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  1. Article ; Online: Bioorthogonal Labeling Enables In Situ Fluorescence Imaging of Expressed Gas Vesicle Nanostructures.

    Schrunk, Erik / Dutka, Przemysław / Hurt, Robert C / Wu, Di / Shapiro, Mikhail G

    Bioconjugate chemistry

    2024  Volume 35, Issue 3, Page(s) 333–339

    Abstract: Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be ...

    Abstract Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' subcellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon reaction with the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. Importantly, this was achieved by replacing only a fraction of GvpA with the tagged version. We used fluorescence images of the tagged GVs to study the GV size and distance distributions within these cells. This bioorthogonal and fractional labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
    MeSH term(s) Proteins/chemistry ; Nanostructures/chemistry ; Optical Imaging
    Chemical Substances Proteins
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1024041-x
    ISSN 1520-4812 ; 1043-1802
    ISSN (online) 1520-4812
    ISSN 1043-1802
    DOI 10.1021/acs.bioconjchem.3c00518
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3400: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article: Structural analysis and conformational dynamics of a holo-adhesion GPCR reveal interplay between extracellular and transmembrane domains.

    Kordon, Szymon P / Cechova, Kristina / Bandekar, Sumit J / Leon, Katherine / Dutka, Przemysław / Siffer, Gracie / Kossiakoff, Anthony A / Vafabakhsh, Reza / Araç, Demet

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Adhesion G Protein-Coupled Receptors (aGPCRs) are key cell-adhesion molecules involved in numerous physiological functions. aGPCRs have large multi-domain extracellular regions (ECR) containing a conserved GAIN domain that precedes their seven-pass ... ...

    Abstract Adhesion G Protein-Coupled Receptors (aGPCRs) are key cell-adhesion molecules involved in numerous physiological functions. aGPCRs have large multi-domain extracellular regions (ECR) containing a conserved GAIN domain that precedes their seven-pass transmembrane domain (7TM). Ligand binding and mechanical force applied on the ECR regulate receptor function. However, how the ECR communicates with the 7TM remains elusive, because the relative orientation and dynamics of the ECR and 7TM within a holoreceptor is unclear. Here, we describe the cryo-EM reconstruction of an aGPCR, Latrophilin3/ADGRL3, and reveal that the GAIN domain adopts a parallel orientation to the membrane and has constrained movement. Single-molecule FRET experiments unveil three slow-exchanging FRET states of the ECR relative to the 7TM within the holoreceptor. GAIN-targeted antibodies, and cancer-associated mutations at the GAIN-7TM interface, alter FRET states, cryo-EM conformations, and receptor signaling. Altogether, this data demonstrates conformational and functional coupling between the ECR and 7TM, suggesting an ECR-mediated mechanism of aGPCR activation.
    Language English
    Publishing date 2024-02-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.25.581807
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures.

    Schrunk, Erik / Dutka, Przemysław / Hurt, Robert C / Wu, Di / Shapiro, Mikhail G

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nano-cages, and other macromolecular assemblies are being developed for potential biomedical applications. To facilitate such development, it would be ...

    Abstract Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nano-cages, and other macromolecular assemblies are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' sub-cellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon binding the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag, and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. We used fluorescence images of the tagged GVs to study GV size and distance distributions within these cells. This bioorthogonal labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
    Language English
    Publishing date 2023-12-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.30.569486
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks.

    Nicolas, William J / Fäßler, Florian / Dutka, Przemysław / Schur, Florian K M / Jensen, Grant / Meyerowitz, Elliot

    Current biology : CB

    2022  Volume 32, Issue 11, Page(s) 2375–2389.e6

    Abstract: One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. ... ...

    Abstract One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall's mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed "meshing," which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is-at least in part-composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at -45° and +45° relative to the cell's long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.
    MeSH term(s) Cell Wall/metabolism ; Cellulose ; Electron Microscope Tomography ; Onions ; Pectins/metabolism
    Chemical Substances Pectins (89NA02M4RX) ; Cellulose (9004-34-6) ; polygalacturonic acid (VV3XD4CL04)
    Language English
    Publishing date 2022-05-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2022.04.024
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3208: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article: Truly tiny acoustic biomolecules for ultrasound imaging and therapy.

    Ling, Bill / Gungoren, Bilge / Yao, Yuxing / Dutka, Przemysław / Smith, Cameron A B / Lee, Justin / Swift, Margaret B / Shapiro, Mikhail G

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of ... ...

    Abstract Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
    Language English
    Publishing date 2023-06-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.27.546773
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening.

    Hurt, Robert C / Jin, Zhiyang / Soufi, Mohamed / Wong, Katie K / Sawyer, Daniel P / Shen, Hao K / Dutka, Przemysław / Deshpande, Ramya / Zhang, Ruby / Mittelstein, David R / Shapiro, Mikhail G

    bioRxiv : the preprint server for biology

    2024  

    Abstract: A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation ... ...

    Abstract A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.30.587094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Truly Tiny Acoustic Biomolecules for Ultrasound Imaging and Therapy.

    Ling, Bill / Gungoren, Bilge / Yao, Yuxing / Dutka, Przemysław / Vassallo, Reid / Nayak, Rohit / Smith, Cameron A B / Lee, Justin / Swift, Margaret B / Shapiro, Mikhail G

    Advanced materials (Deerfield Beach, Fla.)

    2024  , Page(s) e2307106

    Abstract: Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography is challenging due to the size and stability constraints of ... ...

    Abstract Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography is challenging due to the size and stability constraints of conventional bubble-based agents. Here bicones, truly tiny acoustic contrast agents based on gas vesicles (GVs), a unique class of air-filled protein nanostructures naturally produced in buoyant microbes, are described. It is shown that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
    Language English
    Publishing date 2024-02-26
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1474949-X
    ISSN 1521-4095 ; 0935-9648
    ISSN (online) 1521-4095
    ISSN 0935-9648
    DOI 10.1002/adma.202307106
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  8. Article: Ultrasonic reporters of calcium for deep tissue imaging of cellular signals.

    Jin, Zhiyang / Lakshmanan, Anupama / Zhang, Ruby / Tran, Teresa A / Rabut, Claire / Dutka, Przemysław / Duan, Mengtong / Hurt, Robert C / Malounda, Dina / Yao, Yuxing / Shapiro, Mikhail G

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Calcium imaging has enabled major biological discoveries. However, the scattering of light by tissue limits the use of standard fluorescent calcium indicators in living animals. To address this limitation, we introduce the first genetically encoded ... ...

    Abstract Calcium imaging has enabled major biological discoveries. However, the scattering of light by tissue limits the use of standard fluorescent calcium indicators in living animals. To address this limitation, we introduce the first genetically encoded ultrasonic reporter of calcium (URoC). Based on a unique class of air-filled protein nanostructures called gas vesicles, we engineered URoC to produce elevated nonlinear ultrasound signal upon binding to calcium ions. With URoC expressed in mammalian cells, we demonstrate noninvasive ultrasound imaging of calcium signaling
    Language English
    Publishing date 2023-11-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.09.566364
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Morphological remodeling of

    Shepherd, Doulin C / Kaplan, Mohammed / Vankadari, Naveen / Kim, Ki Woo / Larson, Charles L / Dutka, Przemysław / Beare, Paul A / Krzymowski, Edward / Heinzen, Robert A / Jensen, Grant J / Ghosal, Debnath

    iScience

    2023  Volume 26, Issue 7, Page(s) 107210

    Abstract: ... Coxiella ... ...

    Abstract Coxiella burnetii
    Language English
    Publishing date 2023-06-24
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.107210
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder.

    Kordon, Szymon P / Dutka, Przemysław / Adamska, Justyna M / Bandekar, Sumit J / Leon, Katherine / Erramilli, Satchal K / Adams, Brock / Li, Jingxian / Kossiakoff, Anthony A / Araç, Demet

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 635

    Abstract: Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a ... ...

    Abstract Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand - teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand - FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.
    MeSH term(s) Ligands ; Receptors, G-Protein-Coupled/metabolism ; Cell Adhesion ; Binding Sites ; Protein Isoforms/genetics ; Protein Isoforms/metabolism
    Chemical Substances Ligands ; Receptors, G-Protein-Coupled ; Protein Isoforms
    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36312-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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