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Larsen JB, Taebnia N, Dolatshahi-Pirouz A, Eriksen AZ, Hjørringgaard C, Kristensen K, Larsen NW, Larsen NB, Marie R, Mündler AK, Parhamifar L, Urquhart AJ, Weller A, Mortensen KI, Flyvbjerg H, Andresen TL. Imaging therapeutic peptide transport across intestinal barriers. RSC Chem Biol 2021; 2:1115-1143. [PMID: 34458827 PMCID: PMC8341777 DOI: 10.1039/d1cb00024a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.
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Affiliation(s)
- Jannik Bruun Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nayere Taebnia
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Alireza Dolatshahi-Pirouz
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Anne Zebitz Eriksen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Claudia Hjørringgaard
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kasper Kristensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nanna Wichmann Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Niels Bent Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Rodolphe Marie
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ann-Kathrin Mündler
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ladan Parhamifar
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Andrew James Urquhart
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Arjen Weller
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kim I Mortensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Henrik Flyvbjerg
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Thomas Lars Andresen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
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2
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Vestergaard CL, Blainey PC, Flyvbjerg H. Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Res 2019; 46:2446-2458. [PMID: 29361033 PMCID: PMC5861423 DOI: 10.1093/nar/gky004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/05/2018] [Indexed: 12/28/2022] Open
Abstract
We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1’s (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.
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Affiliation(s)
- Christian L Vestergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.,Decision and Bayesian Computation, Pasteur Institute, CNRS UMR 3571, 25-28 rue du Dr Roux, 75015 Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, Pasteur Institute, CNRS USR 3756, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Paul C Blainey
- MIT Department of Biological Engineering and Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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3
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Mortensen KI, Tassone C, Ehrlich N, Andresen TL, Flyvbjerg H. How To Characterize Individual Nanosize Liposomes with Simple Self-Calibrating Fluorescence Microscopy. Nano Lett 2018; 18:2844-2851. [PMID: 29614230 DOI: 10.1021/acs.nanolett.7b05312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanosize lipid vesicles are used extensively at the interface between nanotechnology and biology, e.g., as containers for chemical reactions at minute concentrations and vehicles for targeted delivery of pharmaceuticals. Typically, vesicle samples are heterogeneous as regards vesicle size and structural properties. Consequently, vesicles must be characterized individually to ensure correct interpretation of experimental results. Here we do that using dual-color fluorescence labeling of vesicles-of their lipid bilayers and lumens, separately. A vesicle then images as two spots, one in each color channel. A simple image analysis determines the total intensity and width of each spot. These four data all depend on the vesicle radius in a simple manner for vesicles that are spherical, unilamellar, and optimal encapsulators of molecular cargo. This permits identification of such ideal vesicles. They in turn enable calibration of the dual-color fluorescence microscopy images they appear in. Since this calibration is not a separate experiment but an analysis of images of vesicles to be characterized, it eliminates the potential source of error that a separate calibration experiment would have been. Nonideal vesicles in the same images were characterized by how their four data violate the calibrated relationship established for ideal vesicles. In this way, our method yields size, shape, lamellarity, and encapsulation efficiency of each imaged vesicle. Applying this procedure to extruded samples of vesicles, we found that, contrary to common assumptions, only a fraction of vesicles are ideal.
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Affiliation(s)
- Kim I Mortensen
- Department of Micro- and Nanotechnology , Technical University of Denmark , Kongens Lyngby , DK-2800 , Denmark
| | - Chiara Tassone
- Department of Micro- and Nanotechnology , Technical University of Denmark , Kongens Lyngby , DK-2800 , Denmark
| | - Nicky Ehrlich
- Department of Micro- and Nanotechnology , Technical University of Denmark , Kongens Lyngby , DK-2800 , Denmark
| | - Thomas L Andresen
- Department of Micro- and Nanotechnology , Technical University of Denmark , Kongens Lyngby , DK-2800 , Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology , Technical University of Denmark , Kongens Lyngby , DK-2800 , Denmark
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4
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Łopacińska-Jørgensen JM, Pedersen JN, Bak M, Mehrjouy MM, Sørensen KT, Østergaard PF, Bilenberg B, Kristensen A, Taboryski RJ, Flyvbjerg H, Marie R, Tommerup N, Silahtaroglu A. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing. Sci Rep 2017; 7:17893. [PMID: 29263336 PMCID: PMC5738345 DOI: 10.1038/s41598-017-18091-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022] Open
Abstract
Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so here we introduce a method for selection and enrichment of megabase-sized DNA molecules intended for single-molecule optical mapping: DNA from a human cell line is digested by the NotI rare-cutting enzyme and size-selected by pulsed-field gel electrophoresis. For demonstration, more than 600 sub-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our enrichment method could potentially work with other genomes or target specified regions by applying other genomic editing tools, such as the CRISPR/Cas9 system.
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Affiliation(s)
- Joanna M Łopacińska-Jørgensen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Mads Bak
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Mana M Mehrjouy
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Kristian T Sørensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Peter F Østergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Brian Bilenberg
- NIL Technology ApS, Diplomvej 381, Kongens Lyngby, 2800, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Rafael J Taboryski
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark.
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5
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Abstract
It has been theoretically suggested and experimentally demonstrated that fast and low-cost sequencing of DNA, RNA, and peptide molecules might be achieved by passing such molecules between electrodes embedded in a nanochannel. The experimental realization of this scheme faces major challenges, however. In realistic liquid environments, typical currents in tunneling devices are of the order of picoamps. This corresponds to only six electrons per microsecond, and this number affects the integration time required to do current measurements in real experiments. This limits the speed of sequencing, though current fluctuations due to Brownian motion of the molecule average out during the required integration time. Moreover, data acquisition equipment introduces noise, and electronic filters create correlations in time-series data. We discuss how these effects must be included in the analysis of, e.g., the assignment of specific nucleobases to current signals. As the signals from different molecules overlap, unambiguous classification is impossible with a single measurement. We argue that the assignment of molecules to a signal is a standard pattern classification problem and calculation of the error rates is straightforward. The ideas presented here can be extended to other sequencing approaches of current interest.
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Affiliation(s)
- Jonas Nyvold Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. Center for Nanostructured Graphene (CNG), DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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6
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Pedersen JN, Li L, Grădinaru C, Austin RH, Cox EC, Flyvbjerg H. How to connect time-lapse recorded trajectories of motile microorganisms with dynamical models in continuous time. Phys Rev E 2016; 94:062401. [PMID: 28085401 DOI: 10.1103/physreve.94.062401] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 01/29/2023]
Abstract
We provide a tool for data-driven modeling of motility, data being time-lapse recorded trajectories. Several mathematical properties of a model to be found can be gleaned from appropriate model-independent experimental statistics, if one understands how such statistics are distorted by the finite sampling frequency of time-lapse recording, by experimental errors on recorded positions, and by conditional averaging. We give exact analytical expressions for these effects in the simplest possible model for persistent random motion, the Ornstein-Uhlenbeck process. Then we describe those aspects of these effects that are valid for any reasonable model for persistent random motion. Our findings are illustrated with experimental data and Monte Carlo simulations.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Liang Li
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Cristian Grădinaru
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Edward C Cox
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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7
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Mortensen KI, Flyvbjerg H. "Calibration-on-the-spot": How to calibrate an EMCCD camera from its images. Sci Rep 2016; 6:28680. [PMID: 27381055 PMCID: PMC4933971 DOI: 10.1038/srep28680] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/03/2016] [Indexed: 11/09/2022] Open
Abstract
In order to count photons with a camera, the camera must be calibrated. Photon counting is necessary, e.g., to determine the precision of localization-based super-resolution microscopy. Here we present a protocol that calibrates an EMCCD camera from information contained in isolated, diffraction-limited spots in any image taken by the camera, thus making dedicated calibration procedures redundant by enabling calibration post festum, from images filed without calibration information.
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Affiliation(s)
- Kim I Mortensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark
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8
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Pedersen JN, Marie R, Kristensen A, Flyvbjerg H. How to determine local stretching and tension in a flow-stretched DNA molecule. Phys Rev E 2016; 93:042405. [PMID: 27176327 DOI: 10.1103/physreve.93.042405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/07/2022]
Abstract
We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA-e.g., native DNA extracted from human cells or bacteria-must be stretched with ease for inspection, this method applies.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
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9
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Vestergaard CL, Mikkelsen MB, Reisner W, Kristensen A, Flyvbjerg H. Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment. Nat Commun 2016; 7:10227. [PMID: 26732388 PMCID: PMC5154429 DOI: 10.1038/ncomms10227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/17/2015] [Indexed: 11/25/2022] Open
Abstract
Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds.
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Affiliation(s)
- Christian L. Vestergaard
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Morten Bo Mikkelsen
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Walter Reisner
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
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10
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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11
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Henriksen AD, Ley MWH, Flyvbjerg H, Hansen MF. Configurational Statistics of Magnetic Bead Detection with Magnetoresistive Sensors. PLoS One 2015; 10:e0141115. [PMID: 26496495 PMCID: PMC4619777 DOI: 10.1371/journal.pone.0141115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/04/2015] [Indexed: 11/18/2022] Open
Abstract
Magnetic biosensors detect magnetic beads that, mediated by a target, have bound to a functionalized area. This area is often larger than the area of the sensor. Both the sign and magnitude of the average magnetic field experienced by the sensor from a magnetic bead depends on the location of the bead relative to the sensor. Consequently, the signal from multiple beads also depends on their locations. Thus, a given coverage of the functionalized area with magnetic beads does not result in a given detector response, except on the average, over many realizations of the same coverage. We present a systematic theoretical analysis of how this location-dependence affects the sensor response. The analysis is done for beads magnetized by a homogeneous in-plane magnetic field. We determine the expected value and standard deviation of the sensor response for a given coverage, as well as the accuracy and precision with which the coverage can be determined from a single sensor measurement. We show that statistical fluctuations between samples may reduce the sensitivity and dynamic range of a sensor significantly when the functionalized area is larger than the sensor area. Hence, the statistics of sampling is essential to sensor design. For illustration, we analyze three important published cases for which statistical fluctuations are dominant, significant, and insignificant, respectively.
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Affiliation(s)
- Anders Dahl Henriksen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | | | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Mikkel Fougt Hansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
- * E-mail:
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12
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Mortensen KI, Sung J, Flyvbjerg H, Spudich JA. Optimized measurements of separations and angles between intra-molecular fluorescent markers. Nat Commun 2015; 6:8621. [PMID: 26509412 PMCID: PMC4634324 DOI: 10.1038/ncomms9621] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/11/2015] [Indexed: 11/09/2022] Open
Abstract
We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly.
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Affiliation(s)
- Kim I Mortensen
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
| | - Jongmin Sung
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
| | - James A Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
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13
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Edgar RC, Flyvbjerg H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics 2015; 31:3476-82. [DOI: 10.1093/bioinformatics/btv401] [Citation(s) in RCA: 715] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/27/2015] [Indexed: 12/15/2022] Open
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14
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Chen Y, Abrams ES, Boles TC, Pedersen JN, Flyvbjerg H, Austin RH, Sturm JC. Concentrating genomic length DNA in a microfabricated array. Phys Rev Lett 2015; 114:198303. [PMID: 26024203 DOI: 10.1103/physrevlett.114.198303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Indexed: 05/19/2023]
Abstract
We demonstrate that a microfabricated bump array can concentrate genomic-length DNA molecules efficiently at continuous, high flow velocities, up to 40 μm/s, if the single-molecule DNA globule has a sufficiently large shear modulus. Increase in the shear modulus is accomplished by compacting the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions for next-generation DNA-sequencing libraries will be an important application of this development.
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Affiliation(s)
- Yu Chen
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ezra S Abrams
- Sage Science, Inc., Beverly, Massachusetts 01915, USA
| | | | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Robert H Austin
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - James C Sturm
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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15
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Flyvbjerg H, Mortensen KI. Sifting noisy data for truths about noisy systems: Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar. Phys Life Rev 2015; 13:141-3. [PMID: 25891322 DOI: 10.1016/j.plrev.2015.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Henrik Flyvbjerg
- Stochastic Systems and Signals Group, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| | - Kim I Mortensen
- Stochastic Systems and Signals Group, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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16
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Pedersen JN, Lüscher CJ, Marie R, Thamdrup LH, Kristensen A, Flyvbjerg H. Thermophoretic forces on DNA measured with a single-molecule spring balance. Phys Rev Lett 2014; 113:268301. [PMID: 25615393 DOI: 10.1103/physrevlett.113.268301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement of the thermophoretic force in a static configuration finds forces up to 130 fN. This is eleven times stronger than the force experienced by the same molecule in the same thermal gradient in bulk, where the molecule shields itself. Our stronger forces stretch the middle of the molecule up to 80% of its contour length. We find the Soret coefficient per unit length of DNA at various ionic strengths. It agrees, with novel precision, with results obtained in bulk for DNA too short to shield itself and with the thermodynamic model of thermophoresis.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Christopher J Lüscher
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Lasse H Thamdrup
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark
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17
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Vestergaard CL, Blainey PC, Flyvbjerg H. Optimal estimation of diffusion coefficients from single-particle trajectories. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:022726. [PMID: 25353527 DOI: 10.1103/physreve.89.022726] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Indexed: 05/08/2023]
Abstract
How does one optimally determine the diffusion coefficient of a diffusing particle from a single-time-lapse recorded trajectory of the particle? We answer this question with an explicit, unbiased, and practically optimal covariance-based estimator (CVE). This estimator is regression-free and is far superior to commonly used methods based on measured mean squared displacements. In experimentally relevant parameter ranges, it also outperforms the analytically intractable and computationally more demanding maximum likelihood estimator (MLE). For the case of diffusion on a flexible and fluctuating substrate, the CVE is biased by substrate motion. However, given some long time series and a substrate under some tension, an extended MLE can separate particle diffusion on the substrate from substrate motion in the laboratory frame. This provides benchmarks that allow removal of bias caused by substrate fluctuations in CVE. The resulting unbiased CVE is optimal also for short time series on a fluctuating substrate. We have applied our estimators to human 8-oxoguanine DNA glycolase proteins diffusing on flow-stretched DNA, a fluctuating substrate, and found that diffusion coefficients are severely overestimated if substrate fluctuations are not accounted for.
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Affiliation(s)
- Christian L Vestergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
| | - Paul C Blainey
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
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18
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Bauer DL, Marie RM, Pedersen JN, Rasmussen KH, Yusuf M, Volpi E, Flyvbjerg H, Kristensen A, Mir KU. Nanofluidics to Enhance Single Molecule DNA Imaging: Detecting Genomic Structural Variation in Humans. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Sung J, Nag S, Vestergaard C, Mortensen K, Flyvbjerg H, Spudich J. Harmonic Force Spectroscopy Reveals a Force-Velocity Curve from a Single Human Beta Cardiac Myosin Motor. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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21
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Mortensen KI, Flyvbjerg H. Calibration on the Spot of EMCCD Cameras for Super Resolution Microscopy. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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22
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Grădinaru C, Lopacińska JM, Huth J, Kestler HA, Flyvbjerg H, Mølhave K. Assessment of automated analyses of cell migration on flat and nanostructured surfaces. Comput Struct Biotechnol J 2012; 1:e201207004. [PMID: 24688640 PMCID: PMC3962212 DOI: 10.5936/csbj.201207004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 11/04/2012] [Accepted: 11/07/2012] [Indexed: 11/24/2022] Open
Abstract
Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software.
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Affiliation(s)
- Cristian Grădinaru
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Joanna M Lopacińska
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Johannes Huth
- Neural Information Processing, University of Ulm, Ulm, Germany ; Department of Gastroenterology and Endocrinology, University Hospital of Marburg, Marburg, Germany
| | - Hans A Kestler
- Neural Information Processing, University of Ulm, Ulm, Germany ; Internal Medicine I - Gastroenterology, University Hospital Ulm, Ulm, Germany
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kristian Mølhave
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
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23
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Łopacińska JM, Grădinaru C, Wierzbicki R, Købler C, Schmidt MS, Madsen MT, Skolimowski M, Dufva M, Flyvbjerg H, Mølhave K. Cell motility, morphology, viability and proliferation in response to nanotopography on silicon black. Nanoscale 2012; 4:3739-3745. [PMID: 22614757 DOI: 10.1039/c2nr11455k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Knowledge of cells' interactions with nanostructured materials is fundamental for bio-nanotechnology. We present results for how individual mouse fibroblasts from cell line NIH3T3 respond to highly spiked surfaces of silicon black that were fabricated by maskless reactive ion etching (RIE). We did standard measurements of cell viability, proliferation, and morphology on various surfaces. We also analyzed the motility of cells on the same surfaces, as recorded in time lapse movies of sparsely populated cell cultures. We find that motility and morphology vary strongly with nano-patterns, while viability and proliferation show little dependence on substrate type. We conclude that motility analysis can show a wide range of cell responses e.g. over a factor of two in cell speed to different nano-topographies, where standard assays, such as viability or proliferation, in the tested cases show much less variation of the order 10-20%.
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Affiliation(s)
- Joanna M Łopacińska
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, 2800 Kongens Lyngby, Denmark.
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24
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Abstract
Microtubules polymerize from identical tubulin heterodimers, which form a helical lattice pattern that is the microtubule. This pattern always has left-handed chirality, but it is not known why. But as tubulin, similar to other proteins, evolved for a purpose, the question of the title of this artcile appears to be meaningful. In a computer simulation that explores the 'counterfactual biology' of microtubules without helicity, we demonstrate that these have the same mechanical properties as Nature's microtubules with helicity. Thus only a dynamical reason for helicity is left as potential explanation. We find that helicity solves 'the problem of the blind mason', i.e. how to correctly build a structure, guided only by the shape of the bricks. This answer in turn raises some new questions for researchers to address.
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Affiliation(s)
- Viktória Hunyadi
- Department of Physics of Complex Systems, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary
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25
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Vestergaard CL, Flyvbjerg H, Møller IM. Intracellular signaling by diffusion: can waves of hydrogen peroxide transmit intracellular information in plant cells? Front Plant Sci 2012; 3:295. [PMID: 23293647 PMCID: PMC3533182 DOI: 10.3389/fpls.2012.00295] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/10/2012] [Indexed: 05/21/2023]
Abstract
Amplitude- and frequency-modulated waves of Ca(2+) ions transmit information inside cells. Reactive Oxygen Species (ROS), specifically hydrogen peroxide, have been proposed to have a similar role in plant cells. We consider the feasibility of such an intracellular communication system in view of the physical and biochemical conditions in plant cells. As model system, we use a H(2)O(2) signal originating at the plasma membrane (PM) and spreading through the cytosol. We consider two maximally simple types of signals, isolated pulses and harmonic oscillations. First we consider the basic limits on such signals as regards signal origin, frequency, amplitude, and distance. Then we establish the impact of ROS-removing enzymes on the ability of H(2)O(2) to transmit signals. Finally, we consider to what extent cytoplasmic streaming distorts signals. This modeling allows us to predict the conditions under which diffusion-mediated signaling is possible. We show that purely diffusive transmission of intracellular information by H(2)O(2) over a distance of 1 μm (typical distance between organelles, which may function as relay stations) is possible at frequencies well above 1 Hz, which is the highest frequency observed experimentally. This allows both frequency and amplitude modulation of the signal. Signaling over a distance of 10 μm (typical distance between the PM and the nucleus) may be possible, but requires high signal amplitudes or, equivalently, a very low detection threshold. Furthermore, at this longer distance a high rate of enzymatic degradation is required to make signaling at frequencies above 0.1 Hz possible. In either case, cytoplasmic streaming does not seriously disturb signals. We conclude that although purely diffusion-mediated signaling without relaying stations is theoretically possible, it is unlikely to work in practice, since it requires a much faster enzymatic degradation and a much lower cellular background concentration of H(2)O(2) than observed experimentally.
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Affiliation(s)
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of DenmarkKongens Lyngby, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
- *Correspondence: Ian Max Møller, Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark. e-mail:
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26
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Abstract
We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking by centroid or nucleus. Our data account for cell individuality and dictate a model that extends the cell-type specific models recently derived for mammalian cells. Two generalized Langevin equations model stochastic periodic pseudopod motion parallel and orthogonal to the amoeba's direction of motion. This motion propels the amoeba with a random periodic left-right waddle in a direction that has a long persistence time. The model fully accounts for the statistics of the experimental trajectories, including velocity power spectra and auto-correlations, non-Gaussian velocity distributions, and multiplicative noise. Thus, we find neither need nor place in our data for an interpretation in terms of anomalous diffusion. The model faithfully captures cell individuality as different parameter values in the model, and serves as a basis for integrating the local mechanics of cell motion with our observed long-term behavior.
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Affiliation(s)
- Liang Li
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Edward C. Cox
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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27
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Mikkelsen MB, Reisner W, Flyvbjerg H, Kristensen A. Pressure-driven DNA in nanogroove arrays: complex dynamics leads to length- and topology-dependent separation. Nano Lett 2011; 11:1598-1602. [PMID: 21361348 DOI: 10.1021/nl1044764] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The motion of linear and circular DNA molecules is studied under pressure driven buffer flow in a 50 nm slit channel with arrays of transverse 150 nm deep nanogrooves. Transport occurs through two states of propagation unique to this nanogroove geometry, a slow, stepwise groove-to-groove translation called the "sidewinder" and a fast, continuous tumbling across the grooves called the "tumbleweed". Dynamical transitions between the two states are observed at fixed buffer velocity. Molecules exhibit size- and topology-dependent velocities.
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28
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Nørrelykke SF, Flyvbjerg H. Harmonic oscillator in heat bath: exact simulation of time-lapse-recorded data and exact analytical benchmark statistics. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 83:041103. [PMID: 21599111 DOI: 10.1103/physreve.83.041103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 02/02/2011] [Indexed: 05/30/2023]
Abstract
The stochastic dynamics of the damped harmonic oscillator in a heat bath is simulated with an algorithm that is exact for time steps of arbitrary size. Exact analytical results are given for correlation functions and power spectra in the form they acquire when computed from experimental time-lapse recordings. Three applications are discussed: (i) The effects of finite sampling rate and time, described exactly here, are similar for other stochastic dynamical systems--e.g., motile microorganisms and their time-lapse-recorded trajectories. (ii) The same statistics is satisfied by any experimental system to the extent that it is interpreted as a damped harmonic oscillator at finite temperature-such as an AFM cantilever. (iii) Three other models of fundamental interest are limiting cases of the damped harmonic oscillator at finite temperature; it consequently bridges their differences and describes the effects of finite sampling rate and sampling time for these models as well.
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Affiliation(s)
- Simon F Nørrelykke
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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29
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Sung J, Mortensen KI, Flyvbjerg H, Spudich JA. Optimal Estimation of Location and Orientation of Myosin V Lever Arm from Focused Diffraction-Limited Images of Single, Double-Bound Fluorophore. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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30
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Hagedorn PH, Burton CM, Sahar E, Domany E, Cohen IR, Flyvbjerg H, Iversen M. Integrative analysis correlates donor transcripts to recipient autoantibodies in primary graft dysfunction after lung transplantation. Immunology 2010; 132:394-400. [PMID: 21070236 DOI: 10.1111/j.1365-2567.2010.03373.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Up to one in four lung-transplanted patients develop pulmonary infiltrates and impaired oxygenation within the first days after lung transplantation. Known as primary graft dysfunction (PGD), this condition increases mortality significantly. Complex interactions between donor lung and recipient immune system are the suspected cause. We took an integrative, systems-level approach by first exploring whether the recipient's immune response to PGD includes the development of long-lasting autoreactivity. We next explored whether proteins displaying such differential autoreactivity also display differential gene expression in donor lungs that later develop PGD compared with those that did not. We evaluated 39 patients from whom autoantibody profiles were already available for PGD based on chest radiographs and oxygenation data. An additional nine patients were evaluated for PGD based on their medical records and set aside for validation. From two recent donor lung gene expression studies, we reanalysed and paired gene profiles with autoantibody profiles. Primary graft dysfunction can be distinguished by a profile of differentially reactive autoantibodies binding to 17 proteins. Functional analysis showed that 12 of these proteins are part of a protein-protein interaction network (P=3 x 10⁻⁶) involved in proliferative processes. A nearest centroid classifier assigned correct PGD grades to eight out of the nine patients in the validation cohort (P=0·048). We observed significant positive correlation (r=0·63, P=0·011) between differences in IgM reactivity and differences in gene expression levels. This connection between donor lung gene expression and long-lasting recipient IgM autoantibodies towards a specific set of proteins suggests a mechanism for the development of autoimmunity in PGD.
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Affiliation(s)
- Peter H Hagedorn
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
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31
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Reisner W, Larsen NB, Silahtaroglu A, Kristensen A, Tommerup N, Tegenfeldt JO, Flyvbjerg H. Single-molecule denaturation mapping of DNA in nanofluidic channels. Proc Natl Acad Sci U S A 2010; 107:13294-9. [PMID: 20616076 PMCID: PMC2922186 DOI: 10.1073/pnas.1007081107] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.
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Affiliation(s)
- Walter Reisner
- Department of Physics, McGill University, Montreal, QC, Canada.
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32
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Nørrelykke SF, Flyvbjerg H. Power spectrum analysis with least-squares fitting: amplitude bias and its elimination, with application to optical tweezers and atomic force microscope cantilevers. Rev Sci Instrum 2010; 81:075103. [PMID: 20687755 DOI: 10.1063/1.3455217] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Optical tweezers and atomic force microscope (AFM) cantilevers are often calibrated by fitting their experimental power spectra of Brownian motion. We demonstrate here that if this is done with typical weighted least-squares methods, the result is a bias of relative size between -2/n and +1/n on the value of the fitted diffusion coefficient. Here, n is the number of power spectra averaged over, so typical calibrations contain 10%-20% bias. Both the sign and the size of the bias depend on the weighting scheme applied. Hence, so do length-scale calibrations based on the diffusion coefficient. The fitted value for the characteristic frequency is not affected by this bias. For the AFM then, force measurements are not affected provided an independent length-scale calibration is available. For optical tweezers there is no such luck, since the spring constant is found as the ratio of the characteristic frequency and the diffusion coefficient. We give analytical results for the weight-dependent bias for the wide class of systems whose dynamics is described by a linear (integro)differential equation with additive noise, white or colored. Examples are optical tweezers with hydrodynamic self-interaction and aliasing, calibration of Ornstein-Uhlenbeck models in finance, models for cell migration in biology, etc. Because the bias takes the form of a simple multiplicative factor on the fitted amplitude (e.g. the diffusion coefficient), it is straightforward to remove and the user will need minimal modifications to his or her favorite least-squares fitting programs. Results are demonstrated and illustrated using synthetic data, so we can compare fits with known true values. We also fit some commonly occurring power spectra once-and-for-all in the sense that we give their parameter values and associated error bars as explicit functions of experimental power-spectral values.
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Affiliation(s)
- Simon F Nørrelykke
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
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Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods 2010; 7:377-81. [PMID: 20364147 PMCID: PMC3127582 DOI: 10.1038/nmeth.1447] [Citation(s) in RCA: 539] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 02/22/2010] [Indexed: 11/09/2022]
Abstract
We optimally localize isolated fluorescent beads and molecules imaged as diffraction-limited spots, determine the orientation of molecules, and present reliable formulae for the precisions of various localization methods. For beads, theory and experimental data both show that unweighted least-squares fitting of a Gaussian squanders one third of the available information, a popular formula for its precision exaggerates beyond Fisher's information limit, and weighted least-squares may do worse, while maximum likelihood fitting is practically optimal.
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Affiliation(s)
- Kim I Mortensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
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Hagedorn PH, Burton CM, Carlsen J, Steinbrüchel D, Andersen CB, Sahar E, Domany E, Cohen IR, Flyvbjerg H, Iversen M. Chronic rejection of a lung transplant is characterized by a profile of specific autoantibodies. Immunology 2010; 130:427-35. [PMID: 20201985 DOI: 10.1111/j.1365-2567.2010.03246.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
SUMMARY Obliterative bronchiolitis (OB) continues to be the major limitation to long-term survival after lung transplantation. The specific aetiology and pathogenesis of OB are not well understood. To explore the role of autoreactivity in OB, we spotted 751 different self molecules onto glass slides, and used these antigen microarrays to profile 48 human serum samples for immunoglobulin G (IgG) and IgM autoantibodies; 27 patients showed no or mild bronchiolitis obliterans syndrome (BOS; a clinical correlate of OB) and 15 patients showed medium to severe BOS. We now report that these BOS grades could be differentiated by a profile of autoantibodies binding to 28 proteins or their peptides. The informative autoantibody profile included down-regulation as well as up-regulation of both IgM and IgG specific reactivities. This profile was evaluated for robustness using a panel of six independent test patients. Analysis of the functions of the 28 informative self antigens showed that eight of them are connected in an interaction network involved in apoptosis and protein metabolism. Thus, a profile of autoantibodies may reflect pathological processes in the lung allograft, suggesting a role for autoimmunity in chronic rejection leading to OB.
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Affiliation(s)
- Peter H Hagedorn
- Biosystems Department, Risø National Laboratory, Technical University of Denmark, Roskilde, Denmark.
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35
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Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H. Optimizing Super Resolution Microscopy. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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36
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Sivaramakrishnan S, Sommese R, Sung JM, Ali M, Doniach S, Flyvbjerg H, Spudich JA. Combining Single Molecule Optical Trapping and Small Angle X-Ray Scattering Measurements to Compute the Persistence Length of a Protein Alpha-Helix. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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37
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Vestergaard CL, Blainey P, Xie XS, Flyvbjerg H. Optimal Estimation of the Diffusion Coefficient from Noisy Time-Series Measurements. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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38
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Pedersen JN, Mikkelsen MB, Kristensen A, Flyvbjerg H. Modeling of DNA in Nanochannels using Linear Elasticity Theory. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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39
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Sivaramakrishnan S, Sung J, Ali M, Doniach S, Flyvbjerg H, Spudich J. Combining single-molecule optical trapping and small-angle x-ray scattering measurements to compute the persistence length of a protein ER/K alpha-helix. Biophys J 2009; 97:2993-9. [PMID: 19948129 PMCID: PMC2784555 DOI: 10.1016/j.bpj.2009.09.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/17/2009] [Accepted: 09/04/2009] [Indexed: 11/16/2022] Open
Abstract
A relatively unknown protein structure motif forms stable isolated single alpha-helices, termed ER/K alpha-helices, in a wide variety of proteins and has been shown to be essential for the function of some molecular motors. The flexibility of the ER/K alpha-helix determines whether it behaves as a force transducer, rigid spacer, or flexible linker in proteins. In this study, we quantify this flexibility in terms of persistence length, namely the length scale over which it is rigid. We use single-molecule optical trapping and small-angle x-ray scattering, combined with Monte Carlo simulations to demonstrate that the Kelch ER/K alpha-helix behaves as a wormlike chain with a persistence length of approximately 15 nm or approximately 28 turns of alpha-helix. The ER/K alpha-helix length in proteins varies from 3 to 60 nm, with a median length of approximately 5 nm. Knowledge of its persistence length enables us to define its function as a rigid spacer in a translation initiation factor, as a force transducer in the mechanoenzyme myosin VI, and as a flexible spacer in the Kelch-motif-containing protein.
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Affiliation(s)
| | - J. Sung
- Department of Applied Physics, Stanford University, Stanford, California
| | - M. Ali
- Department of Applied Physics, Stanford University, Stanford, California
| | - S. Doniach
- Department of Applied Physics, Stanford University, Stanford, California
- Department of Physics, Stanford University, Stanford, California
| | - H. Flyvbjerg
- Department of Micro- and Nano-technology, Danmarks Tekniske Universitet, Copenhagen, Denmark
| | - J.A. Spudich
- Department of Biochemistry, Stanford University, Stanford, California
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Hagedorn P, Burton C, Steinbrüchel D, Sahar E, Flyvbjerg H, Iversen M. 530: Microarray Based Measurement of Autoantibodies Identifies Early Development of BOS in Lung Transplant Patients. J Heart Lung Transplant 2008. [DOI: 10.1016/j.healun.2007.11.544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Reisner W, Beech JP, Larsen NB, Flyvbjerg H, Kristensen A, Tegenfeldt JO. Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment. Phys Rev Lett 2007; 99:058302. [PMID: 17930801 DOI: 10.1103/physrevlett.99.058302] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Indexed: 05/21/2023]
Abstract
We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around 100 x 100 nm in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion.
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Affiliation(s)
- Walter Reisner
- Danish Polymer Centre and Biosystems Department, Risø National Laboratory, Technical University of Denmark-DTU, DK-4000 Roskilde, Denmark
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42
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Pedersen L, Flyvbjerg H. Comment on "direct measurement of the oscillation frequency in an optical-tweezers trap by parametric excitation". Phys Rev Lett 2007; 98:189801; author reply 189803. [PMID: 17501617 DOI: 10.1103/physrevlett.98.189801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Indexed: 05/15/2023]
Affiliation(s)
- Lykke Pedersen
- Danish Polymer Centre, BIO-313 RISØ, Technical University of Denmark DK-4000 Roskilde, Denmark
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43
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Abstract
Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even partially covering the loading bay prevent correct parking of the truck. Similarly on DNA, non-specific ligands interfere with the binding and function of sequence-specific proteins. We derive a formula for the probability that the loading bay is free from parked cars. The probability depends on the size of the loading bay and allows an estimation of the size of the footprint on the DNA of the sequence-specific protein by assaying protein binding or function in the presence of increasing concentrations of non-specific ligand. Assaying for function gives an 'activity footprint'; the minimum length of DNA required for function rather than the more commonly measured physical footprint. Assaying the complex type I restriction enzyme, EcoKI, gives an activity footprint of approximately 66 bp for ATP hydrolysis and 300 bp for the DNA cleavage function which is intimately linked with translocation of DNA by EcoKI. Furthermore, considering the coverage of chromosomal DNA by proteins in vivo, our theory shows that the search for a specific DNA sequence is very difficult; most sites are obscured by parked cars. This effectively rules out any significant role in target location for mechanisms invoking one-dimensional, linear diffusion along DNA.
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Affiliation(s)
- Henrik Flyvbjerg
- Risø National Laboratory, Biosystems Department and Danish Polymer Centre Building BIO-776, PO Box 49, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
- Isaac Newton Institute for Mathematical Sciences 20 Clarkson Road, Cambridge, CB3 0EH, UK
| | - Steven A. Keatch
- School of Chemistry, The King's Buildings, The University of Edinburgh Edinburgh, EH9 3JJ, UK
| | - David T.F. Dryden
- School of Chemistry, The King's Buildings, The University of Edinburgh Edinburgh, EH9 3JJ, UK
- Isaac Newton Institute for Mathematical Sciences 20 Clarkson Road, Cambridge, CB3 0EH, UK
- To whom correspondence should be adressed. Tel: +0131 650 4735; Fax: +0131 650 6453;
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Kasimova MR, Grigiene J, Krab K, Hagedorn PH, Flyvbjerg H, Andersen PE, Møller IM. The free NADH concentration is kept constant in plant mitochondria under different metabolic conditions. Plant Cell 2006; 18:688-98. [PMID: 16461578 PMCID: PMC1383643 DOI: 10.1105/tpc.105.039354] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The reduced coenzyme NADH plays a central role in mitochondrial respiratory metabolism. However, reports on the amount of free NADH in mitochondria are sparse and contradictory. We first determined the emission spectrum of NADH bound to proteins using isothermal titration calorimetry combined with fluorescence spectroscopy. The NADH content of actively respiring mitochondria (from potato tubers [Solanum tuberosum cv Bintje]) in different metabolic states was then measured by spectral decomposition analysis of fluorescence emission spectra. Most of the mitochondrial NADH is bound to proteins, and the amount is low in state 3 (substrate + ADP present) and high in state 2 (only substrate present) and state 4 (substrate + ATP). By contrast, the amount of free NADH is low but relatively constant, even increasing a little in state 3. Using modeling, we show that these results can be explained by a 2.5- to 3-fold weaker average binding of NADH to mitochondrial protein in state 3 compared with state 4. This indicates that there is a specific mechanism for free NADH homeostasis and that the concentration of free NADH in the mitochondrial matrix per se does not play a regulatory role in mitochondrial metabolism. These findings have far-reaching consequences for the interpretation of cellular metabolism.
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Affiliation(s)
- Marina R Kasimova
- Optics and Plasma Research Department, Risø National Laboratory, DK-4000 Roskilde, Denmark
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45
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Abstract
When single-molecule fluorescence localization techniques are pushed to their lower limits in attempts to measure ever-shorter distances, measurement errors become important to understand. Here we describe the non-Gaussian distribution of measured distances that is the key to proper interpretation of distance measurements. We test it on single-molecule high-resolution colocalization data for a known distance, 10 nm, and find that it gives the correct result, whereas interpretation of the same data with a Gaussian distribution gives a result that is systematically too large.
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Affiliation(s)
- L Stirling Churchman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
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46
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Abstract
Experimental time series for trajectories of motile cells may contain so much information that a systematic analysis will yield cell-type-specific motility models. Here we demonstrate how, using human keratinocytes and fibroblasts as examples. The two resulting models reflect the cells' different roles in the organism, it seems, and show that a cell has a memory of past velocities. They also suggest how to distinguish quantitatively between various surfaces' compatibility with the two cell types.
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Affiliation(s)
- David Selmeczi
- Danish Polymer Centre, and Biosystems Department, Risø National Laboratory, Roskilde, Denmark
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47
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Abstract
The molecular mechanisms that allow elongation of the unstable microtubule lattice remain unclear. It is usually thought that the GDP-liganded tubulin lattice is capped by a small layer of GTP- or GDP-Pi-liganded molecules, the so called "GTP-cap". Here, we point-out that the elastic properties of the microtubule lattice cause a difference in stability between the elongating tubulin sheet and the completed microtubule wall. The implications of our observations for microtubule structure and dynamics are discussed.
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Affiliation(s)
- D Chrétien
- Laboratoire des Protéines Complexes, Université de Tours, 2 bis Boulevard Tonnellé, F-37032 Tours, France.
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48
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Abstract
NADH is central to the functioning of mitochondrial respiration. It is produced by enzymes in, or associated with, the tricarboxylic acid cycle in the matrix, and it is oxidized by two respiratory chain enzymes in the inner membrane, the rotenone-sensitive complex I and the rotenone-insensitive internal NADH dehydrogenase (ND(in)). A simplified kinetic model for NADH turnover in the matrix of plant mitochondria is presented. Only the two main NADH-producing enzymes, NAD-malate dehydrogenase [EC 1.1.1.37] (MDH) and NAD-malic enzyme [EC 1.1.1.39] (ME), are considered. This model reproduces the complex behaviour of malate oxidation by isolated mitochondria in response to additions of ADP (state 3/state 4), NAD(+) and/or rotenone, as well as to changes in pH. It is found that MDH always operates at or close to equilibrium. Changes in the activity of complex I, ND(in), or ME are predicted to cause clear changes in the pattern of malate oxidation. In general, the model predicts high sensitivity to changes in the ME activity. In contrast, MDH activity can be reduced 100-fold without detectable changes in malate oxidation. It is demonstrated that it is not the high activity, but the equilibrium properties of MDH that are important for the redox-buffering function of MDH in the mitochondrial matrix. Binding of NAD(+) and NADH in the matrix reduces the concentrations of free NAD(+) and NADH, depending on the concentration of binding sites and the binding strength. On the basis of the modelling results it is estimated that a significant proportion of the mitochondrial NAD is bound.
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Affiliation(s)
- Peter H. Hagedorn
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark
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49
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50
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Abstract
Microtubules polymerize from GTP-liganded tubulin dimers, but are essentially made of GDP-liganded tubulin. We investigate the tug-of-war resulting from the fact that GDP-liganded tubulin favors a curved configuration, but is forced to remain in a straight one when part of a microtubule. We point out that near the end of a microtubule, the proximity of the end shifts the balance in this tug-of-war, with some protofilament bending as result. This somewhat relaxes the microtubule lattice near its end, resulting in a structural cap. This structural cap thus is a simple mechanical consequence of two well-established facts: protofilaments made of GDP-liganded tubulin have intrinsic curvature, and microtubules are elastic, made from material that can yield to forces, in casu its own intrinsic forces. We explore possible properties of this structural cap, and demonstrate 1) how it allows both polymerization from GTP-liganded tubulin and rapid depolymerization in its absence; 2) how rescue can occur; 3) how a third, meta-stable intermediate state is possible and can explain some experimental results; and 4) how the tapered tips observed at polymerizing microtubule ends are stabilized during growth, though unable to accommodate a lateral cap. This scenario thus supports the widely accepted GTP-cap model by suggesting a stabilizing mechanism that explains the many aspects of dynamic instability.
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Affiliation(s)
- Imre M Jánosi
- The Niels Bohr Institute, DK-2100 Copenhagen Ø, Denmark.
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