Bianxiao Cui

All Publications

• Actin-driven nanotopography promotes stable integrin adhesion formation in developing tissue. Nature communications Chen, T., Fernández-Espartero, C. H., Illand, A., Tsai, C. T., Yang, Y., Klapholz, B., Jouchet, P., Fabre, M., Rossier, O., Cui, B., Lévêque-Fort, S., Brown, N. H., Giannone, G. 2024; 15 (1): 8691

  Abstract

  Morphogenesis requires building stable macromolecular structures from highly dynamic proteins. Muscles are anchored by long-lasting integrin adhesions to resist contractile force. However, the mechanisms governing integrin diffusion, immobilization, and activation within developing tissues remain elusive. Here, we show that actin polymerization-driven membrane protrusions form nanotopographies that enable strong adhesion at Drosophila muscle attachment sites (MASs). Super-resolution microscopy reveals that integrins assemble adhesive belts around Arp2/3-dependent actin protrusions, forming invadosome-like structures with membrane nanotopographies. Single protein tracking shows that, during MAS development, integrins become immobile and confined within diffusion traps formed by the membrane nanotopographies. Actin filaments also display restricted motion and confinement, indicating strong mechanical connection with integrins. Using isolated muscle cells, we show that substrate nanotopography, rather than rigidity, drives adhesion maturation by regulating actin protrusion, integrin diffusion and immobilization. These results thus demonstrate that actin-polymerization-driven membrane protrusions are essential for the formation of strong integrin adhesions sites in the developing embryo, and highlight the important contribution of geometry to morphogenesis.

  View details for DOI 10.1038/s41467-024-52899-x

  View details for PubMedID 39375335

  View details for PubMedCentralID PMC11458790

• Targeted protein relocalization via protein transport coupling. Nature Ng, C. S., Liu, A., Cui, B., Banik, S. M. 2024

  Abstract

  Subcellular protein localization regulates protein function and can be corrupted in cancers1 and neurodegenerative diseases2,3. The rewiring of localization to address disease-driving phenotypes would be an attractive targeted therapeutic approach. Molecules that harness the trafficking of a shuttle protein to control the subcellular localization of a target protein could enforce targeted protein relocalization and rewire the interactome. Here we identify a collection of shuttle proteins with potent ligands amenable to incorporation into targeted relocalization-activating molecules (TRAMs), and use these to relocalize endogenous proteins. Using a custom imaging analysis pipeline, we show that protein steady-state localization can be modulated through molecular coupling to shuttle proteins containing sufficiently strong localization sequences and expressed in the necessary abundance. We analyse the TRAM-induced relocalization of different proteins and then use nuclear hormone receptors as shuttles to redistribute disease-driving mutant proteins such as SMARCB1Q318X, TDP43ΔNLS and FUSR495X. TRAM-mediated relocalization of FUSR495X to the nucleus from the cytoplasm correlated with a reduction in the number of stress granules in a model of cellular stress. With methionyl aminopeptidase 2 and poly(ADP-ribose) polymerase 1 as endogenous cytoplasmic and nuclear shuttles, respectively, we demonstrate relocalization of endogenous PRMT9, SOS1 and FKBP12. Small-molecule-mediated redistribution of nicotinamide nucleotide adenylyltransferase 1 from nuclei to axons in primary neurons was able to slow axonal degeneration and pharmacologically mimic the genetic WldS gain-of-function phenotype in mice resistant to certain types of neurodegeneration4. The concept of targeted protein relocalization could therefore inspire approaches for treating disease through interactome rewiring.

  View details for DOI 10.1038/s41586-024-07950-8

  View details for PubMedID 39294374

  View details for PubMedCentralID 7429473

• Plasma membrane curvature regulates the formation of contacts with the endoplasmic reticulum. Nature cell biology Yang, Y., Valencia, L. A., Lu, C. H., Nakamoto, M. L., Tsai, C. T., Liu, C., Yang, H., Zhang, W., Jahed, Z., Lee, W. R., Santoro, F., Liou, J., Wu, J. C., Cui, B. 2024

  Abstract

  Contact sites between the endoplasmic reticulum (ER) and plasma membrane (PM) play a crucial role in governing calcium regulation and lipid homeostasis. Despite their significance, the factors regulating their spatial distribution on the PM remain elusive. Inspired by observations in cardiomyocytes, where ER-PM contact sites concentrate on tubular PM invaginations known as transverse tubules, we hypothesize that PM curvature plays a role in ER-PM contact formation. Through precise control of PM invaginations, we show that PM curvatures locally induce the formation of ER-PM contacts in cardiomyocytes. Intriguingly, the junctophilin family of ER-PM tethering proteins, specifically expressed in excitable cells, is the key player in this process, whereas the ubiquitously expressed extended synaptotagmin-2 does not show a preference for PM curvature. At the mechanistic level, we find that the low-complexity region (LCR) and membrane occupation and recognition nexus (MORN) motifs of junctophilins can bind independently to the PM, but both the LCR and MORN motifs are required for targeting PM curvatures. By examining the junctophilin interactome, we identify a family of curvature-sensing proteins-Eps15 homology domain-containing proteins-that interact with the MORN_LCR motifs and facilitate the preferential tethering of junctophilins to curved PM. These findings highlight the pivotal role of PM curvature in the formation of ER-PM contacts in cardiomyocytes and unveil a mechanism for the spatial regulation of ER-PM contacts through PM curvature modulation.

  View details for DOI 10.1038/s41556-024-01511-x

  View details for PubMedID 39289582

  View details for PubMedCentralID 6427007

• Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms. Nature chemical biology Peng, C. S., Zhang, Y., Liu, Q., Marti, G. E., Huang, Y. A., Sudhof, T. C., Cui, B., Chu, S. 2024

  Abstract

  Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.

  View details for DOI 10.1038/s41589-024-01694-2

  View details for PubMedID 39090313

• Light-Inducible Activation of TrkA for Probing Chronic Pain in Mice. ACS chemical biology Liu, A., Mohr, M. A., Hope, J. M., Wang, J., Chen, X., Cui, B. 2024; 19 (7): 1626-1637

  Abstract

  Chronic pain is a prevalent problem that plagues modern society, and better understanding its mechanisms is critical for developing effective therapeutics. Nerve growth factor (NGF) and its primary receptor, Tropomyosin receptor kinase A (TrkA), are known to be potent mediators of chronic pain, but there is a lack of established methods for precisely perturbing the NGF/TrkA signaling pathway in the study of pain and nociception. Optobiological tools that leverage light-induced protein-protein interactions allow for precise spatial and temporal control of receptor signaling. Previously, our lab reported a blue light-activated version of TrkA generated using light-induced dimerization of the intracellular TrkA domain, opto-iTrkA. In this work, we show that opto-iTrkA activation is able to activate endogenous ERK and Akt signaling pathways and causes the retrograde transduction of phospho-ERK signals in dorsal root ganglion (DRG) neurons. Opto-iTrkA activation also sensitizes the transient receptor potential vanilloid 1 (TRPV1) channel in cellular models, further corroborating the physiological relevance of the optobiological stimulus. Finally, we show that opto-iTrkA enables light-inducible potentiation of mechanical sensitization in mice. Light illumination enables nontraumatic and reversible (<2 days) sensitization of mechanical pain in mice transduced with opto-iTrkA, which provides a platform for dissecting TrkA pathways for nociception in vitro and in vivo.

  View details for DOI 10.1021/acschembio.4c00300

  View details for PubMedID 39026469

• Engineering the Cellular Microenvironment: Integrating Three-Dimensional Nontopographical and Two-Dimensional Biochemical Cues for Precise Control of Cellular Behavior. ACS nano Sarikhani, E., Meganathan, D. P., Larsen, A. K., Rahmani, K., Tsai, C. T., Lu, C. H., Marquez-Serrano, A., Sadr, L., Li, X., Dong, M., Santoro, F., Cui, B., Klausen, L. H., Jahed, Z. 2024

  Abstract

  The development of biomaterials capable of regulating cellular processes and guiding cell fate decisions has broad implications in tissue engineering, regenerative medicine, and cell-based assays for drug development and disease modeling. Recent studies have shown that three-dimensional (3D) nanoscale physical cues such as nanotopography can modulate various cellular processes like adhesion and endocytosis by inducing nanoscale curvature on the plasma and nuclear membranes. Two-dimensional (2D) biochemical cues such as protein micropatterns can also regulate cell function and fate by controlling cellular geometries. Development of biomaterials with precise control over nanoscale physical and biochemical cues can significantly influence programming cell function and fate. In this study, we utilized a laser-assisted micropatterning technique to manipulate the 2D architectures of cells on 3D nanopillar platforms. We performed a comprehensive analysis of cellular and nuclear morphology and deformation on both nanopillar and flat substrates. Our findings demonstrate the precise engineering of single cell architectures through 2D micropatterning on nanopillar platforms. We show that the coupling between the nuclear and cell shape is disrupted on nanopillar surfaces compared to flat surfaces. Furthermore, our results suggest that cell elongation on nanopillars enhances nanopillar-induced endocytosis. We believe our platform serves as a versatile tool for further explorations into programming cell function and fate through combined physical cues that create nanoscale curvature on cell membranes and biochemical cues that control the geometry of the cell.

  View details for DOI 10.1021/acsnano.4c03743

  View details for PubMedID 38978500

• Endoplasmic reticulum exit sites are segregated for secretion based on cargo size. Developmental cell Saxena, S., Foresti, O., Liu, A., Androulaki, S., Pena Rodriguez, M., Raote, I., Aridor, M., Cui, B., Malhotra, V. 2024

  Abstract

  TANGO1, TANGO1-Short, and cTAGE5 form stable complexes at the endoplasmic reticulum exit sites (ERES) to preferably export bulky cargoes. Their C-terminal proline-rich domain (PRD) binds Sec23A and affects COPII assembly. The PRD in TANGO1-Short was replaced with light-responsive domains to control its binding to Sec23A in U2OS cells (human osteosarcoma). TANGO1-ShortΔPRD was dispersed in the ER membrane but relocated rapidly, reversibly, to pre-existing ERES by binding to Sec23A upon light activation. Prolonged binding between the two, concentrated ERES in the juxtanuclear region, blocked cargo export and relocated ERGIC53 into the ER, minimally impacting the Golgi complex organization. Bulky collagen VII and endogenous collagen I were collected at less than 47% of the stalled ERES, whereas small cargo molecules were retained uniformly at almost all the ERES. We suggest that ERES are segregated to handle cargoes based on their size, permitting cells to traffic them simultaneously for optimal secretion.

  View details for DOI 10.1016/j.devcel.2024.06.009

  View details for PubMedID 38991587

• Membrane Curvature Promotes ER-PM Contact Formation via Junctophilin-EHD Interactions. bioRxiv : the preprint server for biology Yang, Y., Valencia, L. A., Lu, C. H., Nakamoto, M. L., Tsai, C. T., Liu, C., Yang, H., Zhang, W., Jahed, Z., Lee, W. R., Santoro, F., Liou, J., Wu, J. C., Cui, B. 2024

  Abstract

  Contact sites between the endoplasmic reticulum (ER) and the plasma membrane (PM) play a crucial role in governing calcium regulation and lipid homeostasis. Despite their significance, the factors regulating their spatial distribution on the PM remain elusive. Inspired by observations in cardiomyocytes, where ER-PM contact sites concentrate on tubular PM invaginations known as transverse tubules (T-tubules), we hypothesize that the PM curvature plays a role in ER-PM contact formation. Through precise control of PM invaginations, we show that PM curvatures locally induce the formation of ER-PM contacts in cardiomyocytes. Intriguingly, the junctophilin family of ER-PM tethering proteins, specifically expressed in excitable cells, is the key player in this process, while the ubiquitously expressed extended synaptotagmin 2 does not show a preference for PM curvature. At the mechanistic level, we find that the low complexity region (LCR) and the MORN motifs of junctophilins can independently bind to the PM, but both the LCR and MORN motifs are required for targeting PM curvatures. By examining the junctophilin interactome, we identify a family of curvature-sensing proteins, Eps15-homology domain containing proteins (EHDs), that interact with the MORN_LCR motifs and facilitate junctophilins' preferential tethering to curved PM. These findings highlight the pivotal role of PM curvature in the formation of ER-PM contacts in cardiomyocytes and unveil a novel mechanism for the spatial regulation of ER-PM contacts through PM curvature modulation.

  View details for DOI 10.1101/2024.06.29.601287

  View details for PubMedID 38979311

  View details for PubMedCentralID PMC11230412

• Light-Inducible Activation of TrkA for Probing Chronic Pain in Mice ACS CHEMICAL BIOLOGY Liu, A., Mohr, M. A., Hope, J. M., Wang, J., Chen, X., Cui, B. 2024

  View details for DOI 10.1021/acschembio.4c00300

  View details for Web of Science ID 001251999400001

• Kirigami electronics for long-term electrophysiological recording of human neural organoids and assembloids. Nature biotechnology Yang, X., Forro, C., Li, T. L., Miura, Y., Zaluska, T. J., Tsai, C., Kanton, S., McQueen, J. P., Chen, X., Mollo, V., Santoro, F., Pașca, S. P., Cui, B. 2024

  Abstract

  Realizing the full potential of organoids and assembloids to model neural development and disease will require improved methods for long-term, minimally invasive recording of electrical activity. Current technologies, such as patch clamp, penetrating microelectrodes, planar electrode arrays and substrate-attached flexible electrodes, do not allow chronic recording of organoids in suspension, which is necessary to preserve architecture. Inspired by kirigami art, we developed flexible electronics that transition from a two-dimensional to a three-dimensional basket-like configuration with either spiral or honeycomb patterns to accommodate the long-term culture of organoids in suspension. Here we show that this platform, named kirigami electronics (KiriE), integrates with and enables chronic recording of cortical organoids for up to 120days while preserving their morphology, cytoarchitecture and cell composition. We demonstrate integration of KiriE with optogenetic and pharmacological manipulation and modeling phenotypes related to a genetic disease. Moreover, KiriE can capture corticostriatal connectivity in assembloids following optogenetic stimulation. Thus, KiriE will enable investigation of disease and activity patterns underlying nervous system assembly.

  View details for DOI 10.1038/s41587-023-02081-3

  View details for PubMedID 38253880

• Compact Electrochromic Optical Recording of Bioelectric Potentials. ArXiv Nakasone, K., Zavik, C., Liu, E., Ahmed, B., Griffith, D., Maisenbacher, L., Singh, A., Zhou, Y., Cui, B., Müller, H. 2023

  Abstract

  Electrochromic optical recording (ECORE) is a label-free method that utilizes electrochromism to optically detect electrical signals in biological cells with a high signal-to-noise ratio and is suitable for long-term recording. However, ECORE usually requires a large and intricate optical setup, making it relatively difficult to transport and to study specimens on a large scale. Here, we present a Compact ECORE (CECORE) apparatus that drastically reduces the spatial footprint and complexity of the ECORE setup whilst maintaining high sensitivity. An autobalancing differential photodetector automates common-mode noise rejection, removing the need for manually adjustable optics, and a compact laser module conserves space compared to a typical laser mount. The result is a simple, easy-to-use, and relatively low cost system that achieves a sensitivity of 16.7 μV (within a factor of 5 of the shot noise limit), and reliably detects action potentials from Human-induced pluripotent stem cell (HiPSC) derived cardiomyocytes. This setup can be further improved to within 1.5 dB of the shot noise limit by filtering out power-line interference.

  View details for PubMedID 38076511

  View details for PubMedCentralID PMC10705589

• Curved adhesions mediate cell attachment to soft matrix fibres in three dimensions. Nature cell biology Zhang, W., Lu, C. H., Nakamoto, M. L., Tsai, C. T., Roy, A. R., Lee, C. E., Yang, Y., Jahed, Z., Li, X., Cui, B. 2023

  Abstract

  Integrin-mediated focal adhesions are the primary architectures that transmit forces between the extracellular matrix (ECM) and the actin cytoskeleton. Although focal adhesions are abundant on rigid and flat substrates that support high mechanical tensions, they are sparse in soft three-dimensional (3D) environments. Here we report curvature-dependent integrin-mediated adhesions called curved adhesions. Their formation is regulated by the membrane curvatures imposed by the topography of ECM protein fibres. Curved adhesions are mediated by integrin ɑvβ5 and are molecularly distinct from focal adhesions and clathrin lattices. The molecular mechanism involves a previously unknown interaction between integrin β5 and a curvature-sensing protein, FCHo2. We find that curved adhesions are prevalent in physiological conditions, and disruption of curved adhesions inhibits the migration of some cancer cell lines in 3D fibre matrices. These findings provide a mechanism for cell anchorage to natural protein fibres and suggest that curved adhesions may serve as a potential therapeutic target.

  View details for DOI 10.1038/s41556-023-01238-1

  View details for PubMedID 37770566

  View details for PubMedCentralID 6449687

• Targeted Lysosomal Degradation of Secreted and Cell Surface Proteins through the LRP-1 Pathway. Journal of the American Chemical Society Loppinet, E., Besser, H. A., Lee, C. E., Zhang, W., Cui, B., Khosla, C. 2023

  Abstract

  Protein dysregulation has been characterized as the cause of pathogenesis in many different diseases. For proteins lacking easily druggable pockets or catalytically active sites, targeted protein degradation is an attractive therapeutic approach. While several methods for targeted protein degradation have been developed, there remains a demand for lower molecular weight molecules that promote efficient degradation of their targets. In this work, we describe the synthesis and validation of a series of heterobifunctional molecules that bind a protein of interest through a small molecule ligand while targeting them to the lysosome using a short gluten peptide that leverages the TG2/LRP-1 pathway. We demonstrate that this approach can be used to effectively endocytose and degrade representative secreted, cell surface, and transmembrane proteins, notably streptavidin, the vitamin B12 receptor, cubilin, and integrin αvβ5. Optimization of these prototypical molecules could generate pharmacologically relevant LYTAC agents.

  View details for DOI 10.1021/jacs.3c05109

  View details for PubMedID 37590164

• A NanoCurvS platform for quantitative and multiplex analysis of curvature-sensing proteins. Biomaterials science Lu, C. H., Tsai, C. T., Jones Iv, T., Chim, V., Klausen, L. H., Zhang, W., Li, X., Jahed, Z., Cui, B. 2023

  Abstract

  The cell membrane is characterized by a rich variety of topographical features such as local protrusions or invaginations. Curvature-sensing proteins, including the Bin/Amphiphysin/Rvs (BAR) or epsin N-terminal homology (ENTH) family proteins, sense the bending sharpness and the positive/negative sign of these topographical features to induce subsequent intracellular signaling. A number of assays have been developed to study curvature-sensing properties of proteins in vitro, but it is still challenging to probe low curvature regime with the diameter of curvature from hundreds of nanometers to micrometers. It is particularly difficult to generate negative membrane curvatures with well-defined curvature values in the low curvature regime. In this work, we develop a nanostructure-based curvature sensing (NanoCurvS) platform that enables quantitative and multiplex analysis of curvature-sensitive proteins in the low curvature regime, in both negative and positive directions. We use NanoCurvS to quantitatively measure the sensing range of a negative curvature-sensing protein IRSp53 (an I-BAR protein) and a positive curvature-sensing protein FBP17 (an F-BAR protein). We find that, in cell lysates, the I-BAR domain of IRSp53 is able to sense shallow negative curvatures with the diameter-of-curvature up to 1500 nm, a range much wider than previously expected. NanoCurvS is also used to probe the autoinhibition effect of IRSp53 and the phosphorylation effect of FBP17. Therefore, the NanoCurvS platform provides a robust, multiplex, and easy-to-use tool for quantitative analysis of both positive and negative curvature-sensing proteins.

  View details for DOI 10.1039/d2bm01856j

  View details for PubMedID 37337788

• Curved adhesions mediate cell attachment to soft matrix fibres in 3D. bioRxiv : the preprint server for biology Zhang, W., Lu, C. H., Nakamoto, M. L., Tsai, C. T., Roy, A. R., Lee, C. E., Yang, Y., Jahed, Z., Li, X., Cui, B. 2023

  Abstract

  Mammalian cells adhere to the extracellular matrix (ECM) and sense mechanical cues through integrin-mediated adhesions 1, 2 . Focal adhesions and related structures are the primary architectures that transmit forces between the ECM and the actin cytoskeleton. Although focal adhesions are abundant when cells are cultured on rigid substrates, they are sparse in soft environments that cannot support high mechanical tensions 3 . Here, we report a new class of integrin-mediated adhesions, curved adhesions, whose formation is regulated by membrane curvature instead of mechanical tension. In soft matrices made of protein fibres, curved adhesions are induced by membrane curvatures imposed by the fibre geometry. Curved adhesions are mediated by integrin ɑVβ5 and are molecularly distinct from focal adhesions and clathrin lattices. The molecular mechanism involves a previously unknown interaction between integrin β5 and a curvature-sensing protein FCHo2. We find that curved adhesions are prevalent in physiologically relevant environments. Disruption of curved adhesions by knocking down integrin β5 or FCHo2 abolishes the migration of multiple cancer cell lines in 3D matrices. These findings provide a mechanism of cell anchorage to natural protein fibres that are too soft to support the formation of focal adhesions. Given their functional importance for 3D cell migration, curved adhesions may serve as a therapeutic target for future development.

  View details for DOI 10.1101/2023.03.16.532975

  View details for PubMedID 36993504

  View details for PubMedCentralID PMC10055138

• Expansion microscopy for imaging the cell-material interface. Biophysical journal Nakamoto, M. L., Forro, C., Zhang, W., Tsai, C., Cui, B. 2023; 122 (3S1): 133a

  View details for DOI 10.1016/j.bpj.2022.11.883

  View details for PubMedID 36782597

• Development of an optogenetic TrkB.T1 probe. Biophysical journal Valencia, L. A., Cui, B. 2023; 122 (3S1): 431a-432a

  View details for DOI 10.1016/j.bpj.2022.11.2335

  View details for PubMedID 36784212

• Modulation of nuclear membrane repair machinery by nano-needle arrays. Biophysical journal Hosseini, R., Shukla, S., Sarikhani, E., Meganathan, D., Badle, R., Spain, L., Okerblom, J., Tsai, C., Cui, B., Jahed, Z. 2023; 122 (3S1): 552a

  View details for DOI 10.1016/j.bpj.2022.11.2922

  View details for PubMedID 36784865

• Plasma membrane curvature promotes ER-PM contact formation mediated by junctophilin. Biophysical journal Yang, Y., Cui, B. 2023; 122 (3S1): 379a-380a

  View details for DOI 10.1016/j.bpj.2022.11.2084

  View details for PubMedID 36783923

• High-resolution optical recording of bioelectric signals using electrochromic materials. Biophysical journal Ahmed, B., Nakasone, K., Griffith, D., Zhou, Y., Liu, E., Alfonso, F. S., Cui, B., Mueller, H. 2023; 122 (3S1): 540a

  View details for DOI 10.1016/j.bpj.2022.11.2862

  View details for PubMedID 36784801

• A versatile nanoelectrode platform for electrical recording of diverse cell types. Biophysical journal Shukla, S. R., Tsai, C., Jahed, Z., Cui, B. 2023; 122 (3S1): 431a

  View details for DOI 10.1016/j.bpj.2022.11.2333

  View details for PubMedID 36784209

• Label-free optical detection of cellular action potentials using electrochromic materials. Biophysical journal Liu, E., Zhou, Y., Alfonso, F. S., Yang, Y., Ahmed, B., Nakasone, K., Xu, V., Mueller, H., Cui, B. 2023; 122 (3S1): 540a-541a

  View details for DOI 10.1016/j.bpj.2022.11.2863

  View details for PubMedID 36784800

• Engineering cell morphology using maskless 2D protein micropatterning on 3D nanostructures. Biophysical journal Sarikhani, E., Klausen, L., Pushpa Meganathan, D., Marquez Serrano, A., Tsai, C., Cui, B., Jahed, Z. 2023; 122 (3S1): 553a

  View details for DOI 10.1016/j.bpj.2022.11.2925

  View details for PubMedID 36784871

• Probing mechanical forces in curvature-sensitive cell adhesions. Biophysical journal Lee, C. E., Zhang, W., Cui, B. 2023; 122 (3S1): 532a

  View details for DOI 10.1016/j.bpj.2022.11.2821

  View details for PubMedID 36784754

• A NanoCurvS platform for quantitative and multiplex analysis of curvature-sensing proteins Biomaterials Science Lu, C., et al 2023

  View details for DOI 10.1039/D2BM01856J

• Quantitative phase contrast imaging with a nonlocal angle-selective metasurface. Nature communications Ji, A., Song, J. H., Li, Q., Xu, F., Tsai, C. T., Tiberio, R. C., Cui, B., Lalanne, P., Kik, P. G., Miller, D. A., Brongersma, M. L. 2022; 13 (1): 7848

  Abstract

  Phase contrast microscopy has played a central role in the development of modern biology, geology, and nanotechnology. It can visualize the structure of translucent objects that remains hidden in regular optical microscopes. The optical layout of a phase contrast microscope is based on a 4 f image processing setup and has essentially remained unchanged since its invention by Zernike in the early 1930s. Here, we propose a conceptually new approach to phase contrast imaging that harnesses the non-local optical response of a guided-mode-resonator metasurface. We highlight its benefits and demonstrate the imaging of various phase objects, including biological cells, polymeric nanostructures, and transparent metasurfaces. Our results showcase that the addition of this non-local metasurface to a conventional microscope enables quantitative phase contrast imaging with a 0.02π phase accuracy. At a high level, this work adds to the growing body of research aimed at the use of metasurfaces for analog optical computing.

  View details for DOI 10.1038/s41467-022-34197-6

  View details for PubMedID 36543788

  View details for PubMedCentralID PMC9772391

• Dual-Color Optical Recording of Bioelectric Potentials by Polymer Electrochromism. Journal of the American Chemical Society Zhou, Y., Liu, E., Yang, Y., Alfonso, F. S., Ahmed, B., Nakasone, K., Forro, C., Muller, H., Cui, B. 2022

  Abstract

  Optical recording based on voltage-sensitive fluorescent reporters allows for spatial flexibility of measuring from desired cells, but photobleaching and phototoxicity of the fluorescent labels often limit their sensitivity and recording duration. Voltage-dependent optical absorption, rather than fluorescence, of electrochromic materials, would overcome these limitations to achieve long-term optical recording of bioelectrical signals. Electrochromic materials such as PEDOT:PSS possess the property that an applied voltage can either increase or decrease the light absorption depending on the wavelength. In this work, we harness this anticorrelated light absorption at two different wavelengths to significantly improve the signal detection. With dual-color detection, electrical activity from cells produces signals of opposite polarity, while artifacts, mechanical motions, and technical noises are uncorrelated or positively correlated. Using this technique, we are able to optically record cardiac action potentials with a high signal-to-noise ratio, 10 kHz sampling rate, >15 min recording duration, and no time-dependent degradation of the signal. Furthermore, we can reliably perform multiple recording sessions from the same culture for over 25 days.

  View details for DOI 10.1021/jacs.2c10198

  View details for PubMedID 36525312

• Stretchable mesh microelectronics for the biointegration and stimulation of human neural organoids. Biomaterials Li, T. L., Liu, Y., Forro, C., Yang, X., Beker, L., Bao, Z., Cui, B., Pașca, S. P. 2022; 290: 121825

  Abstract

  Advances in tridimensional (3D) culture approaches have led to the generation of organoids that recapitulate cellular and physiological features of domains of the human nervous system. Although microelectrodes have been developed for long-term electrophysiological interfaces with neural tissue, studies of long-term interfaces between microelectrodes and free-floating organoids remain limited. In this study, we report a stretchable, soft mesh electrode system that establishes an intimate in vitro electrical interface with human neurons in 3D organoids. Our mesh is constructed with poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) based electrically conductive hydrogel electrode arrays and elastomeric poly(styrene-ethylene-butylene-styrene) (SEBS) as the substrate and encapsulation materials. This mesh electrode can maintain a stable electrochemical impedance in buffer solution under 50% compressive and 50% tensile strain. We have successfully cultured pluripotent stem cell-derived human cortical organoids (hCO) on this polymeric mesh for more than 3 months and demonstrated that organoids readily integrate with the mesh. Using simultaneous stimulation and calcium imaging, we show that electrical stimulation through the mesh can elicit intensity-dependent calcium signals comparable to stimulation from a bipolar stereotrode. This platform may serve as a tool for monitoring and modulating the electrical activity of in vitro models of neuropsychiatric diseases.

  View details for DOI 10.1016/j.biomaterials.2022.121825

  View details for PubMedID 36326509

• Maturation and circuit integration of transplanted human cortical organoids. Nature Revah, O., Gore, F., Kelley, K. W., Andersen, J., Sakai, N., Chen, X., Li, M. Y., Birey, F., Yang, X., Saw, N. L., Baker, S. W., Amin, N. D., Kulkarni, S., Mudipalli, R., Cui, B., Nishino, S., Grant, G. A., Knowles, J. K., Shamloo, M., Huguenard, J. R., Deisseroth, K., Pașca, S. P. 2022; 610 (7931): 319-326

  Abstract

  Self-organizing neural organoids represent a promising in vitro platform with which to model human development and disease1-5. However, organoids lack the connectivity that exists in vivo, which limits maturation and makes integration with other circuits that control behaviour impossible. Here we show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. MRI reveals post-transplantation organoid growth across multiple stem cell lines and animals, whereas single-nucleus profiling shows progression of corticogenesis and the emergence of activity-dependent transcriptional programs. Indeed, transplanted cortical neurons display more complex morphological, synaptic and intrinsic membrane properties than their in vitro counterparts, which enables the discovery of defects in neurons derived from individuals with Timothy syndrome. Anatomical and functional tracings show that transplanted organoids receive thalamocortical and corticocortical inputs, and in vivo recordings of neural activity demonstrate that these inputs can produce sensory responses in human cells. Finally, cortical organoids extend axons throughout the rat brain and their optogenetic activation can drive reward-seeking behaviour. Thus, transplanted human cortical neurons mature and engage host circuits that control behaviour. We anticipate that this approach will be useful for detecting circuit-level phenotypes in patient-derived cells that cannot otherwise be uncovered.

  View details for DOI 10.1038/s41586-022-05277-w

  View details for PubMedID 36224417

• Cardiotoxicity drug screening based on whole-panel intracellular recording. Biosensors & bioelectronics Yang, Y., Liu, A., Tsai, C., Liu, C., Wu, J. C., Cui, B. 2022; 216: 114617

  Abstract

  Unintended binding of small-molecule drugs to ion channels affects electrophysiological properties of cardiomyocytes and potentially leads to arrhythmia and heart failure. The waveforms of intracellular action potentials reflect the coordinated activities of cardiac ion channels and serve as a reliable means for assessing drug toxicity, but the implementation is limited by the low throughput of patch clamp for intracellular recording measurements. In the last decade, several new technologies are being developed to address this challenge. We recently developed the nanocrown electrode array (NcEA) technology that allows robust, parallel, and long-duration recording of intracellular action potentials (iAPs). Here, we demonstrate that NcEAs allow comparison of iAP waveforms before and after drug treatment from the same cell. This self-referencing comparison not only shows distinct drug effects of sodium, potassium, and calcium blockers, but also reveals subtle differences among three subclasses of sodium channel blockers with sub-millisecond accuracy. Furthermore, self-referencing comparison unveils heterogeneous drug responses among different cells. In our study, whole-panel simultaneous intracellular recording can be reliably achieved with 94% success rate. The average duration of intracellular recording is 30min and some last longer than 2h. With its high reliability, long recording duration, and easy-to-use nature, NcEA would be useful for iAP-based preclinical drug screening.

  View details for DOI 10.1016/j.bios.2022.114617

  View details for PubMedID 36027802

• A tissue-like neurotransmitter sensor for the brain and gut. Nature Li, J., Liu, Y., Yuan, L., Zhang, B., Bishop, E. S., Wang, K., Tang, J., Zheng, Y., Xu, W., Niu, S., Beker, L., Li, T. L., Chen, G., Diyaolu, M., Thomas, A., Mottini, V., Tok, J. B., Dunn, J. C., Cui, B., Pașca, S. P., Cui, Y., Habtezion, A., Chen, X., Bao, Z. 2022; 606 (7912): 94-101

  Abstract

  Neurotransmitters play essential roles in regulating neural circuit dynamics both in the central nervous system as well as at the peripheral, including the gastrointestinal tract1-3. Their real-time monitoring will offer critical information for understanding neural function and diagnosing disease1-3. However, bioelectronic tools to monitor the dynamics of neurotransmitters in vivo, especially in the enteric nervous systems, are underdeveloped. This is mainly owing to the limited availability of biosensing tools that are capable of examining soft, complex and actively moving organs. Here we introduce a tissue-mimicking, stretchable, neurochemical biological interface termed NeuroString, which is prepared by laser patterning of a metal-complexed polyimide into an interconnected graphene/nanoparticle network embedded in an elastomer. NeuroString sensors allow chronic in vivo real-time, multichannel and multiplexed monoamine sensing in the brain of behaving mouse, as well as measuring serotonin dynamics in the gut without undesired stimulations and perturbing peristaltic movements. The described elastic and conformable biosensing interface has broad potential for studying the impact of neurotransmitters on gut microbes, brain-gut communication and may ultimately be extended to biomolecular sensing in other soft organs across the body.

  View details for DOI 10.1038/s41586-022-04615-2

  View details for PubMedID 35650358

• Expansion Microscopy for Imaging the Cell-Material Interface. ACS nano Nakamoto, M. L., Forro, C., Zhang, W., Tsai, C., Cui, B. 2022

  Abstract

  Surface topography on the scale of tens of nanometers to several micrometers substantially affects cell adhesion, migration, and differentiation. Recent studies using electron microscopy and super-resolution microscopy provide insight into how cells interact with surface nanotopography; however, the complex sample preparation and expensive imaging equipment required for these methods makes them not easily accessible. Expansion microscopy (ExM) is an affordable approach to image beyond the diffraction limit, but ExM cannot be readily applied to image the cell-material interface as most materials do not expand. Here, we develop a protocol that allows the use of ExM to resolve the cell-material interface with high resolution. We apply the technique to image the interface between U2OS cells and nanostructured substrates as well as the interface between primary osteoblasts with titanium dental implants. The high spatial resolution enabled by ExM reveals that although AP2 and F-actin both accumulate at curved membranes induced by vertical nanostructures, they are spatially segregated. Using ExM, we also reliably image how osteoblasts interact with roughened titanium implant surfaces below the diffraction limit; this is of great interest to understand osseointegration of the implants but has up to now been a significant technical challenge due to the irregular shape, the large volume, and the opacity of the titanium implants that have rendered them incompatible with other super-resolution techniques. We believe that our protocol will enable the use of ExM as a powerful tool for cell-material interface studies.

  View details for DOI 10.1021/acsnano.1c11015

  View details for PubMedID 35533401

• Nanocrown electrodes for parallel and robust intracellular recording of cardiomyocytes. Nature communications Jahed, Z., Yang, Y., Tsai, C., Foster, E. P., McGuire, A. F., Yang, H., Liu, A., Forro, C., Yan, Z., Jiang, X., Zhao, M., Zhang, W., Li, X., Li, T., Pawlosky, A., Wu, J. C., Cui, B. 2022; 13 (1): 2253

  Abstract

  Drug-induced cardiotoxicity arises primarily when a compound alters the electrophysiological properties of cardiomyocytes. Features of intracellular action potentials (iAPs) are powerful biomarkers that predict proarrhythmic risks. In the last decade, a number of vertical nanoelectrodes have been demonstrated to achieve parallel and minimally-invasive iAP recordings. However, the large variability in success rate and signal strength have hindered nanoelectrodes from being broadly adopted for proarrhythmia drug assessment. In this work, we develop vertically-aligned nanocrown electrodes that are mechanically robust and achieve>99% success rates in obtaining intracellular access through electroporation. We validate the accuracy of nanocrown electrode recordings by simultaneous patch clamp recording from the same cell. Finally, we demonstrate that nanocrown electrodes enable prolonged iAP recording for continual monitoring of the same cells upon the sequential addition of four incremental drug doses. Our technology development provides an advancement towards establishing an iAP screening assay for preclinical evaluation of drug-induced arrhythmogenicity.

  View details for DOI 10.1038/s41467-022-29726-2

  View details for PubMedID 35474069

• Pericyte-to-endothelial cell signaling via vitronectin-integrin regulates blood-CNS barrier. Neuron Ayloo, S., Lazo, C. G., Sun, S., Zhang, W., Cui, B., Gu, C. 2022

  Abstract

  Endothelial cells of blood vessels of the central nervous system (CNS) constitute blood-CNS barriers. Barrier properties are not intrinsic to these cells; rather they are induced and maintained by CNS microenvironment. Notably, the abluminal surfaces of CNS capillaries are ensheathed by pericytes and astrocytes. However, extrinsic factors from these perivascular cells that regulate barrier integrity are largely unknown. Here, we establish vitronectin, an extracellular matrix protein secreted by CNS pericytes, as a regulator of blood-CNS barrier function via interactions with its integrin receptor, alpha5, in endothelial cells. Genetic ablation of vitronectin or mutating vitronectin to prevent integrin binding, as well as endothelial-specific deletion of integrin alpha5, causes barrier leakage in mice. Furthermore, vitronectin-integrin alpha5 signaling maintains barrier integrity by actively inhibiting transcytosis in endothelial cells. These results demonstrate that signaling from perivascular cells to endothelial cells via ligand-receptor interactions is a key mechanism to regulate barrier permeability.

  View details for DOI 10.1016/j.neuron.2022.02.017

  View details for PubMedID 35294899

• Membrane curvature regulates the spatial distribution of bulky glycoproteins NATURE COMMUNICATIONS Lu, C., Pedram, K., Tsai, C., Jones IV, T., Li, X., Nakamoto, M. L., Bertozzi, C. R., Cui, B. 2022; 13

  View details for DOI 10.1038/s41467-022-30610-2

• Nanotechnology Enables Novel Modalities for Neuromodulation. Advanced materials (Deerfield Beach, Fla.) Yang, X., McGlynn, E., Das, R., Pasca, S. P., Cui, B., Heidari, H. 2021: e2103208

  Abstract

  Neuromodulation is of great importance both as a fundamental neuroscience research tool for analyzing and understanding the brain function, and as a therapeutic avenue for treating brain disorders. Here, an overview of conceptual and technical progress in developing neuromodulation strategies is provided, and it is suggested that recent advances in nanotechnology are enabling novel neuromodulation modalities with less invasiveness, improved biointerfaces, deeper penetration, and higher spatiotemporal precision. The use of nanotechnology and the employment of versatile nanomaterials and nanoscale devices with tailored physical properties have led to considerable research progress. To conclude, an outlook discussing current challenges and future directions for next-generation neuromodulation modalities is presented.

  View details for DOI 10.1002/adma.202103208

  View details for PubMedID 34668249

• Advancing models of neural development with biomaterials. Nature reviews. Neuroscience Roth, J. G., Huang, M. S., Li, T. L., Feig, V. R., Jiang, Y., Cui, B., Greely, H. T., Bao, Z., Pasca, S. P., Heilshorn, S. C. 2021

  Abstract

  Human pluripotent stem cells have emerged as a promising in vitro model system for studying the brain. Two-dimensional and three-dimensional cell culture paradigms have provided valuable insights into the pathogenesis of neuropsychiatric disorders, but they remain limited in their capacity to model certain features of human neural development. Specifically, current models do not efficiently incorporate extracellular matrix-derived biochemical and biophysical cues, facilitate multicellular spatio-temporal patterning, or achieve advanced functional maturation. Engineered biomaterials have the capacity to create increasingly biomimetic neural microenvironments, yet further refinement is needed before these approaches are widely implemented. This Review therefore highlights how continued progression and increased integration of engineered biomaterials may be well poised to address intractable challenges in recapitulating human neural development.

  View details for DOI 10.1038/s41583-021-00496-y

  View details for PubMedID 34376834

• Nanoscale Surface Topography Reduces Focal Adhesions and Cell Stiffness by Enhancing Integrin Endocytosis. Nano letters Li, X., Klausen, L. H., Zhang, W., Jahed, Z., Tsai, C., Li, T. L., Cui, B. 2021

  Abstract

  Both substrate stiffness and surface topography regulate cell behavior through mechanotransduction signaling pathways. Such intertwined effects suggest that engineered surface topographies might substitute or cancel the effects of substrate stiffness in biomedical applications. However, the mechanisms by which cells recognize topographical features are not fully understood. Here we demonstrate that the presence of nanotopography drastically alters cell behavior such that neurons and stem cells cultured on rigid glass substrates behave as if they were on soft hydrogels. With atomic force microscopy, we show that rigid nanotopography resembles the effects of soft hydrogels in reducing cell stiffness and membrane tension. Further, we reveal that nanotopography reduces focal adhesions and cell stiffness by enhancing the endocytosis and the subsequent removal of integrin receptors. This mechanistic understanding will support the rational design of nanotopography that directs cells on rigid materials to behave as if they were on soft ones.

  View details for DOI 10.1021/acs.nanolett.1c01934

  View details for PubMedID 34346220

• Light-inducible deformation of mitochondria in live cells. Cell chemical biology Song, Y., Huang, P., Liu, X., Zhao, Z., Wang, Y., Cui, B., Duan, L. 2021

  Abstract

  Mitochondria, the powerhouse of the cell, are dynamic organelles that undergo constant morphological changes. Increasing evidence indicates that mitochondria morphologies and functions can be modulated by mechanical cues. However, the mechano-sensing and -responding properties of mitochondria and the relation between mitochondrial morphologies and functions are unclear due to the lack of methods to precisely exert mechano-stimulation on and deform mitochondria inside live cells. Here, we present an optogenetic approach that uses light to induce deformation of mitochondria by recruiting molecular motors to the outer mitochondrial membrane via light-activated protein-protein hetero-dimerization. Mechanical forces generated by motor proteins distort the outer membrane, during which the inner mitochondrial membrane can also be deformed. Moreover, this optical method can achieve subcellular spatial precision and be combined with different optical dimerizers and molecular motors. This method presents a mitochondria-specific mechano-stimulator for studying mitochondria mechanobiology and the interplay between mitochondria shapes and functions.

  View details for DOI 10.1016/j.chembiol.2021.05.015

  View details for PubMedID 34157274

• New perspectives on the roles of nanoscale surface topography in modulating intracellular signaling. Current opinion in solid state & materials science Zhang, W., Yang, Y., Cui, B. 2021; 25 (1)

  Abstract

  The physical properties of biomaterials, such as elasticity, stiffness, and surface nanotopography, are mechanical cues that regulate a broad spectrum of cell behaviors, including migration, differentiation, proliferation, and reprogramming. Among them, nanoscale surface topography, i.e. nanotopography, defines the nanoscale shape and spatial arrangement of surface elements, which directly interact with the cell membranes and stimulate changes in the cell signaling pathways. In biological systems, the effects of nanotopography are often entangled with those of other mechanical and biochemical factors. Precise engineering of 2D nanopatterns and 3D nanostructures with well-defined features has provided a powerful means to study the cellular responses to specific topographic features. In this Review, we discuss efforts in the last three years to understand how nanotopography affects membrane receptor activation, curvature-induced cell signaling, and stem cell differentiation.

  View details for DOI 10.1016/j.cossms.2020.100873

  View details for PubMedID 33364912

• Optical Electrophysiology: Toward the Goal of Label-Free Voltage Imaging. Journal of the American Chemical Society Zhou, Y., Liu, E., Müller, H., Cui, B. 2021

  Abstract

  Measuring and monitoring the electrical signals transmitted between neurons is key to understanding the communication between neurons that underlies human perception, information processing, and decision-making. While electrode-based electrophysiology has been the gold standard, optical electrophysiology has opened up a new area in the past decade. Voltage-dependent fluorescent reporters enable voltage imaging with high spatial resolution and flexibility to choose recording locations. However, they exhibit photobleaching as well as phototoxicity and may perturb the physiology of the cell. Label-free optical electrophysiology seeks to overcome these hurdles by detecting electrical activities optically, without the incorporation of exogenous fluorophores in cells. For example, electrochromic optical recording detects neuroelectrical signals via a voltage-dependent color change of extracellular materials, and interferometric optical recording monitors membrane deformations that accompany electrical activities. Label-free optical electrophysiology, however, is in an early stage, and often has limited sensitivity and temporal resolution. In this Perspective, we review the recent progress to overcome these hurdles. We hope this Perspective will inspire developments of label-free optical electrophysiology techniques with high recording sensitivity and temporal resolution in the near future.

  View details for DOI 10.1021/jacs.1c02960

  View details for PubMedID 34191488

• Graphene Electric Field Sensor Enables Single Shot Label-Free Imaging of Bioelectric Potentials. Nano letters Balch, H. B., McGuire, A. F., Horng, J., Tsai, H. Z., Qi, K. K., Duh, Y. S., Forrester, P. R., Crommie, M. F., Cui, B., Wang, F. 2021

  Abstract

  The measurement of electrical activity across systems of excitable cells underlies current progress in neuroscience, cardiac pharmacology, and neurotechnology. However, bioelectricity spans orders of magnitude in intensity, space, and time, posing substantial technological challenges. The development of methods permitting network-scale recordings with high spatial resolution remains key to studies of electrogenic cells, emergent networks, and bioelectric computation. Here, we demonstrate single-shot and label-free imaging of extracellular potentials with high resolution across a wide field-of-view. The critically coupled waveguide-amplified graphene electric field (CAGE) sensor leverages the field-sensitive optical transitions in graphene to convert electric potentials into the optical regime. As a proof-of-concept, we use the CAGE sensor to detect native electrical activity from cardiac action potentials with tens-of-microns resolution, simultaneously map the propagation of these potentials at tissue-scale, and monitor their modification by pharmacological agents. This platform is robust, scalable, and compatible with existing microscopy techniques for multimodal correlative imaging.

  View details for DOI 10.1021/acs.nanolett.1c00543

  View details for PubMedID 34102057

• Exploring Cell Surface-Nanopillar Interactions with 3D Super-Resolution Microscopy. ACS nano Roy, A. R., Zhang, W., Jahed, Z., Tsai, C. T., Cui, B., Moerner, W. E. 2021

  Abstract

  Plasma membrane topography has been shown to strongly influence the behavior of many cellular processes such as clathrin-mediated endocytosis, actin rearrangements, and others. Recent studies have used three-dimensional (3D) nanostructures such as nanopillars to imprint well-defined membrane curvatures (the "nano-bio interface"). In these studies, proteins and their interactions were probed by two-dimensional fluorescence microscopy. However, the low resolution and limited axial detail of such methods are not optimal to determine the relative spatial position and distribution of proteins along a 100 nm-diameter object, which is below the optical diffraction limit. Here, we introduce a general method to explore the nanoscale distribution of proteins at the nano-bio interface with 10-20 nm precision using 3D single-molecule super-resolution (SR) localization microscopy. This is achieved by combining a silicone-oil immersion objective and 3D double-helix point spread function microscopy. We carefully adjust the objective to minimize spherical aberrations between quartz nanopillars and the cell. To validate the 3D SR method, we imaged the 3D shape of surface-labeled nanopillars and compared the results with electron microscopy measurements. Turning to transmembrane-anchored labels in cells, the high quality 3D SR reconstructions reveal the membrane tightly wrapping around the nanopillars. Interestingly, the cytoplasmic protein AP-2 involved in clathrin-mediated endocytosis accumulates along the nanopillar above a specific threshold of 1/R (the reciprocal of the radius) membrane curvature. Finally, we observe that AP-2 and actin preferentially accumulate at positive Gaussian curvature near the pillar caps. Our results establish a general method to investigate the nanoscale distribution of proteins at the nano-bio interface using 3D SR microscopy.

  View details for DOI 10.1021/acsnano.1c05313

  View details for PubMedID 34582687

• Towards biomimetic electronics that emulate cells MRS COMMUNICATIONS Lubrano, C., Matrone, G., Forro, C., Jahed, Z., Offenhaeusser, A., Salleo, A., Cui, B., Santoro, F. 2020; 10 (3): 398–412

  View details for DOI 10.1557/mrc.2020.56

  View details for Web of Science ID 000568782800004

• A hierarchically ordered compacted coil scaffold for tissue regeneration NPG ASIA MATERIALS Su, Y., Zhang, Z., Wan, Y., Zhang, Y., Wang, Z., Klausen, L., Huang, P., Dong, M., Han, X., Cui, B., Chen, M. 2020; 12 (1)

  View details for DOI 10.1038/s41427-020-0234-7

  View details for Web of Science ID 000566899500002

• Nanobar Array Assay Revealed Complementary Roles of BIN1 Splice Isoforms in Cardiac T-Tubule Morphogenesis. Nano letters Li, L., Guo, Q., Lou, H., Liang, J., Yang, Y., Xing, X., Li, H., Han, J., Shen, S., Li, H., Ye, H., Di Wu, H., Cui, B., Wang, S. 2020

  Abstract

  Bridging integrator-1 (BIN1) is a family of banana-shaped molecules implicated in cell membrane tubulation. To understand the curvature sensitivity and functional roles of BIN1 splicing isoforms, we engineered vertical nanobars on a cell culture substrate to create high and low curvatures. When expressed individually, BIN1 isoforms with phosphoinositide-binding motifs (pBIN1) appeared preferentially at high-curvature nanobar ends, agreeing well with their membrane tubulation in cardiomyocytes. In contrast, the ubiquitous BIN1 isoform without phosphoinositide-binding motif (uBIN1) exhibited no affinity to membranes around nanobars but accumulated along Z-lines in cardiomyocytes. Importantly, in pBIN1-uBIN1 coexpression, pBIN1 recruited uBIN1 to high-curvature membranes at nanobar ends, and uBIN1 attached the otherwise messy pBIN1 tubules to Z-lines. The complementary cooperation of BIN1 isoforms (comboBIN1) represents a novel mechanism of T-tubule formation along Z-lines in cardiomyocytes. Dysregulation of BIN1 splicing, e.g., during myocardial infarction, underlied T-tubule disorganization, and correction of uBIN1/pBIN1 stoichiometry rescued T-tubule morphology in heart disease.

  View details for DOI 10.1021/acs.nanolett.0c01957

  View details for PubMedID 32787151

• NOTCH1 is Essential for Ventricular Cardiomyocyte Differentiation of Human Induced Pluripotent Stem Cells Zhao, M., Ye, S., Zhang, J., Shao, N., Liu, C., Zhou, Y., Nishiga, M., Yang, Y., Cui, B., Garg, V., Wu, J. C. LIPPINCOTT WILLIAMS & WILKINS. 2020

  View details for DOI 10.1161/res.127.suppl_1.276

  View details for Web of Science ID 000606541500061

• Production and Isolation of Magnetic Protein Crystals in HEK293T Cells. Bio-protocol Li, T. L., Cui, B. 2020; 10 (14): e3684

  Abstract

  Advances in protein engineering have enabled the production of self-assembled protein crystals within living cells. Our recent publication demonstrates the production of ftn-PAK4, which is a ferritin-containing crystal that can mineralize iron and become magnetic when isolated. We have developed an optimized protocol for the production and isolation of PAK4-based crystals. The crystals are first grown in low-passage HEK293T cells, released using a lysis buffer containing NP-40 and DNase, and collected under careful centrifugation conditions. Our protocol maximizes the purity and yield of crystals and is quick and straightforward.

  View details for DOI 10.21769/BioProtoc.3684

  View details for PubMedID 33659355

  View details for PubMedCentralID PMC7842723

• Production and Isolation of Magnetic Protein Crystals in HEK293T Cells BIO-PROTOCOL Li, T. L., Cui, B. 2020; 10 (14)

  View details for DOI 10.21769/BioProtoc.3684

  View details for Web of Science ID 000583370100007

• Label-free optical detection of bioelectric potentials using electrochromic thin films. Proceedings of the National Academy of Sciences of the United States of America Alfonso, F. S., Zhou, Y., Liu, E., McGuire, A. F., Yang, Y., Kantarci, H., Li, D., Copenhaver, E., Zuchero, J. B., Muller, H., Cui, B. 2020

  Abstract

  Understanding how a network of interconnected neurons receives, stores, and processes information in the human brain is one of the outstanding scientific challenges of our time. The ability to reliably detect neuroelectric activities is essential to addressing this challenge. Optical recording using voltage-sensitive fluorescent probes has provided unprecedented flexibility for choosing regions of interest in recording neuronal activities. However, when recording at a high frame rate such as 500 to 1,000 Hz, fluorescence-based voltage sensors often suffer from photobleaching and phototoxicity, which limit the recording duration. Here, we report an approach called electrochromic optical recording (ECORE) that achieves label-free optical recording of spontaneous neuroelectrical activities. ECORE utilizes the electrochromism of poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) thin films, whose optical absorption can be modulated by an applied voltage. Being based on optical reflection instead of fluorescence, ECORE offers the flexibility of an optical probe without suffering from photobleaching or phototoxicity. Using ECORE, we optically recorded spontaneous action potentials in cardiomyocytes, cultured hippocampal and dorsal root ganglion neurons, and brain slices. With minimal perturbation to cells, ECORE allows long-term optical recording over multiple days.

  View details for DOI 10.1073/pnas.2002352117

  View details for PubMedID 32632007

• Optical Activation of TrkB Signaling. Journal of molecular biology Huang, P., Liu, A., Song, Y., Hope, J. M., Cui, B., Duan, L. 2020

  Abstract

  Brain-derived neurotrophic factor (BDNF), via activation of tropomyosin receptor kinase B (TrkB), plays a critical role in neuronal proliferation, differentiation, survival, and death. Dysregulation of TrkB signaling is implicated in neurodegenerative disorders and cancers. Precise activation of TrkB signaling with spatial and temporal resolution is greatly desired to study the dynamic nature of TrkB signaling and its role in related diseases. Here we develop different optogenetic approaches that use light to activate TrkB signaling. Utilizing the photosensitive protein Arabidopsis thaliana cryptochrome 2 (CRY2), the light-inducible homo-interaction of the intracellular domain of TrkB (iTrkB) in the cytosol or on the plasma membrane is able to induce the activation of downstream MAPK/ERK and PI3K/Akt signaling as well as the neurite outgrowth of PC12 cells. Moreover, we prove that such strategies are generalizable to other optical homo-dimerizers by demonstrating the optical TrkB activation based on the light-oxygen-voltage domain of aureochrome 1 from Vaucheria frigida. The results open up new possibilities of many other optical platforms to activate TrkB signaling to fulfill customized needs. By comparing all the different strategies, we find that the CRY2-integrated approach to achieve light-induced cell membrane recruitment and homo-interaction of iTrkB is most efficient in activating TrkB signaling. The optogenetic strategies presented are promising tools to investigate BDNF/TrkB signaling with tight spatial and temporal control.

  View details for DOI 10.1016/j.jmb.2020.05.002

  View details for PubMedID 32422149

• Construction of Light-Activated Neurotrophin Receptors Using the Improved Light-Induced Dimerizer (iLID). Journal of molecular biology Hope, J. M., Liu, A., Calvin, G. J., Cui, B. 2020

  Abstract

  Receptor tyrosine kinases (RTKs) play crucial roles in human health, and their misregulation is implicated in disorders ranging from neurodegenerative diseases to cancers. The highly conserved mechanism of activation of RTKs makes them especially appealing candidates for control via optogenetic dimerization methods. This work offers a strategy for using the improved Light-Induced Dimer (iLID) system with a constructed tandem-dimer of its binding partner nano (tdnano) to build light-activatable versions of RTKs. In the absence of light, the iLID-RTK is cytosolic, monomeric and inactive. Under blue light, the iLID + tdnano system recruits two copies of iLID-RTK to tdnano, dimerizing and activating the RTK. We demonstrate that iLID opto-iTrkA and opto-iTrkB are capable of reproducing downstream ERK and Akt signaling only in the presence of tdnano. We further show with our opto-iTrkA that the system is compatible with multi-day and population-level activation of TrkA in PC12 cells. By leveraging genetic targeting of tdnano, we achieve RTK activation at a specific subcellular location even with whole-cell illumination, allowing us to confidently probe the impact of context on signaling outcome.

  View details for DOI 10.1016/j.jmb.2020.04.018

  View details for PubMedID 32335036

• Light-Inducible Generation of Membrane Curvature in Live Cells with Engineered BAR Domain Proteins. ACS synthetic biology Jones, T. n., Liu, A. n., Cui, B. n. 2020

  Abstract

  Nanoscale membrane curvature is now understood to play an active role in essential cellular processes such as endocytosis, exocytosis, and actin dynamics. Previous studies have shown that membrane curvature can directly affect protein function and intracellular signaling. However, few methods are able to precisely manipulate membrane curvature in live cells. Here, we report the development of a new method of generating nanoscale membrane curvature in live cells that is controllable, reversible, and capable of precise spatial and temporal manipulation. For this purpose, we make use of Bin/Amphiphysin/Rvs (BAR) domain proteins, a family of well-studied membrane-remodeling and membrane-sculpting proteins. Specifically, we engineered two optogenetic systems, opto-FBAR and opto-IBAR, that allow light-inducible formation of positive and negative membrane curvature, respectively. Using opto-FBAR, blue light activation results in the formation of tubular membrane invaginations (positive curvature), controllable down to the subcellular level. Using opto-IBAR, blue light illumination results in the formation of membrane protrusions or filopodia (negative curvature). These systems present a novel approach for light-inducible manipulation of nanoscale membrane curvature in live cells.

  View details for DOI 10.1021/acssynbio.9b00516

  View details for PubMedID 32212723

• Dynamic Manipulation of Cell Membrane Curvature by Light-Driven Reshaping of Azopolymer. Nano letters De Martino, S., Zhang, W., Klausen, L., Lou, H., Li, X., Alfonso, F. S., Cavalli, S., Netti, P. A., Santoro, F., Cui, B. 2019

  Abstract

  Local curvatures on the cell membrane serve as signaling hubs that promote curvature-dependent protein interactions and modulate a variety of cellular processes including endocytosis, exocytosis, and the actin cytoskeleton. However, precisely controlling the location and the degree of membrane curvature in live cells has not been possible until recently, where studies show that nanofabricated vertical structures on a substrate can imprint their shapes on the cell membrane to induce well-defined curvatures in adherent cells. Nevertheless, the intrinsic static nature of these engineered nanostructures prevents dynamic modulation of membrane curvatures. In this work, we engineer light-responsive polymer structures whose shape can be dynamically modulated by light and thus change the induced-membrane curvatures on-demand. Specifically, we fabricate three-dimensional azobenzene-based polymer structures that change from a vertical pillar to an elongated vertical bar shape upon green light illumination. We observe that U2OS cells cultured on azopolymer nanostructures rapidly respond to the topographical change of the substrate underneath. The dynamically induced high membrane curvatures at bar ends promote local accumulation of actin fibers and actin nucleator Arp2/3 complex. The ability to dynamically manipulate the membrane curvature and analyze protein response in real-time provides a new way to study curvature-dependent processes in live cells.

  View details for DOI 10.1021/acs.nanolett.9b04307

  View details for PubMedID 31846332

• Engineering a Genetically Encoded Magnetic Protein Crystal. Nano letters Li, T. L., Wang, Z., You, H., Ong, Q., Varanasi, V. J., Dong, M., Lu, B., Pasca, S. P., Cui, B. 2019

  Abstract

  Magnetogenetics is a new field that leverages genetically encoded proteins and protein assemblies that are sensitive to magnetic fields to study and manipulate cell behavior. Theoretical studies show that many proposed magnetogenetic proteins do not contain enough iron to generate substantial magnetic forces. Here, we have engineered a genetically encoded ferritin-containing protein crystal that grows inside mammalian cells. Each of these crystals contains more than 10 million ferritin subunits and is capable of mineralizing substantial amounts of iron. When isolated from cells and loaded with iron in vitro, these crystals generate magnetic forces that are 9 orders of magnitude larger than the forces fromthe single ferritin cages used in previous studies. These protein crystals are attracted to an applied magnetic field and move toward magnets even when internalized into cells. While additional studies are needed to realize the full potential of magnetogenetics, these results demonstrate the feasibility of engineering protein assemblies for magnetic sensing.

  View details for DOI 10.1021/acs.nanolett.9b02266

  View details for PubMedID 31552740

• A nanostructure platform for live-cell manipulation of membrane curvature. Nature protocols Li, X., Matino, L., Zhang, W., Klausen, L., McGuire, A. F., Lubrano, C., Zhao, W., Santoro, F., Cui, B. 2019

  Abstract

  Membrane curvatures are involved in essential cellular processes, such as endocytosis and exocytosis, in which they are believed to act as microdomains for protein interactions and intracellular signaling. These membrane curvatures appear and disappear dynamically, and their locations are difficult or impossible to predict. In addition, the size of these curvatures is usually below the diffraction limit of visible light, making it impossible to resolve their values using live-cell imaging. Therefore, precise manipulation of membrane curvature is important to understanding how membrane curvature is involved in intracellular processes. Recent studies show that membrane curvatures can be induced by surface topography when cells are in direct contact with engineered substrates. Here, we present detailed procedures for using nanoscale structures to manipulate membrane curvatures and probe curvature-induced phenomena in live cells. We first describe detailed procedures for the design of nanoscale structures and their fabrication using electron-beam (E-beam) lithography. The fabrication process takes 2 d, but the resultant chips can be cleaned and reused repeatedly over the course of 2 years. Then we describe how to use these nanostructures to manipulate local membrane curvatures and probe intracellular protein responses, discussing surface coating, cell plating, and fluorescence imaging in detail. Finally, we describe a procedure to characterize the nanostructure-cell membrane interface using focused ion beam and scanning electron microscopy (FIB-SEM). Nanotopography-based methods can induce stable membrane curvatures with well-defined curvature values and locations in live cells, which enables the generation of a library of curvatures for probing curvature-related intracellular processes.

  View details for DOI 10.1038/s41596-019-0161-7

  View details for PubMedID 31101905

• Electron Microscopy for 3D Scaffolds-Cell Biointerface Characterization ADVANCED BIOSYSTEMS Iandolo, D., Pennacchio, F. A., Mollo, V., Rossi, D., Dannhauser, D., Cui, B., Owens, R. M., Santoro, F. 2019; 3 (2)

  View details for DOI 10.1002/adbi.201800103

  View details for Web of Science ID 000458425000004

• Electron Microscopy for 3D Scaffolds-Cell Biointerface Characterization. Advanced biosystems Iandolo, D., Pennacchio, F. A., Mollo, V., Rossi, D., Dannhauser, D., Cui, B., Owens, R. M., Santoro, F. 2019; 3 (2): e1800103

  Abstract

  Cell fate is largely determined by interactions that occur at the interface between cells and their surrounding microenvironment. For this reason, especially in the field of tissue-engineering, there is a growing interest in developing techniques that allow evaluating cell-material interaction at the nanoscale, particularly focusing on cell adhesion processes. While for 2D culturing systems a consolidated series of tools already satisfy this need, in 3D environments, more closely recapitulating complex in vivo structures, there is still a lack of procedures furthering the comprehension of cell-material interactions. Here, the use of scanning electron microscopy coupled with a focused ion beam (SEM/FIB) for the characterization of cell interactions with 3D scaffolds obtained by different fabrication techniques is reported for the first time. The results clearly show the capability of the developed approach to preserve and finely resolve scaffold-cell interfaces highlighting details such as plasma membrane arrangement, extracellular matrix architecture and composition, and cellular structures playing a role in cell adhesion to the surface. It is anticipated that the developed approach will be relevant for the design of efficient cell-instructive platforms in the study of cellular guidance strategies for tissue-engineering applications as well as for in vitro 3D models.

  View details for DOI 10.1002/adbi.201800103

  View details for PubMedID 32627375

• Membrane curvature underlies actin reorganization in response to nanoscale surface topography. Proceedings of the National Academy of Sciences of the United States of America Lou, H. Y., Zhao, W. n., Li, X. n., Duan, L. n., Powers, A. n., Akamatsu, M. n., Santoro, F. n., McGuire, A. F., Cui, Y. n., Drubin, D. G., Cui, B. n. 2019

  Abstract

  Surface topography profoundly influences cell adhesion, differentiation, and stem cell fate control. Numerous studies using a variety of materials demonstrate that nanoscale topographies change the intracellular organization of actin cytoskeleton and therefore a broad range of cellular dynamics in live cells. However, the underlying molecular mechanism is not well understood, leaving why actin cytoskeleton responds to topographical features unexplained and therefore preventing researchers from predicting optimal topographic features for desired cell behavior. Here we demonstrate that topography-induced membrane curvature plays a crucial role in modulating intracellular actin organization. By inducing precisely controlled membrane curvatures using engineered vertical nanostructures as topographies, we find that actin fibers form at the sites of nanostructures in a curvature-dependent manner with an upper limit for the diameter of curvature at ∼400 nm. Nanotopography-induced actin fibers are branched actin nucleated by the Arp2/3 complex and are mediated by a curvature-sensing protein FBP17. Our study reveals that the formation of nanotopography-induced actin fibers drastically reduces the amount of stress fibers and mature focal adhesions to result in the reorganization of actin cytoskeleton in the entire cell. These findings establish the membrane curvature as a key linkage between surface topography and topography-induced cell signaling and behavior.

  View details for DOI 10.1073/pnas.1910166116

  View details for PubMedID 31591250

• Soft conductive micropillar electrode arrays for biologically relevant electrophysiological recording PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Liu, Y., McGuire, A. F., Lou, H., Li, T. L., Tok, J. H., Cui, B., Bao, Z. 2018; 115 (46): 11718–23

  View details for DOI 10.1073/pnas.1810827115

  View details for Web of Science ID 000449934400036

• Cells Adhering to 3D Vertical Nanostructures: Cell Membrane Reshaping without Stable Internalization NANO LETTERS Dipalo, M., McGuire, A. F., Lou, H., Caprettini, V., Melle, G., Bruno, G., Lubrano, C., Matino, L., Li, X., De Angelis, F., Cui, B., Santoro, F. 2018; 18 (9): 6100–6105

  Abstract

  The dynamic interface between the cellular membrane and 3D nanostructures determines biological processes and guides the design of novel biomedical devices. Despite the fact that recent advancements in the fabrication of artificial biointerfaces have yielded an enhanced understanding of this interface, there remain open questions on how the cellular membrane reacts and behaves in the presence of sharp objects on the nanoscale. Here we provide a multifaceted characterization of the cellular membrane's mechanical stability when closely interacting with high-aspect-ratio 3D vertical nanostructures, providing strong evidence that vertical nanostructures spontaneously penetrate the cellular membrane to form a steady intracellular coupling only in rare cases and under specific conditions. The cell membrane is able to conform tightly over the majority of structures with various shapes while maintaining its integrity.

  View details for PubMedID 30091365

• The ambipolar transport behavior of WSe2 transistors and its analogue circuits NPG ASIA MATERIALS Wang, Z., Li, Q., Chen, Y., Cui, B., Li, Y., Besenbacher, F., Dong, M. 2018; 10: 703–12

  View details for DOI 10.1038/s41427-018-0062-1

  View details for Web of Science ID 000447953700002

• Optical Activation of TrkA Signaling. ACS synthetic biology Duan, L., Hope, J. M., Guo, S., Ong, Q., Francois, A., Kaplan, L., Scherrer, G., Cui, B. 2018

  Abstract

  Nerve growth factor/tropomyosin receptor kinase A (NGF/TrkA) signaling plays a key role in neuronal development, function, survival, and growth. The pathway is implicated in neurodegenerative disorders including Alzheimer's disease, chronic pain, inflammation, and cancer. NGF binds the extracellular domain of TrkA, leading to the activation of the receptor's intracellular kinase domain. As TrkA signaling is highly dynamic, mechanistic studies would benefit from a tool with high spatial and temporal resolution. Here we present the design and evaluation of four strategies for light-inducible activation of TrkA in the absence of NGF. Our strategies involve the light-sensitive protein Arabidopsis cryptochrome 2 and its binding partner CIB1. We demonstrate successful recapitulation of native NGF/TrkA functions by optical induction of plasma membrane recruitment and homo-interaction of the intracellular domain of TrkA. This approach activates PI3K/AKT and Raf/ERK signaling pathways, promotes neurite growth in PC12 cells, and supports survival of dorsal root ganglion neurons in the absence of NGF. This ability to activate TrkA using light bestows high spatial and temporal resolution for investigating NGF/TrkA signaling.

  View details for PubMedID 29975841

• Dynamic Clustering of Dyneins on Axonal Endosomes: Evidence from High-Speed Darkfield Imaging. Biophysical journal Chowdary, P. D., Kaplan, L., Che, D. L., Cui, B. 2018

  Abstract

  One of the fundamental features that govern the cooperativity of multiple dyneins during cargo trafficking in cells is the spatial distribution of these dyneins on the cargo. Geometric considerations and recent experiments indicate that clustered distributions of dyneins are required for effective cooperation on micron-sized cargos. However, very little is known about the spatial distribution of dyneins and their cooperativity on smaller cargos, such as vesicles or endosomes <200nm in size, which are not amenable to conventional immunostaining and optical trapping methods. In this work, we present evidence that dyneins can dynamically be clustered on endosomes in response to load. Using a darkfield imaging assay, we measured the repeated stalls and detachments of retrograde axonal endosomes under load with <10nm localization accuracy at imaging rates up to 1kHz for over a timescale of minutes. A three-dimensional stochastic model was used to simulate the endosome motility under load to gain insights on the mechanochemical properties and spatial distribution of dyneins on axonal endosomes. Our results indicate that 1) the distribution of dyneins on endosomes is fluid enough to support dynamic clustering under load and 2) the detachment kinetics of dynein on endosomes differs significantly from the invitro measurements possibly due to an increase in the unitary stall force of dynein on endosomes.

  View details for PubMedID 29933888

• Constructing Highly Uniform Onion-Ring-like Graphitic Carbon Nitride for Efficient Visible-Light-Driven Photocatalytic Hydrogen Evolution ACS NANO Cui, L., Song, J., McGuire, A. F., Kang, S., Fang, X., Wang, J., Yin, C., Li, X., Wang, Y., Cui, B. 2018; 12 (6): 5551–58

  Abstract

  The introduction of microstructure to the metal-free graphitic carbon nitride (g-C3N4) photocatalyst holds promise in enhancing its catalytic performance. However, producing such microstructured g-C3N4 remains technically challenging due to a complicated synthetic process and high cost. In this study, we develop a facile and in-air chemical vapor deposition (CVD) method that produces onion-ring-like g-C3N4 microstructures in a simple, reliable, and economical manner. This method involves the use of randomly packed 350 nm SiO2 microspheres as a hard template and melamine as a CVD precursor for the deposition of a thin layer of g-C3N4 in the narrow space between the SiO2 microspheres. After dissolution of the microsphere template, the resultant g-C3N4 exhibits uniquely uniform onion-ring-like microstructures. Unlike previously reported g-C3N4 powder morphologies that show various degrees of agglomeration and irregularity, the onion-ring-like g-C3N4 is highly dispersed and uniform. The calculated band gap for onion-ring-like g-C3N4 is 2.58 eV, which is significantly narrower than that of bulk g-C3N4 at 2.70 eV. Experimental characterization and testing suggest that, in comparison with bulk g-C3N4, onion-ring-like g-C3N4 facilitates charge separation, extends the lifetime of photoinduced carriers, exhibits 5-fold higher photocatalytic hydrogen evolution, and shows great potential for photocatalytic applications.

  View details for PubMedID 29863842

• The Role of Membrane Curvature in Nanoscale Topography-Induced Intracellular Signaling ACCOUNTS OF CHEMICAL RESEARCH Lou, H., Zhao, W., Zeng, Y., Cui, B. 2018; 51 (5): 1046–53

  Abstract

  Over the past decade, there has been growing interest in developing biosensors and devices with nanoscale and vertical topography. Vertical nanostructures induce spontaneous cell engulfment, which enhances the cell-probe coupling efficiency and the sensitivity of biosensors. Although local membranes in contact with the nanostructures are found to be fully fluidic for lipid and membrane protein diffusions, cells appear to actively sense and respond to the surface topography presented by vertical nanostructures. For future development of biodevices, it is important to understand how cells interact with these nanostructures and how their presence modulates cellular function and activities. How cells recognize nanoscale surface topography has been an area of active research for two decades before the recent biosensor works. Extensive studies show that surface topographies in the range of tens to hundreds of nanometers can significantly affect cell functions, behaviors, and ultimately the cell fate. For example, titanium implants having rough surfaces are better for osteoblast attachment and host-implant integration than those with smooth surfaces. At the cellular level, nanoscale surface topography has been shown by a large number of studies to modulate cell attachment, activity, and differentiation. However, a mechanistic understanding of how cells interact and respond to nanoscale topographic features is still lacking. In this Account, we focus on some recent studies that support a new mechanism that local membrane curvature induced by nanoscale topography directly acts as a biochemical signal to induce intracellular signaling, which we refer to as the curvature hypothesis. The curvature hypothesis proposes that some intracellular proteins can recognize membrane curvatures of a certain range at the cell-to-material interface. These proteins then recruit and activate downstream components to modulate cell signaling and behavior. We discuss current technologies allowing the visualization of membrane deformation at the cell membrane-to-substrate interface with nanometer precision and demonstrate that vertical nanostructures induce local curvatures on the plasma membrane. These local curvatures enhance the process of clathrin-mediated endocytosis and affect actin dynamics. We also present evidence that vertical nanostructures can induce significant deformation of the nuclear membrane, which can affect chromatin distribution and gene expression. Finally, we provide a brief perspective on the curvature hypothesis and the challenges and opportunities for the design of nanotopography for manipulating cell behavior.

  View details for PubMedID 29648779

• Swedish Nerve Growth Factor Mutation (NGF(R100W)) Defines a Role for TrkA and p75(NTR) in Nociception JOURNAL OF NEUROSCIENCE Sung, K., Ferrari, L. F., Yang, W., Chung, C., Zhao, X., Gu, Y., Lin, S., Zhang, K., Cui, B., Pearn, M. L., Maloney, M. T., Mobley, W. C., Levine, J. D., Wu, C. 2018; 38 (14): 3394–3413

  Abstract

  Nerve growth factor (NGF) exerts multiple functions on target neurons throughout development. The recent discovery of a point mutation leading to a change from arginine to tryptophan at residue 100 in the mature NGFβ sequence (NGFR100W) in patients with hereditary sensory and autonomic neuropathy type V (HSAN V) made it possible to distinguish the signaling mechanisms that lead to two functionally different outcomes of NGF: trophic versus nociceptive. We performed extensive biochemical, cellular, and live-imaging experiments to examine the binding and signaling properties of NGFR100W Our results show that, similar to the wild-type NGF (wtNGF), the naturally occurring NGFR100W mutant was capable of binding to and activating the TrkA receptor and its downstream signaling pathways to support neuronal survival and differentiation. However, NGFR100W failed to bind and stimulate the 75 kDa neurotrophic factor receptor (p75NTR)-mediated signaling cascades (i.e., the RhoA-Cofilin pathway). Intraplantar injection of NGFR100W into adult rats induced neither TrkA-mediated thermal nor mechanical acute hyperalgesia, but retained the ability to induce chronic hyperalgesia based on agonism for TrkA signaling. Together, our studies provide evidence that NGFR100W retains trophic support capability through TrkA and one aspect of its nociceptive signaling, but fails to engage p75NTR signaling pathways. Our findings suggest that wtNGF acts via TrkA to regulate the delayed priming of nociceptive responses. The integration of both TrkA and p75NTR signaling thus appears to regulate neuroplastic effects of NGF in peripheral nociception.SIGNIFICANCE STATEMENT In the present study, we characterized the naturally occurring nerve growth factor NGFR100W mutant that is associated with hereditary sensory and autonomic neuropathy type V. We have demonstrated for the first time that NGFR100W retains trophic support capability through TrkA, but fails to engage p75NTR signaling pathways. Furthermore, after intraplantar injection into adult rats, NGFR100W induced neither thermal nor mechanical acute hyperalgesia, but retained the ability to induce chronic hyperalgesia. We have also provided evidence that the integration of both TrkA- and p75NTR-mediated signaling appears to regulate neuroplastic effects of NGF in peripheral nociception. Our study with NGFR100W suggests that it is possible to uncouple trophic effect from nociceptive function, both induced by wild-type NGF.

  View details for PubMedID 29483280

• Interfacing Cells with Vertical Nanoscale Devices: Applications and Characterization. Annual review of analytical chemistry (Palo Alto, Calif.) McGuire, A. F., Santoro, F. n., Cui, B. n. 2018

  Abstract

  Measurements of the intracellular state of mammalian cells often require probes or molecules to breach the tightly regulated cell membrane. Mammalian cells have been shown to grow well on vertical nanoscale structures in vitro, going out of their way to reach and tightly wrap the structures. A great deal of research has taken advantage of this interaction to bring probes close to the interface or deliver molecules with increased efficiency or ease. In turn, techniques have been developed to characterize this interface. Here, we endeavor to survey this research with an emphasis on the interface as driven by cellular mechanisms. Expected final online publication date for the Annual Review of Analytical Chemistry Volume 11 is June 12, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  View details for PubMedID 29570360

• Neurospheres on Patterned PEDOT:PSS Microelectrode Arrays Enhance Electrophysiology Recordings ADVANCED BIOSYSTEMS Pas, J., Pitsalidis, C., Koutsouras, D. A., Quilichini, P. P., Santoro, F., Cui, B., Gallais, L., O'Connor, R. P., Malliaras, G. G., Owens, R. M. 2018; 2 (1)

  View details for DOI 10.1002/adbi.201700164

  View details for Web of Science ID 000446966000008

• Rotation of endosomes demonstrates coordination of molecular motors during axonal transport. Science advances Kaplan, L. n., Ierokomos, A. n., Chowdary, P. n., Bryant, Z. n., Cui, B. n. 2018; 4 (3): e1602170

  Abstract

  Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors.

  View details for PubMedID 29536037

  View details for PubMedCentralID PMC5846296

• Visible-Light Neural Stimulation on Graphitic-Carbon Nitride/Graphene Photocatalytic Fibers. ACS applied materials & interfaces Zhang, Z., Xu, R., Wang, Z., Dong, M., Cui, B., Chen, M. 2017; 9 (40): 34736-34743

  Abstract

  Light stimulation allows remote and spatiotemporally accurate operation that has been applied as effective, noninvasive means of therapeutic interventions. Here, visible-light neural stimulation of graphitic carbon nitride (g-C3N4), an emerging photocatalyst with visible-light optoelectronic conversion, was for the first time investigated. Specifically, g-C3N4 was combined with graphene oxide (GO) in a three-dimensional manner on the surfaces of electrospun polycaprolactone/gelatin (PG) fibers and functioned as a biocompatible interface for visible-light stimulating neuronal differentiation. The enhanced photocatalytic function of g-C3N4 was realized by spreading g-C3N4 on GO coated electrospun (PG) microfibers to improve both charge separation and surface area. Ascorbic acid (AA) was used in the cell culture medium not only as a photoexcited hole scavenger but also as a mediator of GO reduction to further improve the electrical conductivity. The successful coatings of g-C3N4, GO, and AA-mediated GO reduction were confirmed using scanning electron microscopy, photoluminescence, Raman spectroscopy, and X-ray photoelectron spectroscopy. Biocompatibility of g-C3N4 (0.01-0.9 mg/mL) to PC12 cells was confirmed by the lactate dehydrogenase (LDH) assay, Live-Dead staining, and colorimetric cell viability assay CCK-8. Under a bidaily, monochromatic light stimulation at a wavelength of 450 nm at 10 mW/cm2, a 18.5-fold increase of neurite outgrowth of PC12 was found on g-C3N4-coated fibers, while AA-reduced GO-g-C3N4 hybrid brought a further 2.6-fold increase, suggesting its great potential as a visible-light neural stimulator that could optically enhance neural growth in a spatiotemporal-specific manner.

  View details for DOI 10.1021/acsami.7b12733

  View details for PubMedID 28929741

• Understanding CRY2 interactions for optical control of intracellular signaling NATURE COMMUNICATIONS Duan, L., Hope, J., Ong, Q., Lou, H., Kim, N., McCarthy, C., Acero, V., Lin, M. Z., Cui, B. 2017; 8: 547

  Abstract

  Arabidopsis cryptochrome 2 (CRY2) can simultaneously undergo light-dependent CRY2-CRY2 homo-oligomerization and CRY2-CIB1 hetero-dimerization, both of which have been widely used to optically control intracellular processes. Applications using CRY2-CIB1 interaction desire minimal CRY2 homo-oligomerization to avoid unintended complications, while those utilizing CRY2-CRY2 interaction prefer robust homo-oligomerization. However, selecting the type of CRY2 interaction has not been possible as the molecular mechanisms underlying CRY2 interactions are unknown. Here we report CRY2-CIB1 and CRY2-CRY2 interactions are governed by well-separated protein interfaces at the two termini of CRY2. N-terminal charges are critical for CRY2-CIB1 interaction. Moreover, two C-terminal charges impact CRY2 homo-oligomerization, with positive charges facilitating oligomerization and negative charges inhibiting it. By engineering C-terminal charges, we develop CRY2high and CRY2low with elevated or suppressed oligomerization respectively, which we use to tune the levels of Raf/MEK/ERK signaling. These results contribute to our understanding of the mechanisms underlying light-induced CRY2 interactions and enhance the controllability of CRY2-based optogenetic systems.Cryptochrome 2 (CRY2) can form light-regulated CRY2-CRY2 homo-oligomers or CRY2-CIB1 hetero-dimers, but modulating these interactions is difficult owing to the lack of interaction mechanism. Here the authors identify the interactions facilitating homo-oligomers and introduce mutations to create low and high oligomerization versions.

  View details for PubMedID 28916751

• Nanoscale manipulation of membrane curvature for probing endocytosis in live cells. Nature nanotechnology Zhao, W., Hanson, L., Lou, H., Akamatsu, M., Chowdary, P. D., Santoro, F., Marks, J. R., Grassart, A., Drubin, D. G., Cui, Y., Cui, B. 2017

  Abstract

  Clathrin-mediated endocytosis (CME) involves nanoscale bending and inward budding of the plasma membrane, by which cells regulate both the distribution of membrane proteins and the entry of extracellular species. Extensive studies have shown that CME proteins actively modulate the plasma membrane curvature. However, the reciprocal regulation of how the plasma membrane curvature affects the activities of endocytic proteins is much less explored, despite studies suggesting that membrane curvature itself can trigger biochemical reactions. This gap in our understanding is largely due to technical challenges in precisely controlling the membrane curvature in live cells. In this work, we use patterned nanostructures to generate well-defined membrane curvatures ranging from +50 nm to -500 nm radius of curvature. We find that the positively curved membranes are CME hotspots, and that key CME proteins, clathrin and dynamin, show a strong preference towards positive membrane curvatures with a radius <200 nm. Of ten CME-related proteins we examined, all show preferences for positively curved membrane. In contrast, other membrane-associated proteins and non-CME endocytic protein caveolin1 show no such curvature preference. Therefore, nanostructured substrates constitute a novel tool for investigating curvature-dependent processes in live cells.

  View details for DOI 10.1038/nnano.2017.98

  View details for PubMedID 28581510

• Accurate nanoelectrode recording of human pluripotent stem cell-derived cardiomyocytes for assaying drugs and modeling disease. Microsystems & nanoengineering Lin, Z. C., McGuire, A. F., Burridge, P. W., Matsa, E., Lou, H. Y., Wu, J. C., Cui, B. 2017; 3: 16080

  Abstract

  The measurement of the electrophysiology of human pluripotent stem cell-derived cardiomyocytes is critical for their biomedical applications, from disease modeling to drug screening. Yet, a method that enables the high-throughput intracellular electrophysiology measurement of single cardiomyocytes in adherent culture is not available. To address this area, we have fabricated vertical nanopillar electrodes that can record intracellular action potentials from up to 60 single beating cardiomyocytes. Intracellular access is achieved by highly localized electroporation, which allows for low impedance electrical access to the intracellular voltage. Herein, we demonstrate that this method provides the accurate measurement of the shape and duration of intracellular action potentials, validated by patch clamp, and can facilitate cellular drug screening and disease modeling using human pluripotent stem cells. This study validates the use of nanopillar electrodes for myriad further applications of human pluripotent stem cell-derived cardiomyocytes such as cardiomyocyte maturation monitoring and electrophysiology-contractile force correlation.

  View details for DOI 10.1038/micronano.2016.80

  View details for PubMedID 31057850

  View details for PubMedCentralID PMC6444980

• Control of cerebral ischemia with magnetic nanoparticles. Nature methods Jia, J., Chowdary, P. D., Gao, X., Ci, B., Li, W., Mulgaonkar, A., Plautz, E. J., Hassan, G., Kumar, A., Stowe, A. M., Yang, S., Zhou, W., Sun, X., Cui, B., Ge, W. 2017; 14 (2): 160-166

  Abstract

  The precise manipulation of microcirculation in mice can facilitate mechanistic studies of brain injury and repair after ischemia, but this manipulation remains a technical challenge, particularly in conscious mice. We developed a technology that uses micromagnets to induce aggregation of magnetic nanoparticles to reversibly occlude blood flow in microvessels. This allowed induction of ischemia in a specific cortical region of conscious mice of any postnatal age, including perinatal and neonatal stages, with precise spatiotemporal control but without surgical intervention of the skull or artery. When combined with longitudinal live-imaging approaches, this technology facilitated the discovery of a feature of the ischemic cascade: selective loss of smooth muscle cells in juveniles but not adults shortly after onset of ischemia and during blood reperfusion.

  View details for DOI 10.1038/nmeth.4105

  View details for PubMedID 27941784

• Dual-Functional Lipid Coating for the Nanopillar-Based Capture of Circulating Tumor Cells with High Purity and Efficiency LANGMUIR Lou, H., Zhao, W., Hanson, L., Zeng, C., Cui, Y., Cui, B. 2017; 33 (4): 1097-1104

  Abstract

  Clinical studies of circulating tumor cells (CTC) have stringent demands for high capture purity and high capture efficiency. Nanostructured surfaces have been shown to significantly increase the capture efficiency yet suffer from low capture purity. Here we introduce a dual-functional lipid coating on nanostructured surfaces. The lipid coating serves both as an effective passivation layer that helps prevent nonspecific cell adhesion and as a functionalized layer for antibody-based specific cell capture. In addition, the fluidity of lipid bilayers enables antibody clustering that enhances the cell-surface interaction for efficient cell capture. As a result, the lipid-coating method helps promote both the capture efficiency and capture purity of nanostructure-based CTC capture.

  View details for DOI 10.1021/acs.langmuir.6b03903

  View details for Web of Science ID 000393269700032

  View details for PubMedID 28059522

• Intracellular TG2 Activity Increases Microtubule Stability but is not Sufficient to Prompt Neurite Growth. Neuroscience bulletin Guo, S. n., Palanski, B. A., Kloeck, C. n., Khosla, C. n., Cui, B. n. 2017; 33 (1): 103–6

  View details for PubMedID 27815680

• Imaging electric field dynamics with graphene optoelectronics NATURE COMMUNICATIONS Horng, J., Balch, H. B., McGuire, A. F., Tsai, H., Forrester, P. R., Crommie, M. F., Cui, B., Wang, F. 2016; 7

  Abstract

  The use of electric fields for signalling and control in liquids is widespread, spanning bioelectric activity in cells to electrical manipulation of microstructures in lab-on-a-chip devices. However, an appropriate tool to resolve the spatio-temporal distribution of electric fields over a large dynamic range has yet to be developed. Here we present a label-free method to image local electric fields in real time and under ambient conditions. Our technique combines the unique gate-variable optical transitions of graphene with a critically coupled planar waveguide platform that enables highly sensitive detection of local electric fields with a voltage sensitivity of a few microvolts, a spatial resolution of tens of micrometres and a frequency response over tens of kilohertz. Our imaging platform enables parallel detection of electric fields over a large field of view and can be tailored to broad applications spanning lab-on-a-chip device engineering to analysis of bioelectric phenomena.

  View details for DOI 10.1038/ncomms13704

  View details for Web of Science ID 000389853500001

  View details for PubMedID 27982125

  View details for PubMedCentralID PMC5172231

• The Timing of Raf/ERK and AKT Activation in Protecting PC12 Cells against Oxidative Stress PLOS ONE Ong, Q., Guo, S., Duan, L., Zhang, K., Collier, E. A., Cui, B. 2016; 11 (4)

  Abstract

  Acute brain injuries such as ischemic stroke or traumatic brain injury often cause massive neural death and irreversible brain damage with grave consequences. Previous studies have established that a key participant in the events leading to neural death is the excessive production of reactive oxygen species. Protecting neuronal cells by activating their endogenous defense mechanisms is an attractive treatment strategy for acute brain injuries. In this work, we investigate how the precise timing of the Raf/ERK and the AKT pathway activation affects their protective effects against oxidative stress. For this purpose, we employed optogenetic systems that use light to precisely and reversibly activate either the Raf/ERK or the AKT pathway. We find that preconditioning activation of the Raf/ERK or the AKT pathway immediately before oxidant exposure provides significant protection to cells. Notably, a 15-minute transient activation of the Raf/ERK pathway is able to protect PC12 cells against oxidant strike that is applied 12 hours later, while the transient activation of the AKT pathway fails to protect PC12 cells in such a scenario. On the other hand, if the pathways are activated after the oxidative insult, i.e. postconditioning, the AKT pathway conveys greater protective effect than the Raf/ERK pathway. We find that postconditioning AKT activation has an optimal delay period of 2 hours. When the AKT pathway is activated 30min after the oxidative insult, it exhibits very little protective effect. Therefore, the precise timing of the pathway activation is crucial in determining its protective effect against oxidative injury. The optogenetic platform, with its precise temporal control and its ability to activate specific pathways, is ideal for the mechanistic dissection of intracellular pathways in protection against oxidative stress.

  View details for DOI 10.1371/journal.pone.0153487

  View details for Web of Science ID 000374291800022

  View details for PubMedID 27082641

  View details for PubMedCentralID PMC4833326

• A close look at axonal transport: Cargos slow down when crossing stationary organelles NEUROSCIENCE LETTERS Che, D. L., Chowdary, P. D., Cui, B. 2016; 610: 110-116

  View details for DOI 10.1016/j.neulet.2015.10.066

  View details for Web of Science ID 000367487400019

• A close look at axonal transport: Cargos slow down when crossing stationary organelles. Neuroscience letters Che, D. L., Chowdary, P. D., Cui, B. 2016; 610: 110-6

  Abstract

  The bidirectional transport of cargos along the thin axon is fundamental for the structure, function and survival of neurons. Defective axonal transport has been linked to the mechanism of neurodegenerative diseases. In this paper, we study the effect of the local axonal environment to cargo transport behavior in neurons. Using dual-color fluorescence imaging in microfluidic neuronal devices, we quantify the transport dynamics of cargos when crossing stationary organelles such as non-moving endosomes and stationary mitochondria in the axon. We show that the axonal cargos tend to slow down, or pause transiently within the vicinity of stationary organelles. The slow-down effect is observed in both retrograde and anterograde transport directions of three different cargos (TrkA, lysosomes and TrkB). Our results agree with the hypothesis that bulky axonal structures can pose as steric hindrance for axonal transport. However, the results do not rule out the possibility that cellular mechanisms causing stationary organelles are also responsible for the delay in moving cargos at the same locations.

  View details for DOI 10.1016/j.neulet.2015.10.066

  View details for PubMedID 26528790

  View details for PubMedCentralID PMC4695265

• Nanoparticle-assisted optical tethering of endosomes reveals the cooperative function of dyneins in retrograde axonal transport SCIENTIFIC REPORTS Chowdary, P. D., Che, D. L., Kaplan, L., Chen, O., Pu, K., Bawendi, M., Cui, B. 2015; 5

  View details for DOI 10.1038/srep18059

  View details for PubMedID 26656461

• A skin-inspired organic digital mechanoreceptor SCIENCE Tee, B. C., Chortos, A., Berndt, A., Nguyen, A. K., Tom, A., McGuire, A., Lin, Z. C., Tien, K., Bae, W., Wang, H., Mei, P., Chou, H., Cui, B., Deisseroth, K., Ng, T. N., Bao, Z. 2015; 350 (6258): 313-?

  Abstract

  Human skin relies on cutaneous receptors that output digital signals for tactile sensing in which the intensity of stimulation is converted to a series of voltage pulses. We present a power-efficient skin-inspired mechanoreceptor with a flexible organic transistor circuit that transduces pressure into digital frequency signals directly. The output frequency ranges between 0 and 200 hertz, with a sublinear response to increasing force stimuli that mimics slow-adapting skin mechanoreceptors. The output of the sensors was further used to stimulate optogenetically engineered mouse somatosensory neurons of mouse cortex in vitro, achieving stimulated pulses in accordance with pressure levels. This work represents a step toward the design and use of large-area organic electronic skins with neural-integrated touch feedback for replacement limbs.

  View details for DOI 10.1126/science.aaa9306

  View details for Web of Science ID 000362838700039

  View details for PubMedID 26472906

• The Dual Characteristics of Light-Induced Cryptochrome 2, Homo-oligomerization and Heterodimerization, for Optogenetic Manipulation in Mammalian Cells. ACS synthetic biology Che, D. L., Duan, L., Zhang, K., Cui, B. 2015; 4 (10): 1124-1135

  View details for DOI 10.1021/acssynbio.5b00048

  View details for PubMedID 25985220

• Activity-dependent BDNF release via endocytic pathways is regulated by synaptotagmin-6 and complexin. Proceedings of the National Academy of Sciences of the United States of America Wong, Y., Lee, C., Xie, W., Cui, B., Poo, M. 2015; 112 (32): E4475-84

  Abstract

  Brain-derived neurotrophic factor (BDNF) is known to modulate synapse development and plasticity, but the source of synaptic BDNF and molecular mechanisms regulating BDNF release remain unclear. Using exogenous BDNF tagged with quantum dots (BDNF-QDs), we found that endocytosed BDNF-QDs were preferentially localized to postsynaptic sites in the dendrite of cultured hippocampal neurons. Repetitive neuronal spiking induced the release of BDNF-QDs at these sites, and this process required activation of glutamate receptors. Down-regulating complexin 1/2 (Cpx1/2) expression eliminated activity-induced BDNF-QD secretion, although the overall activity-independent secretion was elevated. Among eight synaptotagmin (Syt) isoforms examined, down-regulation of only Syt6 impaired activity-induced BDNF-QD secretion. In contrast, activity-induced release of endogenously synthesized BDNF did not depend on Syt6. Thus, neuronal activity could trigger the release of endosomal BDNF from postsynaptic dendrites in a Cpx- and Syt6-dependent manner, and endosomes containing BDNF may serve as a source of BDNF for activity-dependent synaptic modulation.

  View details for DOI 10.1073/pnas.1511830112

  View details for PubMedID 26216953

  View details for PubMedCentralID PMC4538679

• Efficient Radioisotope Energy Transfer by Gold Nanoclusters for Molecular Imaging SMALL Volotskova, O., Sun, C., Stafford, J. H., Koh, A. L., Ma, X., Cheng, Z., Cui, B., Pratx, G., Xing, L. 2015; 11 (32): 4002-4008

  Abstract

  Beta-emitting isotopes Fluorine-18 and Yttrium-90 are tested for their potential to stimulate gold nanoclusters conjugated with blood serum proteins (AuNCs). AuNCs excited by either medical radioisotope are found to be highly effective ionizing radiation energy transfer mediators, suitable for in vivo optical imaging. AuNCs synthesized with protein templates convert beta-decaying radioisotope energy into tissue-penetrating optical signals between 620 and 800 nm. Optical signals are not detected from AuNCs incubated with Technetium-99m, a pure gamma emitter that is used as a control. Optical emission from AuNCs is not proportional to Cerenkov radiation, indicating that the energy transfer between the radionuclide and AuNC is only partially mediated by Cerenkov photons. A direct Coulombic interaction is proposed as a novel and significant mechanism of energy transfer between decaying radionuclides and AuNCs.

  View details for DOI 10.1002/smll.201500907

  View details for Web of Science ID 000360226300016

• Retrograde NGF Axonal Transport-Motor Coordination in the Unidirectional Motility Regime BIOPHYSICAL JOURNAL Chowdary, P. D., Che, D. L., Zhang, K., Cui, B. 2015; 108 (11): 2691-2703

  Abstract

  We present a detailed motion analysis of retrograde nerve growth factor (NGF) endosomes in axons to show that mechanical tugs-of-war and intracellular motor regulation are complimentary features of the near-unidirectional endosome directionality. We used quantum dots to fluorescently label NGF and acquired trajectories of retrograde quantum-dot-NGF-endosomes with <20-nm accuracy at 32 Hz in microfluidic neuron cultures. Using a combination of transient motion analysis and Bayesian parsing, we partitioned the trajectories into sustained periods of retrograde (dynein-driven) motion, constrained pauses, and brief anterograde (kinesin-driven) reversals. The data shows many aspects of mechanical tugs-of-war and multiple-motor mechanics in NGF-endosome transport. However, we found that stochastic mechanical models based on in vitro parameters cannot simulate the experimental data, unless the microtubule-binding affinity of kinesins on the endosome is tuned down by 10 times. Specifically, the simulations suggest that the NGF-endosomes are driven on average by 5-6 active dyneins and 1-2 downregulated kinesins. This is also supported by the dynamics of endosomes detaching under load in axons, showcasing the cooperativity of multiple dyneins and the subdued activity of kinesins. We discuss the possible motor coordination mechanism consistent with motor regulation and tugs-of-war for future investigations.

  View details for DOI 10.1016/j.bpj.2015.04.036

  View details for Web of Science ID 000355668800010

  View details for PubMedID 26039170

  View details for PubMedCentralID PMC4457490

• Nanotechnology and neurophysiology CURRENT OPINION IN NEUROBIOLOGY Angle, M. R., Cui, B., Melosh, N. A. 2015; 32: 132-140

  Abstract

  Neuroscience would be revolutionized by a technique to measure intracellular electrical potentials that would not disrupt cellular physiology and could be massively parallelized. Though such a technology does not yet exist, the technical hurdles for fabricating minimally disruptive, solid-state electrical probes have arguably been overcome in the field of nanotechnology. Nanoscale devices can be patterned with features on the same length scale as biological components, and several groups have demonstrated that nanoscale electrical probes can measure the transmembrane potential of electrogenic cells. Developing these nascent technologies into robust intracellular recording tools will now require a better understanding of device-cell interactions, especially the membrane-inorganic interface. Here we review the state-of-the art in nanobioelectronics, emphasizing the characterization and design of stable interfaces between nanoscale devices and cells.

  View details for DOI 10.1016/j.conb.2015.03.014

  View details for Web of Science ID 000356198900018

• Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells. Nature nanotechnology Hanson, L., Zhao, W., Lou, H., Lin, Z. C., Lee, S. W., Chowdary, P., Cui, Y., Cui, B. 2015; 10 (6): 554-562

  Abstract

  The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells.

  View details for DOI 10.1038/nnano.2015.88

  View details for PubMedID 25984833

• Optogenetic Control of Molecular Motors and Organelle Distributions in Cells CHEMISTRY & BIOLOGY Duan, L., Che, D., Zhang, K., Ong, Q., Guo, S., Cui, B. 2015; 22 (5): 671-682

  Abstract

  Intracellular transport and distribution of organelles play important roles in diverse cellular functions, including cell polarization, intracellular signaling, cell survival, and apoptosis. Here, we report an optogenetic strategy to control the transport and distribution of organelles by light. This is achieved by optically recruiting molecular motors onto organelles through the heterodimerization of Arabidopsis thaliana cryptochrome 2 (CRY2) and its interacting partner CIB1. CRY2 and CIB1 dimerize within subseconds upon exposure to blue light, which requires no exogenous ligands and low intensity of light. We demonstrate that mitochondria, peroxisomes, and lysosomes can be driven toward the cell periphery upon light-induced recruitment of kinesin, or toward the cell nucleus upon recruitment of dynein. Light-induced motor recruitment and organelle movements are repeatable, reversible, and can be achieved at subcellular regions. This light-controlled organelle redistribution provides a new strategy for studying the causal roles of organelle transport and distribution in cellular functions in living cells.

  View details for DOI 10.1016/j.chembiol.2015.04.014

  View details for Web of Science ID 000355153900015

  View details for PubMedID 25963241

  View details for PubMedCentralID PMC4443846

• Efficient Radioisotope Energy Transfer by Gold Nanoclusters for Molecular Imaging. Small (Weinheim an der Bergstrasse, Germany) Volotskova, O., Sun, C., Stafford, J. H., Koh, A. L., Ma, X., Cheng, Z., Cui, B., Pratx, G., Xing, L. 2015

  Abstract

  Beta-emitting isotopes Fluorine-18 and Yttrium-90 are tested for their potential to stimulate gold nanoclusters conjugated with blood serum proteins (AuNCs). AuNCs excited by either medical radioisotope are found to be highly effective ionizing radiation energy transfer mediators, suitable for in vivo optical imaging. AuNCs synthesized with protein templates convert beta-decaying radioisotope energy into tissue-penetrating optical signals between 620 and 800 nm. Optical signals are not detected from AuNCs incubated with Technetium-99m, a pure gamma emitter that is used as a control. Optical emission from AuNCs is not proportional to Cerenkov radiation, indicating that the energy transfer between the radionuclide and AuNC is only partially mediated by Cerenkov photons. A direct Coulombic interaction is proposed as a novel and significant mechanism of energy transfer between decaying radionuclides and AuNCs.

  View details for DOI 10.1002/smll.201500907

  View details for PubMedID 25973916

• Optogenetic control of intracellular signaling pathways TRENDS IN BIOTECHNOLOGY Zhang, K., Cu, B. 2015; 33 (2): 92-100

  View details for DOI 10.1016/j.tibtech.2014.11.007

  View details for Web of Science ID 000349504000007

• U0126 Protects Cells against Oxidative Stress Independent of Its Function as a MEK Inhibitor ACS CHEMICAL NEUROSCIENCE Ong, Q., Guo, S., Zhang, K., Cui, B. 2015; 6 (1): 130-137

  Abstract

  U0126 is a potent and selective inhibitor of MEK1 and MEK2 kinases. It has been widely used as an inhibitor for the Ras/Raf/MEK/ERK signaling pathway with over 5000 references on the NCBI PubMed database. In particular, U0126 has been used in a number of studies to show that inhibition of the Raf/MEK/ERK pathway protects neuronal cells against oxidative stress. Here, we report that U0126 can function as an antioxidant that protects PC12 cells against a number of different oxidative-stress inducers. This protective effect of U0126 is independent of its function as a MEK inhibitor, as several other MEK inhibitors failed to show similar protective effects. U0126 reduces reactive oxygen species (ROS) in cells. We further demonstrate that U0126 is a direct ROS scavenger in vitro, and the oxidation products of U0126 exhibit fluorescence. Our finding that U0126 is a strong antioxidant signals caution for its future usage as a MEK inhibitor and for interpreting some previous results.

  View details for DOI 10.1021/cn500288n

  View details for Web of Science ID 000348338900016

  View details for PubMedID 25544156

  View details for PubMedCentralID PMC4304487

• Enhancing the nanomaterial bio-interface by addition of mesoscale secondary features: crinkling of carbon nanotube films to create subcellular ridges. ACS nano Xie, X., Zhao, W., Lee, H. R., Liu, C., Ye, M., Xie, W., Cui, B., Criddle, C. S., Cui, Y. 2014; 8 (12): 11958-11965

  Abstract

  Biological cells often interact with their local environment through subcellular structures at a scale of tens to hundreds of nanometers. This study investigated whether topographic features fabricated at a similar scale would impact cellular functions by promoting the interaction between subcellular structures and nanomaterials. Crinkling of carbon nanotube films by solvent-induced swelling and shrinkage of substrate resulted in the formation of ridge features at the subcellular scale on both flat and three-dimensional substrates. Biological cells grown upon these crinkled CNT films had enhanced activity: neuronal cells grew to higher density and displayed greater cell polarization; exoelectrogenic micro-organisms transferred electrons more efficiently. The results indicate that crinkling of thin CNT films creates secondary mesoscale features that enhance attachment, growth, and electron transfer.

  View details for DOI 10.1021/nn504898p

  View details for PubMedID 25415858

• Chemically defined generation of human cardiomyocytes. Nature methods Burridge, P. W., Matsa, E., Shukla, P., Lin, Z. C., Churko, J. M., Ebert, A. D., Lan, F., Diecke, S., Huber, B., Mordwinkin, N. M., Plews, J. R., Abilez, O. J., Cui, B., Gold, J. D., Wu, J. C. 2014; 11 (8): 855-860

  Abstract

  Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we systematically developed an optimized cardiac differentiation strategy, using a chemically defined medium consisting of just three components: the basal medium RPMI 1640, L-ascorbic acid 2-phosphate and rice-derived recombinant human albumin. Along with small molecule-based induction of differentiation, this protocol produced contractile sheets of up to 95% TNNT2(+) cardiomyocytes at a yield of up to 100 cardiomyocytes for every input pluripotent cell and was effective in 11 hiPSC lines tested. This chemically defined platform for cardiac specification of hiPSCs will allow the elucidation of cardiomyocyte macromolecular and metabolic requirements and will provide a minimal system for the study of maturation and subtype specification.

  View details for DOI 10.1038/nmeth.2999

  View details for PubMedID 24930130

• Lighting up FGFR signaling. Chemistry & biology Zhang, K., Cui, B. 2014; 21 (7): 806-808

  Abstract

  In this issue of Chemistry & Biology, Kim and colleagues describe their work on optogenetic control of fibroblast growth factor receptor (FGFR) signaling. By engineering a chimeric receptor, the authors demonstrate that FGFR intracellular signaling can be controlled in space and time by blue light.

  View details for DOI 10.1016/j.chembiol.2014.07.004

  View details for PubMedID 25036775

• Divergence of the long-wavelength collective diffusion coefficient in quasi-one- and quasi-two-dimensional colloidal suspensions PHYSICAL REVIEW E Lin, B., Cui, B., Xu, X., Zangi, R., Diamant, H., Rice, S. A. 2014; 89 (2)

  View details for DOI 10.1103/PhysRevE.89.022303

  View details for Web of Science ID 000332176100002

• Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials. Nature communications Lin, Z. C., Xie, C., Osakada, Y., Cui, Y., Cui, B. 2014; 5: 3206-?

  Abstract

  Intracellular recording of action potentials is important to understand electrically-excitable cells. Recently, vertical nanoelectrodes have been developed to achieve highly sensitive, minimally invasive and large-scale intracellular recording. It has been demonstrated that the vertical geometry is crucial for the enhanced signal detection. Here we develop nanoelectrodes of a new geometry, namely nanotubes of iridium oxide. When cardiomyocytes are cultured upon those nanotubes, the cell membrane not only wraps around the vertical tubes but also protrudes deep into the hollow centre. We show that this nanotube geometry enhances cell-electrode coupling and results in larger signals than solid nanoelectrodes. The nanotube electrodes also afford much longer intracellular access and are minimally invasive, making it possible to achieve stable recording up to an hour in a single session and more than 8 days of consecutive daily recording. This study suggests that the nanoelectrode performance can be significantly improved by optimizing the electrode geometry.

  View details for DOI 10.1038/ncomms4206

  View details for PubMedID 24487777

• NANOWIRE TRANSISTORS Room for manoeuvre NATURE NANOTECHNOLOGY Lin, Z. C., Cui, B. 2014; 9 (2): 94-96

  View details for DOI 10.1038/nnano.2014.10

  View details for Web of Science ID 000331069200006

  View details for PubMedID 24496276

• Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials. Nature communications Lin, Z. C., Xie, C., Osakada, Y., Cui, Y., Cui, B. 2014; 5: 3206-?

  Abstract

  Intracellular recording of action potentials is important to understand electrically-excitable cells. Recently, vertical nanoelectrodes have been developed to achieve highly sensitive, minimally invasive and large-scale intracellular recording. It has been demonstrated that the vertical geometry is crucial for the enhanced signal detection. Here we develop nanoelectrodes of a new geometry, namely nanotubes of iridium oxide. When cardiomyocytes are cultured upon those nanotubes, the cell membrane not only wraps around the vertical tubes but also protrudes deep into the hollow centre. We show that this nanotube geometry enhances cell-electrode coupling and results in larger signals than solid nanoelectrodes. The nanotube electrodes also afford much longer intracellular access and are minimally invasive, making it possible to achieve stable recording up to an hour in a single session and more than 8 days of consecutive daily recording. This study suggests that the nanoelectrode performance can be significantly improved by optimizing the electrode geometry.

  View details for DOI 10.1038/ncomms4206

  View details for PubMedID 24487777

• Light-Mediated Kinetic Control Reveals the Temporal Effect of the Raf/MEK/ERK Pathway in PC12 Cell Neurite Outgrowth. PloS one Zhang, K., Duan, L., Ong, Q., Lin, Z., Varman, P. M., Sung, K., Cui, B. 2014; 9 (3)

  View details for DOI 10.1371/journal.pone.0092917

  View details for PubMedID 24667437

• Hard X-ray-induced optical luminescence via biomolecule-directed metal clusters CHEMICAL COMMUNICATIONS Osakada, Y., Pratx, G., Sun, C., Sakamoto, M., Ahmad, M., Volotskova, O., Ong, Q., Teranishi, T., Harada, Y., Xing, L., Cui, B. 2014; 50 (27): 3549-3551

  Abstract

  Here, we demonstrate that biomolecule-directed metal clusters are applicable in the study of hard X-ray excited optical luminescence, promising a new direction in the development of novel X-ray-activated imaging probes.

  View details for DOI 10.1039/c3cc48661c

  View details for Web of Science ID 000332483200003

  View details for PubMedID 24463467

• Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PloS one Zhang, K., Duan, L., Ong, Q., Lin, Z., Varman, P. M., Sung, K., Cui, B. 2014; 9 (3)

  Abstract

  It has been proposed that differential activation kinetics allows cells to use a common set of signaling pathways to specify distinct cellular outcomes. For example, nerve growth factor (NGF) and epidermal growth factor (EGF) induce different activation kinetics of the Raf/MEK/ERK signaling pathway and result in differentiation and proliferation, respectively. However, a direct and quantitative linkage between the temporal profile of Raf/MEK/ERK activation and the cellular outputs has not been established due to a lack of means to precisely perturb its signaling kinetics. Here, we construct a light-gated protein-protein interaction system to regulate the activation pattern of the Raf/MEK/ERK signaling pathway. Light-induced activation of the Raf/MEK/ERK cascade leads to significant neurite outgrowth in rat PC12 pheochromocytoma cell lines in the absence of growth factors. Compared with NGF stimulation, light stimulation induces longer but fewer neurites. Intermittent on/off illumination reveals that cells achieve maximum neurite outgrowth if the off-time duration per cycle is shorter than 45 min. Overall, light-mediated kinetic control enables precise dissection of the temporal dimension within the intracellular signal transduction network.

  View details for DOI 10.1371/journal.pone.0092917

  View details for PubMedID 24667437

  View details for PubMedCentralID PMC3965503

• X-ray excitable luminescent polymer dots doped with an iridium(iii) complex. Chemical communications Osakada, Y., Pratx, G., Hanson, L., Solomon, P. E., Xing, L., Cui, B. 2013; 49 (39): 4319-4321

  Abstract

  In this study, cyclometalated iridium(III) complex-doped polymer dots were synthesized and shown to emit luminescence upon X-ray irradiation, potentially serving as a new probe for molecular imaging during X-ray computed tomography.

  View details for DOI 10.1039/c2cc37169c

  View details for PubMedID 23320256

• Defective Axonal Transport of Rab7 GTPase Results in Dysregulated Trophic Signaling JOURNAL OF NEUROSCIENCE Zhang, K., Ben Kenan, R. F., Osakada, Y., Xu, W., Sinit, R. S., Chen, L., Zhao, X., Chen, J., Cui, B., Wu, C. 2013; 33 (17): 7451-7462

  View details for DOI 10.1523/JNEUROSCI.4322-12.2013

  View details for Web of Science ID 000318419300031

• Light-Controlled Mitogen-Activated Protein Kinase (MAPK) Signaling Pathway in Live Cells 57th Annual Meeting of the Biophysical-Society Zhang, K., Duan, L., Lin, Z., Sung, K., Osakada, Y., Cui, B. CELL PRESS. 2013: 679A–679A

  View details for Web of Science ID 000316074306435

• Accelerating the Development of Hippocampal Neurons using Nanopillar Structures 57th Annual Meeting of the Biophysical-Society Zhao, W., Zhang, K., Xie, W., Hanson, L., Lin, Z., Cui, Y., Cui, B. CELL PRESS. 2013: 675A–675A

  View details for Web of Science ID 000316074306417

• Probing the Mechanical Coupling of the Cell Membrane to the Nucleus with Vertical Nanopillar Arrays 57th Annual Meeting of the Biophysical-Society Hanson, L., Urzay, J., Lin, Z., Zhao, W., Prakash, M., Cui, B. CELL PRESS. 2013: 546A–546A

  View details for Web of Science ID 000316074305286

• Characterization of the Cell-Nanopillar Interface by Transmission Electron Microscopy NANO LETTERS Hanson, L., Lin, Z. C., Xie, C., Cui, Y., Cui, B. 2012; 12 (11): 5815-5820

  Abstract

  Vertically aligned nanopillars can serve as excellent electrical, optical and mechanical platforms for biological studies. However, revealing the nature of the interface between the cell and the nanopillar is very challenging. In particular, a matter of debate is whether the cell membrane remains intact around the nanopillar. Here we present a detailed characterization of the cell-nanopillar interface by transmission electron microscopy. We examined cortical neurons growing on nanopillars with diameter 50-500 nm and heights 0.5-2 μm. We found that on nanopillars less than 300 nm in diameter, the cell membrane wraps around the entirety of the nanopillar without the nanopillar penetrating into the interior of the cell. On the other hand, the cell sits on top of arrays of larger, closely spaced nanopillars. We also observed that the membrane-surface gap of both cell bodies and neurites is smaller for nanopillars than for a flat substrate. These results support a tight interaction between the cell membrane and the nanopillars and previous findings of excellent sealing in electrophysiology recordings using nanopillar electrodes.

  View details for DOI 10.1021/nl303163y

  View details for Web of Science ID 000311244400064

  View details for PubMedID 23030066

• Intracellular recording of action potentials by nanopillar electroporation NATURE NANOTECHNOLOGY Xie, C., Lin, Z., Hanson, L., Cui, Y., Cui, B. 2012; 7 (3): 185-190

  Abstract

  Action potentials have a central role in the nervous system and in many cellular processes, notably those involving ion channels. The accurate measurement of action potentials requires efficient coupling between the cell membrane and the measuring electrodes. Intracellular recording methods such as patch clamping involve measuring the voltage or current across the cell membrane by accessing the cell interior with an electrode, allowing both the amplitude and shape of the action potentials to be recorded faithfully with high signal-to-noise ratios. However, the invasive nature of intracellular methods usually limits the recording time to a few hours, and their complexity makes it difficult to simultaneously record more than a few cells. Extracellular recording methods, such as multielectrode arrays and multitransistor arrays, are non-invasive and allow long-term and multiplexed measurements. However, extracellular recording sacrifices the one-to-one correspondence between the cells and electrodes, and also suffers from significantly reduced signal strength and quality. Extracellular techniques are not, therefore, able to record action potentials with the accuracy needed to explore the properties of ion channels. As a result, the pharmacological screening of ion-channel drugs is usually performed by low-throughput intracellular recording methods. The use of nanowire transistors, nanotube-coupled transistors and micro gold-spine and related electrodes can significantly improve the signal strength of recorded action potentials. Here, we show that vertical nanopillar electrodes can record both the extracellular and intracellular action potentials of cultured cardiomyocytes over a long period of time with excellent signal strength and quality. Moreover, it is possible to repeatedly switch between extracellular and intracellular recording by nanoscale electroporation and resealing processes. Furthermore, vertical nanopillar electrodes can detect subtle changes in action potentials induced by drugs that target ion channels.

  View details for DOI 10.1038/NNANO.2012.8

  View details for Web of Science ID 000301186300012

  View details for PubMedID 22327876

  View details for PubMedCentralID PMC3356686

• Neurotrophin Signaling via Long-Distance Axonal Transport ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 63 Chowdary, P. D., Che, D. L., Cui, B. 2012; 63: 571-594

  Abstract

  Neurotrophins are a family of target-derived growth factors that support survival, development, and maintenance of innervating neurons. Owing to the unique architecture of neurons, neurotrophins that act locally on the axonal terminals must convey their signals across the entire axon for subsequent regulation of gene transcription in the cell nucleus. This long-distance retrograde signaling, a motor-driven process that can take hours or days, has been a subject of intense interest. In the last decade, live-cell imaging with high sensitivity has significantly increased our capability to track the transport of neurotrophins, their receptors, and subsequent signals in real time. This review summarizes recent research progress in understanding neurotrophin-receptor interactions at the axonal terminal and their transport dynamics along the axon. We emphasize high-resolution studies at the single-molecule level and also discuss recent technical advances in the field.

  View details for DOI 10.1146/annurev-physchem-032511-143704

  View details for Web of Science ID 000304203500026

  View details for PubMedID 22404590

• Functional characterization and axonal transport of quantum dot labeled BDNF INTEGRATIVE BIOLOGY Xie, W., Zhang, K., Cui, B. 2012; 4 (8): 953-960

  Abstract

  Brain derived neurotrophic factor (BDNF) plays a key role in the growth, development and maintenance of the central and peripheral nervous systems. Exogenous BDNF activates its membrane receptors at the axon terminal, and subsequently sends regulation signals to the cell body. To understand how a BDNF signal propagates in neurons, it is important to follow the trafficking of BDNF after it is internalized at the axon terminal. Here we labeled BDNF with bright, photostable quantum dots (QD-BDNF) and followed the axonal transport of QD-BDNF in real time in hippocampal neurons. We showed that QD-BDNF was able to bind BDNF receptors and activate downstream signaling pathways. When QD-BDNF was applied to the distal axons of hippocampal neurons, it was observed to be actively transported toward the cell body at an average speed of 1.11 ± 0.05 μm s(-1). A closer examination revealed that QD-BDNF was transported by both discrete endosomes and multivesicular body-like structures. Our results showed that QD-BDNF could be used to track the movement of exogenous BDNF in neurons over long distances and to study the signaling organelles that contain BDNF.

  View details for DOI 10.1039/c2ib20062g

  View details for Web of Science ID 000306708500014

  View details for PubMedID 22772872

  View details for PubMedCentralID PMC3462492

• Diarylethene doped biocompatible polymer dots for fluorescence switching CHEMICAL COMMUNICATIONS Osakada, Y., Hanson, L., Cui, B. 2012; 48 (27): 3285-3287

  Abstract

  The photochromic molecule diarylethene works as a "toggle switch" for biocompatible fluorescence polymer dots and enables fluorescence switching in biological samples.

  View details for DOI 10.1039/c2cc18085e

  View details for Web of Science ID 000301057400004

  View details for PubMedID 22294244

• Automated Image Analysis for Tracking Cargo Transport in Axons MICROSCOPY RESEARCH AND TECHNIQUE Zhang, K., Osakada, Y., Xie, W., Cui, B. 2011; 74 (7): 605-613

  Abstract

  The dynamics of cargo movement in axons encodes crucial information about the underlying regulatory mechanisms of the axonal transport process in neurons, a central problem in understanding many neurodegenerative diseases. Quantitative analysis of cargo dynamics in axons usually includes three steps: (1) acquiring time-lapse image series, (2) localizing individual cargos at each time step, and (3) constructing dynamic trajectories for kinetic analysis. Currently, the later two steps are usually carried out with substantial human intervention. This article presents a method of automatic image analysis aiming for constructing cargo trajectories with higher data processing throughput, better spatial resolution, and minimal human intervention. The method is based on novel applications of several algorithms including 2D kymograph construction, seed points detection, trajectory curve tracing, back-projection to extract spatial information, and position refining using a 2D Gaussian fitting. This method is sufficiently robust for usage on images with low signal-to-noise ratio, such as those from single molecule experiments. The method was experimentally validated by tracking the axonal transport of quantum dot and DiI fluorophore-labeled vesicles in dorsal root ganglia neurons.

  View details for DOI 10.1002/jemt.20934

  View details for Web of Science ID 000292570900005

  View details for PubMedID 20945466

  View details for PubMedCentralID PMC3022967

• A Microfluidic Positioning Chamber for Long-Term Live-Cell Imaging MICROSCOPY RESEARCH AND TECHNIQUE Hanson, L., Cui, L., Xie, C., Cui, B. 2011; 74 (6): 496-501

  Abstract

  We report a microfluidic positioning chamber (MPC) that can rapidly and repeatedly relocate the same imaging area on a microscope stage. The "roof" of the microfluidic chamber was printed with serials of coordinate numbers that act as positioning marks for mammalian cells that grow attached to the "floor" of the microfluidic chamber. MPC cell culture chamber provided a simple solution for tracking the same cell or groups of cells over days or weeks. The positioning marks were used to register time-lapse images of the same imaging area to single-pixel accuracy. Using MPC cell culture chamber, we tracked the migration, division, and differentiation of individual PC12 cells for over a week using bright field and fluorescence imaging.

  View details for DOI 10.1002/jemt.20937

  View details for Web of Science ID 000291539200004

  View details for PubMedID 20936672

  View details for PubMedCentralID PMC3021629

• Vertical nanopillars for highly localized fluorescence imaging PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Xie, C., Hanson, L., Cui, Y., Cui, B. 2011; 108 (10): 3894-3899

  Abstract

  Observing individual molecules in a complex environment by fluorescence microscopy is becoming increasingly important in biological and medical research, for which critical reduction of observation volume is required. Here, we demonstrate the use of vertically aligned silicon dioxide nanopillars to achieve below-the-diffraction-limit observation volume in vitro and inside live cells. With a diameter much smaller than the wavelength of visible light, a transparent silicon dioxide nanopillar embedded in a nontransparent substrate restricts the propagation of light and affords evanescence wave excitation along its vertical surface. This effect creates highly confined illumination volume that selectively excites fluorescence molecules in the vicinity of the nanopillar. We show that this nanopillar illumination can be used for in vitro single-molecule detection at high fluorophore concentrations. In addition, we demonstrate that vertical nanopillars interface tightly with live cells and function as highly localized light sources inside the cell. Furthermore, specific chemical modification of the nanopillar surface makes it possible to locally recruit proteins of interest and simultaneously observe their behavior within the complex, crowded environment of the cell.

  View details for DOI 10.1073/pnas.1015589108

  View details for Web of Science ID 000288120400019

  View details for PubMedID 21368157

  View details for PubMedCentralID PMC3054026

• Vertical Nanopillars For Highly-Localized Fluorescence Imaging in Live Cells 55th Annual Meeting of the Biophysical-Society Cui, B., Xie, C., Hanson, L., Ziliang, C. CELL PRESS. 2011: 188–89

  View details for Web of Science ID 000306288601408

• Real-time visualization of axonal transport in neurons. Methods in molecular biology (Clifton, N.J.) Osakada, Y., Cui, B. 2011; 670: 231-243

  Abstract

  The normal function of neurons depends on the integrity of microtubule-dependent transport of cellular materials and organelles to/from their cell bodies or axon terminus. In this chapter, we describe the design and implementation of a fluorescence imaging method to visualize axonal transport in neurons directly. We combine a pseudo total internal reflection microscopy, quantum dot fluorescence labeling, microfluidic neuronal culture chamber, and single molecule detection methods to achieve a high spatial and temporal resolution in tracking nerve growth factor transport in dorsal root ganglia neurons.

  View details for DOI 10.1007/978-1-60761-744-0_16

  View details for PubMedID 20967594

• Tau Reduction Prevents A beta-Induced Defects in Axonal Transport SCIENCE Vossel, K. A., Zhang, K., Brodbeck, J., Daub, A. C., Sharma, P., Finkbeiner, S., Cui, B., Mucke, L. 2010; 330 (6001): 198-U52

  Abstract

  Amyloid-β (Aβ) peptides, derived from the amyloid precursor protein, and the microtubule-associated protein tau are key pathogenic factors in Alzheimer's disease (AD). How exactly they impair cognitive functions is unknown. We assessed the effects of Aβ and tau on axonal transport of mitochondria and the neurotrophin receptor TrkA, cargoes that are critical for neuronal function and survival and whose distributions are altered in AD. Aβ oligomers rapidly inhibited axonal transport of these cargoes in wild-type neurons. Lowering tau levels prevented these defects without affecting baseline axonal transport. Thus, Aβ requires tau to impair axonal transport, and tau reduction protects against Aβ-induced axonal transport defects.

  View details for DOI 10.1126/science.1194653

  View details for Web of Science ID 000282644600034

  View details for PubMedID 20829454

• Noninvasive Neuron Pinning with Nanopillar Arrays NANO LETTERS Xie, C., Hanson, L., Xie, W., Lin, Z., Cui, B., Cui, Y. 2010; 10 (10): 4020-4024

  Abstract

  Cell migration in a cultured neuronal network presents an obstacle to selectively measuring the activity of the same neuron over a long period of time. Here we report the use of nanopillar arrays to pin the position of neurons in a noninvasive manner. Vertical nanopillars protruding from the surface serve as geometrically better focal adhesion points for cell attachment than a flat surface. The cell body mobility is significantly reduced from 57.8 μm on a flat surface to 3.9 μm on nanopillars over a 5 day period. Yet, neurons growing on nanopillar arrays show a growth pattern that does not differ in any significant way from that seen on a flat substrate. Notably, while the cell bodies of neurons are efficiently anchored by the nanopillars, the axons and dendrites are free to grow and elongate into the surrounding area to develop a neuronal network, which opens up opportunities for long-term study of the same neurons in connected networks.

  View details for DOI 10.1021/nl101950x

  View details for Web of Science ID 000282727600038

  View details for PubMedID 20815404

  View details for PubMedCentralID PMC2955158

• Hydrodynamic interactions in ribbon channels: From quasi-one-dimensional to quasi-two-dimensional behavior PHYSICAL REVIEW E Novikov, S., Rice, S. A., Cui, B., Diamant, H., Lin, B. 2010; 82 (3)

  Abstract

  We present a study of the dynamics of confined suspensions whose dimensionality is intermediate between quasi-one-dimensional and quasi-two-dimensional (q2D) using microfluidic channels of various widths. The crossover between the two limiting behaviors is found to occur to different extent for different dynamic correlations between a pair of particles. In particular, the transverse coupling diffusion coefficient of particle pairs significantly deviates from its q2D form even in surprisingly wide channels.

  View details for DOI 10.1103/PhysRevE.82.031403

  View details for Web of Science ID 000281741000002

  View details for PubMedID 21230073

• Spreading of colloid clusters in a quasi-one-dimensional channel JOURNAL OF CHEMICAL PHYSICS Xu, X., Lin, B., Cui, B., Dinner, A. R., Rice, S. A. 2010; 132 (8)

  Abstract

  The effect of hydrodynamic interactions on the spreading of clusters of colloid particles in a quasi-one-dimensional channel is analyzed both experimentally and theoretically. An n-particle cluster spreading diffusion coefficient is defined, in terms of the displacement Deltax(t) in time t, by D(n)[triple bond]<[Sigma(i=1)(n)Deltax(i)(t)](2)>/2nt, where the average is taken over all groups of n adjacent particles. Our study focuses on the n-dependence of D(n) with some attention to the dependence of D(n) on colloid packing fraction. We find that the ratio of D(n) to the infinite dilution self-diffusion coefficient D(S)(0) increases as n increases, eventually saturating for large n. The observed dependence of D(n) on n is in satisfactory agreement with the predictions obtained from both Stokesian dynamics simulations and hydrodynamic calculations using the method of reflections.

  View details for DOI 10.1063/1.3330414

  View details for Web of Science ID 000275029200035

  View details for PubMedID 20192315

• Single-molecule imaging of NGF axonal transport in microfluidic devices LAB ON A CHIP Zhang, K., Osakada, Y., Vrljic, M., Chen, L., Mudrakola, H. V., Cui, B. 2010; 10 (19): 2566-2573

  Abstract

  Nerve growth factor (NGF) signaling begins at the nerve terminal, where it binds and activates membrane receptors and subsequently carries the cell-survival signal to the cell body through the axon. A recent study revealed that the majority of endosomes contain a single NGF molecule, which makes single-molecule imaging an essential tool for NGF studies. Despite being an increasingly popular technique, single-molecule imaging in live cells is often limited by background fluorescence. Here, we employed a microfluidic culture platform to achieve background reduction for single-molecule imaging in live neurons. Microfluidic devices guide the growth of neurons and allow separately controlled microenvironment for cell bodies or axon termini. Designs of microfluidic devices were optimized and a three-compartment device successfully achieved direct observation of axonal transport of single NGF when quantum dot labeled NGF (Qdot-NGF) was applied only to the distal-axon compartment while imaging was carried out exclusively in the cell-body compartment. Qdot-NGF was shown to move exclusively toward the cell body with a characteristic stop-and-go pattern of movements. Measurements at various temperatures show that the rate of NGF retrograde transport decreased exponentially over the range of 36-14 degrees C. A 10 degrees C decrease in temperature resulted in a threefold decrease in the rate of NGF retrograde transport. Our successful measurements of NGF transport suggest that the microfluidic device can serve as a unique platform for single-molecule imaging of molecular processes in neurons.

  View details for DOI 10.1039/c003385e

  View details for Web of Science ID 000281614900012

  View details for PubMedID 20623041

  View details for PubMedCentralID PMC2935512

• Optically Resolving Individual Microtubules in Live Axons STRUCTURE Mudrakola, H. V., Zhang, K., Cui, B. 2009; 17 (11): 1433-1441

  Abstract

  Microtubules are essential cytoskeletal tracks for cargo transportation in axons and also serve as the primary structural scaffold of neurons. Structural assembly, stability, and dynamics of axonal microtubules are of great interest for understanding neuronal functions and pathologies. However, microtubules are so densely packed in axons that their separations are well below the diffraction limit of light, which precludes using optical microscopy for live-cell studies. Here, we present a single-molecule imaging method capable of resolving individual microtubules in live axons. In our method, unlabeled microtubules are revealed by following individual axonal cargos that travel along them. We resolved more than six microtubules in a 1 microm diameter axon by real-time tracking of endosomes containing quantum dots. Our live-cell study also provided direct evidence that endosomes switch between microtubules while traveling along axons, which has been proposed to be the primary means for axonal cargos to effectively navigate through the crowded axoplasmic environment.

  View details for DOI 10.1016/j.str.2009.09.008

  View details for Web of Science ID 000272011500005

  View details for PubMedID 19913478

  View details for PubMedCentralID PMC2927971

• The Quasi-One-Dimensional Colloid Fluid Revisited JOURNAL OF PHYSICAL CHEMISTRY B Lin, B., Valley, D., Meron, M., Cui, B., Ho, H. M., Rice, S. A. 2009; 113 (42): 13742-13751

  Abstract

  We report the results of studies of the pair correlation function and equation of state of a quasi-one-dimensional colloid suspension, focusing attention on the behavior in the density range near close packing. Our data show that, despite deviations from true one-dimensional geometry, the colloid fluid is well described as a hard rod Tonks fluid. In our experimental realization, the colloid suspension does not wet the confining walls, one consequence of which is a surface tension induced weak attractive interaction between the particles. The reality of this interaction is confirmed after correction of the raw experimental data for overlap of the optical images of particles that are nearly in contact and by an alternative particle location algorithm based on edge location.

  View details for DOI 10.1021/jp9018734

  View details for Web of Science ID 000270670800010

  View details for PubMedID 19569626

• Structure of quasi-one-dimensional ribbon colloid suspensions PHYSICAL REVIEW E Stratton, T. R., Novikov, S., Qato, R., Villarreal, S., Cui, B., Rice, S. A., Lin, B. 2009; 79 (3)

  Abstract

  We report the results of an experimental study of a colloid fluid confined to a quasi-one-dimensional (q1D) ribbon channel as a function of channel width and colloid density. Our findings confirm the principal predictions of previous theoretical studies of such systems. These are (1) that the density distribution of the liquid transverse to the ribbon channel exhibits stratification; (2) that even at the highest density the order along the strata, as measured by the longitudinal pair correlation function, is characteristic of a liquid; and (3) the q1D pair correlation functions in different strata exhibit anisotropic behavior resembling that found in a Monte Carlo simulation for the in-plane pair correlation function of a hard sphere fluid in a planar slit.

  View details for DOI 10.1103/PhysRevE.79.031406

  View details for Web of Science ID 000264767300067

  View details for PubMedID 19391943

• The coming of age of axonal neurotrophin signaling endosomes JOURNAL OF PROTEOMICS Wu, C., Cui, B., He, L., Chen, L., Mobley, W. C. 2009; 72 (1): 46-55

  Abstract

  Neurons of both the central and the peripheral nervous system are critically dependent on neurotrophic signals for their survival and differentiation. The trophic signal is originated at the axonal terminals that innervate the target(s). It has been well established that the signal must be retrogradely transported back to the cell body to exert its trophic effect. Among the many forms of transmitted signals, the signaling endosome serves as a primary means to ensure that the retrograde signal is delivered to the cell body with sufficient fidelity and specificity. Recent evidence suggests that disruption of axonal transport of neurotrophin signals may contribute to neurodegenerative diseases such as Alzheimer's disease and Down syndrome. However, the identity of the endocytic vesicular carrier(s), and the mechanisms involved in retrogradely transporting the signaling complexes remain a matter of debate. In this review, we summarize current insights that are mainly based on classical hypothesis-driven research, and we emphasize the urgent needs to carry out proteomics to resolve the controversies in the field.

  View details for DOI 10.1016/j.jprot.2008.10.007

  View details for Web of Science ID 000264320700006

  View details for PubMedID 19028611

  View details for PubMedCentralID PMC2677075

• Pair diffusion in quasi-one- and quasi-two-dimensional binary colloid suspensions JOURNAL OF CHEMICAL PHYSICS Valley, D. T., Rice, S. A., Cui, B., Ho, H. M., Diamant, H., Lin, B. 2007; 126 (13)

  Abstract

  The authors report the results of measurements of the center of mass and relative pair diffusion coefficients in quasi-one-dimensional (q1D) and quasi-two-dimensional (q2D) binary colloid suspensions. The new results extend the findings of similar studies of one-component quasi-one-dimensional and quasi-two-dimensional colloid suspensions. Our principal new finding is that the presence of the smaller diameter component can destroy the oscillatory structure of the separation dependence of the q2D relative pair diffusion coefficient of the large particles even though the oscillatory character of the large particle equilibrium pair correlation function remains prominent, and that no such effect occurs with the q1D suspension. An interpretation of these results is proposed.

  View details for DOI 10.1063/1.2719191

  View details for Web of Science ID 000245512400059

  View details for PubMedID 17430068

• Correlated particle dynamics in concentrated quasi-two-dimensional suspensions JOURNAL OF PHYSICS-CONDENSED MATTER Diamant, H., Cui, B., Lin, B., Rice, S. A. 2005; 17 (49): S4047-S4058

  View details for DOI 10.1088/0953-8984/17/49/003

  View details for Web of Science ID 000235147000004

• Hydrodynamic interaction in quasi-two-dimensional suspensions International Workshop on Physics of Soft Matter Complexes Diamant, H., Cui, B., Lin, B., Diamant', H. IOP PUBLISHING LTD. 2005: S2787–S2793

  View details for DOI 10.1088/0953-8984/17/31/003

  View details for Web of Science ID 000231935000004

• Anomalous behavior of the depletion potential in quasi-two-dimensional binary mixtures PHYSICAL REVIEW E Cui, B., Lin, B., Frydel, D., Rice, S. A. 2005; 72 (2)

  Abstract

  We report an experimental determination of the depletion interaction between a pair of large colloid particles present in a binary colloid mixture that has a high density of large particles and is tightly confined between two parallel plates, as a function of the small colloid particle density. The bare interaction between the large particles in the one component large colloid suspension, and the effective potential between the large particles in the binary colloid suspension represented as a pseudo-one-component fluid, were obtained by inverting the Ornstein-Zernike equation with the hypernetted chain closure. The depletion interaction is defined by subtracting the bare potential from the effective potential at fixed large colloid density. We find that the depletion potential in the quasi-two-dimensional (Q2D) system is purely attractive and short ranged as described by Asakura-Oosawa model. However, the depth of the depletion potential is found to be almost an order of magnitude larger than the counterpart depletion potential predicted for the same density and diameter ratio in a three-dimensional system. Although it is expected that the confining walls in the Q2D geometry enhance the excluded volume effects that generate entropic attraction, the observed enhancement is much larger than predicted for a Q2D binary mixture of hard spheres. We speculate that this anomalously strong confinement-induced depletion potential is a signature of characteristics of the real confined binary colloid mixture that are not included in any extant theory of the depletion interaction, specifically the omission of the role of the solvent in those theories. One such characteristic could be differential wall or particle wetting that generates a wall induced one-particle effective potential that confines the centers of the small particles to lie closer to the midplane between the walls than expected from the wall separation and the direct particle-wall interaction, thereby enhancing the depletion interaction.

  View details for DOI 10.1103/PhysRevE.72.021402

  View details for Web of Science ID 000231564000027

  View details for PubMedID 16196560

• From random walk to single-file diffusion PHYSICAL REVIEW LETTERS Lin, B. H., Meron, M., Cui, B. X., Rice, S. A., Diamant, H. 2005; 94 (21)

  Abstract

  We report an experimental study of diffusion in a quasi-one-dimensional (q1D) colloid suspension which behaves like a Tonks gas. The mean squared displacement as a function of time is described well with an ansatz encompassing a time regime that is both shorter and longer than the mean time between collisions. The ansatz asserts that the inverse mean squared displacement is the sum of the inverse mean squared displacement for short time normal diffusion (random walk) and the inverse mean squared displacement for asymptotic single-file diffusion (SFD). The dependence of the 1D mobility in the SFD on the concentration of the colloids agrees quantitatively with that derived for a hard rod model, which confirms for the first time the validity of the hard rod SFD theory. We also show that a recent SFD theory by Kollmann leads to the hard rod SFD theory for a Tonks gas.

  View details for DOI 10.1103/PhysRevLett.94.216001

  View details for Web of Science ID 000229543900028

  View details for PubMedID 16090331

• Neuronal network in a microfluidic device 49th Annual Meeting of the Biophysical-Society Cui, B. X., Wu, C. B., Mobley, W., Chu, S. CELL PRESS. 2005: 519A–520A

  View details for Web of Science ID 000226378502540

• Anomalous hydrodynamic interaction in a quasi-two-dimensional suspension PHYSICAL REVIEW LETTERS Cui, B. X., Diamant, H., Lin, B. H., Rice, S. A. 2004; 92 (25)

  Abstract

  We study the correlated Brownian motion of micron-sized particles suspended in water and confined between two plates. The hydrodynamic interaction between the particles exhibits three anomalies. (i) The transverse coupling is negative; i.e., particles exert "antidrag" on one another when moving perpendicular to their connecting line. (ii) The interaction decays with interparticle distance r as 1/r(2), faster than in unconfined suspensions but slower than near a single wall. (iii) At large distances, the pair interaction is independent of concentration within the experimental accuracy. The confined suspension thus provides an unusual example of long-range, yet essentially pairwise, correlations even at high concentration. These effects are shown to arise from the two-dimensional dipolar form of the flow induced by single-particle motion.

  View details for DOI 10.1103/PhysRevLett.92.258301

  View details for Web of Science ID 000222266100081

  View details for PubMedID 15245065

• Structure and phase transitions in confined binary colloid mixtures JOURNAL OF CHEMICAL PHYSICS Cui, B., Lin, B., Rice, S. A. 2003; 119 (4): 2386-2398

  View details for DOI 10.1063/1.1583674

  View details for Web of Science ID 000184103000062

• Screened hydrodynamic interaction in a narrow channel PHYSICAL REVIEW LETTERS Cui, B. X., Diamant, H., Lin, B. H. 2002; 89 (18)

  Abstract

  We study experimentally and theoretically the hydrodynamic coupling between Brownian colloidal particles diffusing along a linear channel. The quasi-one-dimensional confinement, unlike other constrained geometries, leads to a sharply screened interaction. Consequently, particles move in concert only when their mutual distance is smaller than the channel width, and two-body interactions remain dominant up to high particle densities. The coupling in a cylindrical channel is predicted to reverse sign at a certain distance, yet this unusual effect is too small to be currently detectable.

  View details for DOI 10.1103/PhysRevLett.89.188302

  View details for Web of Science ID 000178622000060

  View details for PubMedID 12398643

• Hydrodynamic coupling in diffusion of quasi-one-dimensional Brownian particles EUROPHYSICS LETTERS Lin, B. H., Cui, B. X., Lee, J. H., Yu, J. 2002; 57 (5): 724-730

  View details for Web of Science ID 000174179900016

• Equilibrium structure and effective pair interaction in a quasi-one-dimensional colloid liquid JOURNAL OF CHEMICAL PHYSICS Cui, B. X., Lin, B. H., Sharma, S., Rice, S. A. 2002; 116 (7): 3119-3127

  View details for Web of Science ID 000173618900051

• Dynamical heterogeneity in a dense quasi-two-dimensional colloidal liquid JOURNAL OF CHEMICAL PHYSICS Cui, B. X., Lin, B. H., Rice, S. A. 2001; 114 (20): 9142-9155

  View details for Web of Science ID 000168580500046