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Guo J, Artur C, Womack T, Eriksen JL, Mayerich D. Multiplex protein-specific microscopy with ultraviolet surface excitation. BIOMEDICAL OPTICS EXPRESS 2020; 11:99-108. [PMID: 32010503 PMCID: PMC6968765 DOI: 10.1364/boe.11.000099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 06/01/2023]
Abstract
Immunohistochemical techniques, such as immunofluorescence (IF) staining, enable microscopic imaging of local protein expression within tissue samples. Molecular profiling enabled by IF is critical to understanding pathogenesis and is often involved in complex diagnoses. A recent innovation, known as microscopy with ultraviolet surface excitation (MUSE), uses deep ultraviolet (≈280 nm) illumination to excite labels at the tissue surface, providing equivalent images without fixation, embedding, and sectioning. However, MUSE has not yet been integrated into traditional IF pipelines. This limits its application in more complex diagnoses that rely on protein-specific markers. This paper aims to broaden the applicability of MUSE to multiplex immunohistochemistry using quantum dot nanoparticles. We demonstrate the advantages of quantum dot labels for protein-specific MUSE imaging on both paraffin-embedded and intact tissue, significantly expanding MUSE applicability to protein-specific applications. Furthermore, with recent innovations in three-dimensional ultraviolet fluorescence microscopy, this opens the door to three-dimensional IF imaging with quantum dots using ultraviolet excitation.
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Affiliation(s)
- Jiaming Guo
- University of Houston, Department of Electrical and Computer Engineering, Houston, TX 77004, USA
- These authors contributed equally to this work
| | - Camille Artur
- University of Houston, Department of Electrical and Computer Engineering, Houston, TX 77004, USA
- These authors contributed equally to this work
| | - Tasha Womack
- University of Houston, Department of Pharmacology, Houston, TX 77004, USA
| | - Jason L. Eriksen
- University of Houston, Department of Pharmacology, Houston, TX 77004, USA
| | - David Mayerich
- University of Houston, Department of Electrical and Computer Engineering, Houston, TX 77004, USA
- University of Houston, NSF I/UCRC BRAIN Center, Houston, TX 77004, USA
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52
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Abstract
The selective immobilization of proteins represents an essential step in the selection of binding proteins such as antibodies. The immobilization strategy determines how the target protein is presented to the binders and thereby directly affects the experimental outcome. This poses specific challenges for membrane proteins due to their inherent lack of stability and limited exposed hydrophilic surfaces. Here we detail methodologies for the selective immobilization of membrane proteins based on the strong biotin-avidin interaction and with a specific focus on its application for the selection of nanobodies and sybodies. We discuss the challenges in generating and benefits of obtaining an equimolar biotin to target-protein ratio.
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53
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Hendler-Neumark A, Bisker G. Fluorescent Single-Walled Carbon Nanotubes for Protein Detection. SENSORS (BASEL, SWITZERLAND) 2019; 19:E5403. [PMID: 31817932 PMCID: PMC6960995 DOI: 10.3390/s19245403] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/06/2023]
Abstract
Nanosensors have a central role in recent approaches to molecular recognition in applications like imaging, drug delivery systems, and phototherapy. Fluorescent nanoparticles are particularly attractive for such tasks owing to their emission signal that can serve as optical reporter for location or environmental properties. Single-walled carbon nanotubes (SWCNTs) fluoresce in the near-infrared part of the spectrum, where biological samples are relatively transparent, and they do not photobleach or blink. These unique optical properties and their biocompatibility make SWCNTs attractive for a variety of biomedical applications. Here, we review recent advancements in protein recognition using SWCNTs functionalized with either natural recognition moieties or synthetic heteropolymers. We emphasize the benefits of the versatile applicability of the SWCNT sensors in different systems ranging from single-molecule level to in-vivo sensing in whole animal models. Finally, we discuss challenges, opportunities, and future perspectives.
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Affiliation(s)
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel-Aviv University, Tel Aviv 6997801, Israel;
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Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A. Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B. subtilis. Cell Rep 2019; 24:1890-1901.e8. [PMID: 30110644 DOI: 10.1016/j.celrep.2018.07.047] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 07/02/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022] Open
Abstract
The ubiquitous coenzyme nicotinamide adenine dinucleotide (NAD) decorates various RNAs in different organisms. In the proteobacterium Escherichia coli, the NAD-cap confers stability against RNA degradation. To date, NAD-RNAs have not been identified in any other bacterial microorganism. Here, we report the identification of NAD-RNA in the firmicute Bacillus subtilis. In the late exponential growth phase, predominantly mRNAs are NAD modified. NAD is incorporated de novo into RNA by the cellular RNA polymerase using non-canonical transcription initiation. The incorporation efficiency depends on the -1 position of the promoter but is independent of sigma factors or mutations in the rifampicin binding pocket. RNA pyrophosphohydrolase BsRppH is found to decap NAD-RNA. In vitro, the decapping activity is facilitated by manganese ions and single-stranded RNA 5' ends. Depletion of BsRppH influences the gene expression of ∼13% of transcripts in B. subtilis. The NAD-cap stabilizes RNA against 5'-to-3'-exonucleolytic decay by RNase J1.
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Affiliation(s)
- Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Yaqing Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Gabriele Nübel
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Masroor Kahloon
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Leonie Kolmar
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Group, Core Facility Genomics and Proteomics, German Cancer Research Center (DKFZ), DKFZ-Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Alliance, 69120 Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany.
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55
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Stevens LM, Zhang Y, Volnov Y, Chen G, Stein DS. Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation. PLoS One 2019; 14:e0219878. [PMID: 31658274 PMCID: PMC6816556 DOI: 10.1371/journal.pone.0219878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
The extraordinarily strong non-covalent interaction between biotin and avidin (kD = 10-14-10-16) has permitted this interaction to be used in a wide variety of experimental contexts. The Biotin Acceptor Peptide (BAP), a 15 amino acid motif that can be biotinylated by the E. coli BirA protein, has been fused to proteins-of-interest, making them substrates for in vivo biotinylation. Here we report on the construction and characterization of a modified BirA bearing signals for secretion and endoplasmic reticulum (ER) retention, for use in experimental contexts requiring biotinylation of secreted proteins. When expressed in the Drosophila female germline or ovarian follicle cells under Gal4-mediated transcriptional control, the modified BirA protein could be detected and shown to be enzymatically active in ovaries and progeny embryos. Surprisingly, however, it was not efficiently retained in the ER, and instead appeared to be secreted. To determine whether this secreted protein, now designated secBirA, could biotinylate secreted proteins, we generated BAP-tagged versions of two secreted Drosophila proteins, Torsolike (Tsl) and Gastrulation Defective (GD), which are normally expressed maternally and participate in embryonic pattern formation. Both Tsl-BAP and GD-BAP were shown to exhibit normal patterning activity. Co-expression of Tsl-BAP together with secBirA in ovarian follicle cells resulted in its biotinylation, which permitted its isolation from both ovaries and progeny embryos using Avidin-coupled affinity matrix. In contrast, co-expression with secBirA in the female germline did not result in detectable biotinylation of GD-BAP, possibly because the C-terminal location of the BAP tag made it inaccessible to BirA in vivo. Our results indicate that secBirA directs biotinylation of proteins bound for secretion in vivo, providing access to powerful experimental approaches for secreted proteins-of-interest. However, efficient biotinylation of target proteins may vary depending upon the location of the BAP tag or other structural features of the protein.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuan Zhang
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuri Volnov
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Geng Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - David S. Stein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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56
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Wan Y, McDole K, Keller PJ. Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes. Annu Rev Cell Dev Biol 2019; 35:655-681. [PMID: 31299171 DOI: 10.1146/annurev-cellbio-100818-125311] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability to visualize and quantitatively measure dynamic biological processes in vivo and at high spatiotemporal resolution is of fundamental importance to experimental investigations in developmental biology. Light-sheet microscopy is particularly well suited to providing such data, since it offers exceptionally high imaging speed and good spatial resolution while minimizing light-induced damage to the specimen. We review core principles and recent advances in light-sheet microscopy, with a focus on concepts and implementations relevant for applications in developmental biology. We discuss how light-sheet microcopy has helped advance our understanding of developmental processes from single-molecule to whole-organism studies, assess the potential for synergies with other state-of-the-art technologies, and introduce methods for computational image and data analysis. Finally, we explore the future trajectory of light-sheet microscopy, discuss key efforts to disseminate new light-sheet technology, and identify exciting opportunities for further advances.
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Affiliation(s)
- Yinan Wan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
| | - Katie McDole
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA;
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57
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58
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Reshetniak S, Rizzoli SO. Interrogating Synaptic Architecture: Approaches for Labeling Organelles and Cytoskeleton Components. Front Synaptic Neurosci 2019; 11:23. [PMID: 31507402 PMCID: PMC6716447 DOI: 10.3389/fnsyn.2019.00023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 01/06/2023] Open
Abstract
Synaptic transmission has been studied for decades, as a fundamental step in brain function. The structure of the synapse, and its changes during activity, turned out to be key aspects not only in the transfer of information between neurons, but also in cognitive processes such as learning and memory. The overall synaptic morphology has traditionally been studied by electron microscopy, which enables the visualization of synaptic structure in great detail. The changes in the organization of easily identified structures, such as the presynaptic active zone, or the postsynaptic density, are optimally studied via electron microscopy. However, few reliable methods are available for labeling individual organelles or protein complexes in electron microscopy. For such targets one typically relies either on combination of electron and fluorescence microscopy, or on super-resolution fluorescence microscopy. This review focuses on approaches and techniques used to specifically reveal synaptic organelles and protein complexes, such as cytoskeletal assemblies. We place the strongest emphasis on methods detecting the targets of interest by affinity binding, and we discuss the advantages and limitations of each method.
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Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
- International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Silvio O. Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
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59
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Li N, Zhang W, Li Y, Lin JM. Analysis of cellular biomolecules and behaviors using microfluidic chip and fluorescence method. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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60
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Chadha A, Volland S, Baliaouri NV, Tran EM, Williams DS. The route of the visual receptor rhodopsin along the cilium. J Cell Sci 2019; 132:jcs.229526. [PMID: 30975916 DOI: 10.1242/jcs.229526] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
The photoreceptor outer segment is the most elaborate primary cilium, containing large amounts of rhodopsin (RHO) in disk membranes that grow from a connecting cilium. The movement of RHO along the connecting cilium precedes formation of the disk membranes. However, the route that RHO takes has not been clearly determined; some reports suggest that it follows an intracellular, vesicular route along the axoneme, possibly as an adaptation for the high load of delivery or the morphogenesis of the disk endomembranes. We addressed this question by studying RHO in cilia of IMCD3 cells and mouse rod photoreceptors. In IMCD3 cilia, fluorescence recovery after photobleaching (FRAP) experiments with fluorescently tagged RHO supported the idea of RHO motility in the ciliary plasma membrane and was inconsistent with the hypothesis of RHO motility within the lumen of the cilium. In rod photoreceptors, FRAP of RHO-EGFP was altered by externally applied lectin, supporting the idea of plasmalemmal RHO dynamics. Quantitative immunoelectron microscopy corroborated our live-cell conclusions, as RHO was found to be distributed along the plasma membrane of the connecting cilium, with negligible labeling within the axoneme. Taken together, the present findings demonstrate RHO trafficking entirely via the ciliary plasma membrane.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Abhishek Chadha
- Departments of Ophthalmology and Neurobiology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - Stefanie Volland
- Departments of Ophthalmology and Neurobiology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - Natella V Baliaouri
- Departments of Ophthalmology and Neurobiology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - Elaine M Tran
- Departments of Ophthalmology and Neurobiology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - David S Williams
- Departments of Ophthalmology and Neurobiology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA .,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.,Brain Research Institute, University of California, Los Angeles, CA 90095, USA
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61
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Temporal dependence of shifts in mu opioid receptor mobility at the cell surface after agonist binding observed by single-particle tracking. Sci Rep 2019; 9:7297. [PMID: 31086197 PMCID: PMC6514008 DOI: 10.1038/s41598-019-43657-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 04/24/2019] [Indexed: 01/13/2023] Open
Abstract
Agonist binding to the mu opioid receptor (MOR) results in conformational changes that allow recruitment of G-proteins, activation of downstream effectors and eventual desensitization and internalization, all of which could affect receptor mobility. The present study employed single particle tracking (SPT) of quantum dot labeled FLAG-tagged MORs to examine shifts in MOR mobility after agonist binding. FLAG-MORs on the plasma membrane were in both mobile and immobile states under basal conditions. Activation of FLAG-MORs with DAMGO caused an acute increase in the fraction of mobile MORs, and free portions of mobile tracks were partially dependent on interactions with G-proteins. In contrast, 10-minute exposure to DAMGO or morphine increased the fraction of immobile FLAG-MORs. While the decrease in mobility with prolonged DAMGO exposure corresponded to an increase in colocalization with clathrin, the increase in colocalization was present in both mobile and immobile FLAG-MORs. Thus, no single mobility state of the receptor accounted for colocalization with clathrin. These findings demonstrate that SPT can be used to track agonist-dependent changes in MOR mobility over time, but that the mobility states observed likely arise from a diverse set of interactions and will be most informative when examined in concert with particular downstream effectors.
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62
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Fathi P, Khamo JS, Huang X, Srivastava I, Esch MB, Zhang K, Pan D. Bulk-state and single-particle imaging are central to understanding carbon dot photo-physics and elucidating the effects of precursor composition and reaction temperature. CARBON 2019; 145:10.1016/j.carbon.2018.12.105. [PMID: 34795455 PMCID: PMC8596966 DOI: 10.1016/j.carbon.2018.12.105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Carbon dots have garnered attention for their strong multi-color luminescence properties and unprecedented biocompatibility. Despite significant progress in the recent past, a fundamental understanding of their photoluminescence and structure-properties relationships, especially at the bulk vs. single-particle level, has not been well established. Here we present a comparative study of bulk- and single-particle properties as a function of precursor composition and reaction temperature. The synthesis and characterization of multicolored inherently functionalized carbon dots were achieved from a variety of carbon sources, and at synthesis temperatures of 150 °C and 200 °C. Solvothermal synthesis at 200 °C led to quantum yields as high as 86%, smaller particle sizes, and a narrowed fluorescence emission, while synthesis at 150 °C resulted in a greater UV-visible absorbance, increase in nanoparticle stability, red-shifted fluorescence, and a greater resistance to bulk photobleaching. These results suggest the potential for synthesis temperature to be utilized as a simple tool for modulating carbon dot photophysical properties. Single-particle imaging resolved that particle brightness was determined by both the instantaneous intensity and the on-time duty cycle. Increasing the synthesis temperature caused an enhancement in blinking frequency, which led to an increase in on-time duty cycle in three out of four precursors.
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Affiliation(s)
- Parinaz Fathi
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
- Biomedical Technologies Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - John S. Khamo
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xuedong Huang
- Department of Chemistry, Fudan University, Shanghai, PR China
| | - Indrajit Srivastava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
| | - Mandy B. Esch
- Biomedical Technologies Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kai Zhang
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Dipanjan Pan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
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63
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Granhøj J, Dimke H, Svenningsen P. A bacterial display system for effective selection of protein-biotin ligase BirA variants with novel peptide specificity. Sci Rep 2019; 9:4118. [PMID: 30858523 PMCID: PMC6411976 DOI: 10.1038/s41598-019-40984-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/14/2019] [Indexed: 11/09/2022] Open
Abstract
Biotinylation creates a sensitive and specific tag for purification and detection of target proteins. The E. coli protein-biotin ligase BirA biotinylates a lysine within a synthetic biotin acceptor peptide (AP) and allow for specific tagging of proteins fused to the AP. The approach is not applicable to unmodified proteins, and we sought to develop an effective selection system that could form the basis for directed evolution of novel BirA variants with specificity towards unmodified proteins. The system was based on bacterial display of a target peptide sequence, which could be biotinylated by cytosolic BirA variants before being displayed on the surface. In a model selection, the bacterial display system accomplished >1.000.000 enrichment in a single selection step. A randomly mutated BirA library was used to identify novel variants. Bacteria displaying peptide sequences from 13 out of 14 tested proteins were strongly enriched after 3-5 selection rounds. Moreover, a clone selected for biotinylation of a C-terminal peptide from red-fluorescent protein TagRFP showed biotinylation of the native protein. Thus, active BirA variants with novel activity are effectively isolated with our bacterial display system and provides a basis for the development of BirA variants for site-selective biotinylation.
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Affiliation(s)
- Jeff Granhøj
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Henrik Dimke
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Per Svenningsen
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
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64
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Chamma I, Sainlos M, Thoumine O. Biophysical mechanisms underlying the membrane trafficking of synaptic adhesion molecules. Neuropharmacology 2019; 169:107555. [PMID: 30831159 DOI: 10.1016/j.neuropharm.2019.02.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/14/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
Abstract
Adhesion proteins play crucial roles at synapses, not only by providing a physical trans-synaptic linkage between axonal and dendritic membranes, but also by connecting to functional elements including the pre-synaptic neurotransmitter release machinery and post-synaptic receptors. To mediate these functions, adhesion proteins must be organized on the neuronal surface in a precise and controlled manner. Recent studies have started to describe the mobility, nanoscale organization, and turnover rate of key synaptic adhesion molecules including cadherins, neurexins, neuroligins, SynCAMs, and LRRTMs, and show that some of these proteins are highly mobile in the plasma membrane while others are confined at sub-synaptic compartments, providing evidence for different regulatory pathways. In this review article, we provide a biophysical view of the diffusional trapping of adhesion molecules at synapses, involving both extracellular and intracellular protein interactions. We review the methodology underlying these measurements, including biomimetic systems with purified adhesion proteins, means to perturb protein expression or function, single molecule imaging in cultured neurons, and analytical models to interpret the data. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Ingrid Chamma
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France
| | - Matthieu Sainlos
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France
| | - Olivier Thoumine
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France.
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65
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Lukashev EP, Petrovskaya LE, Tretyak MV, Kryukova EA, Sizova SV, Oleinikov VA. Formation of an Efficient Energy Transfer Complex between Quantum Dots and Exiguobacterium sibiricum Retinal Protein via the Histidine-Cysteine Anchor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162018050114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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66
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Bercier V, Rosello M, Del Bene F, Revenu C. Zebrafish as a Model for the Study of Live in vivo Processive Transport in Neurons. Front Cell Dev Biol 2019; 7:17. [PMID: 30838208 PMCID: PMC6389722 DOI: 10.3389/fcell.2019.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Motor proteins are responsible for transport of vesicles and organelles within the cell cytoplasm. They interact with the actin cytoskeleton and with microtubules to ensure communication and supply throughout the cell. Much work has been done in vitro and in silico to unravel the key players, including the dynein motor complex, the kinesin and myosin superfamilies, and their interacting regulatory complexes, but there is a clear need for in vivo data as recent evidence suggests previous models might not recapitulate physiological conditions. The zebrafish embryo provides an excellent system to study these processes in intact animals due to the ease of genetic manipulation and the optical transparency allowing live imaging. We present here the advantages of the zebrafish embryo as a system to study live in vivo processive transport in neurons and provide technical recommendations for successful analysis.
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Affiliation(s)
- Valérie Bercier
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France.,Laboratory of Neurobiology, Center for Brain and Disease Research, Research Group Experimental Neurology, Department of Neurosciences, VIB-KU Leuven, Leuven, Belgium
| | - Marion Rosello
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Céline Revenu
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
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67
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Song D, Jung Y. Homo-molecular Fluorescence Complementation for Direct Visualization of Receptor Oligomerization in Living Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daesun Song
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
| | - Yongwon Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
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68
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Tian X, Hussain S, de Pace C, Ruiz-Pérez L, Battaglia G. Zn II Complexes for Bioimaging and Correlated Applications. Chem Asian J 2019; 14:509-526. [PMID: 30716209 DOI: 10.1002/asia.201801437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/31/2018] [Indexed: 11/09/2022]
Abstract
Zinc is a biocompatible element that exists as the second most abundant transition metal ion and an indispensable trace element in the human body. Compared to traditional metal-organic complexes systems, d10 metal ZnII complexes not only exhibit a large Stokes shift and good photon stability but also possess strong emission and low cytotoxicity with a relatively small molecular weight. The use of ZnII complexes has emerged in the last decade as a versatile and convenient tool for numerous biological applications, including bioimaging, molecular and protein recognition, as well as photodynamic therapy. Herein, we review recent developments involving ZnII metal complexes applied as specific subcellular compartment imaging probes and their correlated utilizations.
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Affiliation(s)
- Xiaohe Tian
- School of life science, Anhui University, Hefei, 230039, P.R. China
| | - Sajid Hussain
- School of life science, Anhui University, Hefei, 230039, P.R. China.,School of Applied Sciences and Humanities (NUSASH), National University of Technology, Sector I-12, Islamabad, Pakistan
| | - Cesare de Pace
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Lorena Ruiz-Pérez
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Giuseppe Battaglia
- School of life science, Anhui University, Hefei, 230039, P.R. China.,Department of Chemistry, University College London, London, WC1H 0AJ, UK
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69
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Choi H, Lee JM, Jung Y. Monomeric Covalent-Avidin for Rapid and Covalent Labeling of Quantum Dots to Cell Surface Proteins. ACTA ACUST UNITED AC 2019; 3:e1800288. [PMID: 32627405 DOI: 10.1002/adbi.201800288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/26/2018] [Indexed: 01/25/2023]
Abstract
With high brightness and photostability, quantum dots (QDs) are potent probes for long-term imaging of dynamic cell surface proteins, but practical methods to covalently label QDs to target proteins for stable imaging are largely lacking. Here, a small covalent-bond forming protein (Covalent-avidin)/peptide pair is introduced, which provides a recombinant protein-based rapid and covalent QD labeling strategy. Covalent-avidin is constructed by optimized fusion of circular permuted monomeric avidin to SpyCatcher, which forms an isopeptide bond with the SpyTag peptide. Covalent-avidin-conjugated QDs allow for strong and irreversible QD labeling to the biotinylated SpyTag-fused adrenergic receptor on live cells in 2 min. In addition, QDs with only a minimum number of conjugated Covalent-avidin show more stable receptor labeling than commercially available streptavidin-conjugated QDs, also with minimal unwanted clustering of labeled receptors. Monomeric Covalent-avidin will be a valuable protein linker for diverse other nanolabeling structures with beneficial properties such as covalent linkages and facile valency control.
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Affiliation(s)
- Hyeokjune Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Jeong Min Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Yongwon Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
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70
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Song D, Jung Y. Homo-molecular Fluorescence Complementation for Direct Visualization of Receptor Oligomerization in Living Cells. Angew Chem Int Ed Engl 2019; 58:2045-2049. [PMID: 30561874 DOI: 10.1002/anie.201812780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 01/14/2023]
Abstract
Cell surface receptor oligomerization is an attractive target process for drug screening. However, simple but reliable (and thus high-throughput) visualization methods for receptor oligomerization are still lacking. Herein, we report on a new single-construct homo-molecular fluorescence complementation (Homo-FC) probe, which shows strong fluorescence signals by oligomerization of fused receptors in living cells with unexpectedly low background signals. Importantly, this high signal-to-noise ratio was not affected by expression level variations of fused receptors. The Homo-FC probe was developed by optimized flopped fusion of split fragments of superfolder green fluorescence protein and subsequent surface charge engineering. Homo-FC reliably visualized the oligomerization of diverse natural receptors such as GPCR, EGFR, and even cytosolic DAI.
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Affiliation(s)
- Daesun Song
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Yongwon Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
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71
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Zhang F, Yan S, Guo H, Chen Q, Fang Q. Characterization of viral entry and infection of quantum dot-labeled grass carp reovirus. Virol Sin 2018; 32:163-166. [PMID: 28466443 DOI: 10.1007/s12250-016-3903-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Fuxian Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shicui Yan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hong Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qingxiu Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qin Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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72
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Letellier M, Szíber Z, Chamma I, Saphy C, Papasideri I, Tessier B, Sainlos M, Czöndör K, Thoumine O. A unique intracellular tyrosine in neuroligin-1 regulates AMPA receptor recruitment during synapse differentiation and potentiation. Nat Commun 2018; 9:3979. [PMID: 30266896 PMCID: PMC6162332 DOI: 10.1038/s41467-018-06220-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/13/2018] [Indexed: 01/08/2023] Open
Abstract
To better understand the molecular mechanisms by which early neuronal connections mature into synapses, we examined the impact of neuroligin-1 (Nlg1) phosphorylation on synapse differentiation, focusing on a unique intracellular tyrosine (Y782), which differentially regulates Nlg1 binding to PSD-95 and gephyrin. By expressing Nlg1 point mutants (Y782A/F) in hippocampal neurons, we show using imaging and electrophysiology that Y782 modulates the recruitment of functional AMPA receptors (AMPARs). Nlg1-Y782F impaired both dendritic spine formation and AMPAR diffusional trapping, but not NMDA receptor recruitment, revealing the assembly of silent synapses. Furthermore, replacing endogenous Nlg1 with either Nlg1-Y782A or -Y782F in CA1 hippocampal neurons impaired long-term potentiation (LTP), demonstrating a critical role of AMPAR synaptic retention. Screening of tyrosine kinases combined with pharmacological inhibitors point to Trk family members as major regulators of endogenous Nlg1 phosphorylation and synaptogenic function. Thus, Nlg1 tyrosine phosphorylation signaling is a critical event in excitatory synapse differentiation and LTP. Neuroligins are postsynaptic cell adhesion molecules thought to play roles in synaptic development and function. Here, authors show that phosphorylation of Y782 in neuroligin-1 modulates its role in differentiation and ability to recruit AMPARs including during long-term potentiation.
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Affiliation(s)
- Mathieu Letellier
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France. .,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France.
| | - Zsófia Szíber
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Ingrid Chamma
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Camille Saphy
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Ioanna Papasideri
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Béatrice Tessier
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Matthieu Sainlos
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Katalin Czöndör
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France
| | - Olivier Thoumine
- Interdisciplinary Institute for Neuroscience, UMR 5297, Univ. Bordeaux, F-33000, Bordeaux, France. .,Interdisciplinary Institute for Neuroscience, UMR 5297, CNRS, F-33000, Bordeaux, France.
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73
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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74
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Delgado JY, Selvin PR. A Revised View on the Role of Surface AMPAR Mobility in Tuning Synaptic Transmission: Limitations, Tools, and Alternative Views. Front Synaptic Neurosci 2018; 10:21. [PMID: 30079019 PMCID: PMC6062754 DOI: 10.3389/fnsyn.2018.00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
Calcium dynamics in presynaptic terminals regulate the response dynamics of most central excitatory synapses. However, this dogma has been challenged by the hypothesis that mobility of the postsynaptic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype glutamate receptors (AMPAR) plays a role in tuning fast excitatory synaptic transmission. In this review, we reevaluate the factors regulating postsynaptic AMPAR mobility, reassess the modeling parameters, analyze the experimental tools, and end by providing alternative ideas stemming from recent results. In particular, newer methods of labeling AMPARs with small fluorophores in live neurons, combined with super-resolution microscopy and sub-second dynamics, lends support to the idea that AMPARs are primarily within the synapse, are greatly constrained, and have much slower mobility than previously thought. We discuss new experiments which may be necessary to readdress the role of postsynaptic AMPAR mobility in tuning fast excitatory synaptic transmission.
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Affiliation(s)
- Jary Y Delgado
- Department of Neurobiology, The University of Chicago, Chicago, IL, United States
| | - Paul R Selvin
- Department of Physics, Biophysics, and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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75
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Synthesis of Metallic Silver Nanoparticles by Fluconazole Drug and Gamma Rays to Inhibit the Growth of Multidrug-Resistant Microbes. J CLUST SCI 2018. [DOI: 10.1007/s10876-018-1411-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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76
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Manzoor O, Soleja N, Mohsin M. Nanoscale gizmos - the novel fluorescent probes for monitoring protein activity. Biochem Eng J 2018; 133:83-95. [PMID: 32518506 PMCID: PMC7270366 DOI: 10.1016/j.bej.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/27/2017] [Accepted: 02/06/2018] [Indexed: 11/15/2022]
Abstract
Genetically-encoded FRET, organic dye, QD based sensors. Real-time monitoring of the respective metabolite level at sub cellular level. Spatio temporal resolution of the fluorophores by low intensity light. Monitoring of various metabolite levels in any cell type prokaryotic and eukaryotic as well. Functional analysis of the role of proteases in several diseases.
Nanobiotechnology has emerged inherently as an interdisciplinary field, with collaborations from researchers belonging to diverse backgrounds like molecular biology, materials science and organic chemistry. Till the current times, researchers have been able to design numerous types of nanoscale fluorescent tool kits for monitoring protein–protein interactions through real time cellular imagery in a fluorescence microscope. It is apparent that supplementing any protein of interest with a fluorescence habit traces its function and regulation within a cell. Our review therefore highlights the application of several fluorescent probes such as molecular organic dyes, quantum dots (QD) and fluorescent proteins (FPs) to determine activity state, expression and localization of proteins in live and fixed cells. The focus is on Fluorescence Resonance Energy Transfer (FRET) based nanosensors that have been developed by researchers to visualize and monitor protein dynamics and quantify metabolites of diverse nature. FRET based toolkits permit the resolution of ambiguities that arise due to the rotation of sensor molecules and flexibility of the probe. Achievements of live cell imaging and efficient spatiotemporal resolution however have been possible only with the advent of fluorescence microscopic technology, equipped with precisely sensitive automated softwares.
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77
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Kwon SJ, Kim D, Lee I, Nam J, Kim J, Dordick JS. Sensitive multiplex detection of whole bacteria using self-assembled cell binding domain complexes. Anal Chim Acta 2018; 1030:156-165. [PMID: 30032765 DOI: 10.1016/j.aca.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/14/2018] [Accepted: 05/02/2018] [Indexed: 11/29/2022]
Abstract
Detecting bacterial cells at low levels is critical in public health, the food industry and first response. Current processes typically involve laborious cell lysis and genomic DNA extraction to achieve 100-1000 CFU mL-1 levels for detecting gram-positive bacteria. As an alternative to DNA-based methods, cell wall binding domains (CBDs) derived from lysins having a modular structure with an N-terminal catalytic domain and a C-terminal CBD, can be used to detect bacterial pathogens as a result of their exceptionally specific binding to target bacteria with great avidity. We have developed a highly sensitive method for multiplex detection of whole bacterial cells using self-assembled CBD complexes. Self-assembled CBD-SA-reporter complexes were generated using streptavidin (SA), biotin-CBDs, and biotinylated reporters, such as glucose oxidase (GOx) and specific DNA sequences. The simultaneous detection of three test bacteria, Staphylococcus aureus, Bacillus anthracis-Sterne, and Listeria innocua cells in PBS could be accomplished with a 96-well plate-based sandwich method using CBD-SA-GOx complex-coupled spectrophotometric assay to achieve a detection limit of >100 CFU mL-1. To achieve greater detection sensitivity, we used CBD-SA-DNA complexes and qPCR of specific DNA barcodes selectively bound to the surface of target bacterial cells, which resulted in a detection sensitivity as low as 1-10 CFU mL-1 without cross-reactivity. This sensitive multiplex detection of bacterial pathogens using both CBD-SA-GOx and CBD-SA-DNA complexes has the potential to be quickly combined with point-of-care compatible diagnostics for the rapid detection of pathogens in test samples.
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Affiliation(s)
- Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Domyoung Kim
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Inseon Lee
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jahyun Nam
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
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78
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Oliveira D, de Melo FM, Toma HE. One-pot single step to label microtubule with MPA-capped CdTe quantum dots. Micron 2018; 108:19-23. [DOI: 10.1016/j.micron.2018.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
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79
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McHugh KJ, Jing L, Behrens AM, Jayawardena S, Tang W, Gao M, Langer R, Jaklenec A. Biocompatible Semiconductor Quantum Dots as Cancer Imaging Agents. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706356. [PMID: 29468747 DOI: 10.1002/adma.201706356] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/26/2017] [Indexed: 05/20/2023]
Abstract
Approximately 1.7 million new cases of cancer will be diagnosed this year in the United States leading to 600 000 deaths. Patient survival rates are highly correlated with the stage of cancer diagnosis, with localized and regional remission rates that are much higher than for metastatic cancer. The current standard of care for many solid tumors includes imaging and biopsy with histological assessment. In many cases, after tomographical imaging modalities have identified abnormal morphology consistent with cancer, surgery is performed to remove the primary tumor and evaluate the surrounding lymph nodes. Accurate identification of tumor margins and staging are critical for selecting optimal treatments to minimize recurrence. Visible, fluorescent, and radiolabeled small molecules have been used as contrast agents to improve detection during real-time intraoperative imaging. Unfortunately, current dyes lack the tissue specificity, stability, and signal penetration needed for optimal performance. Quantum dots (QDs) represent an exciting class of fluorescent probes for optical imaging with tunable optical properties, high stability, and the ability to target tumors or lymph nodes based on surface functionalization. Here, state-of-the-art biocompatible QDs are compared with current Food and Drug Administration approved fluorophores used in cancer imaging and a perspective on the pathway to clinical translation is provided.
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Affiliation(s)
- Kevin J McHugh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Lihong Jing
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing, 100190, China
| | - Adam M Behrens
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Surangi Jayawardena
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Wen Tang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Mingyuan Gao
- Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing, 100190, China
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Ana Jaklenec
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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80
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Sung K, Ferrari LF, Yang W, Chung C, Zhao X, Gu Y, Lin S, Zhang K, Cui B, Pearn ML, Maloney MT, Mobley WC, Levine JD, Wu C. Swedish Nerve Growth Factor Mutation (NGF R100W) Defines a Role for TrkA and p75 NTR in Nociception. J Neurosci 2018; 38:3394-3413. [PMID: 29483280 PMCID: PMC5895035 DOI: 10.1523/jneurosci.1686-17.2018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
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.
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Affiliation(s)
| | - Luiz F Ferrari
- Department of Oral Surgery, University of California San Francisco, San Francisco, California 94143
| | - Wanlin Yang
- Department of Neurosciences
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China 200025
| | - ChiHye Chung
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 143-701, South Korea
| | | | - Yingli Gu
- Department of Neurosciences
- Department of Neurology, the Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, China 150001
| | - Suzhen Lin
- Department of Neurosciences
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China 200025
| | - Kai Zhang
- Department of Chemistry
- Department of Biochemistry, Neuroscience Program, Center for Biophysics and Quantitative Biology, Chemistry-Biology Interface Training Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | | | - Matthew L Pearn
- Department of Anesthesiology, University of California San Diego, School of Medicine, La Jolla, California 92093
- V.A. San Diego Healthcare System, San Diego, California 92161
| | - Michael T Maloney
- Department of Neurosciences, Stanford University, Stanford, California 94305
| | | | - Jon D Levine
- Department of Oral Surgery, University of California San Francisco, San Francisco, California 94143
| | - Chengbiao Wu
- Department of Neurosciences,
- V.A. San Diego Healthcare System, San Diego, California 92161
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81
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Bi X, Yin J, Chen Guanbang A, Liu CF. Chemical and Enzymatic Strategies for Bacterial and Mammalian Cell Surface Engineering. Chemistry 2018; 24:8042-8050. [DOI: 10.1002/chem.201705049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaobao Bi
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Juan Yin
- Current address: Program in Neuroscience and behavioural disorders; Duke-NUS Medical School; 8 College Road Singapore 169857 Singapore
| | - Ashley Chen Guanbang
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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82
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Abstract
Ferritin subunits of heavy and light polypeptide chains self-assemble into a spherical nanocage that serves as a natural transport vehicle for metals but can include diverse cargoes. Ferritin nanoparticles are characterized by remarkable stability, small and uniform size. Chemical modifications and molecular re-engineering of ferritin yield a versatile platform of nanocarriers capable of delivering a broad range of therapeutic and imaging agents. Targeting moieties conjugated to the ferritin external surface provide multivalent anchoring of biological targets. Here, we highlight some of the current work on ferritin as well as examine potential strategies that could be used to functionalize ferritin via chemical and genetic means to enable its utility in vascular drug delivery.
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83
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Abstract
The visualization of membrane protein complexes in their natural membrane environment is a major goal in an emerging area of research termed structural cell biology. Such approaches provide important information on the spatial distribution of protein complexes in their resident cellular membrane systems and on the structural organization of multi-subunit membrane protein assemblies. We have developed a method to specifically label active membrane protein complexes in their native membrane environment with electron-dense nanoparticles coupled to an activating ligand, in order to visualize them by electron cryo-tomography. As an example, we describe here the depiction of preprotein import sites of mitochondria, formed by the translocase of the outer membrane (TOM complex) and the presequence translocase of the inner membrane (TIM23 complex). Active import sites are selectively labeled via a biotinylated, quantum dot-coupled preprotein that is arrested in translocation across the outer and inner mitochondrial membranes. Additionally, a related method is described for direct labeling of mitochondrial outer membrane proteins that does not depend on binding of a ligand.
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84
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Liao TYA, Lau A, Sunil J, Hytönen V, Hmama Z. Expression of Exogenous Antigens in the Mycobacterium bovis BCG Vaccine via Non-genetic Surface Decoration with the Avidin-biotin System. J Vis Exp 2018. [PMID: 29443102 DOI: 10.3791/56421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Tuberculosis (TB) is a serious infectious disease and the only available vaccine M. bovis bacillus Calmette-Guérin (BCG) is safe and effective for protection against children's severe TB meningitis and some forms of disseminated TB, but fails to protect against pulmonary TB, which is the most prevalent form of the disease. Promising strategies to improve BCG currently rely either on its transformation with genes encoding immunodominant M. tuberculosis (Mtb)-specific antigens and/or complementation with genes encoding co-factors that would stimulate antigen presenting cells. Major limitations to these approaches include low efficiency, low stability, and the uncertain level of safety of expression vectors. In this study, we present an alternative approach to vaccine improvement, which consists of BCG complementation with exogenous proteins of interest on the surface of bacteria, rather than transformation with plasmids encoding corresponding genes. First, proteins of interest are expressed in fusion with monomeric avidin in standard E. coli expression systems and then used to decorate the surface of biotinylated BCG. Animal experiments using BCG surface decorated with surrogate ovalbumin antigen demonstrate that the modified bacterium is fully immunogenic and capable of inducing specific T cell responses. Altogether, the data presented here strongly support a novel and efficient method for reshaping the current BCG vaccine that replaces the laborious conventional approach of complementation with exogenous nucleic acids.
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Affiliation(s)
- Ting-Yu Angela Liao
- Division of Infectious Diseases, Department of Medicine and Vancouver Costal Health Research Institute, University of British Columbia
| | - Alice Lau
- Division of Infectious Diseases, Department of Medicine and Vancouver Costal Health Research Institute, University of British Columbia
| | - Joseph Sunil
- Division of Infectious Diseases, Department of Medicine and Vancouver Costal Health Research Institute, University of British Columbia
| | - Vesa Hytönen
- Institute of Biomedical Technology, University of Tampere
| | - Zakaria Hmama
- Division of Infectious Diseases, Department of Medicine and Vancouver Costal Health Research Institute, University of British Columbia;
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85
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Youn Y, Ishitsuka Y, Jin C, Selvin PR. Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy. OPTICS EXPRESS 2018; 26:1670-1680. [PMID: 29402038 PMCID: PMC5901072 DOI: 10.1364/oe.26.001670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Localization-based super-resolution microscopy enables imaging of biological structures with sub-diffraction-limited accuracy, but generally requires extended acquisition time. Consequently, stage drift often limits the spatial precision. Previously, we reported a simple method to correct for this by creating an array of 1 μm3 fiducial markers, every ~8 μm, on the coverslip, using UV-nanoimprint lithography (UV-NIL). While this allowed reliable and accurate 3D drift correction, it suffered high autofluorescence background with shorter wavelength illumination, unstable adsorption to the substrate glass surface, and suboptimal biocompatibility. Here, we present an improved fiducial micro-pattern prepared by thermal nanoimprint lithography (T-NIL). The new pattern is made of a thermal plastic material with low fluorescence backgrounds across the wide excitation range, particularly in the blue-region; robust structural stability under cell culturing condition; and a high bio-compatibility in terms of cell viability and adhesion. We demonstrate drift precision to 1.5 nm for lateral (x, y) and 6.1 nm axial (z) axes every 0.2 seconds for a total of 1 min long image acquisition. As a proof of principle, we acquired 4-color wide-field fluorescence images of live mammalian cells; we also acquired super-resolution images of fixed hippocampal neurons, and super-resolution images of live glutamate receptors and postsynaptic density proteins.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Yuji Ishitsuka
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Chaoyi Jin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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86
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Cordova JC, Olivares AO, Lang MJ. Mechanically Watching the ClpXP Proteolytic Machinery. Methods Mol Biol 2018; 1486:317-341. [PMID: 27844434 DOI: 10.1007/978-1-4939-6421-5_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Energy-dependent protein degradation is studied through the dual bead ClpXP motility assay. Processing of folded proteins involves recognition, unfolding, translocation, and degradation stages. A dual optical trap, in a passive force-clamp geometry, exhibits bead-to-bead displacements that directly follow subprocesses underlying protein degradation. Discrete nanometer-scale displacements of the bead position reveal steps, dwells and pauses during the unfolding and translocation substeps. With a few structural modifications to the protease machinery and an engineered substrate, the assay represents a "chassis" for the measurement of a wide range of substrates and related machinery. The methods described faithfully record our assay as implemented, including substrate design, wet assay preparation, and the motility assay experiment protocol. The strategies herein permit adaptation of the ClpXP mechanical assay to a wide range of protein degradation systems.
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Affiliation(s)
- Juan Carlos Cordova
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA
| | - Adrian O Olivares
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 308-A Olin Hall, VU Mailbox: PMB 351604, Nashville, TN, 37235, USA.
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87
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Castellanos-Rubio I, Munshi R, Qadri S, Pralle A. Nanoparticle Preparation for Magnetothermal Genetic Stimulation in Cell Culture and in the Brain of Live Rodents. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-1-4939-7584-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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88
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Enzyme-Based Labeling Strategies for Antibody-Drug Conjugates and Antibody Mimetics. Antibodies (Basel) 2018; 7:antib7010004. [PMID: 31544857 PMCID: PMC6698867 DOI: 10.3390/antib7010004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
Strategies for site-specific modification of proteins have increased in number, complexity, and specificity over the last years. Such modifications hold the promise to broaden the use of existing biopharmaceuticals or to tailor novel proteins for therapeutic or diagnostic applications. The recent quest for next-generation antibody–drug conjugates (ADCs) sparked research into techniques with site selectivity. While purely chemical approaches often impede control of dosage or locus of derivatization, naturally occurring enzymes and proteins bear the ability of co- or post-translational protein modifications at particular residues, thus enabling unique coupling reactions or protein fusions. This review provides a general overview and focuses on chemo-enzymatic methods including enzymes such as formylglycine-generating enzyme, sortase, and transglutaminase. Applications for the conjugation of antibodies and antibody mimetics are reported.
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89
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Yoon JG, Hwang HJ, Cho JA. Application of the biotin-labeled toxin mutant for affinity isolation of associated proteins in the mammalian cells. J Biosci Bioeng 2018; 125:497-504. [PMID: 29291913 DOI: 10.1016/j.jbiosc.2017.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
Cholera toxin (CT), one of the AB5 bacterial toxin families, is produced by Vibrio cholerae, breeches the intestinal epithelial barrier and enters host epithelial cells to cause the massive secretory diarrhea. This study focused on understanding the retro-translocation machinery of the bacterial toxin using biotin-avidin technology to explain toxin trafficking from the endoplasmic reticulum (ER) to the cytosol. Because the association between the A1 chain of CT and other components of the retro-translocation machinery is likely transient or very weak, the successful bioengineering of such a mutant to be trapped as an intermediate in ER is essential for affinity isolation and further analysis. Here, we prepared a mutant toxin that 15 amino acid Biotin Acceptor Peptide (BAP) was fused to the C-terminal of A1 chain of CT. Biotinylation efficiency of the BAP-inserted cholera toxin (BT) was nearly 100%. Moreover, BT was functionally toxic and successfully pulled down by NeutrAvidin in vitro and in vivo. However, NeutrAvidin-bound biotinylated BT was not toxic. These results suggest the possibility of a plug effect of the biotin-NeutrAvidin-BT complex stuck in the ER without retro-translocation to the cytosol. Therefore, this model might identify the interacting proteins with A1 chain of CT in the host cells by holding the moment of retro-translocation of the bacterial toxin. In conclusion, this study established the model using biotin-avidin technology to elucidate the molecular basis for retro-translocation of bacterial toxin from within the lumen of ER to the cytosol.
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Affiliation(s)
- Ju-Gyeong Yoon
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea
| | - Hye-Jeong Hwang
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea
| | - Jin Ah Cho
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Dae-Jeon 34134, South Korea.
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90
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Abstract
Here, we describe protocols for three-dimensional tracking of single quantum dot-conjugated molecules with nanometer accuracy in living cells using conventional fluorescence microscopy. The technique exploits out-of-focus images of single emitters combined with an automated pattern-recognition open-source software that fits the images with proper model functions to extract the emitter coordinates. We describe protocols for targeting quantum dots to both membrane components and cytosolic proteins.
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91
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Identification of the caveolae/raft-mediated endocytosis as the primary entry pathway for aquareovirus. Virology 2018; 513:195-207. [DOI: 10.1016/j.virol.2017.09.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022]
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92
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HUANG H, WANG B, CHEN M, ZHANG W, LI Y, LIU Z. A Graphene Quantum Dots-Enzyme Hybrid System for the Fluorescence Assay of Alkaline Phosphatase Activity and Inhibitor Screening. ANAL SCI 2018; 34:131-136. [DOI: 10.2116/analsci.34.131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hui HUANG
- College of Food Science and Engineering, Jilin University
- Key Laboratory of Bionic Engineering (Ministry of Education), College of Biological and Agricultural Engineering, Jilin University
| | - Bingdi WANG
- College of Food Science and Engineering, Jilin University
- Key Laboratory of Bionic Engineering (Ministry of Education), College of Biological and Agricultural Engineering, Jilin University
| | - Meng CHEN
- College of Food Science and Engineering, Jilin University
| | - Wenjing ZHANG
- College of Food Science and Engineering, Jilin University
| | - Yongxin LI
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
| | - Zhenning LIU
- Key Laboratory of Bionic Engineering (Ministry of Education), College of Biological and Agricultural Engineering, Jilin University
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93
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Sedlak SM, Bauer MS, Kluger C, Schendel LC, Milles LF, Pippig DA, Gaub HE. Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry. PLoS One 2017; 12:e0188722. [PMID: 29206886 PMCID: PMC5716544 DOI: 10.1371/journal.pone.0188722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/07/2017] [Indexed: 11/18/2022] Open
Abstract
The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.
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Affiliation(s)
- Steffen M. Sedlak
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Magnus S. Bauer
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carleen Kluger
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leonard C. Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas F. Milles
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Diana A. Pippig
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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94
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Kumar A, Tan A, Wong J, Spagnoli JC, Lam J, Blevins BD, G N, Thorne L, Ashkan K, Xie J, Liu H. Nanotechnology for Neuroscience: Promising Approaches for Diagnostics, Therapeutics and Brain Activity Mapping. ADVANCED FUNCTIONAL MATERIALS 2017; 27:1700489. [PMID: 30853878 PMCID: PMC6404766 DOI: 10.1002/adfm.201700489] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Unlocking the secrets of the brain is a task fraught with complexity and challenge - not least due to the intricacy of the circuits involved. With advancements in the scale and precision of scientific technologies, we are increasingly equipped to explore how these components interact to produce a vast range of outputs that constitute function and disease. Here, an insight is offered into key areas in which the marriage of neuroscience and nanotechnology has revolutionized the industry. The evolution of ever more sophisticated nanomaterials culminates in network-operant functionalized agents. In turn, these materials contribute to novel diagnostic and therapeutic strategies, including drug delivery, neuroprotection, neural regeneration, neuroimaging and neurosurgery. Further, the entrance of nanotechnology into future research arenas including optogenetics, molecular/ion sensing and monitoring, and piezoelectric effects is discussed. Finally, considerations in nanoneurotoxicity, the main barrier to clinical translation, are reviewed, and direction for future perspectives is provided.
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Affiliation(s)
- Anil Kumar
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Aaron Tan
- UCL Medical School, University College London (UCL), London, United Kingdom
| | - Joanna Wong
- Imperial College School of Medicine, Imperial College London,London, United Kingdom
| | - Jonathan Clayton Spagnoli
- Department of Chemistry, Bio-Imaging Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - James Lam
- UCL Medical School, University College London (UCL), London, United Kingdom
| | - Brianna Diane Blevins
- Department of Chemistry, Bio-Imaging Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Natasha G
- UCL Medical School, University College London (UCL), London, United Kingdom
| | - Lewis Thorne
- Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, Queen Square, London, United Kingdom
| | - Keyoumars Ashkan
- Department of Neurosurgery, King's College Hospital NHS Foundation Trust, King's College London, London, United Kingdom
| | - Jin Xie
- Department of Chemistry, Bio-Imaging Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Hong Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
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95
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Hippocampal LTP and contextual learning require surface diffusion of AMPA receptors. Nature 2017; 549:384-388. [PMID: 28902836 PMCID: PMC5683353 DOI: 10.1038/nature23658] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
Abstract
Long-term potentiation (LTP) of excitatory synaptic transmission has long been considered a cellular correlate for learning and memory1,2. Early LTP (eLTP, <1 hour) had initially been explained either by presynaptic increases in glutamate release3–5 or by direct modification of post-synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) function6,7. Compelling models have more recently proposed that synaptic potentiation can occur by the recruitment of additional post-synaptic AMPARs8, sourced either from an intracellular reserve pool by exocytosis or from nearby extra synaptic receptors pre-existing on the neuronal surface9–12. However, the exact mechanism through which synapses can rapidly recruit new AMPARs during eLTP is still unknown. In particular, direct evidence for a pivotal role of AMPAR surface diffusion as a trafficking mechanism in synaptic plasticity is still lacking. Using AMPAR immobilization approaches, we show that interfering with AMPAR surface diffusion dramatically impaired synaptic potentiation of Schaffer collateral/commissural inputs to cornu ammonis area 1 (CA1) in cultured slices, acute slices and in vivo. Our data also identifies distinct contributions of various AMPAR trafficking routes to the temporal profile of synaptic potentiation. In addition, AMPAR immobilization in vivo in the dorsal hippocampus (DH) before fear conditioning, indicated that AMPAR diffusion is important for the early phase of contextual learning. Therefore, our results provide a direct demonstration that the recruitment of new receptors to synapses by surface diffusion is a critical mechanism for the expression of LTP and hippocampal learning. Since AMPAR surface diffusion is dictated by weak Brownian forces that are readily perturbed by protein-protein interactions, we anticipate that this fundamental trafficking mechanism will be a key target for modulating synaptic potentiation and learning.
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96
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Limitations of Qdot labelling compared to directly-conjugated probes for single particle tracking of B cell receptor mobility. Sci Rep 2017; 7:11379. [PMID: 28900238 PMCID: PMC5595841 DOI: 10.1038/s41598-017-11563-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022] Open
Abstract
Single-particle tracking (SPT) is a powerful method for exploring single-molecule dynamics in living cells with nanoscale spatiotemporal resolution. Photostability and bright fluorescence make quantum dots (Qdots) a popular choice for SPT. However, their large size could potentially alter the mobility of the molecule of interest. To test this, we labelled B cell receptors on the surface of B-lymphocytes with monovalent Fab fragments of antibodies that were either linked to Qdots via streptavidin or directly conjugated to the small organic fluorophore Cy3. Imaging of receptor mobility by total internal reflection fluorescence microscopy (TIRFM), followed by quantitative single-molecule diffusion and confinement analysis, definitively showed that Qdots sterically hinder lateral mobility regardless of the substrate to which the cells were adhered. Qdot labelling also drastically altered the frequency with which receptors transitioned between apparent slow- and fast-moving states and reduced the size of apparent confinement zones. Although we show that Qdot-labelled probes can detect large differences in receptor mobility, they fail to resolve subtle differences in lateral diffusion that are readily detectable using Cy3-labelled Fabs. Our findings highlight the utility and limitations of using Qdots for TIRFM and wide-field-based SPT, and have significant implications for interpreting SPT data.
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97
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Munshi R, Qadri SM, Zhang Q, Castellanos Rubio I, Del Pino P, Pralle A. Magnetothermal genetic deep brain stimulation of motor behaviors in awake, freely moving mice. eLife 2017; 6:27069. [PMID: 28826470 PMCID: PMC5779110 DOI: 10.7554/elife.27069] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/14/2017] [Indexed: 01/07/2023] Open
Abstract
Establishing how neurocircuit activation causes particular behaviors requires modulating the activity of specific neurons. Here, we demonstrate that magnetothermal genetic stimulation provides tetherless deep brain activation sufficient to evoke motor behavior in awake mice. The approach uses alternating magnetic fields to heat superparamagnetic nanoparticles on the neuronal membrane. Neurons, heat-sensitized by expressing TRPV1 are activated with magnetic field application. Magnetothermal genetic stimulation in the motor cortex evoked ambulation, deep brain stimulation in the striatum caused rotation around the body-axis, and stimulation near the ridge between ventral and dorsal striatum caused freezing-of-gait. The duration of the behavior correlated tightly with field application. This approach provides genetically and spatially targetable, repeatable and temporarily precise activation of deep-brain circuits without the need for surgical implantation of any device.
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Affiliation(s)
- Rahul Munshi
- Department of Physics, University at Buffalo, Buffalo, United States
| | - Shahnaz M Qadri
- Department of Physics, University at Buffalo, Buffalo, United States
| | - Qian Zhang
- Department of Physics, Philipps University Marburg, Marburg, Germany
| | | | | | - Arnd Pralle
- Department of Physics, University at Buffalo, Buffalo, United States
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98
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Lee SH, Jin C, Cai E, Ge P, Ishitsuka Y, Teng KW, de Thomaz AA, Nall D, Baday M, Jeyifous O, Demonte D, Dundas CM, Park S, Delgado JY, Green WN, Selvin PR. Super-resolution imaging of synaptic and Extra-synaptic AMPA receptors with different-sized fluorescent probes. eLife 2017; 6:27744. [PMID: 28749340 PMCID: PMC5779237 DOI: 10.7554/elife.27744] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, post-synaptic densities (PSDs) from rats. Organic fluorescent dyes (≈4 nm), quantum dots, either small (≈10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
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Affiliation(s)
- Sang Hak Lee
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Chaoyi Jin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - En Cai
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Pinghua Ge
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Yuji Ishitsuka
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Kai Wen Teng
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Andre A de Thomaz
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Duncan Nall
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Murat Baday
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Okunola Jeyifous
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Christopher M Dundas
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Sheldon Park
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Jary Y Delgado
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - William N Green
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Paul R Selvin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
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99
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Park D, Na M, Kim JA, Lee U, Cho E, Jang M, Chang S. Activation of CaMKIV by soluble amyloid-β 1-42 impedes trafficking of axonal vesicles and impairs activity-dependent synaptogenesis. Sci Signal 2017; 10:10/487/eaam8661. [PMID: 28698220 DOI: 10.1126/scisignal.aam8661] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The prefibrillar form of soluble amyloid-β (sAβ1-42) impairs synaptic function and is associated with the early phase of Alzheimer's disease (AD). We investigated how sAβ1-42 led to presynaptic defects using a quantum dot-based, single particle-tracking method to monitor synaptic vesicle (SV) trafficking along axons. We found that sAβ1-42 prevented new synapse formation induced by chemical long-term potentiation (cLTP). In cultured rat hippocampal neurons, nanomolar amounts of sAβ1-42 impaired Ca2+ clearance from presynaptic terminals and increased the basal Ca2+ concentration. This caused an increase in the phosphorylation of Ca2+/calmodulin-dependent protein kinase IV (CaMKIV) and its substrate synapsin, which markedly inhibited SV trafficking along axons between synapses. Neurons derived from a transgenic AD mouse model had similar defects, which were prevented by an inhibitor of CaMK kinase (CaMKK; which activates CaMKIV), by antibodies against Aβ1-42, or by expression a phosphodeficient synapsin mutant. The CaMKK inhibitor also abolished the defects in activity-dependent synaptogenesis caused by sAβ1-42 Our results suggest that by disrupting SV reallocation between synapses, sAβ1-42 prevents neurons from forming new synapses or adjusting strength and activity among neighboring synapses. Targeting this mechanism might prevent synaptic dysfunction in AD patients.
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Affiliation(s)
- Daehun Park
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Myeongsu Na
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Jung Ah Kim
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea.,Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Unghwi Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Eunji Cho
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Mirye Jang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea.,Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 110-799, South Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea. .,Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 110-799, South Korea.,Biomembrane Plasticity Research Center, Seoul National University College of Medicine, Seoul 110-799, South Korea
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100
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Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
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Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
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