Relevant bibliographies by topics / Biophysical Investigations

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Biophysical Investigations'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Biophysical Investigations"

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Becker, R., J. Bienen, U. Carl, P. Cloth, M. Dellert, V. Dr ke, W. Eyrich, et al. "Biophysical Investigations of Therapeutic Proton Beams." Radiation Protection Dosimetry 70, no. 1 (April 1, 1997): 485–92. http://dx.doi.org/10.1093/oxfordjournals.rpd.a032002.

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Hosur, R. V., P. K. Radha, Anup Madan, and L. C. Padhy. "Biophysical investigations on the myb-DNA system." Biophysical Chemistry 68, no. 1-3 (October 1997): 147–59. http://dx.doi.org/10.1016/s0301-4622(97)00026-4.

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Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (December 24, 2021): 7. http://dx.doi.org/10.3390/photonics9010007.

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Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.
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Rounsevell, Ross W. S., Annette Steward, and Jane Clarke. "Biophysical Investigations of Engineered Polyproteins: Implications for Force Data." Biophysical Journal 88, no. 3 (March 2005): 2022–29. http://dx.doi.org/10.1529/biophysj.104.053744.

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Brandenburg, K., I. Moriyon, M. D. Arraiza, G. Lewark-Yvetot, M. H. J. Koch, and U. Seydel. "Biophysical investigations into the interaction of lipopolysaccharide with polymyxins." Thermochimica Acta 382, no. 1-2 (January 2002): 189–98. http://dx.doi.org/10.1016/s0040-6031(01)00731-6.

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Kenkare, U. W., G. K. Jarori, S. R. Kasturi, A. Mehta, and M. P. Pitale. "Biophysical investigations on the active site of brain hexokinase." Journal of Biosciences 8, no. 1-2 (August 1985): 107–19. http://dx.doi.org/10.1007/bf02703970.

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De, Kathakali, Christopher Aisenbrey, Jayanta Haldar, Sophie Faure, Christiane Forestier, Nicolas Charbonnel, and Burkhard Bechinger. "Biophysical investigations of antimicrobial peptide mimics for mechanistic studies." Biophysical Journal 122, no. 3 (February 2023): 368a. http://dx.doi.org/10.1016/j.bpj.2022.11.2030.

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Chen, F., X. W. Shen, D. F. Huang, and Y. X. Huang. "THERMAL ENVIRONMENT OF RESIDENTIAL COMMUNITIES OVER A COAST AREA IN SOUTHEASTERN CHINA." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLVIII-3/W2-2022 (October 27, 2022): 9–14. http://dx.doi.org/10.5194/isprs-archives-xlviii-3-w2-2022-9-2022.

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Abstract. The characters of the residential communities over Tong’an District of Xiamen City in thermal environment as well as in biophysical factors were investigated mainly based on the Lansat-8 OLI/TIRS Collection 2 Level-2 products. Specifically, the surface temperature product was used in measuring thermal environment, and the surface reflectance product was used to derive biophysical factors through the tasseled cap transformation as well as the normalized difference vegetation index (NDVI). Among the four types of residential community, the old community in urban area was generally lower in NDVI and in the Wetness component and therefore had higher surface temperature. Varied relationships of surface temperature with biophysical factors among four types were observed, which also demonstrated seasonal variation. At the same time, the preliminary investigation showed that the residential communities located in rural-urban fringe and a small portion of village communities had confronted with problems in thermal environment as well as in surface biophysical conditions. Furthermore, limitations of this study were discussed, mainly in spatial resolution and temporal representativeness of the Landsat-8 OLI/TIRS data, in biophysical components derived from the multi-spectral reflectance without depicting actual landscape, and in no consideration for the background of individual community. As the whole district covers wide and complex territory along with different local climate types, more investigations in details are required.
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Plotegher, Nicoletta, Elisa Greggio, Marco Bisaglia, and Luigi Bubacco. "Biophysical groundwork as a hinge to unravel the biology of α-synuclein aggregation and toxicity." Quarterly Reviews of Biophysics 47, no. 1 (January 21, 2014): 1–48. http://dx.doi.org/10.1017/s0033583513000097.

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AbstractAlpha-synuclein (aS) and its aggregation properties are central in the development and spread of Parkinson's disease. Point mutations and multiplications of the SNCA gene encoding aS cause autosomal dominant forms of the disorder. Moreover, protein inclusions found in the surviving neurons of parkinsonian brains consist mainly of a fibrillar form of aS. Aggregates of aS, which form a transient, complex and heterogeneous ensemble, participate in a wide variety of toxic mechanisms that may be amplified by aS spreading among neighbouring neurons. Recently, significant effort has been directed into the study of the aS aggregation process and the impact of aS aggregates on neuron survival. In this review, we present state-of-the-art biophysical studies on the aS aggregation process in vitro and in cellular models. We comprehensively review the new insights generated by the recent biophysical investigations, which could provide a solid basis from which to design future biomedical studies. The diverse cellular models of aS toxicity and their potential use in the biophysical investigation are also discussed.
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Fukuoka, Satoshi, Walter Richter, Jörg Howe, Jörg Andrä, Manfred Rössle, Christian Alexander, Thomas Gutsmann, and Klaus Brandenburg. "Biophysical investigations into the interactions of endotoxins with bile acids." Innate Immunity 18, no. 2 (September 27, 2011): 307–17. http://dx.doi.org/10.1177/1753425911404093.

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Dissertations / Theses on the topic "Biophysical Investigations"

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Forman, J. R. "Biophysical investigations of PKD domains : mechanosensation and pathogenesis." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599119.

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Autosomal dominant polycystic kidney disease is one of the most common human genetic disorders, and most cases are linked to mutations in the protein polycystin-1. In 2003, polycystin-1 was proposed to function as a mechanosensor, sensing changes in kidney tubule fluid flow. This dissertation presents investigations into the mechanical properties of PKD domains, which constitute approximately half of the extracellular region of the transmembrane polycystin-1 protein. Using single molecule force spectroscopy, PKD domains of polycystin-1 were shown to exhibit a phenomenal resistance to unfolding under applied external forces. These results demonstrate that PKD domains would remain folded under the physiological forces of fluid flow and suggest that polycystin-1 has evolved to fulfil a mechanical function. How do proteins resist unfolding under applied forces? Computer simulations, protein engineering, and force spectroscopy were employed to investigate the unfolding pathway of PKD domains under force. This work reveals the formation of force-induced non-native contacts in the PKD domains. These non-native contacts appear to be the critical feature for stabilising PKD domains against unfolding. Finally, this dissertation presents the thermodynamic effects of pathogenic mutations in the PKD domains of polycystin-1. These data suggest that a significant proportion of pathogenic mutations will act to destabilise protein domains, sometimes preventing folding. Thermodynamic destabilisation is likely to be the molecular pathogenic mechanism for a large fraction of genetic diseases. Further research in this vein, to elucidate the molecular biophysical effects of mutations, will be vital for our understanding of genetic diseases.
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Hands, Sarah Louise. "Biophysical investigations of the mechanism of colicin translocation." Thesis, University of Nottingham, 2005. http://eprints.nottingham.ac.uk/10102/.

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Colicins are a family of bacterial toxins, which kill Escherichia coli cells and other closely related species. Their mode of action requires binding to an outer membrane receptor, translocation across the outer membrane and periplasm and cytotoxic action on a specific target. Colicins usually kill cells either by attacking the bacterial RNA or DNA or by forming pores in the inner membrane of the cell. Their cytotoxic activity can be inhibited by the high affinity binding of an immunity protein. For Group A colicins, translocation requires interaction between the N-terminal domain of the colicin and a series of membrane bound and periplasmic proteins called the Tol system (TolB, TolR, TolA, TolQ and Pal). Three residues of colicin E9 have previously been shown to be essential for an interaction with TolB. This study suggests that these residues play differing roles in the interaction with TolB. Other residues surrounding these previously identified residues are also shown to be involved in the interaction with TolB. In order to allow cytotoxicity, the immunity protein of colicins E3 and E9 must be lost on entry of the colicin to a target cell. This work has demonstrated by Surface Plasmon Resonance and Atomic Force Microscopy that the affinity of colicins E3 and E9 for TolB is increased when the immunity protein is removed. This observation has implications for the mechanism by which the immunity protein dissociates from the colicin. Finally this study has used Surface Plasmon Resonance to explore differences between pore-forming and enzymatic colicins in their interactions with Tol proteins. Although the pore-former colicin A interacts with TolR, TolA and TolB, the endonuclease colicins E3 and E9 were shown only to interact with TolB. This suggests that pore-forming and endonuclease colicins use the Tol system in different ways in order to translocate across the periplasm.
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Patel, Amesh Babubhai. "Biophysical and computational investigations into receptor-ligand complexes." Thesis, University of Nottingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435998.

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Garner, Thomas Peter. "Structural and biophysical investigations into ubiquitin binding proteins." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/12100/.

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The complicated task of interpreting the many ubiquitin signals is mediated by specific ubiquitin binding domains. The investigations discussed in this thesis focus on two very different ubiquitin binding domains. Chapters 3 to 5 detail the structural characterisation of the ubiquitin binding protein ZNF216. The structure of the ubiquitin binding Znf_A20 domain has been determined using multidimensional NMR techniques. A thermodynamic and structural characterisation of the interaction between the Znf_A20 and ubiquitin has been performed utilising chemical shift mapping, PRE based approaches, ESI-MS and ITC. The Znf_A20 domain forms a high affinity complex with Ub utilising a non-canonical binding site on ubiquitin centred at Asp58. The investigation was extended to the function of the Znf_A20 domain in the context of the full length protein. ZNF216, like many other ubiquitin receptors, has a ‘hook and line’ domain architecture with two independent domain separated by a long disordered linker. Chapters 6, 7 and 8 focus on the UBA domain of p62. The p62-UBA domain has been identified as a ‘hot spot’ for mutations linked to Paget’s disease of bone, a bone disorder which affects >3% of the over 55s. The dimerisation of the p62-UBA domain has been shown here to be a novel regulatory mechanism for the ubiquitin binding properties of p62. Modulation of both dimerisation and ubiquitin recognition are potential mechanisms by which mutations may disrupt p62 function and this prospect has been investigated here. The final chapter of this thesis examines the possibility of cooperation between different ubiquitin binding domains by simultaneous interaction with Ub to form ternary complexes. Using the Znf_A20 and the p62-UBA as an example the formation of a ternary complex has been demonstrated. By examining the available ubiquitin complexes it has been suggested that the formation of Ub mediated ternary complexes is limited to only a few UBD pairings. The cormation of Ub mediated ternary complexes may have interesting implications for the formation of larger multi-protein complexes utilising ubiquitin as an interaction hub on the recognition of poly-Ub with chain linkage specificity; and for Ub mediated signalling in general.
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Yin, Daniel. "Biophysical investigations into membrane-active peptides and proteins." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:25401447-e37b-4c07-a22d-29718958ac48.

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The inexorable spread of antibiotic or antimicrobial resistance is a global problem, described by the UK Chief Medical Officer to be "as big a threat as terrorism". Due to uncontrolled, unnecessary overuse of antibiotics in medicine and agriculture, bacterial resistance has evolved to even the antibiotics of last resort. Antimicrobial peptides (AMPs) are a promising class of organic molecule that have been proposed to exert a potent antimicrobial effect, which, directly or indirectly, involve complex interactions with cell membranes. Three broad mechanisms have been proposed for AMPs: carpet, barrel-stave and toroidal pore. However, the molecular basis for the mode of action of AMPs, and the relationship between primary structure and antimicrobial activity, remains poorly understood. In this thesis, interactions of membrane-active peptides and proteins with model lipid membranes are studied, to understand better the peptide-lipid interactions of two de novo AMPs and a functionally related protein puroindoline-b (pinB), which is implicated in antimicrobial plant defence. Quartz crystal microbalance (QCM), solid-state nuclear magnetic resonance (ssNMR), electron paramagnetic resonance (EPR) and neutron reflectivity (NR) are used to achieve this. The two AMPs were designed rationally with their primary structure predicted to display specific peptide-lipid interactions. Tilamin (tilted antimicrobial insert) was designed by modifying amhelin (antimicrobial insert), a pore-forming AMP. The modified peptide was predicted to disrupt model membranes mimicking bacterial membranes via a different mode of action to transmembrane barrel stave pore formation. Chom (chopped cecropin mutant) was designed by shortening the length of a natural AMP, cecropin-B, and was predicted to operate via a carpet mechanism. To model the biophysical properties such as morphology, thickness and charge of native membranes, simplified phospholipid liposomes were used to better understand the membrane-perturbing influence of the AMPs, and whether this was correlated with antimicrobial activity. In the presence of anionic model membranes (mimicking Gram-negative inner membranes and Gram-positive membranes), tilamin and chom adopt amphipathic alpha helix conformations as determined by circular dichroism, while remaining unstructured in solution and in the presence of zwitterionic model membranes mimicking mammalian model membranes. Adoption of a folded conformation appears to be important for the lytic effect of the AMPs. Calcein leakage experiments performed show that the AMPs induce leakage of calcein from the interior of anionic liposomes, consistent with the proposal that membrane permeabilisation is important for antimicrobial activity. The peptide-lipid interactions of the AMPs were then probed using QCM and ssNMR, giving mechanistic evidence that chom operates via the carpet mechanism as predicted. The nature of the mode of action of tilamin remained uncertain. From order parameters of lipids in bilayers, obtained using ssNMR upon interaction with tilamin, a toroidal pore mechanism was proposed, along with a new mode of action that caused monoleaflet poration, though it was not possible to resolve the two mechanism based on data obtained from symmetrical vesicles alone. Adapting a newly established protocol to control the leaflet distribution of lipids in model membranes, an asymmetrically distributed nitroxide probe reveals for the first time leaflet-specific peptide-lipid interactions using cw-EPR. Tilamin shows changes in bilayer lipid order parameters that do not match those seen for either an all-surface or transmembrane control peptide, indicating more complex interactions. Unique QCM data, heterogeneous changes in order parameter profiles observed with acylchain 2H ssNMR, as well as a lack of interaction with the inner leaflets of anionic model membranes seen by cw-EPR taken in combination suggest tilamin operates via a more complicated mechanism. Supported by tilt angles obtained by geometric analysis of labelled alanines (GALA) of deuterium-labelled tilamin and atomic force microscopy (AFM) imaging performed with collaborators, the results are consistent with a new mechanism; monolayer poration. The puroindolines are also studied, due to their potential role as antimicrobial proteins in food safety, and in controlling wheat endosperm texture. The mode of insertion of wild-type puroindoline-B (pinB+) and a single-point mutant (pinBs) into bacterial model bilayers was probed for the first time with ssNMR, EPR and NR. In contrast to previous work on monolayers, pinBs does not cause changes in bilayer lipid order in the gel phase, while pinB+ forms a protein layer on the surface of a membrane. The results suggest that in more native-like model membranes, the tryptophan-rich domain (TRD) of pinBs and pinB+ greatly affects the membrane binding properties, with implications for the role of the proteins in vivo.
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Fyfe, Paul Kelman. "Biophysical investigations of photosynthetic reaction centres from Rhodobacter sphaeroides." Thesis, University of Glasgow, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.263434.

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Shnoudeh, Abeer Jabra. "Biochemical and biophysical investigations of novel phosphodiesterase-5 inhibitors." Thesis, King's College London (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.429578.

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Haggarty-Weir, Christopher Neil. "Biochemical and biophysical investigations into key malaria parasite proteins." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/29617.

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Plasmodium falciparum, the most pestilential of the malaria parasite species, is responsible for ~450,000 direct deaths annually. Clinical disease is a consequence of the blood stage of the parasite’s lifecycle involving a plethora of host-parasite interactions. Key to these interactions are the P. falciparum reticulocyte binding-like homologue (PfRh) proteins responsible for binding erythrocyte receptors and gaining entry to host cells. For example, PfRh4 binds to human complement receptor-1 (CR1) on erythrocytes for sialic-acid-independent invasion. Another protein important for invasion is the PfRh5-interacting protein (PfRipr), an essential member of the PfRh5-associated invasion complex (PAIN-complex) along with CyRPA, the cysteine-rich protective antigen. Loss of function of PfRipr in P. falciparum parasites prevents erythrocyte entry and ablates Ca2+-influx into the erythrocyte; essential events during invasion. This study aimed to biochemically and structurally investigate truncated recombinant versions of PfRh4 and PfRipr. Homology modelling suggested that PfRh4 is rich in alpha-helical secondary structure. The sequence of PfRipr suggested the presence of ten epidermal growth factor-like (EGF) modules, two towards the N-terminus and eight in the C-terminal domain. In this project, monoclonal antibodies made against recombinant PfRh4 were shown, via indirect immunofluorescent assays, to localize to the apical tip of merozoites. Monoclonal antibody 5H12, raised against PfRh4, reduces parasite invasion of erythrocytes by ~75% in growth-inhibition assays with neuraminidase pre-treated erythrocytes. Attempts to produce a stable truncated recombinant PfRh4 protein for structural studies were unsuccessful. An ELISA-based assay using ten alanine-scan mutants suggested the CR1-binding site lies outside of amino acids 283 – 341 of PfRh4. PfRipr truncations, defined by the boundaries of EGF-like repeats predicted based on sequence homology, were produced recombinantly in Escherichia coli and Pichia pastoris. These proteins had a circular dichroism signature suggestive of β-strand-containing proteins with disordered regions. EGF-containing PfRipr truncations did not bind recombinant PfRh5 according to ELISA and size-exclusion chromatography assays. EGFs 1-2, 5-7 and 7-10 of PfRipr did not bind CyRPA via size-exclusion chromatography or NMR. Crystallisation trials performed on EGF modules failed to yield crystals suitable for data collection. A 15N isotopically-labelled sample of EGF5-7 gave good quality HSQC NMR spectra. A suite of three-dimensional NMR spectra collected on a 13C,15N-EGF5-7 sample, at three different temperatures, allowed for >86% of backbone assignments. T1/T2 relaxation analysis and heteronuclear NOE data were suggestive of an elongated, rigid protein undergoing intermolecular self-association. Further evidence for EGF5-7 being an elongated protein was provided via SAXS analysis. Chemical shifts facilitated prediction of secondary structure in EGF 5-7 consistent with an EGF-like fold. Melting studies performed on EGF5-7 showed no evidence of denaturation over the temperature range 20 °C - 95 °C indicating a thermally-stable protein. The addition of Ca2+ to the 15N-EGF5-7 sample caused chemical shift perturbations consistent with high-affinity binding. The discovery of inhibitory monoclonal antibodies recognising a conformational epitope on EGF7 provided evidence of the functional importance of this region within PfRipr. The work described in this thesis provides methods for the industrially-scalable production and biophysical investigations of P. pastoris or E. coli-produced disulfide-rich P. falciparum antigens of interest to vaccinologists.
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Colledge, Vicki Louise. "Stuructural and biophysical investigations of bacillus subtillis transition-state regulators." Thesis, University of York, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535053.

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Hansen, R. K. "Biophysical and biochemical investigations of the M2 peptide of influenza A." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603662.

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Membrane proteins, especially passive ion channels, are very difficult to characterise using normal biophysical methods. This thesis used the transmembrane domain of the M2 proton channel of Influenza A (M2-TM) as a model system for biophysical investigations. Patch clamping is the most accurate method for assessing ion channel function, but requires rigid liposomes that can withstand mechanical stress, but are not usually optimal for structural investigations. Here a new hydrogen deuterium exchange (HDX) method has been optimised for the analysis of a membrane spanning peptides in lipid vesicles. A simple electrospray ionisation mass spectrometry method is introduced for HDX studies of carefully prepared aqueous proteoliposome samples. 11 backbone amide sites of M2-TM in lipid vesicles were shown to be resistant to HDX for several weeks. By contrast, HDX of M2-TM in methanol or in detergent micelles was complete within an hour, indicating that the peptide adopts a non-nativee conformation. A solution state nuclear magnetic resonance (NMR) strategy relying on quenching the exchange reaction at low pH, lyophilisation and resuspension in acidified methanol was applied to studies of HDX in a transmembrane peptide for the first and revealed site specific information. His16 and Leu17 exchanged much faster than neighbouring residues consistent with a "flip-open" mechanism for proton conduction. Binding of the drug amantadine weakly perturbs the HDX of Ala8 and Ala9 in agreement with neutron scattering data showing an interaction with the N-terminus of the channel. NMR studies investigated details of the binding and release of fluoroamantadine to liposomes in the presence and absence of M2-TM consistent with the drug binding only to the closed state of the channel in DMPC vesicles. HDX studies have great potential to reveal details of the structure, dynamics and intermolecular interactions of membrane proteins.
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Books on the topic "Biophysical Investigations"

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Li, Mi. Investigations of Cellular and Molecular Biophysical Properties by Atomic Force Microscopy Nanorobotics. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-6829-4.

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Li, Mi. Investigations of Cellular and Molecular Biophysical Properties by Atomic Force Microscopy Nanorobotics. Springer, 2017.

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Li, Mi. Investigations of Cellular and Molecular Biophysical Properties by Atomic Force Microscopy Nanorobotics. Springer, 2019.

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Biophysical Analysis of Membrane Proteins: Investigating Structure and Function. Wiley-VCH, 2007.

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Biophysical analysis of membrane proteins: Investigating structure and function. Weinheim: Wiley-VCH, 2008.

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Pebay-Peyroula, Eva. Biophysical Analysis of Membrane Proteins: Investigating Structure and Function. Wiley & Sons, Incorporated, John, 2008.

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Pebay-Peyroula, Eva. Biophysical Analysis of Membrane Proteins: Investigating Structure and Function. Wiley & Sons, Limited, John, 2008.

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Safar, Jiri G. Prion Paradigm of Human Neurodegenerative Diseases Caused by Protein Misfolding. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190233563.003.0005.

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Data accumulated from different laboratories argue that a growing number of proteins causing neurodegeneration share certain characteristics with prions. Prion-like particles were produced from synthetic amyloid beta (Aβ‎) peptides of Alzheimer’s disease (AD), from recombinant α‎-synuclein linked to Parkinson’s disease (PD), and from recombinant tau associated with frontotemporal dementias (FTD). Evidence from human prions reveals that variable disease phenotypes, rates of propagation, and targeting of different brain structures are determined by distinct conformers (strains) of pathogenic prion protein. Recent progress in the development of advanced biophysical tools identified the structural characteristics of Aβ‎ in the brain cortex of phenotypically diverse AD patients and thus allowed an investigation of the prion paradigm of AD. The findings of distinctly structured strains of human brain Aβ‎, forming a unique spectrum of oligomeric particles in the cortex of rapidly progressive cases, implicates these structures in variable rates of propagation in the brain.
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Chalecki, Elizabeth L. Environment and Security. Oxford University Press, 2017. http://dx.doi.org/10.1093/acrefore/9780190846626.013.165.

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The term environment is often used as a short form for the biophysical environment, which refers to the biotic and abiotic surrounding of an organism or population, and consequently includes the factors that have an influence in their survival, development, and evolution. All life that has survived must have adapted to conditions of its environment. On one hand, part of the study of environmental science is the investigation of the effect of human activity on the environment. On the other hand, scholars also examine threats posed by environmental events and trends to individuals, communities, or nations, otherwise known as environmental security. It studies the impact of human conflict and international relations on the environment, or on how environmental problems cross state borders. Environmental security is a significant concept in two fields: international relations and international development. Within international development, projects may aim to improve aspects of environmental security such as food security or water security, along with connected aspects such as energy security. The importance of environmental security lies in the fact that it affects humankind and its institutions anywhere and at anytime. To the extent that humankind neglects to maintain the planet’s life-supporting eco-systems generating water, food, medicine, and clean air, current and future generations will be confronted with increasingly severe instances of environmentally induced changes.
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Book chapters on the topic "Biophysical Investigations"

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Phillips, William J., and Richard A. Cerione. "Fluorescence Investigations of Receptor-Mediated Processes." In Biophysical and Biochemical Aspects of Fluorescence Spectroscopy, 135–67. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4757-9513-4_5.

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Drew, Simon C., and Kevin J. Barnham. "Biophysical Investigations of the Prion Protein Using Electron Paramagnetic Resonance." In Methods in Molecular Biology, 173–96. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-234-2_13.

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Walter, Maria, and Ramona Schlesinger. "Nanodisc Reconstitution of Channelrhodopsins Heterologously Expressed in Pichia pastoris for Biophysical Investigations." In Methods in Molecular Biology, 29–48. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0830-2_3.

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Liashkovich, Ivan, Gonzalo Rosso, and Victor Shahin. "Atomic Force Microscopy for Structural and Biophysical Investigations on Nuclear Pore Complexes." In Methods in Molecular Biology, 299–310. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2337-4_20.

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Aisenbrey, Christopher, Arnaud Marquette, and Burkhard Bechinger. "The Mechanisms of Action of Cationic Antimicrobial Peptides Refined by Novel Concepts from Biophysical Investigations." In Advances in Experimental Medicine and Biology, 33–64. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-3588-4_4.

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Lammers, Michael. "Expression and Purification of Site-Specifically Lysine-Acetylated and Natively-Folded Proteins for Biophysical Investigations." In Methods in Molecular Biology, 169–90. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7574-7_11.

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Fasolato, Claudia. "Investigation on Nanoparticles and Their Molecular Functionalization." In Surface Enhanced Raman Spectroscopy for Biophysical Applications, 57–83. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-03556-3_3.

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Thornton, K. L., R. C. Findlay, P. B. Walrad, and L. G. Wilson. "Investigating the Swimming of Microbial Pathogens Using Digital Holography." In Biophysics of Infection, 17–32. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-32189-9_3.

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Takahashi, Satoshi, and Kiyoto Kamagata. "Staring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics." In Single-Molecule Biophysics, 1–22. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118131374.ch1.

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Wen, Zai-Qing, Gianni Torraca, Guiyang Li, Xiaolin Cao, and Chanel K. Yee. "Investigation of Nonconformance During Protein Therapeutic Manufacturing." In Biophysics for Therapeutic Protein Development, 245–60. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-4316-2_10.

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Conference papers on the topic "Biophysical Investigations"

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Baibyrin, V. B., P. I. Anisimov, N. P. Konnov, A. A. Shcherbakov, and U. P. Volkov. "Near field scanning optical microscope for biological applications." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/lacea.1996.lwd.9.

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In our biophysical laboratory systematic investigations of plague and choler microbes are carried out by different methods (conventional electron microscopy, scanning tunneling microscopy and atomic force microscopy). At present for the investigations we have develop a near field scanning optical microscope (NSOM).
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Mofrad, Mohammad R. K. "Molecular Mechanosensors and Focal Adhesion Mechanotransduction." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19707.

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Cellular response to mechanical stimulation is mediated by both biochemical mechanisms via changes in gene expression and by biophysical mechanisms via mechanically induced changes in specific molecules’ structure and function. These mechanically responsive molecules can be described as the cell’s mechanosensors and can function to initiate processes such as focal adhesion formation. A series of molecular dynamics investigations explore the mechanosensor function of key molecules involved in focal adhesion formation and cytoskeletal dynamics.
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Vickerman Kelley, Vernella V., and Roger D. Kamm. "Microfluidics Bioreactor: A Platform for Studying Capillary Morphogenesis in Response to Biochemical and Biophysical Cues." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-176655.

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The in vivo microvasculature is a dynamic structure which is influenced by both biochemical (e.g. cytokines, growth factors) and biophysical factors (e.g. shear stress, interstitial flow). Important regulators of this structure are the endothelial cells which are normally quiescent but under certain conditions are able to form new vascular sprouts. Investigations into the mechanism of capillary morphogenesis of human endothelial cells warrant an in vitro model that closely mimics the physiological in vivo microenvironment. To this end, we have developed a novel microfabricated system which permits 2D and 3D culture of endothelial cells in biologically derived (e.g. type I collagen) or synthetic (self assembling peptides) scaffolds and delivers control flow rates and pressures. This system offers tremendous flexibility with regard to scaffold physical and chemical properties, physiologically relevant mechanical stress induced by surface shear and interstitial flow as well as chemotactic gradients. In addition we are able to directly monitor the progression of vascular networks in response to these critical factors.
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Maftouni, Negin, Mehriar Amininasab, MohammadReza Ejtehadi, and Farshad Kowsari. "Multiscale Molecular Dynamics Simulation of Nanobio Membrane in Interaction With Protein." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93054.

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One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of lateral pressure. Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a result of a change in the contribution of the various intermolecular forces may be expressed morphologically and lead to deformation of the lipid membrane.
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Conchello, Jose A., J. Peter Zelten, Frank C. Miele, Bruce H. Davis, and Eric W. Hansen. "Enhanced 3-D reconstruction from confocal microscope images." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1988. http://dx.doi.org/10.1364/oam.1988.thff1.

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Confocal scanning microscopes are known to possess superior optical sectioning capabilities compared to conventional microscopes. Out-of-focus contributions in a through-focus series of images are significantly reduced by the confocal geometry but not completely removed. This paper reports our initial investigations Into a posterioriimage processing (i.e., deconvolution) for further improvement of depth resolution in confocal microscopy. This project is part of a larger effort In laser scanning fluorescence microscopy for biological and biophysical analyses in living cells. The instrument is built around a standard inverted microscope stand, enabling the use of standard optics, micromanipulation apparatus, and conventional (including video) microscopy in conjunction with laser scanning. The beam is scanned across the specimen by a pair of galvanometer-mounted mirrors driven by a programmable controller which can operate In three modes: full raster scan; region of interest; and random-access (point-hopping). After taking a scout image with laser scanning or video, the user will select isolated points or regions of interest for further analysis via a graphic user interface implemented on the system’s host computer. Experimental parameters such as detector integration times are set up with a window-style menu.
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Salamon, Zdzislaw, Gordon Tollin, Angus Macleod, and Ian C. Stevenson. "Spectroscopic studies of membrane protein-lipid bilayer systems deposited on multilayer thin film coatings." In Optical Interference Coatings. Washington, D.C.: Optica Publishing Group, 1997. http://dx.doi.org/10.1364/oic.1998.thd.1.

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Although thin film coatings have been used for many years in optical investigations of biological systems (especially as narrow band light filters), more recent applications of such films in two types of spectroscopic devices, surface plasmon resonance (SPR) and optical waveguides, have provided new biophysical tools for the study of protein-protein and protein-lipid membrane interactions [1]. Although both of these techniques are based on different physical phenomena, the thin film coatings have the same function, i.e. coupling devices in which incident light, under the appropriate optical conditions, can generate an evanescent surface-bound electromagnetic field, which propagates along the interface between the thin film and the emergent dielectric medium in a manner which depends on the interface characteristics. The resulting electric field intensity is concentrated at the outer surface of the film, and diminishes exponentially on both sides of the interface. As a consequence of these properties, it is possible to use SPR and waveguide spectroscopy to probe a few nanometers from the coated surface, a distance well below the wavelength of the light used to generate the evanescent waves, and hence these phenomena have been utilized extensively in studies of surfaces and thin films [for references see 1,2]. Although numerous other optical techniques have also been applied to such systems (e.g. ellipsometry, interferometry, spectrophotometry, and various forms of microscopy), the SPR method has very recently regained its popularity, mainly because of its superior sensitivity, as well as some additional very important advantages over these other methodologies [1,2]. These latter advantages include the following. First, the complete system of measurement is located on the side of the apparatus which is remote from the sample, and thus there is no optical interference from the bulk medium. Second, the outer surface of the sample needs no treatment to increase reflectance, because the necessary high reflectivity is achieved by using total internal reflectance. Third, there are three principal parameters of the resonance that can readily be measured, thereby yielding much more information about the sample and changes within it than the simple interferometric step height used in other sensitive optical techniques.
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Fathi Salmi, Ebrahim, Raphael Costa Picorelli, and Ewan Sellers. "Investigating the biophysical challenges associated with mine closure in different mining methods." In Mine Closure 2022: 15th Conference on Mine Closure. Australian Centre for Geomechanics, Perth, 2022. http://dx.doi.org/10.36487/acg_repo/2215_38.

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Dimitrov, Petar. "Investigation of dynamics of some biophysical parameters of Norway spruce stands by MODIS data." In 2009 4th International Conference on Recent Advances in Space Technologies (RAST). IEEE, 2009. http://dx.doi.org/10.1109/rast.2009.5158232.

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Chaikovsky, Illya, Ilya Syropyatov, Mykola Budnyk, Georg Mjasnikov, Anatoly Kazmirchyk, and Victor Dykhanovskiy. "Investigation of the ECG Leads Sensitivity to Myocardial Ischemia by Means of Biophysical Model." In 2019 IEEE 39th International Conference on Electronics and Nanotechnology (ELNANO). IEEE, 2019. http://dx.doi.org/10.1109/elnano.2019.8783855.

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Malevich, E. S., M. S. Mikhailov, and V. A. Permyakov. "Investigation of Biophysical Parameters of Forests Using Experimental Data and Results of Forest Environment Simulation." In 2019 PhotonIcs & Electromagnetics Research Symposium - Spring (PIERS-Spring). IEEE, 2019. http://dx.doi.org/10.1109/piers-spring46901.2019.9017866.

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Reports on the topic "Biophysical Investigations"

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Gates, Sean Damien. Biophysical analysis of bacterial and viral systems. A shock tube study of bio-aerosols and a correlated AFM/nanosims investigation of vaccinia virus. Office of Scientific and Technical Information (OSTI), May 2013. http://dx.doi.org/10.2172/1108845.

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Azem, Abdussalam, George Lorimer, and Adina Breiman. Molecular and in vivo Functions of the Chloroplast Chaperonins. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697111.bard.

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We present here the final report for our research project entitled "The molecular and in vivo functions of the chloroplast chaperonins”. Over the past few decades, intensive investigation of the bacterial GroELS system has led to a basic understanding of how chaperonins refold denatured proteins. However, the parallel is limited in its relevance to plant chaperonins, since the plant system differs from GroEL in genetic complexity, physiological roles of the chaperonins and precise molecular structure. Due to the importance of plant chaperonins for chloroplast biogenesis and Rubisco assembly, research on this topic will have implications for many vital applicative fields such as crop hardiness and efficiency of plant growth as well as the production of alternative energy sources. In this study, we set out to investigate the structure and function of chloroplast chaperonins from A. thaliana. Most plants harbor multiple genes for chaperonin proteins, making analysis of plant chaperonin systems more complicated than the GroEL-GroES system. We decided to focus on the chaperonins from A. thaliana since the genome of this plant has been well defined and many materials are available which can help facilitate studies using this system. Our proposal put forward a number of goals including cloning, purification, and characterization of the chloroplast cpn60 subunits, antibody preparation, gene expression patterns, in vivo analysis of oligomer composition, preparation and characterization of plant deletion mutants, identification of substrate proteins and biophysical studies. In this report, we describe the progress we have made in understanding the structure and function of chloroplast chaperonins in each of these categories.
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Shahak, Yosepha, and Donald R. Ort. Physiological Bases for Impaired Photosynthetic Performance of Chilling-Sensitive Fruit Trees. United States Department of Agriculture, May 2001. http://dx.doi.org/10.32747/2001.7575278.bard.

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Chilling-sensitivity is an important agricultural problem in both the U.S. and Israel. Most research attention has focused so far on herbaceous crop plants, even though the problem is also acute in the fruit tree industry. Under BARD funding we made substantial progress in identifying the mechanisms involved in the disruption of photosynthesis following a chill in mango. Our investigation with fruit trees has been substantially accelerated by drawing on our knowledge and experience with herbaceous crops. The four original research objectives, focused or discovering the underlying mechanisms of chill-induced inhibition of photosynthesis in fruit trees, and the main achievements are listed below. [1] Separating stomatal from non-stomatal components of chilling on photosynthesis in fruit trees. We found evidence that the dark chill-induced inhibition of photosynthesis in mango was E combination of both stomatal and mesophyll components. [2] Differentiating photo damage from light-induced photo protection of photosystem II (PSII). Dark chilling exacerbate high light photoinhibition, as a result of primary inhibition in the carbor reduction cycle. Nevertheless, in Israeli orchards we observed chronic photoinhibition of PSII photochemistry in the winter. This photo damage was reversible over a few days if sunlight was attenuated with filters or night temperature rose. Practical implications of this finding deserve further investment. Additional achievement was the development of a new biophysical tool to study macro-structural changes of LHCII particles in intact, attached leaves. [3] Determine the role of oxidative stress in the dark-chilling-induced inhibition, with emphasis on oxygen radical scavenging, lipid peroxidation and redox-controlled carbon-cycle enzymes. We found an increase in lipid peroxidation following a dark chill, and partial protective effects or an antioxidant. However, the photoinhibition observed in mango orchards in Israel during the winter did not appear to be a general oxidative stress. [4] Investigate whether chilling interferes with the diurnal and circadian rhythm of gene expression of key photosynthetic proteins as has been shown for chilling-sensitive crop plants. The results indicated that most of the circadian rhythm in photosynthesis was due to reduced lea: internal CO2 concentrations during the subjective night, as a result of rhythmic stomatal closure Chilling-induced interference with circadian timing in mango, does not play the central role in chilling inhibition of photosynthesis that has previously been demonstrated in certain chilling sensitive herbaceous plants. Practical implications of the research achievements are feasible, but require few more years of research.
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