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1.
Mol Biol Cell ; 32(21): ar35, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34586828

RESUMO

The counting of discrete photobleaching steps in fluorescence microscopy is ideally suited to study protein complex stoichiometry in situ. The counting range of photobleaching step analysis has been significantly improved with more-sophisticated algorithms for step detection, albeit at an increasing computational cost and with the necessity for high-quality data. Here, we address concerns regarding robustness, automation, and experimental validation, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labeling strategies with respect to their molecular brightness, photostability, and photoblinking. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we validate the developed methods with experimental data acquired on DNA origami labeled with defined fluorophore numbers, demonstrating counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis by counting labeled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated manner.

2.
ACS Cent Sci ; 7(9): 1561-1571, 2021 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-34584958

RESUMO

Small-molecule fluorophores enable the observation of biomolecules in their native context with fluorescence microscopy. Specific labeling via bio-orthogonal tetrazine chemistry combines minimal label size with rapid labeling kinetics. At the same time, fluorogenic tetrazine-dye conjugates exhibit efficient quenching of dyes prior to target binding. However, live-cell compatible long-wavelength fluorophores with strong fluorogenicity have been difficult to realize. Here, we report close proximity tetrazine-dye conjugates with minimal distance between tetrazine and the fluorophore. Two synthetic routes give access to a series of cell-permeable and -impermeable dyes including highly fluorogenic far-red emitting derivatives with electron exchange as the dominant excited-state quenching mechanism. We demonstrate their potential for live-cell imaging in combination with unnatural amino acids, wash-free multicolor and super-resolution STED, and SOFI imaging. These dyes pave the way for advanced fluorescence imaging of biomolecules with minimal label size.

3.
Nat Commun ; 12(1): 4565, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34315910

RESUMO

High-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffraction-resolution.


Assuntos
Imageamento Tridimensional , Microscopia de Fluorescência , Análise de Célula Única , Animais , Células COS , Chlorocebus aethiops , Citoesqueleto/metabolismo , Íons , Imagem Óptica , Tubulina (Proteína)/metabolismo
4.
Int J Biochem Cell Biol ; 135: 105978, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33865985

RESUMO

Quantitative assessment of protein complexes, such as receptor clusters in the context of cellular signalling, has become a pressing objective in cell biology. The advancements in the field of single molecule fluorescence microscopy have led to different approaches for counting protein copy numbers in various cellular structures. This has resulted in an increasing interest in robust calibration protocols addressing photophysical properties of fluorescent labels and the effect of labelling efficiencies. Here, we want to give an update on recent methods for protein counting with a focus on novel calibration protocols. In this context, we discuss different types of calibration samples and identify some of the challenges arising in molecular counting experiments. Some recently published applications offer potential approaches to tackle these challenges.


Assuntos
Fluorescência , Microscopia de Fluorescência/métodos , Proteínas/química , Imagem Individual de Molécula/métodos , Animais , Humanos
5.
Thromb Haemost ; 121(11): 1435-1447, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33638140

RESUMO

Collagen has been proposed to bind to a unique epitope in dimeric glycoprotein VI (GPVI) and the number of GPVI dimers has been reported to increase upon platelet activation. However, in contrast, the crystal structure of GPVI in complex with collagen-related peptide (CRP) showed binding distinct from the site of dimerization. Further fibrinogen has been reported to bind to monomeric but not dimeric GPVI. In the present study, we have used the advanced fluorescence microscopy techniques of single-molecule microscopy, fluorescence correlation spectroscopy (FCS) and bioluminescence resonance energy transfer (BRET), and mutagenesis studies in a transfected cell line model to show that GPVI is expressed as a mixture of monomers and dimers and that dimerization through the D2 domain is not critical for activation. As many of these techniques cannot be applied to platelets to resolve this issue, due to the high density of GPVI and its anucleate nature, we used Förster resonance energy transfer (FRET) to show that endogenous GPVI is at least partially expressed as a dimer on resting and activated platelet membranes. We propose that GPVI may be expressed as a monomer on the cell surface and it forms dimers in the membrane through diffusion, giving rise to a mixture of monomers and dimers. We speculate that the formation of dimers facilitates ligand binding through avidity.

6.
J Phys Chem B ; 124(29): 6358-6368, 2020 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-32589422

RESUMO

Time-resolved spectroscopies have been playing an essential role in the elucidation of the fundamental mechanisms of light-driven processes, particularly in exploring relaxation models for electronically excited molecules. However, the determination of such models from experimentally obtained time-resolved and spectrally resolved data still demands a high degree of intuition, frequently poses numerical challenges, and is often not free from ambiguities. Here, we demonstrate the analysis of time-resolved laser spectroscopy data via a deep learning network to obtain the correct relaxation kinetic model. In its current design, the presented Deep Spectroscopy Kinetic Analysis Network (DeepSKAN) can predict kinetic models (involved states and relaxation pathways) consisting of up to five states, which results in 103 possible different classes, by estimating the probability of occurrence of a given kinetic model class. DeepSKAN was trained with synthetic time-resolved spectra spanning over 4 orders of magnitude in time with a unitless time axis, thereby demonstrating its potential as a universal approach for analyzing data from various time-resolved spectroscopy techniques in different time ranges. By adding the probabilities of each pathway of the top-k models normalized by the total probability, we can determine the relaxation pathways for a given data set with high certainty (up to 99%). Due to its architecture and training, DeepSKAN is robust against experimental noise and typical preanalysis errors like time-zero corrections. Application of DeepSKAN to experimental data is successfully demonstrated for three different photoinduced processes: transient absorption of the retinal isomerization, transient IR spectroscopy of the relaxation of the photoactivated DRONPA, and transient absorption of the dynamics in lycopene. This approach delivers kinetic models and could be a unifying asset in several areas of spectroscopy.

7.
Mol Cell ; 78(2): 236-249.e7, 2020 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-32101700

RESUMO

The formation of silenced and condensed heterochromatin foci involves enrichment of heterochromatin protein 1 (HP1). HP1 can bridge chromatin segments and form liquid droplets, but the biophysical principles underlying heterochromatin compartmentalization in the cell nucleus are elusive. Here, we assess mechanistically relevant features of pericentric heterochromatin compaction in mouse fibroblasts. We find that (1) HP1 has only a weak capacity to form liquid droplets in living cells; (2) the size, global accessibility, and compaction of heterochromatin foci are independent of HP1; (3) heterochromatin foci lack a separated liquid HP1 pool; and (4) heterochromatin compaction can toggle between two "digital" states depending on the presence of a strong transcriptional activator. These findings indicate that heterochromatin foci resemble collapsed polymer globules that are percolated with the same nucleoplasmic liquid as the surrounding euchromatin, which has implications for our understanding of chromatin compartmentalization and its functional consequences.


Assuntos
Cromatina/genética , Proteínas Cromossômicas não Histona/genética , Eucromatina/genética , Heterocromatina/genética , Animais , Fibroblastos , Camundongos
8.
Nat Commun ; 11(1): 32, 2020 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-31896744

RESUMO

Many intracellular pathogens, such as mammalian reovirus, mimic extracellular matrix motifs to specifically interact with the host membrane. Whether and how cell-matrix interactions influence virus particle uptake is unknown, as it is usually studied from the dorsal side. Here we show that the forces exerted at the ventral side of adherent cells during reovirus uptake exceed the binding strength of biotin-neutravidin anchoring viruses to a biofunctionalized substrate. Analysis of virus dissociation kinetics using the Bell model revealed mean forces higher than 30 pN per virus, preferentially applied in the cell periphery where close matrix contacts form. Utilizing 100 nm-sized nanoparticles decorated with integrin adhesion motifs, we demonstrate that the uptake forces scale with the adhesion energy, while actin/myosin inhibitions strongly reduce the uptake frequency, but not uptake kinetics. We hypothesize that particle adhesion and the push by the substrate provide the main driving forces for uptake.


Assuntos
Interações Hospedeiro-Patógeno/fisiologia , Orthoreovirus Mamífero 3/fisiologia , Nanopartículas Metálicas/química , Actinas/metabolismo , Animais , Avidina/química , Biotina/química , Capsídeo/química , Células Cultivadas , Fibroblastos/virologia , Ouro , Células HeLa , Humanos , Integrinas/metabolismo , Cinética , Orthoreovirus Mamífero 3/química , Orthoreovirus Mamífero 3/patogenicidade , Nanopartículas Metálicas/virologia , Modelos Teóricos , Miosinas/metabolismo , Ratos , Vírion/patogenicidade , Vírion/fisiologia
9.
Angew Chem Int Ed Engl ; 59(2): 804-810, 2020 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-31638314

RESUMO

Recent developments in fluorescence microscopy call for novel small-molecule-based labels with multiple functionalities to satisfy different experimental requirements. A current limitation in the advancement of live-cell single-molecule localization microscopy is the high excitation power required to induce blinking. This is in marked contrast to the minimal phototoxicity required in live-cell experiments. At the same time, quality of super-resolution imaging depends on high label specificity, making removal of excess dye essential. Approaching both hurdles, we present the design and synthesis of a small-molecule label comprising both fluorogenic and self-blinking features. Bioorthogonal click chemistry ensures fast and highly selective attachment onto a variety of biomolecular targets. Along with spectroscopic characterization, we demonstrate that the probe improves quality and conditions for regular and single-molecule localization microscopy on live-cell samples.


Assuntos
Química Click/métodos , Microscopia de Fluorescência/métodos , Imagem Óptica/métodos
10.
Methods Mol Biol ; 1663: 127-138, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28924664

RESUMO

Measuring the kinetics of protein-protein interactions between molecules in the plasma membrane of live cells provides valuable information for understanding dynamic processes, like cellular signaling, on a molecular scale. Two-color single-molecule tracking is a fluorescence microscopy-based method to detect and quantify specific protein-protein interactions on a single-event level, providing sensitivity to heterogeneities and rare events. Fundamentally, it allows following the movement of single molecules of two different protein species in live cells with a localization precision beyond the diffraction limit of light in real time. It hence provides information about the diffusion behavior of every protein as well as about their dimerization kinetics. Here, we describe all the necessary steps to obtain two-color tracking data of plasma membrane-associated proteins in live cells using SNAP-tag and HaloTag fusion constructs and total internal reflection fluorescence (TIRF) microscopy. Also, we outline the main steps needed for analyzing the recorded data.


Assuntos
Proteínas de Membrana/metabolismo , Imagem Individual de Molécula/métodos , Cinética , Proteínas de Membrana/química , Microscopia de Fluorescência/métodos , Ligação Proteica , Multimerização Proteica
11.
PLoS Comput Biol ; 13(9): e1005779, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28945754

RESUMO

Cells typically vary in their response to extracellular ligands. Receptor transport processes modulate ligand-receptor induced signal transduction and impact the variability in cellular responses. Here, we quantitatively characterized cellular variability in erythropoietin receptor (EpoR) trafficking at the single-cell level based on live-cell imaging and mathematical modeling. Using ensembles of single-cell mathematical models reduced parameter uncertainties and showed that rapid EpoR turnover, transport of internalized EpoR back to the plasma membrane, and degradation of Epo-EpoR complexes were essential for receptor trafficking. EpoR trafficking dynamics in adherent H838 lung cancer cells closely resembled the dynamics previously characterized by mathematical modeling in suspension cells, indicating that dynamic properties of the EpoR system are widely conserved. Receptor transport processes differed by one order of magnitude between individual cells. However, the concentration of activated Epo-EpoR complexes was less variable due to the correlated kinetics of opposing transport processes acting as a buffering system.


Assuntos
Transporte Biológico/fisiologia , Modelos Biológicos , Receptores de Superfície Celular/metabolismo , Análise de Célula Única/métodos , Linhagem Celular Tumoral , Biologia Computacional , Corantes Fluorescentes/análise , Corantes Fluorescentes/química , Corantes Fluorescentes/metabolismo , Humanos , Processamento de Imagem Assistida por Computador/métodos , Cinética , Microscopia Confocal , Receptores de Superfície Celular/análise , Receptores de Superfície Celular/química , Receptores da Eritropoetina
12.
Angew Chem Int Ed Engl ; 56(17): 4724-4728, 2017 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-28328078

RESUMO

Chemical fixation of living cells for microscopy is commonly achieved by crosslinking of intracellular proteins with dialdehydes prior to examination. We herein report a photocleavable protecting group for glutaraldehyde that results in a light-triggered and membrane-permeable fixative, which is nontoxic prior to photocleavage. Lipophilic ester groups allow for diffusion across the cell membrane and intracellular accumulation after enzymatic hydrolysis. Irradiation with UV light releases glutaraldehyde. The in situ generated fixative crosslinks intracellular proteins and preserves and stabilizes the cell so that it is ready for microscopy. In contrast to conventional glutaraldehyde fixation, tissue autofluorescence does not increase after fixation. Caged glutaraldehyde may in future enable functional experiments on living cells under a light microscope in which events of interest can be stopped in spatially confined volumes at defined time points. Samples with individually stopped events could then later be analyzed in ultrastructural studies.

13.
Chemistry ; 23(50): 12264-12274, 2017 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-28339125

RESUMO

Dinuclear CuII -patellamide complexes (patellamides are naturally occurring cyclic pseudo-octapeptides) are known to be efficient catalysts for hydrolysis reactions of biological importance, for example, those of phosphatase, carbonic anhydrase, and glycosidase. However, the biological role of patellamides is still unknown. Patellamides were originally extracted from the sea squirt Lissoclinum patella, but are now known to be ribosomally expressed by the blue-green algae Prochloron that live in symbiosis with L. patella. In a further step to unravel the metabolic significance of the patellamide complexes, the question as to whether these are also formed inside Prochloron cells is addressed. In this study, a biocompatible patellamide-fluorescent dye conjugate has been introduced into living Prochloron cells and, by means of flow cytometry and confocal microscopy, it is shown that CuII ions are coordinated to patellamides in vivo.

14.
Org Biomol Chem ; 14(24): 5606-11, 2016 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-27072883

RESUMO

A small synthetic calcium sensor that can be site-specifically coupled to proteins in living cells by utilizing the bio-orthogonal HaloTag labeling strategy is presented. We synthesized an iodo-derivatized BAPTA chelator with a tetramethyl rhodamine fluorophore that allows further modification by Sonogashira cross-coupling. The presented calcium sensitive dye shows a 200-fold increase in fluorescence upon calcium binding. The derivatization with an aliphatic linker bearing a terminal haloalkane-function by Sonogashira cross-coupling allows the localization of the calcium sensor to Halo fusion proteins which we successfully demonstrate in in vitro and in vivo experiments. The herein reported highly sensitive tetramethyl rhodamine based calcium indicator, which can be selectively localized to proteins, is a powerful tool to determine changes in calcium levels inside living cells with spatiotemporal resolution.


Assuntos
Cálcio/metabolismo , Corantes Fluorescentes/metabolismo , Proteínas/metabolismo , Rodaminas/metabolismo , Animais , Sobrevivência Celular , Células HeLa , Humanos , Camundongos , Células NIH 3T3 , Coloração e Rotulagem
15.
Biophys J ; 109(11): 2352-62, 2015 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-26636946

RESUMO

The number of fluorophores within a molecule complex can be revealed by single-molecule photobleaching imaging. A widely applied strategy to analyze intensity traces over time is the quantification of photobleaching step counts. However, several factors can limit and bias the detection of photobleaching steps, including noise, high numbers of fluorophores, and the possibility that several photobleaching events occur almost simultaneously. In this study, we propose a new approach, to our knowledge, to determine the fluorophore number that correlates the intensity decay of a population of molecule complexes with the decay of the number of visible complexes. We validated our approach using single and fourfold Atto-labeled DNA strands. As an example we estimated the subunit stoichiometry of soluble CD95L using GFP fusion proteins. To assess the precision of our method we performed in silico experiments showing that the estimates are not biased for experimentally observed intensity fluctuations and that the relative precision remains constant with increasing number of fluorophores. In case of fractional fluorescent labeling, our simulations predicted that the fluorophore number estimate corresponds to the product of the true fluorophore number with the labeling fraction. Our method, denoted by spot number and intensity correlation (SONIC), is fully automated, robust to noise, and does not require the counting of photobleaching events.


Assuntos
Corantes Fluorescentes/química , Modelos Estatísticos , Fotodegradação , Automação , Sequência de Bases , DNA/química , DNA/genética , Processamento de Imagem Assistida por Computador , Microscopia , Modelos Moleculares , Conformação de Ácido Nucleico , Multimerização Proteica , Estrutura Quaternária de Proteína , Receptor fas/química
16.
Chemphyschem ; 16(17): 3578-83, 2015 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-26490757

RESUMO

Blinking of the photoluminescence (PL) emitted from individual conjugated polymer chains is one of the central observations made by single-molecule spectroscopy (SMS). Important information, for example regarding excitation energy transfer, can be extracted by evaluating dynamic quenching. However, the nature of trap states, which are responsible for PL quenching, often remains obscured. We present a detailed investigation of the photon statistics of single poly(3-hexylthiophene) (P3HT) chains obtained by SMS. The photon statistics provide a measure of the number and brightness of independently emitting areas on a single chain. These observables can be followed during blinking. A decrease in PL intensity is shown to be correlated with either 1) a decrease in the average brightness of the emitting sites; or 2) a decrease in the number of emitting regions. We attribute these phenomena to the formation of 1) shallow charge traps, which can weakly affect all emitting areas of a single chain at once; and 2) deep traps, which have a strong effect on small regions within the single chains.

17.
J Inorg Biochem ; 148: 78-83, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26048430

RESUMO

The substitution of tetradentate bispidine ligands with rhodamine and cyanine dye molecules, coupled to an amine donor, forming an amide as potential fifth donor, is described. Bispidines are known to lead to very stable Cu(II) complexes, and the coordination to Cu(II) was expected to efficiently quench the fluorescence of dye molecules. However, at physiological pH the amide is not coordinated, as shown by titration experiments and crystallographic structural data of three possible isomers of these complexes. This may be due to the specific cavity shape of bispidines and the Jahn-Teller lability of the Cu(II) center. While Cu(II) coordination in aqueous solution leads to efficient fluorescence quenching, experiments show that the complex stabilities are not large enough for Cu(II) sensing in biological media, and possibilities are discussed, how this may be achieved by optimized bispidine-dye conjugates.


Assuntos
Compostos Bicíclicos Heterocíclicos com Pontes/química , Corantes/química , Cobre/química , Compostos Organometálicos/química , Compostos Bicíclicos Heterocíclicos com Pontes/síntese química , Cristalografia por Raios X , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Isomerismo , Ligantes , Modelos Químicos , Estrutura Molecular , Compostos Organometálicos/síntese química , Hidróxido de Sódio/química , Espectrometria de Fluorescência , Espectrofotometria
18.
Dalton Trans ; 44(7): 3467-85, 2015 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-25604703

RESUMO

In this work the first phenazine derivatives with guanidino substituents were prepared and their structural and electronic properties studied in detail. The guanidino groups decrease the HOMO-LUMO gap, massively increase the quantum yield for fluorescence and offer sites for metal coordination. The yellow-orange colored 2,3,7,8-tetraguanidino-substituted phenazine shows intense fluorescence. The wavelength of the fluorescence signal is strongly solvent dependent, covering a region from 515 nm in Et2O solution (with a record quantum yield of 0.39 in Et2O) to 640 nm in water. 2,3-Bisguanidino-substituted phenazine is less fluorescent (maximum quantum yield of 0.17 in THF), but exhibits extremely large Stokes shifts. In contrast, guanidino-functionalized fluorenes emit only very weakly. Subsequently, the influence of coordination on the electronic properties and especially the fluorescence of the phenazine system was analysed. Coordination first takes place at the guanidino groups, and leads to a blue shift of the luminescence signal as well as a massive decrease of the luminescence lifetime. Luminescence is almost quenched completely upon Cu(I) coordination. On the other hand, in the case of Zn(II) coordination the fluorescence signal remains strong (quantum yield of 0.36 in CH3CN). In the case of strong zinc Lewis acids, an excess of metal compound leads to additional coordination at the phenazine N atoms. This is accompanied by significant red-shifts of the lowest-energy transition in the absorption and fluorescence spectra. Pentanuclear complexes with two phenazine units were isolated and structurally characterized, and further aggregation leads to chain polymers.

19.
Methods Appl Fluoresc ; 3(4): 044001, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-29148507

RESUMO

We describe a fluorogenic ruthenium (II) carbene complex in which the chromophore is directly connected to the metal center. The compound introduces a boron dipyrromethene (BODIPY) moiety into target double bonds by metathesis. Tagging of terminal double bonds is demonstrated on immobilized styrene units on a glass surface. We also show that two compounds with distinguishable fluorescence properties are formed in the model reaction with styrene. The outcome of the metathesis reaction is characterized by 19F-NMR, optical spectroscopy, and, finally, single-molecule trajectories. This labeling scheme, in our perception, is of particular interest in the fields of interfacial science and biorthogonal ligation in combination with super-resolution imaging.

20.
Chemphyschem ; 15(17): 3832-8, 2014 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-25212489

RESUMO

The effect of solute affinity on solute diffusion in binary liquids well below the lower critical solution temperature (LCST) was studied by using fluorescence correlation spectroscopy. We measured the hydrodynamic radii of a hydrophobic and an amphiphilic fluorescent dye under systematic variation of the relative molar fractions of water/2-butoxyethanol and, for comparison, of water/methanol mixtures, which do not show phase separation. We found that the apparent hydrodynamic radius of the hydrophobic dye almost doubled in water/2-butoxyethanol, whereas it remained largely unchanged for the amphiphilic dye and in water/methanol mixtures. Our results indicate that the translational diffusion of solutes is influenced by transient local solution structures, even at temperatures well below the LCST. We conclude that, even far below LCST, different solutes can experience different environments in binary liquid mixtures depending on both the solute and solvent properties, all of which impact their reactivity.

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