1
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Korb A, Tajbakhsh S, Comai GE. Functional specialisation and coordination of myonuclei. Biol Rev Camb Philos Soc 2024; 99:1164-1195. [PMID: 38477382 DOI: 10.1111/brv.13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Myofibres serve as the functional unit for locomotion, with the sarcomere as fundamental subunit. Running the entire length of this structure are hundreds of myonuclei, located at the periphery of the myofibre, juxtaposed to the plasma membrane. Myonuclear specialisation and clustering at the centre and ends of the fibre are known to be essential for muscle contraction, yet the molecular basis of this regionalisation has remained unclear. While the 'myonuclear domain hypothesis' helped explain how myonuclei can independently govern large cytoplasmic territories, novel technologies have provided granularity on the diverse transcriptional programs running simultaneously within the syncytia and added a new perspective on how myonuclei communicate. Building upon this, we explore the critical cellular and molecular sources of transcriptional and functional heterogeneity within myofibres, discussing the impact of intrinsic and extrinsic factors on myonuclear programs. This knowledge provides new insights for understanding muscle development, repair, and disease, but also opens avenues for the development of novel and precise therapeutic approaches.
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Affiliation(s)
- Amaury Korb
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Shahragim Tajbakhsh
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Glenda E Comai
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
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2
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Wagner WJ, Moyle AB, Wagner ND, Rempel DL, Gross ML. Evaluating Chemical Footprinting-Induced Perturbation of Protein Higher Order Structure. Anal Chem 2024; 96:9693-9703. [PMID: 38815160 PMCID: PMC11238718 DOI: 10.1021/acs.analchem.4c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Specific amino acid footprinting mass spectrometry (MS) is an increasingly utilized method for elucidating protein higher order structure (HOS). It does this by adding to certain amino acid residues a mass tag, whose reaction extent depends on solvent accessibility and microenvironment of the protein. Unlike reactive free radicals and carbenes, these specific footprinters react slower than protein unfolding. Thus, their footprinting, under certain conditions, provokes structural changes to the protein, leading to labeling on non-native structures. It is critical to establish conditions (i.e., reagent concentrations, time of reaction) to ensure that the structure of the protein following footprinting remains native. Here, we compare the efficacy of five methods in assessing protein HOS following footprinting at the intact protein level and then further localize the perturbation at the peptide level. Three are MS-based methods that provide dose-response plot analysis, evaluation of Poisson distributions of precursor and products, and determination of the average number of modifications. These MS-based methods reliably and effectively indicate HOS perturbation at the intact protein level, whereas spectroscopic methods (circular dichroism (CD) and dynamic light scattering (DLS)) are less sensitive in monitoring subtle HOS perturbation caused by footprinting. Evaluation of HOS at the peptide level indicates regions that are sensitive to localized perturbations. Peptide-level analysis also provides higher resolution of the HOS perturbation, and we recommend using it for future footprinting studies. Overall, this work shows conclusive evidence for HOS perturbation caused by footprinting. Implementation of quality control workflows can identify conditions to avoid the perturbation, for footprinting, allowing accurate and reliable identification of protein structural changes that accompany, for example, ligand interactions, mutations, and changes in solution environment.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 United States
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3
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Wong W, Bravo P, Yunker PJ, Ratcliff WC, Burnetti AJ. Examining the role of oxygen-binding proteins on the early evolution of multicellularity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569647. [PMID: 38106219 PMCID: PMC10723371 DOI: 10.1101/2023.12.01.569647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Oxygen availability is a key factor in the evolution of multicellularity, as larger and more sophisticated organisms often require mechanisms allowing efficient oxygen delivery to their tissues. One such mechanism is the presence of oxygen-binding proteins, such as globins and hemerythrins, which arose in the ancestor of bilaterian animals. Despite their importance, the precise mechanisms by which oxygen-binding proteins influenced the early stages of multicellular evolution under varying environmental oxygen levels are not yet clear. We addressed this knowledge gap by heterologously expressing the oxygen binding proteins myoglobin and myohemerythrin in snowflake yeast, a model system of simple, undifferentiated multicellularity. These proteins increased the depth and rate of oxygen diffusion, increasing the fitness of snowflake yeast growing aerobically. Experiments show that, paradoxically, oxygen-binding proteins confer a greater fitness benefit for larger organisms under high, not low, O2 conditions. We show via biophysical modeling that this is because facilitated diffusion is more efficient when oxygen is abundant, transporting a greater quantity of O2 which can be used for metabolism. By alleviating anatomical diffusion limitations to oxygen consumption, the evolution of O2-binding proteins in the oxygen-rich Neoproterozoic may have been a key breakthrough enabling the evolution of increasingly large, complex multicellular metazoan lineages.
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Affiliation(s)
- Whitney Wong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pablo Bravo
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony J Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Schuknecht F, Kołątaj K, Steinberger M, Liedl T, Lohmueller T. Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment. Nat Commun 2023; 14:7192. [PMID: 37938571 PMCID: PMC10632510 DOI: 10.1038/s41467-023-42943-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.
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Affiliation(s)
- Francis Schuknecht
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Karol Kołątaj
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Département de Physique, Université de Fribourg, Chemin du Musée 3, 1700, Fribourg, Switzerland
| | - Michael Steinberger
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Tim Liedl
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
| | - Theobald Lohmueller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany.
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5
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Hansson KA, Eftestøl E. Scaling of nuclear numbers and their spatial arrangement in skeletal muscle cell size regulation. Mol Biol Cell 2023; 34:pe3. [PMID: 37339435 PMCID: PMC10398882 DOI: 10.1091/mbc.e22-09-0424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/29/2023] [Accepted: 04/28/2023] [Indexed: 06/22/2023] Open
Abstract
Many cells display considerable functional plasticity and depend on the regulation of numerous organelles and macromolecules for their maintenance. In large cells, organelles also need to be carefully distributed to supply the cell with essential resources and regulate intracellular activities. Having multiple copies of the largest eukaryotic organelle, the nucleus, epitomizes the importance of scaling gene products to large cytoplasmic volumes in skeletal muscle fibers. Scaling of intracellular constituents within mammalian muscle fibers is, however, poorly understood, but according to the myonuclear domain hypothesis, a single nucleus supports a finite amount of cytoplasm and is thus postulated to act autonomously, causing the nuclear number to be commensurate with fiber volume. In addition, the orderly peripheral distribution of myonuclei is a hallmark of normal cell physiology, as nuclear mispositioning is associated with impaired muscle function. Because underlying structures of complex cell behaviors are commonly formalized by scaling laws and thus emphasize emerging principles of size regulation, the work presented herein offers more of a unified conceptual platform based on principles from physics, chemistry, geometry, and biology to explore cell size-dependent correlations of the largest mammalian cell by means of scaling.
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Affiliation(s)
- Kenth-Arne Hansson
- Section for Health and Exercise Physiology, Inland Norway University of Applied Sciences, 2624 Lillehammer, Norway
| | - Einar Eftestøl
- Department of Biosciences, University of Oslo, 0371 Oslo, Norway
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6
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Bulthuis EP, Dieteren CEJ, Bergmans J, Berkhout J, Wagenaars JA, van de Westerlo EMA, Podhumljak E, Hink MA, Hesp LFB, Rosa HS, Malik AN, Lindert MKT, Willems PHGM, Gardeniers HJGE, den Otter WK, Adjobo-Hermans MJW, Koopman WJH. Stress-dependent macromolecular crowding in the mitochondrial matrix. EMBO J 2023; 42:e108533. [PMID: 36825437 PMCID: PMC10068333 DOI: 10.15252/embj.2021108533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/25/2023] Open
Abstract
Macromolecules of various sizes induce crowding of the cellular environment. This crowding impacts on biochemical reactions by increasing solvent viscosity, decreasing the water-accessible volume and altering protein shape, function, and interactions. Although mitochondria represent highly protein-rich organelles, most of these proteins are somehow immobilized. Therefore, whether the mitochondrial matrix solvent exhibits macromolecular crowding is still unclear. Here, we demonstrate that fluorescent protein fusion peptides (AcGFP1 concatemers) in the mitochondrial matrix of HeLa cells display an elongated molecular structure and that their diffusion constant decreases with increasing molecular weight in a manner typical of macromolecular crowding. Chloramphenicol (CAP) treatment impaired mitochondrial function and reduced the number of cristae without triggering mitochondrial orthodox-to-condensed transition or a mitochondrial unfolded protein response. CAP-treated cells displayed progressive concatemer immobilization with increasing molecular weight and an eightfold matrix viscosity increase, compatible with increased macromolecular crowding. These results establish that the matrix solvent exhibits macromolecular crowding in functional and dysfunctional mitochondria. Therefore, changes in matrix crowding likely affect matrix biochemical reactions in a manner depending on the molecular weight of the involved crowders and reactants.
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Affiliation(s)
- Elianne P Bulthuis
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Cindy E J Dieteren
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands.,Department of Cell Biology and Electron Microscopy Center, Radboudumc, Nijmegen, The Netherlands
| | - Jesper Bergmans
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Job Berkhout
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Jori A Wagenaars
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Els M A van de Westerlo
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Emina Podhumljak
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Mark A Hink
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura F B Hesp
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Hannah S Rosa
- Department of Diabetes, King's College London, London, UK
| | - Afshan N Malik
- Department of Diabetes, King's College London, London, UK
| | - Mariska Kea-Te Lindert
- Department of Cell Biology and Electron Microscopy Center, Radboudumc, Nijmegen, The Netherlands
| | - Peter H G M Willems
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Han J G E Gardeniers
- Mesoscale Chemical Systems, University of Twente, Enschede, The Netherlands.,MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Wouter K den Otter
- MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands.,Thermal and Fluid Engineering, Faculty of Engineering Technology, University of Twente, Enschede, The Netherlands
| | - Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Centre (Radboudumc), Nijmegen, The Netherlands
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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7
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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8
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Ojima K, Kigaki M, Ichimura E, Suzuki T, Kobayashi K, Muroya S, Nishimura T. Endogenous slow and fast myosin dynamics in myofibers isolated from mice expressing GFP-Myh7 and Kusabira Orange-Myh1. Am J Physiol Cell Physiol 2022; 323:C520-C535. [PMID: 35759444 DOI: 10.1152/ajpcell.00415.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Skeletal muscle consists of slow and fast myofibers in which different myosin isoforms are expressed. Approximately 300 myosins form a single thick filament in the myofibrils, where myosin is continuously exchanged. However, endogenous slow and fast myosin dynamics have not been fully understood. To elucidate those dynamics, here we generated mice expressing green fluorescence protein-tagged slow myosin heavy chain (GFP-Myh7) and Kusabira Orange fluorescence protein-tagged fast myosin heavy chain (KuO-Myh1). First, these mice enabled us to distinguish between GFP- and KuO-myofibers under fluorescence microscopy: GFP-Myh7 and KuO-Myh1 were exclusively expressed in slow myofibers and fast myofibers, respectively. Next, to monitor endogenous myosin dynamics, fluorescence recovery after photobleaching (FRAP) was conducted. The mobile fraction (Mf) of GFP-Myh7 and that of KuO-Myh1 were almost constant values independent of the regions of the myofibers and the muscle portions where the myofibers were isolated. Intriguingly, proteasome inhibitor treatment significantly decreased the Mf in GFP-Myh7 but not in KuO-Myh1 myofibers, indicating that the response to a disturbance in protein turnover depended on muscle fiber type. Taken together, the present results indicated that the mice we generated are promising tools not only for distinguishing between GFP- and KuO-myofibers but also for studying the dynamics of endogenous myosin isoforms by live-cell fluorescence imaging.
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Affiliation(s)
- Koichi Ojima
- Muscle Biology Research Unit, Division of Animal Products Research, Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, Japan
| | - Masahiro Kigaki
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Emi Ichimura
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takahiro Suzuki
- Laboratory of Muscle and Meat Science, Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Ken Kobayashi
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Susumu Muroya
- Muscle Biology Research Unit, Division of Animal Products Research, Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, Japan
| | - Takanori Nishimura
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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9
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Buckley KH, Nestor-Kalinoski AL, Pizza FX. Positional Context of Myonuclear Transcription During Injury-Induced Muscle Regeneration. Front Physiol 2022; 13:845504. [PMID: 35492593 PMCID: PMC9040890 DOI: 10.3389/fphys.2022.845504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/02/2022] [Indexed: 01/31/2023] Open
Abstract
Fundamental aspects underlying downstream processes of skeletal muscle regeneration, such as myonuclear positioning and transcription are poorly understood. This investigation begins to address deficiencies in knowledge by examining the kinetics of myonuclear accretion, positioning, and global transcription during injury-induced muscle regeneration in mice. We demonstrate that myonuclear accretion plateaus within 7 days of an injury and that the majority (∼70%) of myonuclei are centrally aligned in linear arrays (nuclear chains) throughout the course of regeneration. Relatively few myonuclei were found in a peripheral position (∼20%) or clustered (∼10%) together during regeneration. Importantly, transcriptional activity of individual myonuclei in nuclear chains was high, and greater than that of peripheral or clustered myonuclei. Transcription occurring primarily in nuclear chains elevated the collective transcriptional activity of regenerating myofibers during the later stage of regeneration. Importantly, the number of myonuclei in chains and their transcriptional activity were statistically correlated with an increase in myofiber size during regeneration. Our findings demonstrate the positional context of transcription during regeneration and highlight the importance of centralized nuclear chains in facilitating hypertrophy of regenerating myofibers after injury.
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Affiliation(s)
- Kole H. Buckley
- School of Exercise and Rehabilitation Sciences, University of Toledo, Toledo, OH, United States
| | | | - Francis X. Pizza
- School of Exercise and Rehabilitation Sciences, University of Toledo, Toledo, OH, United States
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10
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Mechanobiology of muscle and myofibril morphogenesis. Cells Dev 2021; 168:203760. [PMID: 34863916 DOI: 10.1016/j.cdev.2021.203760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 01/05/2023]
Abstract
Muscles generate forces for animal locomotion. The contractile apparatus of muscles is the sarcomere, a highly regular array of large actin and myosin filaments linked by gigantic titin springs. During muscle development many sarcomeres assemble in series into long periodic myofibrils that mechanically connect the attached skeleton elements. Thus, ATP-driven myosin forces can power movement of the skeleton. Here we review muscle and myofibril morphogenesis, with a particular focus on their mechanobiology. We describe recent progress on the molecular structure of sarcomeres and their mechanical connections to the skeleton. We discuss current models predicting how tension coordinates the assembly of key sarcomeric components to periodic myofibrils that then further mature during development. This requires transcriptional feedback mechanisms that may help to coordinate myofibril assembly and maturation states with the transcriptional program. To fuel the varying energy demands of muscles we also discuss the close mechanical interactions of myofibrils with mitochondria and nuclei to optimally support powerful or enduring muscle fibers.
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11
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Microtubule-based transport is essential to distribute RNA and nascent protein in skeletal muscle. Nat Commun 2021; 12:6079. [PMID: 34707124 PMCID: PMC8551216 DOI: 10.1038/s41467-021-26383-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
While the importance of RNA localization in highly differentiated cells is well appreciated, basic principles of RNA localization in skeletal muscle remain poorly characterized. Here, we develop a method to detect and quantify single molecule RNA localization patterns in skeletal myofibers, and uncover a critical role for directed transport of RNPs in muscle. We find that RNAs localize and are translated along sarcomere Z-disks, dispersing tens of microns from progenitor nuclei, regardless of encoded protein function. We find that directed transport along the lattice-like microtubule network of myofibers becomes essential to achieve this localization pattern as muscle development progresses; disruption of this network leads to extreme accumulation of RNPs and nascent protein around myonuclei. Our observations suggest that global active RNP transport may be required to distribute RNAs in highly differentiated cells and reveal fundamental mechanisms of gene regulation, with consequences for myopathies caused by perturbations to RNPs or microtubules.
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12
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Tanwar S, Kaur V, Kaur G, Sen T. Broadband SERS Enhancement by DNA Origami Assembled Bimetallic Nanoantennas with Label-Free Single Protein Sensing. J Phys Chem Lett 2021; 12:8141-8150. [PMID: 34410129 DOI: 10.1021/acs.jpclett.1c02272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Engineering hotspots in surface-enhanced Raman spectroscopy (SERS) through precisely controlled assembly of plasmonic nanostructures capable of expanding intense field enhancement are highly desirable to enhance the potentiality of SERS as a label-free optical tool for single molecule detection. Inspired by DNA origami technique, we constructed plasmonic dimer nanoantennas with a tunable gap decorated with Ag-coated Au nanostars on origami. Herein, we demonstrate the single-molecule SERS enhancements of three dyes with emission in different spectral regions after incorporation of single dye molecules in between two nanostars. The enhancement factors (EFs) achieved in the range of 109-1010 for all the single dye molecules, under both resonant and nonresonant excitation conditions, would enable enhanced photostability during time-series measurement. We further successfully explored the potential of our designed nanoantennas to accommodate and detect a single thrombin protein molecule after selective placement in the wide nanogap of 10 nm. Our results suggest that such nanoantennas can serve as a broadband SERS enhancer and enable specific detection of target biological molecules with single-molecule sensitivity.
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Affiliation(s)
- Swati Tanwar
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Vishaldeep Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Gagandeep Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Tapasi Sen
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
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13
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Why exercise builds muscles: titin mechanosensing controls skeletal muscle growth under load. Biophys J 2021; 120:3649-3663. [PMID: 34389312 PMCID: PMC8456289 DOI: 10.1016/j.bpj.2021.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022] Open
Abstract
Muscles sense internally generated and externally applied forces, responding to these in a coordinated hierarchical manner at different timescales. The center of the basic unit of the muscle, the sarcomeric M-band, is perfectly placed to sense the different types of load to which the muscle is subjected. In particular, the kinase domain of titin (TK) located at the M-band is a known candidate for mechanical signaling. Here, we develop a quantitative mathematical model that describes the kinetics of TK-based mechanosensitive signaling and predicts trophic changes in response to exercise and rehabilitation regimes. First, we build the kinetic model for TK conformational changes under force: opening, phosphorylation, signaling, and autoinhibition. We find that TK opens as a metastable mechanosensitive switch, which naturally produces a much greater signal after high-load resistance exercise than an equally energetically costly endurance effort. Next, for the model to be stable and give coherent predictions, in particular for the lag after the onset of an exercise regime, we have to account for the associated kinetics of phosphate (carried by ATP) and for the nonlinear dependence of protein synthesis rates on muscle fiber size. We suggest that the latter effect may occur via the steric inhibition of ribosome diffusion through the sieve-like myofilament lattice. The full model yields a steady-state solution (homeostasis) for muscle cross-sectional area and tension and, a quantitatively plausible hypertrophic response to training, as well as atrophy after an extended reduction in tension.
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Berry DB, Englund EK, Galinsky V, Frank LR, Ward SR. Varying diffusion time to discriminate between simulated skeletal muscle injury models using stimulated echo diffusion tensor imaging. Magn Reson Med 2021; 85:2524-2536. [PMID: 33226163 PMCID: PMC8204931 DOI: 10.1002/mrm.28598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE Evaluate the relationship between muscle microstructure, diffusion time (Δ), and the diffusion tensor (DT) to identify the optimal Δ where changes in muscle fiber size may be detected. METHODS The DT was simulated in models with histology informed geometry over a range of Δ with a stimulated echo DT imaging (DTI) sequence using the numerical simulation application DifSim. The difference in the DT at each Δ between healthy and injured skeletal muscle models was calculated, to identify the optimal Δ at which changes in muscle fiber size may be detected. The random permeable barrier model (RPBM) was used to estimate muscle microstructure from the simulated DT measurements, which were compared to the ground truth. RESULTS Across all models, fractional anisotropy provided greater contrast between injured and control models than diffusivity measurements. Compared to control models, in atrophic injury models, the greatest difference in the DT was found between 90 ms and 250 ms. In models with acute edema, the contrast between injured and control muscle increased with increasing diffusion time, although these models had smaller mean fiber areas. RPBM systematically underestimated fiber size but accurately estimated surface area-to-volume ratio of simulated models. CONCLUSION These findings may better inform pulse sequence parameter selection when performing DTI experiments in vivo. If only a single diffusion experiment can be performed, the selected Δ should be ~170 ms to maximize the ability to discriminate between different injury models. Ideally several diffusion times between 90 ms and 500 ms should be sampled in order to maximize diffusion contrast, particularly when the disease process is unknown.
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Affiliation(s)
- David B. Berry
- Department of Nanoengineering, University of California San Diego, San Diego, California, USA
| | - Erin K. Englund
- Department of Orthopaedic Surgery, University of California San Diego, San Diego, California, USA
| | - Vitaly Galinsky
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, California, USA
- Center for Scientific Computation in Imaging, University of California San Diego, San Diego, California, USA
| | - Lawrence R. Frank
- Center for Scientific Computation in Imaging, University of California San Diego, San Diego, California, USA
- Center for Functional MRI, University of California San Diego, San Diego, California, USA
| | - Samuel R. Ward
- Department of Orthopaedic Surgery, University of California San Diego, San Diego, California, USA
- Department of Radiology, University of California San Diego, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
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15
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Ntamo Y, Samodien E, Burger J, Muller N, Muller CJF, Chellan N. In vitro Characterization of Insulin-Producing β-Cell Spheroids. Front Cell Dev Biol 2021; 8:623889. [PMID: 33585464 PMCID: PMC7876261 DOI: 10.3389/fcell.2020.623889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022] Open
Abstract
Over the years, immortalized rodent β-cell lines such as RIN, HIT, MIN, βTC, and INS-1 have been used to investigate pancreatic β-cell physiology using conventional two-dimensional (2D) culture techniques. However, physical and physiological limitations inherent to 2D cell culture necessitates confirmatory follow up studies using sentient animals. Three-dimensional (3D) culture models are gaining popularity for their recapitulation of key features of in vivo organ physiology, and thus could pose as potential surrogates for animal experiments. In this study, we aimed to develop and characterize a rat insulinoma INS-1 3D spheroid model to compare with 2D monolayers of the same cell line. Ultrastructural verification was done by transmission electron microscopy and toluidine blue staining, which showed that both 2D monolayers and 3D spheroids contained highly granulated cells with ultrastructural features synonymous with mature pancreatic β-cells, with increased prominence of these features observed in 3D spheroids. Viability, as assessed by cellular ATP quantification, size profiling and glucose utilization, showed that our spheroids remained viable for the experimental period of 30 days, compared to the limiting 5-day passage period of INS-1 monolayers. In fact, increasing ATP content together with spheroid size was observed over time, without adverse changes in glucose utilization. Additionally, β-cell function, assessed by determining insulin and amylin secretion, showed that the 3D spheroids retained glucose sensing and insulin secretory capability, that was more acute when compared to 2D monolayer cultures. Thus, we were able to successfully demonstrate that our in vitro INS-1 β-cell 3D spheroid model exhibits in vivo tissue-like structural features with extended viability and lifespan. This offers enhanced predictive capacity of the model in the study of metabolic disease, β-cell pathophysiology and the potential treatment thereof.
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Affiliation(s)
- Yonela Ntamo
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa.,Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa, South Africa
| | - Ebrahim Samodien
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
| | - Joleen Burger
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nolan Muller
- National Health Laboratory Service, Anatomical Pathology, Tygerberg Hospital, Cape Town, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa.,Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa, South Africa.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nireshni Chellan
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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16
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Kim M, Franke V, Brandt B, Lowenstein ED, Schöwel V, Spuler S, Akalin A, Birchmeier C. Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nat Commun 2020; 11:6375. [PMID: 33311457 PMCID: PMC7732842 DOI: 10.1038/s41467-020-20064-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022] Open
Abstract
Syncytial skeletal muscle cells contain hundreds of nuclei in a shared cytoplasm. We investigated nuclear heterogeneity and transcriptional dynamics in the uninjured and regenerating muscle using single-nucleus RNA-sequencing (snRNAseq) of isolated nuclei from muscle fibers. This revealed distinct nuclear subtypes unrelated to fiber type diversity, previously unknown subtypes as well as the expected ones at the neuromuscular and myotendinous junctions. In fibers of the Mdx dystrophy mouse model, distinct subtypes emerged, among them nuclei expressing a repair signature that were also abundant in the muscle of dystrophy patients, and a nuclear population associated with necrotic fibers. Finally, modifications of our approach revealed the compartmentalization in the rare and specialized muscle spindle. Our data identifies nuclear compartments of the myofiber and defines a molecular roadmap for their functional analyses; the data can be freely explored on the MyoExplorer server ( https://shiny.mdc-berlin.de/MyoExplorer/ ).
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Affiliation(s)
- Minchul Kim
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Bettina Brandt
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Elijah D Lowenstein
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Verena Schöwel
- Muscle Research Unit, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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Jain A, Trindade GF, Hicks JM, Potts JC, Rahman R, Hague RJM, Amabilino DB, Pérez-García L, Rawson FJ. Modulating the biological function of protein by tailoring the adsorption orientation on nanoparticles. J Colloid Interface Sci 2020; 587:150-161. [PMID: 33360888 DOI: 10.1016/j.jcis.2020.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 11/25/2022]
Abstract
Protein orientation in nanoparticle-protein conjugates plays a crucial role in binding to cell receptors and ultimately, defines their targeting efficiency. Therefore, understanding fundamental aspects of the role of protein orientation upon adsorption on the surface of nanoparticles (NPs) is vital for the development of clinically important protein-based nanomedicines. In this work, new insights on the effect of the different orientation of cytochrome c (cyt c) bound to gold nanoparticles (GNPs) using various ligands on its apoptotic activity is reported. Time-of-Flight Secondary-Ion Mass Spectrometry (ToF-SIMS), electrochemical and circular dichroism (CD) analyses are used to investigate the characteristics of cyt c orientation and structure on functionalized GNPs. These studies indicate that the orientation and position of the heme ring inside the cyt c structure can be altered by changing the surface chemistry on the GNPs. A difference in the apoptosis inducing capability because of different orientation of cyt c bound to the GNPs is observed. These findings indicate that the biological activity of a protein can be modulated on the surface of NPs by varying its adsorption orientation. This study will impact on the rational design of new nanoscale biosensors, bioelectronics, and nanoparticle-protein based drugs.
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Affiliation(s)
- Akhil Jain
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Gustavo F Trindade
- Division of Advanced Materials and Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jacqueline M Hicks
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jordan C Potts
- Division of Advanced Materials and Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Ruman Rahman
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Richard J M Hague
- Centre for Additive Manufacturing, Faculty of Engineering, University of Nottingham, Nottingham NG8 1BB, UK
| | - David B Amabilino
- GSK Carbon Neutral Laboratories for Sustainable Chemistry, School of Chemistry, University of Nottingham, Nottingham NG7 2TU, UK
| | - Lluïsa Pérez-García
- Division of Advanced Materials and Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Frankie J Rawson
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK.
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18
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Tuchina DK, Meerovich IG, Sindeeva OA, Zherdeva VV, Savitsky AP, Bogdanov AA, Tuchin VV. Magnetic resonance contrast agents in optical clearing: Prospects for multimodal tissue imaging. JOURNAL OF BIOPHOTONICS 2020; 13:e201960249. [PMID: 32687263 DOI: 10.1002/jbio.201960249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Skin optical clearing effect ex vivo and in vivo was achieved by topical application of low molecular weight paramagnetic magnetic resonance contrast agents. This novel feature has not been explored before. By using collimated transmittance the diffusion coefficients of three clinically used magnetic resonance contrast agents, that is Gadovist, Magnevist and Dotarem as well as X-ray contrast agent Visipaque in mouse skin were determined ex vivo as (4.29 ± 0.39) × 10-7 cm2 /s, (5.00 ± 0.72) × 10-7 cm2 /s, (3.72 ± 0.67) × 10-7 cm2 /s and (1.64 ± 0.18) × 10-7 cm2 /s, respectively. The application of gadobutrol (Gadovist) resulted in efficient optical clearing that in general, was superior to other contrast agents tested and allowed to achieve: (a) more than 12-fold increase of transmittance over 10 minutes after application ex vivo; (b) markedly improved images of skin architecture obtained with optical coherence tomography; (c) an increase of the fluorescence intensity/background ratio in TagRFP-red fluorescent marker protein expressing tumor by five times after 15 minutes application into the skin in vivo. The obtained results have immediate implications for multimodality imaging because many contrast agents are capable of simultaneously enhancing the contrast of multiple imaging modalities.
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Affiliation(s)
- Daria K Tuchina
- Saratov State University, Saratov, Russia
- Tomsk State University, Tomsk, Russia
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina G Meerovich
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Victoria V Zherdeva
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander P Savitsky
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexei A Bogdanov
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Valery V Tuchin
- Saratov State University, Saratov, Russia
- Tomsk State University, Tomsk, Russia
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Saratov, Russia
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Computational Assessment of Transport Distances in Living Skeletal Muscle Fibers Studied In Situ. Biophys J 2020; 119:2166-2178. [PMID: 33121941 DOI: 10.1016/j.bpj.2020.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 11/22/2022] Open
Abstract
Transport distances in skeletal muscle fibers are mitigated by these cells having multiple nuclei. We have studied mouse living slow (soleus) and fast (extensor digitorum longus) muscle fibers in situ and determined cellular dimensions and the positions of all the nuclei within fiber segments. We modeled the effect of placing nuclei optimally and randomly using the nuclei as the origin of a transportation network. It appeared that an equidistant positioning of nuclei minimizes transport distances along the surface for both muscles. In the soleus muscle, however, which were richer in nuclei, positioning of nuclei to reduce transport distances to the cytoplasm were of less importance, and these fibers exhibit a pattern not statistically different from a random positioning of nuclei. We also simulated transport times for myoglobin and found that they were remarkably similar between the two muscles despite differences in nuclear patterning and distances. Together, these results highlight the importance of spatially distributed nuclei to minimize transport distances to the surface when nuclear density is low, whereas it appears that the distribution are of less importance at higher nuclear densities.
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20
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Davis PR, Miller SG, Verhoeven NA, Morgan JS, Tulis DA, Witczak CA, Brault JJ. Increased AMP deaminase activity decreases ATP content and slows protein degradation in cultured skeletal muscle. Metabolism 2020; 108:154257. [PMID: 32370945 PMCID: PMC7319876 DOI: 10.1016/j.metabol.2020.154257] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Protein degradation is an energy-dependent process, requiring ATP at multiple steps. However, reports conflict as to the relationship between intracellular energetics and the rate of proteasome-mediated protein degradation. METHODS To determine whether the concentration of the adenine nucleotide pool (ATP + ADP + AMP) affects protein degradation in muscle cells, we overexpressed an AMP degrading enzyme, AMP deaminase 3 (AMPD3), via adenovirus in C2C12 myotubes. RESULTS Overexpression of AMPD3 resulted in a dose- and time-dependent reduction of total adenine nucleotides (ATP, ADP and AMP) without increasing the ADP/ATP or AMP/ATP ratios. In agreement, the reduction of total adenine nucleotide concentration did not result in increased Thr172 phosphorylation of AMP-activated protein kinase (AMPK), a common indicator of intracellular energetic state. Furthermore, LC3 protein accumulation and ULK1 (Ser 555) phosphorylation were not induced. However, overall protein degradation and ubiquitin-dependent proteolysis were slowed by overexpression of AMPD3, despite unchanged content of several proteasome subunit proteins and proteasome activity in vitro under standard conditions. CONCLUSIONS Altogether, these findings indicate that a physiologically relevant decrease in ATP content, without a concomitant increase in ADP or AMP, is sufficient to decrease the rate of protein degradation and activity of the ubiquitin-proteasome system in muscle cells. This suggests that adenine nucleotide degrading enzymes, such as AMPD3, may be a viable target to control muscle protein degradation and perhaps muscle mass.
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Affiliation(s)
- Patrick R Davis
- Department of Kinesiology, East Carolina University, United States of America
| | - Spencer G Miller
- Department of Kinesiology, East Carolina University, United States of America
| | - Nicolas A Verhoeven
- Department of Kinesiology, East Carolina University, United States of America
| | - Joshua S Morgan
- Department of Physiology, Brody School of Medicine, East Carolina University, United States of America
| | - David A Tulis
- Department of Physiology, Brody School of Medicine, East Carolina University, United States of America
| | - Carol A Witczak
- Department of Kinesiology, East Carolina University, United States of America; Department of Physiology, Brody School of Medicine, East Carolina University, United States of America; Department of Biochemistry & Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States of America
| | - Jeffrey J Brault
- Department of Kinesiology, East Carolina University, United States of America; Department of Physiology, Brody School of Medicine, East Carolina University, United States of America; Department of Biochemistry & Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States of America.
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21
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Parui PP, Sarakar Y, Majumder R, Das S, Yang H, Yasuhara K, Hirota S. Determination of proton concentration at cardiolipin-containing membrane interfaces and its relation with the peroxidase activity of cytochrome c. Chem Sci 2019; 10:9140-9151. [PMID: 31827756 PMCID: PMC6889831 DOI: 10.1039/c9sc02993a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/03/2019] [Indexed: 01/04/2023] Open
Abstract
The activities of biomolecules are affected by the proton concentrations at biological membranes. Here, we succeeded in evaluating the interface proton concentration (-log[H+] defined as pH') of cardiolipin (CL)-enriched membrane models of the inner mitochondrial membrane (IMM) using a spiro-rhodamine-glucose molecule (RHG). According to fluorescence microscopy and 1H-NMR studies, RHG interacted with the Stern layer of the membrane. The acid/base equilibrium of RHG between its protonated open form (o-RHG) and deprotonated closed spiro-form (c-RHG) at the membrane interface was monitored with UV-vis absorption and fluorescence spectra. The interface pH' of 25% cardiolipin (CL)-containing large unilamellar vesicles (LUVs), which possess similar lipid properties to those of the IMM, was estimated to be ∼3.9, when the bulk pH was similar to the mitochondrial intermembrane space pH (6.8). However, for the membranes containing mono-anionic lipids, the interface pH' was estimated to be ∼5.3 at bulk pH 6.8, indicating that the local negative charges of the lipid headgroups in the lipid membranes are responsible for the deviation of the interface pH' from the bulk pH. The peroxidase activity of cyt c increased 5-7 fold upon lowering the pH to 3.9-4.3 or adding CL-containing (10-25% of total lipids) LUVs compared to that at bulk pH 6.8, indicating that the pH' decrease at the IMM interface from the bulk pH enhances the peroxidase activity of cyt c. The peroxidase activity of cyt c at the membrane interface of tetraoleoyl CL (TOCL)-enriched (50% of total lipids) LUVs was higher than that estimated from the interface pH', while the peroxidase activity was similar to that estimated from the interface pH' for tetramyristoyl CL (TMCL)-enriched LUVs, supporting the hypothesis that when interacting with TOCL (not TMCL), cyt c opens the heme crevice to substrates. The present simple methodology allows us to estimate the interface proton concentrations of complex biological membranes.
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Affiliation(s)
- Partha Pratim Parui
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Yeasmin Sarakar
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Rini Majumder
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
| | - Sanju Das
- Department of Chemistry , Jadavpur University , Kolkata 700032 , India . ; ; Tel: +91-9433490492
- Department of Chemistry , Maulana Azad College , Kolkata 700013 , India
| | - Hongxu Yang
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Kazuma Yasuhara
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
| | - Shun Hirota
- Division of Materials Science , Nara Institute of Science and Technology , Nara 630-0192 , Japan
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Sutisna B, Musteata V, Pulido B, Puspasari T, Smilgies DM, Hadjichristidis N, Nunes SP. High flux membranes, based on self-assembled and H-bond linked triblock copolymer nanospheres. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
Significance: In addition to their classical role in cellular ATP production, mitochondria are of key relevance in various (patho)physiological mechanisms including second messenger signaling, neuro-transduction, immune responses and death induction. Recent Advances: Within cells, mitochondria are motile and display temporal changes in internal and external structure ("mitochondrial dynamics"). During the last decade, substantial empirical and in silico evidence was presented demonstrating that mitochondrial dynamics impacts on mitochondrial function and vice versa. Critical Issues: However, a comprehensive and quantitative understanding of the bidirectional links between mitochondrial external shape, internal structure and function ("morphofunction") is still lacking. The latter particularly hampers our understanding of the functional properties and behavior of individual mitochondrial within single living cells. Future Directions: In this review we discuss the concept of mitochondrial morphofunction in mammalian cells, primarily using experimental evidence obtained within the last decade. The topic is introduced by briefly presenting the central role of mitochondria in cell physiology and the importance of the mitochondrial electron transport chain (ETC) therein. Next, we summarize in detail how mitochondrial (ultra)structure is controlled and discuss empirical evidence regarding the equivalence of mitochondrial (ultra)structure and function. Finally, we provide a brief summary of how mitochondrial morphofunction can be quantified at the level of single cells and mitochondria, how mitochondrial ultrastructure/volume impacts on mitochondrial bioreactions and intramitochondrial protein diffusion, and how mitochondrial morphofunction can be targeted by small molecules.
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Affiliation(s)
- Elianne P. Bulthuis
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Merel J.W. Adjobo-Hermans
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter H.G.M. Willems
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Werner J.H. Koopman
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Address correspondence to: Dr. Werner J.H. Koopman, Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, P.O. Box 9101, Nijmegen NL-6500 HB, The Netherlands
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Wu X, Dai H, Xu C, Liu L, Li S. Citric acid modification of a polymer exhibits antioxidant and anti‐inflammatory properties in stem cells and tissues. J Biomed Mater Res A 2019; 107:2414-2424. [DOI: 10.1002/jbm.a.36748] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/19/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Xiaopei Wu
- State Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology Wuhan China
| | - Honglian Dai
- State Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology Wuhan China
- Biomedical Materials and Engineering Research Center of Hubei Province Wuhan China
| | - Chao Xu
- State Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology Wuhan China
| | - Langlang Liu
- State Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology Wuhan China
| | - Shipu Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and ProcessingWuhan University of Technology Wuhan China
- Biomedical Materials and Engineering Research Center of Hubei Province Wuhan China
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25
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Ojima K. Myosin: Formation and maintenance of thick filaments. Anim Sci J 2019; 90:801-807. [PMID: 31134719 PMCID: PMC6618170 DOI: 10.1111/asj.13226] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/27/2019] [Accepted: 04/18/2019] [Indexed: 12/17/2022]
Abstract
Skeletal muscle consists of bundles of myofibers containing millions of myofibrils, each of which is formed of longitudinally aligned sarcomere structures. Sarcomeres are the minimum contractile unit, which mainly consists of four components: Z‐bands, thin filaments, thick filaments, and connectin/titin. The size and shape of the sarcomere component is strictly controlled. Surprisingly, skeletal muscle cells not only synthesize a series of myofibrillar proteins but also regulate the assembly of those proteins into the sarcomere structures. However, authentic sarcomere structures cannot be reconstituted by combining purified myofibrillar proteins in vitro, therefore there must be an elaborate mechanism ensuring the correct formation of myofibril structure in skeletal muscle cells. This review discusses the role of myosin, a main component of the thick filament, in thick filament formation and the dynamics of myosin in skeletal muscle cells. Changes in the number of myofibrils in myofibers can cause muscle hypertrophy or atrophy. Therefore, it is important to understand the fundamental mechanisms by which myofibers control myofibril formation at the molecular level to develop approaches that effectively enhance muscle growth in animals.
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Affiliation(s)
- Koichi Ojima
- Muscle Biology Research Unit, Division of Animal Products Research, National Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
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Antunes GC, Dias CS, Telo da Gama MM, Araújo NAM. Optimal number of linkers per monomer in linker-mediated aggregation. SOFT MATTER 2019; 15:3712-3718. [PMID: 30977508 DOI: 10.1039/c9sm00483a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study the dynamics of diffusion-limited irreversible aggregation of monomers, where bonds are mediated by linkers. We combine kinetic Monte Carlo simulations of a lattice model with a mean-field theory to study the dynamics when the diffusion of aggregates is negligible and only monomers diffuse. We find two values of the number of linkers per monomer which maximize the size of the largest aggregate. We explain the existence of the two maxima based on the distribution of linkers per monomer. This observation is well described by a simple mean-field model. We also show that a relevant parameter is the ratio of the diffusion coefficients of monomers and linkers. In particular, when this ratio is close to ten, the two maxima merge at a single maximum.
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Affiliation(s)
- G C Antunes
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Development of Tubing-based Stationary Liquid-phase Enzyme-linked Immunosorbent Assay. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-018-3208-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rogers C, Erkes DA, Nardone A, Aplin AE, Fernandes-Alnemri T, Alnemri ES. Gasdermin pores permeabilize mitochondria to augment caspase-3 activation during apoptosis and inflammasome activation. Nat Commun 2019; 10:1689. [PMID: 30976076 PMCID: PMC6459836 DOI: 10.1038/s41467-019-09397-2] [Citation(s) in RCA: 489] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/05/2019] [Indexed: 12/14/2022] Open
Abstract
Gasdermin E (GSDME/DFNA5) cleavage by caspase-3 liberates the GSDME-N domain, which mediates pyroptosis by forming pores in the plasma membrane. Here we show that GSDME-N also permeabilizes the mitochondrial membrane, releasing cytochrome c and activating the apoptosome. Cytochrome c release and caspase-3 activation in response to intrinsic and extrinsic apoptotic stimuli are significantly reduced in GSDME-deficient cells comparing with wild type cells. GSDME deficiency also accelerates cell growth in culture and in a mouse model of melanoma. Phosphomimetic mutation of the highly conserved phosphorylatable Thr6 residue of GSDME, inhibits its pore-forming activity, thus uncovering a potential mechanism by which GSDME might be regulated. Like GSDME-N, inflammasome-generated gasdermin D-N (GSDMD-N), can also permeabilize the mitochondria linking inflammasome activation to downstream activation of the apoptosome. Collectively, our results point to a role of gasdermin proteins in targeting the mitochondria to promote cytochrome c release to augment the mitochondrial apoptotic pathway. Gasdermins mediate lytic cell death by forming pores in the plasma membrane. Here the authors show that gasdermins also permeabilize mitochondrial membrane, thereby facilitating intrinsic apoptosis pathway, downstream of apoptotic (Gasdermin E) and inflammatory (Gasdermin D) caspase activation.
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Affiliation(s)
- Corey Rogers
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Dan A Erkes
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Alexandria Nardone
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Teresa Fernandes-Alnemri
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
| | - Emad S Alnemri
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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OSAKAI T, YAMAMOTO T, UEKI M. Directional Electron Transfer from Ubiquinone-10 to Cytochrome c at a Biomimetic Self-Assembled Monolayer Modified Electrode. ELECTROCHEMISTRY 2019. [DOI: 10.5796/electrochemistry.18-00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Toshiyuki OSAKAI
- Department of Chemistry, Graduate School of Science, Kobe University
| | - Takuya YAMAMOTO
- Department of Chemistry, Graduate School of Science, Kobe University
| | - Misato UEKI
- Department of Chemistry, Graduate School of Science, Kobe University
- Present address: Analysis Technology Research Center, Sumitomo Electric Industries Ltd
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Citrate reduced oxidative damage in stem cells by regulating cellular redox signaling pathways and represent a potential treatment for oxidative stress-induced diseases. Redox Biol 2018; 21:101057. [PMID: 30576924 PMCID: PMC6302140 DOI: 10.1016/j.redox.2018.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/14/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
Chemical substances containing citrate such as calcium citrate, citrate esters and citric acid exhibit anti-oxidant and anti-inflammatory properties in different cells and tissues. However, data on the anti-oxidant and anti-inflammatory properties and mechanisms of action of citrate are insufficient. In this study, we systematically evaluated the anti-oxidant capacity of citrate using chemical, cellular and animal assays. Citrate showed a stable molecular structure and did not directly react with oxides. Citrate exerted protective and anti-apoptotic effects on BMSCs and also showed significant inhibitory effects on the oxidative stress and inflammatory reactions in the rat air pouch model. By using proteomics, we found that PPARγ contributed to the upregulation of various free radical scavenging proteins and the downregulation of diverse components of the inflammatory responses. Citrate-regulated global PPARγ expression was evidenced by the significant increase expression of PPARγ in PC12 cell line. Our results provide novel insights into the role of citrate in regulating cellular redox signaling and the function of PPARγ signaling in this process and also provide basic molecular cell biology information to improve the applications of biomaterials or stem cells as treatments for oxidative stress-induced degenerative diseases and inflammatory diseases. Citrate exerts anti-oxidant and anti-inflammatory properties in BMSCs and tissues. Citrate can upregulate and downregulate anti-oxidant and anti-inflammatory proteins in BMSCs. Citrate can regulate anti-oxidant and anti-inflammatory proteins via PPARγ dependent and independent pathways.
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Samant P, Burt TA, Zhao ZJ, Xiang L. Nanoscale photoacoustic tomography for label-free super-resolution imaging: simulation study. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-10. [PMID: 30411552 DOI: 10.1117/1.jbo.23.11.116501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/12/2018] [Indexed: 06/08/2023]
Abstract
Resolutions higher than the optical diffraction limit are often desired in the context of cellular imaging and the study of disease progression at the cellular level. However, three-dimensional super-resolution imaging without reliance on exogenous contrast agents has so far not been achieved. We present nanoscale photoacoustic tomography (nPAT), an imaging modality based on the photoacoustic effect. nPAT can achieve a dramatic improvement in the axial resolution of the photoacoustic imaging. We derive the theoretical resolution and sensitivity of nPAT and demonstrate that nPAT can achieve a maximum axial resolution of 9.2 nm. We also demonstrate that nPAT can theoretically detect smaller numbers of molecules (∼273) than conventional photoacoustic microscopy due to its ability to detect acoustic signals very close to the photoacoustic source. We simulate nPAT imaging of malaria-infected red blood cells (RBCs) using digital phantoms generated from real biological samples, showing nPAT imaging of the RBC at different stages of infection. These simulations show the potential of nPAT to nondestructively image RBCs at the nanometer resolutions for in vivo samples without the use of exogenous contrast agents. Simulations of nPAT-enabled functional imaging show that nPAT can yield insight into malarial metabolism and biocrystallization processes. We believe that the experimental realization of nPAT has important applications in biomedicine.
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Affiliation(s)
- Pratik Samant
- University of Oklahoma, Stephenson School of Biomedical Engineering, Norman, Oklahoma, United States
| | - Timothy A Burt
- University of Oklahoma, Homer L. Dodge Department of Physics and Astronomy, Norman, Oklahoma, United States
| | - Zhizhuang Joe Zhao
- University of Oklahoma Health Sciences Center, Department of Pathology, Oklahoma City, Oklahoma, United States
| | - Liangzhong Xiang
- University of Oklahoma, School of Electric and Computer Engineering, Norman, Oklahoma, United States
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Berry DB, Regner B, Galinsky V, Ward SR, Frank LR. Relationships between tissue microstructure and the diffusion tensor in simulated skeletal muscle. Magn Reson Med 2018; 80:317-329. [PMID: 29090480 PMCID: PMC5876103 DOI: 10.1002/mrm.26993] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
PURPOSE To establish a series of relationships defining how muscle microstructure and diffusion tensor imaging (DTI) are related. METHODS The relationship among key microstructural features of skeletal muscle (fiber size, fibrosis, edema, and permeability) and the diffusion tensor were systematically simulated over physiologically relevant dimensions individually, and in combination, using a numerical simulation application. Stepwise multiple regression was used to identify which microstructural features of muscle significantly predict the diffusion tensor using single-echo and multi-echo DTI pulse sequences. Simulations were also performed in models with histology-informed geometry to investigate the relationship between fiber size and the diffusion tensor in models with real muscle geometry. RESULTS Fiber size is the strongest predictor of λ2, λ3, mean diffusivity, and fractional anisotropy in skeletal muscle, accounting for approximately 40% of the variance in the diffusion model when calculated with single-echo DTI. This increased to approximately 70% when diffusion measures were calculated from the short T2 component of the multi-echo DTI sequence. This nonlinear relationship begins to plateau in fibers with greater than 60-μm diameter. CONCLUSIONS As the normal fiber size of a human muscle fiber is 40 to 60 μm, this suggests that DTI is a sensitive tool to monitor muscle atrophy, but may be limited in measurements of muscle with larger fibers. Magn Reson Med 80:317-329, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- David B Berry
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Benjamin Regner
- Institute of Engineering in Medicine, San Diego, California, USA
| | - Vitaly Galinsky
- Institute of Engineering in Medicine, San Diego, California, USA
| | - Samuel R Ward
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Radiology, University of California San Diego, La Jolla, California, USA
- Department of Orthopedic Surgery, University of California San Diego, La Jolla, California, USA
| | - Lawrence R Frank
- Department of Radiology, University of California San Diego, La Jolla, California, USA
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Volfkovich YM, Goroncharovskaya IV, Evseev AK, Sosenkin VE, Goldin MM. The Effect of Electrochemical Modification of Activated Carbons by Polypyrrole on Their Structure Characteristics, Composition of Surface Compounds, and Adsorption Properties. RUSS J ELECTROCHEM+ 2018. [DOI: 10.1134/s1023193517120126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Barredo WI, Bernido CC, Carpio-Bernido MV, Bornales JB. Modelling non-Markovian fluctuations in intracellular biomolecular transport. Math Biosci 2018; 297:27-31. [PMID: 29337131 DOI: 10.1016/j.mbs.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 04/02/2017] [Accepted: 01/08/2018] [Indexed: 11/25/2022]
Abstract
To model non-Markovian fluctuations arising in biomolecular transport, we introduce a stochastic process with memory where Brownian motion is modulated sinusoidally. The probability density function and moments of this non-Markovian process are evaluated analytically as Hida stochastic functional integrals. Comparison of graphs of computed variance vis-á-vis empirical data for protein diffusion coefficients closely match with both exhibiting emergent superdiffusive then subdiffusive behavior for longer proteins.
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Affiliation(s)
- Wilson I Barredo
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Physics Department, Mindanao State University, Marawi City, 9700, Philippines
| | - Christopher C Bernido
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, 6308, Philippines; Physics Department, University of San Carlos, Cebu City, 6000, Philippines.
| | - M Victoria Carpio-Bernido
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, 6308, Philippines; Physics Department, University of San Carlos, Cebu City, 6000, Philippines
| | - Jinky B Bornales
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines
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Mishra K, Chakrabarti A, Das PK. Protein-Protein Interaction Probed by Label-free Second Harmonic Light Scattering: Hemoglobin Adsorption on Spectrin Surface as a Case Study. J Phys Chem B 2017; 121:7797-7802. [PMID: 28753013 DOI: 10.1021/acs.jpcb.7b04503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this article, we have studied the binding of different naturally occurring hemoglobin (Hb) variants on erythrocyte skeletal protein, spectrin surface using the label free nondestructive second harmonic light scattering (SHLS) technique in aqueous buffer. Hemoglobin variants like sickle hemoglobin (HbS) and hemoglobin E (HbE) were chosen as they associate with sickle cell disease and HbEβ-thalassemia, respectively, and their interaction with spectrin is compared with normal adult hemoglobin (HbA). The concentration dependent change in the second harmonic light intensity from nanomolar spectrin solution has been measured after addition of small aliquots of hemoglobins. From the second harmonic titration data, the binding constant is calculated using a modified Langmuir adsorption model of hemoglobin binding to the spectrin surface. Interestingly, it is found that the binding constant for HbE (13.8 × 108 M-1) is 1 order of magnitude higher than that of HbS (1.6 × 108 M-1) or HbA (2.1 × 108 M-1) which indicates higher affinity of HbE for spectrin compared to HbA and HbS. The number of the Hb molecules bound to the spectrin surface was estimated to be of the order of hundred's which is determined for the first time.
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Affiliation(s)
- Kamini Mishra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560 012, India
| | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Div., Saha Institute of Nuclear Physics, HBNI , 1/AF Bidhannagar, Kolkata 700 064, India
| | - Puspendu K Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560 012, India
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Madrigal JL, Stilhano R, Silva EA. Biomaterial-Guided Gene Delivery for Musculoskeletal Tissue Repair. TISSUE ENGINEERING. PART B, REVIEWS 2017; 23:347-361. [PMID: 28166711 PMCID: PMC5749599 DOI: 10.1089/ten.teb.2016.0462] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/11/2017] [Indexed: 02/07/2023]
Abstract
Gene therapy is a promising strategy for musculoskeletal tissue repair and regeneration where local and sustained expression of proteins and/or therapeutic nucleic acids can be achieved. However, the musculoskeletal tissues present unique engineering and biological challenges as recipients of genetic vectors. Targeting specific cell populations, regulating expression in vivo, and overcoming the harsh environment of damaged tissue accompany the general concerns of safety and efficacy common to all applications of gene therapy. In this review, we will first summarize these challenges and then discuss how biomaterial carriers for genetic vectors can address these issues. Second, we will review how limitations specific to given vectors further motivate the utility of biomaterial carriers. Finally, we will discuss how these concepts have been combined with tissue engineering strategies and approaches to improve the delivery of these vectors for musculoskeletal tissue regeneration.
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Affiliation(s)
- Justin L Madrigal
- Department of Biomedical Engineering, University of California , Davis, Davis, California
| | - Roberta Stilhano
- Department of Biomedical Engineering, University of California , Davis, Davis, California
| | - Eduardo A Silva
- Department of Biomedical Engineering, University of California , Davis, Davis, California
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Tillo SE, Xiong WH, Takahashi M, Miao S, Andrade AL, Fortin DA, Yang G, Qin M, Smoody BF, Stork PJS, Zhong H. Liberated PKA Catalytic Subunits Associate with the Membrane via Myristoylation to Preferentially Phosphorylate Membrane Substrates. Cell Rep 2017; 19:617-629. [PMID: 28423323 DOI: 10.1016/j.celrep.2017.03.070] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 12/20/2016] [Accepted: 03/23/2017] [Indexed: 10/19/2022] Open
Abstract
Protein kinase A (PKA) has diverse functions in neurons. At rest, the subcellular localization of PKA is controlled by A-kinase anchoring proteins (AKAPs). However, the dynamics of PKA upon activation remain poorly understood. Here, we report that elevation of cyclic AMP (cAMP) in neuronal dendrites causes a significant percentage of the PKA catalytic subunit (PKA-C) molecules to be released from the regulatory subunit (PKA-R). Liberated PKA-C becomes associated with the membrane via N-terminal myristoylation. This membrane association does not require the interaction between PKA-R and AKAPs. It slows the mobility of PKA-C and enriches kinase activity on the membrane. Membrane-residing PKA substrates are preferentially phosphorylated compared to cytosolic substrates. Finally, the myristoylation of PKA-C is critical for normal synaptic function and plasticity. We propose that activation-dependent association of PKA-C renders the membrane a unique PKA-signaling compartment. Constrained mobility of PKA-C may synergize with AKAP anchoring to determine specific PKA function in neurons.
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Affiliation(s)
- Shane E Tillo
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Wei-Hong Xiong
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maho Takahashi
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Sheng Miao
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Adriana L Andrade
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Dale A Fortin
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Guang Yang
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maozhen Qin
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Barbara F Smoody
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Philip J S Stork
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA.
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40
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Govada L, Leese HS, Saridakis E, Kassen S, Chain B, Khurshid S, Menzel R, Hu S, Shaffer MSP, Chayen NE. Exploring Carbon Nanomaterial Diversity for Nucleation of Protein Crystals. Sci Rep 2016; 6:20053. [PMID: 26843366 PMCID: PMC4740738 DOI: 10.1038/srep20053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/06/2015] [Indexed: 11/21/2022] Open
Abstract
Controlling crystal nucleation is a crucial step in obtaining high quality protein crystals for structure determination by X-ray crystallography. Carbon nanomaterials (CNMs) including carbon nanotubes, graphene oxide, and carbon black provide a range of surface topographies, porosities and length scales; functionalisation with two different approaches, gas phase radical grafting and liquid phase reductive grafting, provide routes to a range of oligomer functionalised products. These grafted materials, combined with a range of controls, were used in a large-scale assessment of the effectiveness for protein crystal nucleation of 20 different carbon nanomaterials on five proteins. This study has allowed a direct comparison of the key characteristics of carbon-based nucleants: appropriate surface chemistry, porosity and/or roughness are required. The most effective solid system tested in this study, carbon black nanoparticles functionalised with poly(ethylene glycol) methyl ether of mean molecular weight 5000, provides a novel highly effective nucleant, that was able to induce crystal nucleation of four out of the five proteins tested at metastable conditions.
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Affiliation(s)
- Lata Govada
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Hannah S Leese
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Emmanuel Saridakis
- Laboratory of Structural and Supramolecular Chemistry, Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research 'Demokritos' Athens, Greece
| | - Sean Kassen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Benny Chain
- Division of infection and immunity, The Cruciform Building, UCL, Gower St., London WC1E 6BT
| | - Sahir Khurshid
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Robert Menzel
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Sheng Hu
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Milo S P Shaffer
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Naomi E Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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Ojima K, Ichimura E, Yasukawa Y, Wakamatsu JI, Nishimura T. Dynamics of myosin replacement in skeletal muscle cells. Am J Physiol Cell Physiol 2015; 309:C669-79. [PMID: 26377314 DOI: 10.1152/ajpcell.00170.2015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/06/2015] [Indexed: 01/04/2023]
Abstract
Highly organized thick filaments in skeletal muscle cells are formed from ~300 myosin molecules. Each thick-filament-associated myosin molecule is thought to be constantly exchanged. However, the mechanism of myosin replacement remains unclear, as does the source of myosin for substitution. Here, we investigated the dynamics of myosin exchange in the myofibrils of cultured myotubes by fluorescent recovery after photobleaching and found that myofibrillar myosin is actively replaced with an exchange half-life of ~3 h. Myosin replacement was not disrupted by the absence of the microtubule system or by actomyosin interactions, suggesting that known cytoskeletal systems are dispensable for myosin substitution. Intriguingly, myosin replacement was independent of myosin binding protein C, which links myosin molecules together to form thick filaments. This implies that an individual myosin molecule rather than a thick filament functions as an exchange unit. Furthermore, the myosin substitution rate was decreased by the inhibition of protein synthesis, suggesting that newly synthesized myosin, as well as preexisting cytosolic myosin, contributes to myosin replacement in myofibrils. Notably, incorporation and release of myosin occurred simultaneously in myofibrils, but rapid myosin release from myofibrils was observed without protein synthesis. Collectively, our results indicate that myosin shuttles between myofibrils and the nonmyofibrillar cytosol to maintain a dynamic equilibrium in skeletal muscle cells.
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Affiliation(s)
- Koichi Ojima
- Animal Products Research Division, NARO Institute of Livestock and Grassland Science, Ibaraki, Japan; and
| | - Emi Ichimura
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Yuya Yasukawa
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Jun-Ichi Wakamatsu
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Takanori Nishimura
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
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Zhang X, Tian Y, Zhang H, Kavishwar A, Lynes M, Brownell AL, Sun H, Tseng YH, Moore A, Ran C. Curcumin analogues as selective fluorescence imaging probes for brown adipose tissue and monitoring browning. Sci Rep 2015; 5:13116. [PMID: 26269357 PMCID: PMC4534785 DOI: 10.1038/srep13116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/16/2015] [Indexed: 01/10/2023] Open
Abstract
Manipulation of brown adipose tissue (BAT) and browning of white adipose tissue (WAT) can be promising new approaches to counter metabolic disorder diseases in humans. Imaging probes that could consistently monitor BAT mass and browning of WAT are highly desirable. In the course of our imaging probe screening, we found that BAT could be imaged with curcumin analogues in mice. However, the poor BAT selectivity over WAT and short emissions of the lead probes promoted further lead optimization. Limited uptake mechanism studies suggested that CD36/FAT (fatty acid transporter) probably contributed to the facilitated uptake of the probes. By increasing the stereo-hindrance of the lead compound, we designed CRANAD-29 to extend the emission and increase the facilitated uptake, thus increasing its BAT selectivity. Our data demonstrated that CRANAD-29 had significantly improved selectivity for BAT over WAT, and could be used for imaging BAT mass change in a streptozotocin-induced diabetic mouse model, as well as for monitoring BAT activation under cold exposure. In addition, CRANAD-29 could be used for monitoring the browning of subcutaneous WAT (sWAT) induced by β3-adrenoceptor agonist CL-316, 243.
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Affiliation(s)
- Xueli Zhang
- 1] Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA [2] School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China [3] Department of pharmacy, ZhongDa Hospital, Southeast University, Nanjing 210009, China
| | - Yanli Tian
- 1] Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA [2] Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hongbin Zhang
- Joslin Diabetes Center, Harvard Medical School, and Harvard Stem Cell Institute, Boston, MA 02215
| | - Amol Kavishwar
- Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Matthew Lynes
- Joslin Diabetes Center, Harvard Medical School, and Harvard Stem Cell Institute, Boston, MA 02215
| | - Anna-Liisa Brownell
- Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Hongbin Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yu-Hua Tseng
- Joslin Diabetes Center, Harvard Medical School, and Harvard Stem Cell Institute, Boston, MA 02215
| | - Anna Moore
- Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Chongzhao Ran
- Molecular Imaging Laboratory, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Boston, MA
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Analytical mitigation of solute–capillary interactions in double detection Taylor Dispersion Analysis. J Chromatogr A 2015; 1408:255-60. [DOI: 10.1016/j.chroma.2015.07.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/25/2015] [Accepted: 07/02/2015] [Indexed: 11/22/2022]
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Rico-Varela J, Singh T, McCutcheon S, Vazquez M. EGF as a New Therapeutic Target for Medulloblastoma Metastasis. Cell Mol Bioeng 2015; 8:553-565. [PMID: 26594253 DOI: 10.1007/s12195-015-0395-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Medulloblastoma (MB) is a malignant pediatric brain tumor known for its aggressive metastatic potential. Despite the well-documented migration of MB cells to other parts of the brain and spinal column, MB chemotaxis is poorly understood. Herein, we examined the in vitro migratory and cellular responses of MB-derived cells to external signaling of Epidermal Growth Factor (EGF), hepatocyte growth factor (HGF), platelet-derived growth factor (PDGF-BB), and the stromal cell-derived factors 1-alpha (SDF-1). Experiments utilized transwell assays and immunocytochemistry to identify receptor activation in MB migration, and used a microfluidic platform to examine directionality, trajectory, and gradient-dependence of motile cells. Data illustrates that MB-derived cells respond strongly to EGF in a dosage and gradient-dependent manner with increased EGF-R activation, and show that high EGF gradient fields cause an increased number of cells to migrate longer directed distances. Our results provide evidence that EGF and its receptor play an important role than previously documented in MB chemotactic migration than previously documented and should be considered for developing migration-target therapies against MB metastasis.
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Affiliation(s)
- Jennifer Rico-Varela
- Department of Biomedical Engineering, The City College of New York, 160 Convent Avenue, ST-403D, New York, NY 10031
| | - Tanya Singh
- Department of Biomedical Engineering, The City College of New York, 160 Convent Avenue, ST-403D, New York, NY 10031
| | - Sean McCutcheon
- Department of Biomedical Engineering, The City College of New York, 160 Convent Avenue, ST-403D, New York, NY 10031
| | - Maribel Vazquez
- Department of Biomedical Engineering, The City College of New York, 160 Convent Avenue, ST-403D, New York, NY 10031
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45
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Exosomes as drug delivery vehicles for Parkinson's disease therapy. J Control Release 2015; 207:18-30. [PMID: 25836593 DOI: 10.1016/j.jconrel.2015.03.033] [Citation(s) in RCA: 1290] [Impact Index Per Article: 143.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/24/2015] [Accepted: 03/28/2015] [Indexed: 01/12/2023]
Abstract
Exosomes are naturally occurring nanosized vesicles that have attracted considerable attention as drug delivery vehicles in the past few years. Exosomes are comprised of natural lipid bilayers with the abundance of adhesive proteins that readily interact with cellular membranes. We posit that exosomes secreted by monocytes and macrophages can provide an unprecedented opportunity to avoid entrapment in mononuclear phagocytes (as a part of the host immune system), and at the same time enhance delivery of incorporated drugs to target cells ultimately increasing drug therapeutic efficacy. In light of this, we developed a new exosomal-based delivery system for a potent antioxidant, catalase, to treat Parkinson's disease (PD). Catalase was loaded into exosomes ex vivo using different methods: the incubation at room temperature, permeabilization with saponin, freeze-thaw cycles, sonication, or extrusion. The size of the obtained catalase-loaded exosomes (exoCAT) was in the range of 100-200nm. A reformation of exosomes upon sonication and extrusion, or permeabilization with saponin resulted in high loading efficiency, sustained release, and catalase preservation against proteases degradation. Exosomes were readily taken up by neuronal cells in vitro. A considerable amount of exosomes was detected in PD mouse brain following intranasal administration. ExoCAT provided significant neuroprotective effects in in vitro and in vivo models of PD. Overall, exosome-based catalase formulations have a potential to be a versatile strategy to treat inflammatory and neurodegenerative disorders.
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46
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Li R, Todd BA. Diffusion-limited encounter rate in a three-dimensional lattice of connected compartments studied by Brownian-dynamics simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032801. [PMID: 25871151 DOI: 10.1103/physreve.91.032801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Indexed: 06/04/2023]
Abstract
We considered the rate at which a diffusing particle encounters a target in a three-dimensional lattice of compartments with semipermeable walls. This work expands a previous theory [Li et al., Phys. Rev. Lett. 113, 028303 (2014)] for the encounter rate in the dilute limit of targets to the general case of any density of targets. We also used Brownian dynamics simulations to evaluate the approximations in the analytical theory. We find that the largest errors in the analytical theory are on the order of 10%. This work therefore demonstrates an analytical theory capable of describing the encounter rates in compartmentalized environments for any level of confinement and any target density.
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Affiliation(s)
- Ran Li
- School of Electrical and Computer Engineering and Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Brian A Todd
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
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47
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Guadalupe E, Ramos D, Shelke NB, James R, Gibney C, Kumbar SG. Bioactive polymeric nanofiber matrices for skin regeneration. J Appl Polym Sci 2015. [DOI: 10.1002/app.41879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Eross Guadalupe
- Department of Biomedical Engineering; University of Connecticut; Connecticut 06269
| | - Daisy Ramos
- Institute for Regenerative Engineering; University of Connecticut Health Center; Connecticut 06030
- The Raymond and Beverly Sackler Center for Biomedical; Biological, Physical and Engineering Sciences; Connecticut 06030
- Department of Orthopaedic Surgery; University of Connecticut Health Center; Connecticut 06030
- Department of Materials Science and Engineering; University of Connecticut; Connecticut 06269
| | - Namdev B. Shelke
- Institute for Regenerative Engineering; University of Connecticut Health Center; Connecticut 06030
- The Raymond and Beverly Sackler Center for Biomedical; Biological, Physical and Engineering Sciences; Connecticut 06030
- Department of Orthopaedic Surgery; University of Connecticut Health Center; Connecticut 06030
| | - Roshan James
- Institute for Regenerative Engineering; University of Connecticut Health Center; Connecticut 06030
- The Raymond and Beverly Sackler Center for Biomedical; Biological, Physical and Engineering Sciences; Connecticut 06030
- Department of Orthopaedic Surgery; University of Connecticut Health Center; Connecticut 06030
| | - Christian Gibney
- Department of Biomedical Engineering; University of Connecticut; Connecticut 06269
| | - Sangamesh G. Kumbar
- Institute for Regenerative Engineering; University of Connecticut Health Center; Connecticut 06030
- The Raymond and Beverly Sackler Center for Biomedical; Biological, Physical and Engineering Sciences; Connecticut 06030
- Department of Orthopaedic Surgery; University of Connecticut Health Center; Connecticut 06030
- Department of Materials Science and Engineering; University of Connecticut; Connecticut 06269
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48
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Balabushevich NG, Lopez de Guerenu AV, Feoktistova NA, Volodkin D. Protein loading into porous CaCO3 microspheres: adsorption equilibrium and bioactivity retention. Phys Chem Chem Phys 2015; 17:2523-30. [DOI: 10.1039/c4cp04567j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Here we focus on understanding protein interactions with mesoporous CaCO3 microspheres (vaterite form), which are nowadays very actively used as decomposable templates for biomolecule encapsulation under mild conditions.
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Affiliation(s)
| | | | - N. A. Feoktistova
- Fraunhofer Institute for Cell Therapy and Immunology
- 14476 Potsdam-Golm
- Germany
| | - D. Volodkin
- Lomonosov Moscow State University
- Department of Chemistry
- 119991 Moscow
- Russia
- Fraunhofer Institute for Cell Therapy and Immunology
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49
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Guimarães-Ferreira L. Role of the phosphocreatine system on energetic homeostasis in skeletal and cardiac muscles. EINSTEIN-SAO PAULO 2014; 12:126-31. [PMID: 24728259 PMCID: PMC4898252 DOI: 10.1590/s1679-45082014rb2741] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 12/12/2013] [Indexed: 02/03/2023] Open
Abstract
Adenosine triphosphate is the present energy currency in the body, and is used in various cellular and indispensable processes for the maintenance of cell homeostasis. The regeneration mechanisms of adenosine triphosphate, from the product of its hydrolysis - adenosine diphosphate - are therefore necessary. Phosphocreatine is known as its quickest form of regeneration, by means of the enzyme creatine kinase. Thus, the primary function of this system is to act as a temporal energy buffer. Nevertheless, over the years, several other functions were attributed to phosphocreatine. This occurs as various isoforms of creatine kinase isoforms have been identified with a distinct subcellular location and functionally coupled with the sites that generate and use energy, in the mitochondria and cytosol, respectively. The present study discussed the central and complex role that the phosphocreatine system performs in energy homeostasis in muscle cells, as well as its alterations in pathological conditions.
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50
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Carlson BE, Vigoreaux JO, Maughan DW. Diffusion coefficients of endogenous cytosolic proteins from rabbit skinned muscle fibers. Biophys J 2014; 106:780-92. [PMID: 24559981 DOI: 10.1016/j.bpj.2013.12.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 12/19/2013] [Accepted: 12/31/2013] [Indexed: 10/25/2022] Open
Abstract
Efflux time courses of endogenous cytosolic proteins were obtained from rabbit psoas muscle fibers skinned in oil and transferred to physiological salt solution. Proteins were separated by gel electrophoresis and compared to load-matched standards for quantitative analysis. A radial diffusion model incorporating the dissociation and dissipation of supramolecular complexes accounts for an initial lag and subsequent efflux of glycolytic and glycogenolytic enzymes. The model includes terms representing protein crowding, myofilament lattice hindrance, and binding to the cytomatrix. Optimization algorithms returned estimates of the apparent diffusion coefficients, D(r,t), that were very low at the onset of diffusion (∼10(-10) cm(2) s(-1)) but increased with time as cytosolic protein density, which was initially high, decreased. D(r,t) at later times ranged from 2.11 × 10(-7) cm(2) s(-1) (parvalbumin) to 0.20 × 10(-7) cm(2) s(-1) (phosphofructose kinase), values that are 3.6- to 12.3-fold lower than those predicted in bulk water. The low initial values are consistent with the presence of complexes in situ; the higher later values are consistent with molecular sieving and transient binding of dissociated proteins. Channeling of metabolic intermediates via enzyme complexes may enhance production of adenosine triphosphate at rates beyond that possible with randomly and/or sparsely distributed enzymes, thereby matching supply with demand.
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Affiliation(s)
- Brian E Carlson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Jim O Vigoreaux
- Department of Molecular Physiology and Biophysics, Health Science Research Facility, University of Vermont College of Medicine, Burlington, Vermont; Department of Biology, University of Vermont, Burlington, Vermont
| | - David W Maughan
- Department of Molecular Physiology and Biophysics, Health Science Research Facility, University of Vermont College of Medicine, Burlington, Vermont.
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