We are a discovery-driven research group working at the interface between developmental biology, bioengineering, and statistical physics. We combine quantitative organism-wide fluorescence imaging, functional genomics, and physical modeling to understand the fundamental rules that control collective cell behaviors to optimize tissue regeneration, adaptation, and evolution.
Honors & Awards
SN10: Scientists to Watch, Science News (2020)
Young Investigator Award, Human Frontier Science Program (2019)
Beckman Young Investigator Award, Arnold and Mabel Beckman Foundation (2017)
Hellman Faculty Scholar Award, Hellman Fellows Fund (2017)
Baxter Faculty Scholar Award, Donald E. and Delia B. Baxter Foundation (2016)
Career Award at the Scientific Interface, Burroughs Wellcome Fund (2013)
Victor K. LaMer Award, American Chemical Society (2012)
Frank J. Padden, Jr. Award, American Physical Society (2010)
Ph.D., University of Illinois, Urbana-Champaign, Materials Science (2011)
M.S., B.S., Zhejiang University, Materials Science (2006)
Current Research and Scholarly Interests
(1) Systems biology of whole-body regeneration
(2) Cell type evolution through the lens of single-cell multiomic sequencing analysis
(3) Quantitative biology of brain regeneration
(4) Regeneration of animal-algal photosymbiotic systems
- Fundamentals of Regeneration Biology
BIOE 219 (Win)
Independent Studies (7)
- Bioengineering Problems and Experimental Investigation
BIOE 191 (Aut, Win, Spr)
- Directed Investigation
BIOE 392 (Aut, Win, Spr)
- Directed Reading in Biophysics
BIOPHYS 399 (Aut, Win, Spr)
- Directed Studies in Applied Physics
APPPHYS 290 (Aut, Win, Spr)
- Directed Study
BIOE 391 (Aut)
- Graduate Research
BIOPHYS 300 (Aut, Win, Spr)
- Out-of-Department Graduate Research
BIO 300X (Aut, Win, Spr)
- Bioengineering Problems and Experimental Investigation
- Prior Year Courses
Doctoral Dissertation Reader (AC)
James Hemker, Lauren Lubeck, R. Andres Parra Sperberg, Pam Rios Coronado, Hannah Rosenblatt, Jiawei Sun, Miriam Sun, Macy Vollbrecht, Pranav Vyas, Xinzhi Zou
Postdoctoral Faculty Sponsor
Doctoral Dissertation Advisor (AC)
Chew Chai, Yuhang Fan, Jesse Gibson, Nelson Hall, Prateek Kalakuntla, Dania Nanes Sarfati, Eun Sun Song, Sidney Vermeulen, Livia Wyss
Master's Program Advisor
Woo Joo Kwon, Xuetong Zhou
Chew Chai, Ray Chang, Yilin Chen, Yuhang Fan, Isabel Goldaracena Aguirre, Esther Mozipo, Misha Raffiee, Soham Sinha, Pranav Vyas, Yixin Wang, Livia Wyss, Helen Yue Zhang
Mapping single-cell atlases throughout Metazoa unravels cell type evolution.
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
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.
2021; 12 (1): 485
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.
2020; 16 (5): 553-557
View details for DOI 10.1038/s41567-020-0809-9
Mechanically resolved imaging of bacteria using expansion microscopy.
2019; 17 (10): e3000268
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.
2019; 8: e48994
View details for DOI 10.7554/eLife.48994
- Stem cell heterogeneity drives the parasitic life cycle of Schistosoma mansoni ELIFE 2018; 7
Memoryless self-reinforcing directionality in endosomal active transport within living cells
2015; 14 (6): 589-593
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
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
Adult somatic stem cells in the human parasite Schistosoma mansoni
2013; 494 (7438): 476-479
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
- When Brownian diffusion is not Gaussian NATURE MATERIALS 2012; 11 (6): 481-485
Anomalous yet Brownian
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (36): 15160-15164
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
2008; 105 (47): 18171-18175
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
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
2022; 119 (25): e2203179119
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.
2022; 13 (1): 13
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
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
2021; 161: 125–46
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.) 2021; 374 (6568): 717-723
Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS.
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
2020; 16 (6): e1008021
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
2020; 14 (3): e0008150
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 2019; 16 (4)
Deep line-temporal focusing with high axial resolution and a large field-of-view using intracavity control and incoherent pulse shaping
2018; 43 (20): 4919–22
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
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.
2017; 11 (12): 11831–38
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
2014; 8 (4): 3331-3336
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
2013; 111 (20)
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
2013; 7 (10): 8634-8644
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
2013; 135 (16): 6006-6009
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
Automated Single-Molecule Imaging To Track DNA Shape
2011; 27 (10): 6149-6154
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 2010; 48 (24): 2542-2543
Confining Potential when a Biopolymer Filament Reptates
PHYSICAL REVIEW LETTERS
2010; 104 (11)
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
Influence of assembling pH on the stability of poly(L-glutamic acid) and poly(L-lysine) multilayers against urea treatment
COLLOIDS AND SURFACES B-BIOINTERFACES
2008; 62 (2): 250-257
Polyelectrolyte multilayers of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) were built up using the layer-by-layer (LbL) technique in low pH (3.6, PM3.6) and in neutral pH (7.4, PM7.4) solutions. The multilayers were then treated with a concentrated urea (one kind of denaturant for proteins and polypeptides) solution (8M) and rinsed with corresponding buffer. The buildup and treatment processes were investigated by ultraviolet visible spectroscopy and ellipsometry. The surface morphology was observed by scanning force microscopy (SFM). The inner structures were determined by X-ray reflectometry and circular dichroism spectroscopy (CD). An exponential growth of the optical mass and the layer thickness was observed for both PM3.6 and PM7.4. After urea treatment, a significant mass loss for PM3.6 was found, while no mass change was recorded for PM7.4. The dominant driving force for PM7.4 is electrostatic interaction, resulting in multilayers with an abundant beta-sheet structure, which has higher stability against urea treatment. By contrast, the dominant driving force for PM3.6 is hydrogen bonding and hydrophobic interaction, which are sensitive to the urea treatment. The mechanism is substantiated by molecular mechanics calculation. This has offered a convenient pathway to mediate the multilayer properties, which is of great importance for potential applications.
View details for DOI 10.1016/j.colsurfb.2007.10.017
View details for Web of Science ID 000254606900012
View details for PubMedID 18068958
The influence of polycaprolactone coating on the internalization and cytotoxicity of gold nanoparticles
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
2007; 3 (3): 215-223
The interaction between mesoscopic colloids and cells is largely dependent on the particle size and surface properties. Under a mild reaction condition, gold particles with an average diameter of approximately 100 nm were prepared by incubating poly(dimethylsiloxane) film in HAuCl4/acetic acid solution. The particles were then transferred into a polycaprolactone (PCL) film by thermal pressing. Bare and PCL-coated particles were obtained by control over the extent of rinsing. The bare and PCL-coated gold particles were co-cultured with ECV-304 cells to examine the particle internalization and their influence on the cell morphology and cytotoxicity. Transmission electron microcopy observed the subcellular distribution of the gold particles, which were found in the cell compartments (endosomes or lysosomes), cytoplasm, nucleic envelope, and even nucleus regardless of the existence of PCL coating. However, scanning electron microscopy and beta-tubulin staining revealed a significant change in terms of the cell morphology and cytoskeleton caused by the bare gold particles. Higher cytotoxicity was also determined for the bare gold particles. By contrast, no significant difference of the cell morphology and cytoskeleton change was caused by the PCL-coated gold particles, which have also shown lower cytotoxicity.
View details for DOI 10.1016/j.nano.2007.04.001
View details for Web of Science ID 000249325500006
View details for PubMedID 17706466
Stepwise interfacial self-assembly of nanoparticles via specific DNA pairing
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
2007; 9 (48): 6313-6318
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
2006; 7 (4): 1203-1209
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 2006; 45 (10): 1560-1563
- Irreversible compression of polyelectrolyte multilayers MACROMOLECULES 2004; 37 (24): 8836-8839
- Selective adsorption of microcapsules on patterned polyelectrolyte multilayers ADVANCED MATERIALS 2004; 16 (21): 1940-?