J. n., Gisselberg, J. n., Yeh, E. n., Wang, S. C., Company, A. H., Monti, L. n., Caffrey, C. R., Huston, C. D., Wang, B. n., Singh, U. n. 2020; 14 (3): e0008150

  Abstract

  Parasitic infections are a major source of human suffering, mortality, and economic loss, but drug development for these diseases has been stymied by the significant expense involved in bringing a drug though clinical trials and to market. Identification of single compounds active against multiple parasitic pathogens could improve the economic incentives for drug development as well as simplifying treatment regimens. We recently performed a screen of repurposed compounds against the protozoan parasite Entamoeba histolytica, causative agent of amebic dysentery, and identified four compounds (anisomycin, prodigiosin, obatoclax and nithiamide) with low micromolar potency and drug-like properties. Here, we extend our investigation of these drugs. We assayed the speed of killing of E. histolytica trophozoites and found that all four have more rapid action than the current drug of choice, metronidazole. We further established a multi-institute collaboration to determine whether these compounds may have efficacy against other parasites and opportunistic pathogens. We found that anisomycin, prodigiosin and obatoclax all have broad-spectrum antiparasitic activity in vitro, including activity against schistosomes, T. brucei, and apicomplexan parasites. In several cases, the drugs were found to have significant improvements over existing drugs. For instance, both obatoclax and prodigiosin were more efficacious at inhibiting the juvenile form of Schistosoma than the current standard of care, praziquantel. Additionally, low micromolar potencies were observed against pathogenic free-living amebae (Naegleria fowleri, Balamuthia mandrillaris and Acanthamoeba castellanii), which cause CNS infection and for which there are currently no reliable treatments. These results, combined with the previous human use of three of these drugs (obatoclax, anisomycin and nithiamide), support the idea that these compounds could serve as the basis for the development of broad-spectrum anti-parasitic drugs.

  View details for DOI 10.1371/journal.pntd.0008150

  View details for PubMedID 32196500

• Phase transitions in mutualistic communities under invasion PHYSICAL BIOLOGY Bray, S. R., Fan, Y., Wang, B. 2019; 16 (4)

  View details for DOI 10.1088/1478-3975/ab0946

  View details for Web of Science ID 000464498800001

• Deep line-temporal focusing with high axial resolution and a large field-of-view using intracavity control and incoherent pulse shaping OPTICS LETTERS Lou, K., Wang, B., Jee, A., Granick, S., Amblard, F. 2018; 43 (20): 4919–22

  Abstract

  Line-temporal focusing has been recognized as an elegant strategy that provides two-photon microscopy with an effective means for fast imaging through parallelization, together with an improved resilience to scattering for deep imaging. However, the axial resolution remains sub-optimal, except when using high NA objectives and a small field-of-view. With the introduction of an intracavity control of the spectral width of the femtosecond laser to adaptively fill the back aperture of the objective lens, line-temporal focusing two-photon microscopy is demonstrated to reach near-diffraction-limited axial resolution with a large back-aperture objective lens, and improved immunity to sample scattering. In addition, a new incoherent flattop beam shaping method is proposed which provides a uniform contrast with little degradation of the axial resolution along the focus line, even deep in the sample. This is demonstrated in large volumetric imaging of mouse lung samples.

  View details for DOI 10.1364/OL.43.004919

  View details for Web of Science ID 000447265700017

  View details for PubMedID 30320783

• Nanomedicine Approaches Against Parasitic Worm Infections. Advanced healthcare materials Li, P., Rios Coronado, P. E., Longstaff, X. R., Tarashansky, A. J., Wang, B. 2018: e1701494

  Abstract

  Nanomedicine approaches have the potential to transform the battle against parasitic worm (helminth) infections, a major global health scourge from which billions are currently suffering. It is anticipated that the intersection of two currently disparate fields, nanomedicine and helminth biology, will constitute a new frontier in science and technology. This progress report surveys current innovations in these research fields and discusses research opportunities. In particular, the focus is on: (1) major challenges that helminth infections impose on mankind; (2) key aspects of helminth biology that inform future research directions; (3) efforts to construct nanodelivery platforms to target drugs and genes to helminths hidden in their hosts; (4) attempts in applying nanotechnology to enable vaccination against helminth infections; (5) outlooks in utilizing nanoparticles to enhance immunomodulatory activities of worm-derived factors to cure allergy and autoimmune diseases. In each section, achievements are summarized, limitations are explored, and future directions are assessed.

  View details for PubMedID 29602254

• Biomimetic Virulomics for Capture and Identification of Cell-Type Specific Effector Proteins. ACS nano Lapek, J. D., Fang, R. H., Wei, X. n., Li, P. n., Wang, B. n., Zhang, L. n., Gonzalez, D. J. 2017; 11 (12): 11831–38

  Abstract

  An unmet challenge in the study of disease is to accurately streamline the identification of important virulence factors. Traditional, genetically driven approaches miss biologically relevant markers due to discordance between the genome and proteome. Here, we developed a nanotechnology-enabled affinity enrichment strategy coupled with multiplexed quantitative proteomics, namely Biomimetic Virulomics, for successful identification of cell-type specific effector proteins of both prokaryotic and eukaryotic pathogens. We highlight the power of Biomimetic Virulomics by capturing known virulence factors in a high-throughput, cell-type guided fashion. Additionally, a comprehensive characterization of the membrane protein component of biomimetics utilized in this strategy is provided. Interfacing cell-derived nanomaterials with multiplexed quantitative proteomics allow for a specific targeting strategy of virulence factors that can be utilized for drug discovery against prominent human diseases.

  View details for PubMedID 28892626

• Even Hard-Sphere Colloidal Suspensions Display Fickian Yet Non-Gaussian Diffusion ACS NANO Guan, J., Wang, B., Granick, S. 2014; 8 (4): 3331-3336

  Abstract

  We scrutinize three decades of probability density displacement distribution in a simple colloidal suspension with hard-sphere interactions. In this index-matched and density-matched solvent, fluorescent tracer nanoparticles diffuse among matrix particles that are eight times larger, at concentrations from dilute to concentrated, over times up to when the tracer diffuses a few times its size. Displacement distributions of tracers, Gaussian in pure solvent, broaden systematically with increasing obstacle density. The onset of non-Gaussian dynamics is seen in even modestly dilute suspensions, which traditionally would be assumed to follow classic Gaussian expectation. The findings underscore, in agreement with recent studies of more esoteric soft matter systems, the prevalence of non-Gaussian yet Fickian diffusion.

  View details for DOI 10.1021/nn405476t

  View details for Web of Science ID 000334990600023

  View details for PubMedID 24646449

• Bursts of Active Transport in Living Cells PHYSICAL REVIEW LETTERS Wang, B., Kuo, J., Granick, S. 2013; 111 (20)

  Abstract

  We show, using a large new data set, that the temporally resolved speed of active cargo transport in living cells follows a scaling law over several decades of time and length. The statistical regularities display a time-averaged shape that we interpret to reflect stress buildup, followed by rapid release. The scaling power law agrees quantitatively with those reported in inanimate systems (jammed colloids and granular media, and magnetic Barkhausen noise), suggesting a common origin in pushing through a crowded environment in a weak force regime. The implied regulation of the speed of active cellular transport due to environmental obstruction results in bursts of speed and acceleration. These findings extend the classical notion of molecular crowding.

  View details for DOI 10.1103/PhysRevLett.111.208102

  View details for Web of Science ID 000327243600026

  View details for PubMedID 24289710

• Diagnosing Heterogeneous Dynamics in Single-Molecule/Particle Trajectories with Multiscale Wavelets ACS NANO Chen, K., Wang, B., Guan, J., Granick, S. 2013; 7 (10): 8634-8644

  Abstract

  We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large data sets generated in single-molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw data to locally match dynamics of interest. This is accomplished using statistically adaptive universal thresholding, whose advantage is to avoid a single arbitrary threshold that might conceal individual variability across populations. How to implement this multiscale method is described, focusing on local confined diffusion separated by transient transport periods or hopping events, with three specific examples: in cell biology, biotechnology, and glassy colloid dynamics. The discussion is generalized within the framework of continuous time random walk. This computationally efficient method can run routinely on hundreds of millions of data points analyzed within an hour on a desktop personal computer.

  View details for DOI 10.1021/nn402787a

  View details for Web of Science ID 000326209100033

  View details for PubMedID 23971739

• Modular Stitching To Image Single-Molecule DNA Transport JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Guan, J., Wang, B., Bae, S. C., Granick, S. 2013; 135 (16): 6006-6009

  Abstract

  For study of time-dependent conformation, all previous single-molecule imaging studies of polymer transport involve fluorescence labeling uniformly along the chain, which suffers from limited resolution due to the diffraction limit. Here we demonstrate the concept of submolecular single-molecule imaging with DNA chains assembled from DNA fragments such that a chain is labeled at designated spots with covalently attached fluorescent dyes and the chain backbone with dyes of different color. High density of dyes ensures good signal-to-noise ratio to localize the designated spots in real time with nanometer precision and prevents significant photobleaching for long-time tracking purposes. To demonstrate usefulness of this approach, we image electrophoretic transport of λ-DNA through agarose gels. The unexpected pattern is observed that one end of each molecule tends to stretch out in the electric field while the other end remains quiescent for some time before it snaps forward and the stretch-recoil cycle repeats. These features are neither predicted by prevailing theories of electrophoresis mechanism nor detectable by conventional whole-chain labeling methods, which demonstrate pragmatically the usefulness of modular stitching to reveal internal chain dynamics of single molecules.

  View details for DOI 10.1021/ja4020138

  View details for Web of Science ID 000318204800019

  View details for PubMedID 23570269

• Adult somatic stem cells in the human parasite Schistosoma mansoni NATURE Collins, J. J., Wang, B., Lambrus, B. G., Tharp, M. E., Iyer, H., Newmark, P. A. 2013; 494 (7438): 476-479

  Abstract

  Schistosomiasis is among the most prevalent human parasitic diseases, affecting more than 200 million people worldwide. The aetiological agents of this disease are trematode flatworms (Schistosoma) that live and lay eggs within the vasculature of the host. These eggs lodge in host tissues, causing inflammatory responses that are the primary cause of morbidity. Because these parasites can live and reproduce within human hosts for decades, elucidating the mechanisms that promote their longevity is of fundamental importance. Although adult pluripotent stem cells, called neoblasts, drive long-term homeostatic tissue maintenance in long-lived free-living flatworms (for example, planarians), and neoblast-like cells have been described in some parasitic tapeworms, little is known about whether similar cell types exist in any trematode species. Here we describe a population of neoblast-like cells in the trematode Schistosoma mansoni. These cells resemble planarian neoblasts morphologically and share their ability to proliferate and differentiate into derivatives of multiple germ layers. Capitalizing on available genomic resources and RNA-seq-based gene expression profiling, we find that these schistosome neoblast-like cells express a fibroblast growth factor receptor orthologue. Using RNA interference we demonstrate that this gene is required for the maintenance of these neoblast-like cells. Our observations indicate that adaptation of developmental strategies shared by free-living ancestors to modern-day schistosomes probably contributed to the success of these animals as long-lived obligate parasites. We expect that future studies deciphering the function of these neoblast-like cells will have important implications for understanding the biology of these devastating parasites.

  View details for DOI 10.1038/nature11924

  View details for Web of Science ID 000315661500038

  View details for PubMedID 23426263

  View details for PubMedCentralID PMC3586782

• Automated Single-Molecule Imaging To Track DNA Shape LANGMUIR Guan, J., Wang, B., Granick, S. 2011; 27 (10): 6149-6154

  Abstract

  We describe a straightforward, automated line tracking method to visualize linear macromolecules as they rearrange shape by brownian diffusion and under external fields such as electrophoresis. The analysis, implemented here with 30 ms time resolution, identifies contour lines from one end of the molecule to the other without attention to structure smaller than the optical resolution. There are three sequential stages of analysis: first, "feature finding" to discriminate signal from noise; second, "line tracking" to approximate those shapes as lines; and third, "temporal consistency check" to discriminate reasonable from unreasonable fitted conformations in the time domain. Automation makes it straightforward to accumulate vast quantities of data while excluding the unreliable parts of it. We implement this analysis on fluorescence images of λ-DNA molecules in agarose gel to demonstrate its capability to produce large data sets for subsequent statistical analysis.

  View details for DOI 10.1021/la200433r

  View details for Web of Science ID 000290292900050

  View details for PubMedID 21510676

• Single-Molecule Methods in Polymer Science JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS Granick, S., Bae, S. C., Wang, B., Kumar, S., Guan, J., Yu, C., Chen, K., Kuo, J. 2010; 48 (24): 2542-2543

  View details for DOI 10.1002/polb.22133

  View details for Web of Science ID 000284228300003

• Confining Potential when a Biopolymer Filament Reptates PHYSICAL REVIEW LETTERS Wang, B., Guan, J., Anthony, S. M., Bae, S. C., Schweizer, K. S., Granick, S. 2010; 104 (11)

  Abstract

  Using single-molecule fluorescence imaging, we track Brownian motion perpendicular to the contour of tightly entangled F-actin filaments and extract the confining potential. The chain localization presents a small-displacement Hookean regime followed by a large amplitude regime where the effective restoring force is independent of displacement. The implied heterogeneity characterized by a distribution of tube width is modeled.

  View details for DOI 10.1103/PhysRevLett.104.118301

  View details for Web of Science ID 000275802600045

  View details for PubMedID 20366503

• Stepwise interfacial self-assembly of nanoparticles via specific DNA pairing PHYSICAL CHEMISTRY CHEMICAL PHYSICS Wang, B., Wang, M., Zhang, H., Sobal, N. S., Tong, W., Gao, C., Wang, Y., Giersig, M., Wang, D., Moehwald, H. 2007; 9 (48): 6313-6318

  Abstract

  In the present work, we succeeded in alternatively depositing inorganic nanoparticles and functionalized DNA bases onto the water/oil interface from the water and oil bulk phases. The ligands used were functional thymines and adenines. Their thiol and phosphate groups were used to cap inorganic nanoparticles and their thymine and adenine groups to alter the surface functionality of the nanoparticles, thus enabling a layer-by-layer growth fashion of nanoparticles at the interface. The multiple particle ligation rendered the resulting nanoparticle films rather mechanically robust. As results, the freestanding asymmetric bilayer and trilayer films, composed of negatively-charged Au, positively-charged CdTe, and/or organic Ag nanoparticles were constructed; their areas were as large as over several centimetres, depending on the sizes of the containers used. Our work should bring up a novel methodology to generate asymmetric multilayer films of nanoparticles with a defined control of electron or charge across the films.

  View details for Web of Science ID 000251441100004

  View details for PubMedID 18060160

• Chitosan-mediated synthesis of gold nanoparticles on patterned poly(dimethylsiloxane) surfaces BIOMACROMOLECULES Wang, B., Chen, K., Jiang, S., Reincke, F., Tong, W. J., Wang, D. Y., Gao, C. Y. 2006; 7 (4): 1203-1209

  Abstract

  Synthesis of gold nanoparticles on surfaces has been accomplished by the incubation of poly(dimethylsiloxane) (PDMS) films in tetrachloroauric(III) acid and chitosan solution at room temperature and 4 degrees C. One important point in the present study is that the synthesis selectively occurred on the PDMS surface. These observations are substantially different from the reaction in solution, in which no particles can be formed at room temperature. Computation of surface plasmon bands (SPBs) based on Mie theory suggests that the particles are partially coated by chitosan molecules, and the experimental results confirm the theoretical calculations. The proposed mechanism is that chitosan molecules adsorbed or printed on the PDMS surfaces act as reducing/stabilizing agents. Furthermore, PDMS films patterned with chitosan could induce localized synthesis of gold nanoparticles in regions capped with chitosan only. In this way, colloidal patterns were fabricated on the surfaces with high spatial selectivity simultaneously with the synthesis of the particles. Surface-induced fluorescence quenching was observed in the regions capped with gold nanoparticles as well.

  View details for DOI 10.1021/bm060030f

  View details for Web of Science ID 000236868800027

  View details for PubMedID 16602739

• Biologically driven assembly of polyelectrolyte microcapsule patterns to fabricate microreactor arrays ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Wang, B., Zhao, Q. H., Wang, F., Gao, C. Y. 2006; 45 (10): 1560-1563

  View details for DOI 10.1002/anie.200502822

  View details for Web of Science ID 000235752600009

  View details for PubMedID 16440395

• Irreversible compression of polyelectrolyte multilayers MACROMOLECULES Gao, C. Y., Wang, B., Feng, J., Shen, J. C. 2004; 37 (24): 8836-8839

  View details for DOI 10.1021/ma048930g

  View details for Web of Science ID 000225371200008

• Selective adsorption of microcapsules on patterned polyelectrolyte multilayers ADVANCED MATERIALS Feng, J., Wang, B., Gao, C. Y., Shen, J. C. 2004; 16 (21): 1940-?

  View details for DOI 10.1002/adma.200400573

  View details for Web of Science ID 000225848000017