Relevant bibliographies by topics / Protein Dynamics - Confocal Microscopy

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  2. Dissertations / Theses
  3. Books
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  5. Conference papers
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Academic literature on the topic 'Protein Dynamics - Confocal Microscopy'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Protein Dynamics - Confocal Microscopy"

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Volkov, I. A., N. V. Frigo, L. F. Znamenskaya, and O. R. Katunina. "Application of Confocal Laser Scanning Microscopy in Biology and Medicine." Vestnik dermatologii i venerologii 90, no. 1 (February 24, 2014): 17–24. http://dx.doi.org/10.25208/0042-4609-2014-90-1-17-24.

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Fluorescence confocal laser scanning microscopy and reflectance confocal laser scanning microscopy are up-to-date highend study methods. Confocal microscopy is used in cell biology and medicine. By using confocal microscopy, it is possible to study bioplasts and localization of protein molecules and other compounds relative to cell or tissue structures, and to monitor dynamic cell processes. Confocal microscopes enable layer-by-layer scanning of test items to create demonstrable 3D models. As compared to usual fluorescent microscopes, confocal microscopes are characterized by a higher contrast ratio and image definition.
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Eggeling, Christian. "Super-resolution optical microscopy of lipid plasma membrane dynamics." Essays in Biochemistry 57 (February 6, 2015): 69–80. http://dx.doi.org/10.1042/bse0570069.

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Plasma membrane dynamics are an important ruler of cellular activity, particularly through the interaction and diffusion dynamics of membrane-embedded proteins and lipids. FCS (fluorescence correlation spectroscopy) on an optical (confocal) microscope is a popular tool for investigating such dynamics. Unfortunately, its full applicability is constrained by the limited spatial resolution of a conventional optical microscope. The present chapter depicts the combination of optical super-resolution STED (stimulated emission depletion) microscopy with FCS, and why it is an important tool for investigating molecular membrane dynamics in living cells. Compared with conventional FCS, the STED-FCS approach demonstrates an improved possibility to distinguish free from anomalous molecular diffusion, and thus to give new insights into lipid–protein interactions and the traditional lipid ‘raft’ theory.
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WANG, XIAO-PING, HUAI-NA YU, and TONG-SHENG CHEN. "QUANTITATIVE FRET MEASUREMENT BASED ON CONFOCAL MICROSCOPY IMAGING AND PARTIAL ACCEPTOR PHOTOBLEACHING." Journal of Innovative Optical Health Sciences 05, no. 03 (July 2012): 1250015. http://dx.doi.org/10.1142/s1793545812500150.

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Fluorescence resonance energy transfer (FRET) technology had been widely used to study protein–protein interactions in living cells. In this study, we developed a ROI-PbFRET method to real-time quantitate the FRET efficiency of FRET construct in living cells by combining the region of interest (ROI) function of confocal microscope and partial acceptor photobleaching. We validated the ROI-PbFRET method using GFPs-based FRET constructs including 18AA and SCAT3, and used it to quantitatively monitor the dynamics of caspase-3 activation in single live cells stably expressing SCAT3 during staurosporine (STS)-induced apoptosis. Our results for the first demonstrate that ROI-PbFRET method is a powerful potential tool for detecting the dynamics of molecular interactions in live cells.
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Wüstner, Daniel. "Dynamic Mode Decomposition of Fluorescence Loss in Photobleaching Microscopy Data for Model-Free Analysis of Protein Transport and Aggregation in Living Cells." Sensors 22, no. 13 (June 23, 2022): 4731. http://dx.doi.org/10.3390/s22134731.

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The phase separation and aggregation of proteins are hallmarks of many neurodegenerative diseases. These processes can be studied in living cells using fluorescent protein constructs and quantitative live-cell imaging techniques, such as fluorescence recovery after photobleaching (FRAP) or the related fluorescence loss in photobleaching (FLIP). While the acquisition of FLIP images is straightforward on most commercial confocal microscope systems, the analysis and computational modeling of such data is challenging. Here, a novel model-free method is presented, which resolves complex spatiotemporal fluorescence-loss kinetics based on dynamic-mode decomposition (DMD) of FLIP live-cell image sequences. It is shown that the DMD of synthetic and experimental FLIP image series (DMD-FLIP) allows for the unequivocal discrimination of subcellular compartments, such as nuclei, cytoplasm, and protein condensates based on their differing transport and therefore fluorescence loss kinetics. By decomposing fluorescence-loss kinetics into distinct dynamic modes, DMD-FLIP will enable researchers to study protein dynamics at each time scale individually. Furthermore, it is shown that DMD-FLIP is very efficient in denoising confocal time series data. Thus, DMD-FLIP is an easy-to-use method for the model-free detection of barriers to protein diffusion, of phase-separated protein assemblies, and of insoluble protein aggregates. It should, therefore, find wide application in the analysis of protein transport and aggregation, in particular in relation to neurodegenerative diseases and the formation of protein condensates in living cells.
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Yang, Kun, Shu Bai, and Yan Sun. "Protein adsorption dynamics in cation-exchange chromatography quantitatively studied by confocal laser scanning microscopy." Chemical Engineering Science 63, no. 16 (August 2008): 4045–54. http://dx.doi.org/10.1016/j.ces.2008.05.013.

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Olmsted, J. B., K. R. Olson, M. L. Gonzalez-Garay, and F. Cabral. "Green fluorescent protein: Use of GFP-chimeras in the analysis of microtubule-associated protein 4 domains and microtubule dynamics." Proceedings, annual meeting, Electron Microscopy Society of America 54 (August 11, 1996): 888–89. http://dx.doi.org/10.1017/s0424820100166907.

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Green Fluorescent Protein (GFP) is an endogenous 27 kDa fluorophore of the jellyfish, Aequorea victoria. Chalfie et al., first described the exogenous expression of this molecule in bacteria, and its utility as a reporter in higher eukaryotes. Potential applications of GFP have been expanded through the construction of variants with enhanced brightness and/or different spectral properties.We have explored using GFP for the analysis of the real-time behaviors of microtubules and their associated proteins. Constructs of microtubule-associated protein 4 (MAP 4) or β-tubulin were generated in pRC/CMV vectors and used in either transient or stable transfection assays in a variety of cultured cell lines (3T3, PtKl, BHK, CHO, Cos). The GFP-chimeras were visualized using conventional fluorescence microscopy and confocal laser scanning microscopy. Unusual features of the GFP reporter are that fluorescence intensity increased 2-10 fold upon illumination, and that phototoxicity was low.
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Waterman-Storer, C. M., and W. C. Salmon. "Fluorescent Speckle Microscopy in Studies of Cytoskeletal Dynamics During Cell Motility." Microscopy and Microanalysis 7, S2 (August 2001): 6–7. http://dx.doi.org/10.1017/s1431927600026106.

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We have discovered a new method, Fluorescent Speckle Microscopy (FSM), for analyzing the dynamic movement and turnover of macromolecular protein assemblies, such as the cytoskeleton, in living cells (Waterman-Storer et al., 1998). FSM compliments or replaces the techniques of fluorescence recovery after photobleaching or photoactivation of fluorescence for measuring protein dynamics in vivo. For FSM, cells are microinjected with a very low fraction of fluorescently labeled subunits that co-assemble with unlabeled subunits to give a structure with a fluorescent speckled appearance in diffraction-limited wide-field or confocal digital fluorescence images. At low fractions of fluorescent subunits relative to unlabeled subunits, fluorescent speckles vary randomly in intensity according to the number of fluorescent subunits within a diffraction-limited region. in time-lapse FSM image series, movement of the fluorescent speckle pattern indicates translocation of structures, while changes in speckle intensity indicate subunit turnover. We have used FSM to study microtubule and actin behavior in interphase and mitotic cells. We use kymograph analysis to quantitate the movement of speckled structures (Fig 1) and are currently developing analysis procedures to quantify subunit turnover in structures.We have applied these methods to the study of microtubule and actin cytoskeletal dynamics in migrating vertebrate cells in culture. Interactions between the microtubule and actin cytoskeletons underlie fundamental cellular processes such as cytokinesis and cell locomotion, but are poorly understood.
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Chiodi, I., M. Biggiogera, M. Denegri, M. Corioni, F. Weighardt, F. Cobianchi, S. Riva, and G. Biamonti. "Structure and dynamics of hnRNP-labelled nuclear bodies induced by stress treatments." Journal of Cell Science 113, no. 22 (November 15, 2000): 4043–53. http://dx.doi.org/10.1242/jcs.113.22.4043.

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We have previously described HAP, a novel hnRNP protein that is identical both to SAF-B, a component of the nuclear scaffold, and to HET, a transcriptional regulator of the gene for heat shock protein 27. After heat shock, HAP is recruited to a few nuclear bodies. Here we report the characterisation of these bodies, which are distinct from other nuclear components such as coiled bodies and speckles. The formation of HAP bodies is part of a general cell response to stress agents, such as heat shock and cadmium sulfate, which also affect the distribution of hnRNP protein M. Electron microscopy demonstrates that in untreated cells, similar to other hnRNP proteins, HAP is associated to perichromatin fibrils. Instead, in heat shocked cells the protein is preferentially associated to clusters of perichromatin granules, which correspond to the HAP bodies observed in confocal microscopy. Inside such clusters, perichromatin granules eventually merge into a highly packaged ‘core’. HAP and hnRNP M mark different districts of these structures. HAP is associated to perichromatin granules surrounding the core, while hnRNP M is mostly detected within the core. BrU incorporation experiments demonstrate that no transcription occurs within the stress-induced clusters of perichromatin granules, which are depots for RNAs synthesised both before and after heat shock.
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Aymerich, María S., J. López-Azcárate, J. Bonaventura, G. Navarro, D. Fernández-Suárez, V. Casadó, F. Mayor, et al. "Real-Time G-Protein-Coupled Receptor Imaging to Understand and Quantify Receptor Dynamics." Scientific World JOURNAL 11 (2011): 1995–2010. http://dx.doi.org/10.1100/2011/690858.

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Understanding the trafficking of G-protein-coupled receptors (GPCRs) and their regulation by agonists and antagonists is fundamental to develop more effective drugs. Optical methods using fluorescent-tagged receptors and spinning disk confocal microscopy are useful tools to investigate membrane receptor dynamics in living cells. The aim of this study was to develop a method to characterize receptor dynamics using this system which offers the advantage of very fast image acquisition with minimal cell perturbation. However, in short-term assays photobleaching was still a problem. Thus, we developed a procedure to perform a photobleaching-corrected image analysis. A study of short-term dynamics of the long isoform of the dopamine type 2 receptor revealed an agonist-induced increase in the mobile fraction of receptors with a rate of movement of 0.08 μm/s For long-term assays, the ratio between the relative fluorescence intensity at the cell surface versus that in the intracellular compartment indicated that receptor internalization only occurred in cells co-expressing G protein-coupled receptor kinase 2. These results indicate that the lateral movement of receptors and receptor internalization are not directly coupled. Thus, we believe that live imaging of GPCRs using spinning disk confocal image analysis constitutes a powerful tool to study of receptor dynamics.
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Wilkins, Ngozi A., Brian Storrie, and Jeffrey A. Kamykowski. "Characterization of Platelet Alpha-Granule Dynamics." Blood 116, no. 21 (November 19, 2010): 327. http://dx.doi.org/10.1182/blood.v116.21.327.327.

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Abstract Abstract 327 Background: Platelets, anucleated cells that play a critical role in blood clotting, store proteins and small molecules in alpha-granules and dense granules, respectively, for secretion. Alpha-granules contain several proteins including von Willebrand factor and fibrinogen and dense granules contain serotonin. Rab4, a marker for the early endosomes has been implicated in regulating alpha granule secretions (Sirakawa et al, 2010). Previous fluorescence microscopy mapping of alpha-granule protein distributions suggested that there are either two different alpha-granule types or subdomains within a single granule population (Storrie and Seghal, 2007; Italiano et al, 2008). More recent work based on electron tomography (Kamykowski et al, manuscript in preparation) indicates that human platelets are comprised of one alpha granule population. We hypothesized that there was a single population of alpha-granules in which all fibrinogen is similarly compartmentalized. Hence, fibrinogen endocytocized by guinea pig megakaryocytes and platelets in vivo at 4 h (short label) and 24 h (long label) would map to the same location. Aims: We carried out several experiments to form a basis for future high-resolution (5 nm) electron tomography to establish packaging of HRP-conjugated fibrinogen or nanogold conjugated fibrinogen into platelet alpha-granules. (a) Using PD-10 columns, we prepared Cy3 conjugated fibrinogen. Using an in vivo guinea pig model to test the ability of guinea pig platelets to take up fluorescently labeled fibrinogen, we injected 10 mg/ml of Cy3 conjugated fibrinogen (short label, 4 h) and 10 mg/ml of commercially purchased AlexaFluor 488 conjugated fibrinogen (long label, 28 h) into guinea pigs. Platelets were then fixed, purified and confocal microscopy performed. (b) Using triple immunofluorescence, serotonin antibody was applied to fixed and purified resting state human and guinea pig platelets and immunofluorescence microscopy was performed to provide whole platelet information on the staining pattern of the dense granules in comparison to the alpha-granules and early endosomes. (c) Preliminary Electron Microscopy fixation conditions were also tested on guinea pig platelets. Results: For the uptake experiment, spinning-disk confocal microscopy was used to collect full platelet volume image stacks which were then deconvolved, pixel shift corrected for red and green channels and analyzed. Overlap of green and red fibrinogen conjugates was observed where the fluorescently tagged fibrinogens were taken up by structures presumed to be alpha-granules. For the triple labeling experiments, the distribution of serotonin, Rab4 and von Willebrand factor was observed in resting state platelets. Using spinning-disk confocal microscopy, full platelet volume image stacks were collected, deconvolved, pixel shift corrected for red, far red and green channels and analyzed. Serotonin antibody gave an abundant punctate staining pattern in both the triple-labeled human and guinea pig platelets. In both the human platelets and the guinea pig platelets, the serotonin positive punctate granules, presumed to be dense granules, had a more similar pattern to the von Willebrand factor positive punctate alpha granules, than to the Rab4 positive punctate granules, presumed to be the early endosomes. The triple label results were unexpected because previous electron microscopy studies have indicated that the dense granules in human platelets are fewer in number than the alpha-granules and fewer than the corresponding dense granules in guinea pig platelets. Results of the electron microscopy preparations are pending. Conclusions: Our results indicate that the guinea pig model, while its platelets are a much smaller size than human platelets, is a good system for loading alpha-granules with labeled proteins for electron tomography. The serotonin distribution results together with previous electron tomography also raise the question as to whether dense granules could be a specialized form of the alpha-granules. A summary of this research will be presented at the Promoting Minorities in Hematology event during the 2010 ASH meeting. Disclosures: No relevant conflicts of interest to declare.
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Dissertations / Theses on the topic "Protein Dynamics - Confocal Microscopy"

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Nilufar, Rahimova. "Real-time dynamics of IκBαdegradation studied with Kusabira-Orange 2 fusion proteins." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/217147.

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Gösch, Michael. "Microfluidic analysis and parallel confocal detection of single molecules /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-663-4/.

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Piguet, Joachim. "Advanced Fluorescence Microscopy to Study Plasma Membrane Protein Dynamics." Doctoral thesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-178147.

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Membrane protein dynamics is of great importance for living organisms. The precise localization of proteins composing a synapse on the membrane facing a nerve terminus is essential for proper functioning of the nervous system. In muscle fibers, the nicotinic acetylcholine is densely packed under the motor nerve termini. A receptor associated protein, rapsyn, acts as a linker between the receptor and the other components of the synaptic suramolecular assembly. Advances in fluorescence microscopy have allowed to measure the behavior of a single receptor in the cell membrane. In this work single-molecule microscopy was used to track the motion of ionotropic acetylcholine (nAChR) and serotonin (5HT3R) receptors in the plasma membrane of cells. We present methods for measuring single-molecule diffusion and their analysis. Single molecule tracking has shown a high dependence of acetylcholine receptors diffusion on its associated protein rapsyn. Comparing muscle cells that either express rapsyn or are devoid of it, we found that rapsyn plays an important role on receptor immobilization. A three-fold increase of receptor mobility was observed in muscle cells devoid of rapsyn. However, in these cells, a certain fraction of immobilized receptors was also found immobile. Furthermore, nAChR were strongly confined in membrane domains of few tens of nanometers. This showed that membrane composition and membrane associated proteins influence on receptor localization. During muscle cell differentiation, the fraction of immobile nAChR diminished along with the decreasing nAChR and stable rapsyn expression levels. The importance of rapsyn in nAChR immobilization has been further confirmed by measurements in HEK 293 cells, where co-expression of rapsyn increased immobilization of the receptor. nAChR is a ligand-gated ion-channel of the Cys-loop family. In mammals, members of this receptor family share general structural and functional features. They are homo- or hetero-pentamers and form a membrane-spanning ion channel. Subunits have three major regions, an extracellular ligand binding domain, a transmembrane channel and a large intracellular loop. 5HT3R was used as a model to study the effect of this loop on receptor mobility. Single-molecule tracking experiments on receptors with progressively larger deletions in the intracellular loop did not show a dependence of the size of the loop on the diffusion coefficient of mobile receptors. However, two regions were identified to play a role in receptor mobility by changing the fractions of immobile and directed receptors. Interestingly, a prokaryotic homologue of cys-loop receptors, ELIC, devoid of a large cytoplasmic loop was found to be immobile or to show directed diffusion similar as the wild-type 5HT3R. The scaffolding protein rapsyn stabilizes nAChR clusters in a concentration dependent manner. We have measured the density and self-interactions of rapsyn using FRET microscopy. Point-mutations of rapsyn, known to provoke myopathies, destabilized rapsyn self-interactions. Rapsyn-N88K, and R91L were found at high concentration in the cytoplasm suggesting that this modification disturbs membrane association of rapsyn. A25V was found to accumulate in the endoplasmic reticulum. Fluorescent tools to measure intracellular concentration of calcium ions are of great value to study the function of neurons. Rapsyn is highly abundant at the neuromuscular junction and thus is a genuine synaptic marker. A fusion protein of rapsyn with a genetically encoded ratiometric calcium sensor has been made to probe synapse activity. This thesis has shown that the combined use of biologically relevant system and modern fluorescence microscopy techniques deliver important information on pLGIC behaviour in the cell membrane.

QC 20151217

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Elmlund, Hans. "Protein structure dynamics and interplay : by single-particle electron microscopy." Doctoral thesis, Stockholm : Teknik och hälsa, Technology and Health, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4669.

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Guo, Qing. "Single Molecule Optical Magnetic Tweezers Microscopy Studies of Protein Dynamics." Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1435334948.

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SCIPIONI, LORENZO. "Local image correlation methods for the characterization of subcellular structure and dynamics by confocal and super-resolution microscopy." Doctoral thesis, Università degli studi di Genova, 2018. http://hdl.handle.net/11567/929279.

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This thesis work aspires to present a new concept for the application of correlation techniques to the study of the cellular environment. By exploiting local analysis in combination to a fast fit-free technique (the phasor approach) we provide an exhaustive high-resolution analysis of structural and dynamic properties while maintaining a reasonable computation time. The dissertation will be articulated as follows: In CHAPTER 1 we aim to provide the reader with a description of the techniques that will be exploited during the rest of the dissertation together with the open questions and problematics that our techniques will try to answer to. In CHAPTER 2 we present the local analysis concept and its application to a correlation technique capable of measuring size and concentration (ICS). We will show how we coupled ICS to the phasor approach to create a technique (PLICS) for the assessment of size heterogeneity. PLICS will be demonstrated with simulations as well as with cellular samples and will be applied to the study of endocytic vesicles uptake and to the characterization of other organelles. In CHAPTER 3 the concept is extended to two-colors samples for the determination of local inter-structure distance (PLICCS). We will present a pattern analysis method we developed that exploits this information in order to evaluate the relative distribution of the structures imaged in the two channels, comparing it to a random distribution. This method will be validated with simulations and applied to the study of replication-transcription collisions. Successively, we will show that PLICCS can be converted to a localization algorithm for single particle tracking that will be used for tracking membrane receptors in living neurons. CHAPTER 4 will describe the extension of our local analysis to RICS, a correlation technique capable of measuring the diffusion coefficient of a fluorescent probe. The resulting algorithm (L-RICS) provides high resolution diffusion maps that will be used to characterize the diffusion of a fluorescent probe (GFP) within the nucleus and nucleolus of living cells. We will show that the algorithm can be implemented also in non-linear scanning systems. CHAPTER 5 will conclude the dissertation by introducing advanced correlation methods for the analysis of non-Brownian diffusion and their coupling to super-resolution techniques. In particular, we will present a super-resolution correlation technique (SPLIT) recently developed capable of analyzing the cellular environment and a microcamera-based approach (Airyscan comprehensive correlation analysis) we developed for the parallel implementation, in super-resolution, of several complementary correlation techniques.
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Vallejo, Rodriguez Johana. "Compartmentation of glycolysis to a plasma membrane domain : role of caveolin-1 as a scaffolding protein for phosphofructokinase /." Free to MU Campus, others may purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3137759.

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Ljunglöf, Anders. "Direct observation of biomolecule adsorption and spatial distribution of functional groups in chromatographic adsorbent particles." Doctoral thesis, Uppsala University, Surface Biotechnology, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1602.

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Confocal microscopy has been used as a tool for studying adsorption of biomolecules to individual chromatographic adsorbent particles. By coupling a fluorescent dye to protein molecules, their penetration into single adsorbent particles could be observed visually at different times during batch uptake. By relating the relative fluorescence intensity obtained at different times to the value at equilibrium, the degree of saturation versus time could be constructed. The use of two different fluorescent dyes for protein labeling and two independent detectors, allowed direct observation of a two-component adsorption process. The confocal technique was also applied for visualization of nucleic acids. Plasmid DNA and RNA were visualized with fluorescent probes that binds to double stranded DNA and RNA respectively. Confocal measurements following single component adsorption to ion exchange particles, revealed an interesting phenomenon. Under certain experimental conditions, development of "inner radial concentration rings" (i.e. adsorbed phase concentrations that are higher at certain radial positions within the particle) were observed. Some examples are given that show how such concentration rings are formed within a particle.

Methods were also developed for measurement of the spatial distribution of immobilized functional groups. Confocal microscopy was used to investigate the immobilization of trypsin on porous glycidyl methacrylate beads. Artefacts relating to optical length differences could be reduced by use of "contrast matching". Confocal microscopy and confocal micro-Raman spectroscopy, were used to analyze the spatial distribution of IgG antibodies immobilized on BrCN-activated agarose beads. Both these measurement methods indicate an even ligand distribution. Finally, confocal Raman and fluorescence spectroscopy was applied for measurement of the spatial distribution of iminodiacetic- and sulphopropyl groups, using Nd3+ ions as fluorescent probes. Comparison of different microscope objectives showed that an immersion objective should be used for measurement of wet adsorbent particles.

Direct experimental information from the interior of individual adsorbent particles will increase the scientific understanding of intraparticle mass transport and adsorption mechanisms, and is an essential step towards the ultimate understanding of the behaviour of chromatographic adsorbents.

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des, Georges Amédée. "Regulation of tubulin dynamics by the +Tip tracking protein Mal3." Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/256531.

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The Microtubule (MT) network is a central component of the eukaryotic cell cytoskeleton. In the fission yeast S. pombe, a complex of three proteins specifically tracks MT +ends and stabilizes MTs in the cell. It is composed of the proteins Mal3, Tip1 and Tea2. Mal3, the S. pombe homologue of EB1, is a highly conserved ubiquitous protein found to be at the centre of many MT related processes. Tip1 is a CLIP170 homologue and Tea2 a kinesin-like motor protein. The mechanism by which they target the growing end of MTs and stabilize them is still unknown. A combination of biochemistry, electron microscopy and crystallography were used in an attempt to get a more precise understanding of the MT stabilization by this +Tip complex. Protein-A pull-down of the endogenous complex and analysis of its constituents by mass spectrometry revealed that Tea2 and Tip1 form a tight stoichiometric complex, making a much more labile interaction with Mal3. Biochemical experiments, light scattering and DIC microscopy demonstrate that Mal3 stabilizes the MT structure in a stoichiometric fashion by suppressing catastrophe events. 3D helical reconstruction of electron micrographs of Mal3 bound to the MT show that it most probably stabilizes the MT structure by bridging protofilaments together. Deletion mutant analysis suggests that contact with one of the protofilaments is via an interaction between the charged tails of tubulin and Mal3. Mal3 MT binding domain structure was solved by X-ray crystallography so that eventually it may be docked into a higher resolution electron microscopy map to provide a more precise structural insight on how Mal3 stabilizes the MT lattice. The EM analysis also shows that Mal3 regulates MT structure in vitro by restraining their protofilament number to 13, which is the number always found in vivo, and by driving the assembly of MTs with a high proportion of A-lattice. It is the first time that a protein is found to promote formation of A-lattice MTs. The fact that EB1 is such a ubiquitous protein reopens the question of MT structure in cells and has important implications for in vivo MT dynamics.
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Roy, Chowdhury Susovan. "Single-Molecule Force Manipulation and Nanoscopic Imaging of Protein Structure-Dynamics-Function Relationship." Bowling Green State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu162707900722617.

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Books on the topic "Protein Dynamics - Confocal Microscopy"

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Tony, Wilson, Society of Photo-optical Instrumentation Engineers., Optical Society of America, and European Physical Society, eds. Confocal, multiphoton, and nonlinear microscopic imaging: 22-23 June 2003, Munich, Germany. Bellingham, Wash., USA: SPIE, 2003.

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Society, European Physical. Confocal, Multiphoton, and Nonlinear Microscopic Imaging II: 12-16 June 2005, Munich, Germany (Progress in Biomedical Optics and Imaging,). SPIE-International Society for Optical Engine, 2005.

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Appasani, Krishnarao, and Raghu Kiran Appasani, eds. Single-Molecule Science. Cambridge University Press, 2022. http://dx.doi.org/10.1017/9781108525909.

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Single Molecule Science (SMS) has emerged from developing, using and combining technologies such as super-resolution microscopy, atomic force microscopy, and optical and magnetic tweezers, alongside sophisticated computational and modelling techniques. This comprehensive, edited volume brings together authoritative overviews of these methods from a biological perspective, and highlights how they can be used to observe and track individual molecules and monitor molecular interactions in living cells. Pioneers in this fast-moving field cover topics such as single molecule optical maps, nanomachines, and protein folding and dynamics. A particular emphasis is also given to mapping DNA molecules for diagnostic purposes, and the study of gene expression. With numerous illustrations, this book reveals how SMS has presented us with a new way of understanding life processes. A must-have for researchers and graduate students, as well as those working in industry, primarily in the areas of biophysics, biological imaging, genomics and structural biology.
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Book chapters on the topic "Protein Dynamics - Confocal Microscopy"

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Tillberg, Paul. "Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy." In Confocal Microscopy, 147–56. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1402-0_7.

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Akkaya, Billur, Olena Kamenyeva, Juraj Kabat, and Ryan Kissinger. "Visualizing the Dynamics of T Cell–Dendritic Cell Interactions in Intact Lymph Nodes by Multiphoton Confocal Microscopy." In Confocal Microscopy, 243–63. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1402-0_13.

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Tan, Yan-Wen, Jeffrey A. Hanson, Jhih-Wei Chu, and Haw Yang. "Confocal Single-Molecule FRET for Protein Conformational Dynamics." In Protein Dynamics, 51–62. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_3.

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Mullineaux, Conrad W. "Localization and Mobility of Bacterial Proteins by Confocal Microscopy and Fluorescence Recovery After Photobleaching." In Protein Targeting Protocols, 3–16. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-466-7_1.

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Shenoy, Sudha K. "Visualizing G Protein-Coupled Receptor Signalsomes Using Confocal Immunofluorescence Microscopy." In Methods in Molecular Biology, 333–42. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-160-4_20.

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Käs, Josef, Jochen Guck, and David Humphrey. "Dynamics of Single Protein Polymers Visualized by Fluorescence Microscopy." In Modern Optics, Electronics and High Precision Techniques in Cell Biology, 101–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-80370-3_6.

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Sharma, Ved P., David Entenberg, and John Condeelis. "High-Resolution Live-Cell Imaging and Time-Lapse Microscopy of Invadopodium Dynamics and Tracking Analysis." In Adhesion Protein Protocols, 343–57. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-538-5_21.

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Larsen, DeLaine D., Regina Wai-Yan Choy, and Minjong Park. "Concurrent Imaging of Receptor Trafficking and Calcium Dynamics by Spinning Disk Confocal Microscopy." In Methods in Molecular Biology, 249–59. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6688-2_17.

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Chang, Jerry C., and Sandra J. Rosenthal. "Quantum Dot-Based Single-Molecule Microscopy for the Study of Protein Dynamics." In Methods in Molecular Biology, 71–84. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-468-5_6.

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Rao, Tejeshwar C., Tomasz J. Nawara, and Alexa L. Mattheyses. "Live-Cell Total Internal Reflection Fluorescence (TIRF) Microscopy to Investigate Protein Internalization Dynamics." In Methods in Molecular Biology, 45–58. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2035-9_3.

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Conference papers on the topic "Protein Dynamics - Confocal Microscopy"

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Wijarnprecha, Khakhanang, Philipp Fuhrmann, Christopher Gregson, Matt Sillick, Sopark Sonwai, and Derick Rousseau. "Temperature-dependent Microstructure and Rheology of Fat in Adipose Tissue in Pork, Beef and Lamb." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/urjw5726.

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Matching the texture of fat in plant-based meat alternatives requires an in-depth understanding of the structure and rheology of animal adipose tissue which, to-date, remains under-studied. We investigated the temperature-dependent microstructure and thermal properties of adipose tissue from pork, beef and lamb. Microstructural characterisation via electron, confocal and light microscopy showed that the back fats were structurally similar and consisted of fat dispersed in discrete units within a protein matrix akin to a closed cell foam. Differential scanning calorimetry showed distinct fat melting profiles in each of the tissues, which were ascribed to differences in fatty acid profile. Fat crystal organisation, melting and re-solidification signatures unique to each adipose tissue were found via X-ray diffraction and Raman spectroscopy. The dynamic rheological behaviour of the back fats was characterised via frequency and amplitude sweeps as well as texture analysis via puncture tests. At 20 °C, prior to heating, the small and large deformation properties of adipose tissue were dominated by the solid fat phase in the adipose cells. Upon heating to 80 °C, with the fat phase molten, the protein network underpinning the structure of the back fats conferred elastic behaviour to the tissues, and the now-molten oil partly leaked from the adipocytes into the surrounding interstitial space. Upon re-cooling, a bicontinuous network of fat crystals and protein contributed to back fat rheology. Large deformation rheology revealed animal species-specific differences in back fat rheology. Overall, we found that the temperature-dependent microstructure of adipose fat was intricately linked to the fat phase melting behaviour, and importantly, to its protein matrix at elevated temperatures. Such understanding is necessary to provide the required insights to effectively replicate the functionality of adipose tissue using plant-based materials.
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Nicolau, Dan V., Robert A. Cross, Nick Carter, and Takahisa Taguchi. "Protein patterning using bilayer lithography and confocal microscopy." In Microlithography '99, edited by Will Conley. SPIE, 1999. http://dx.doi.org/10.1117/12.350244.

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Marchello, Gabriele. "Analysis of protein dynamics via Deep Learning." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.1077.

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Nicolau, Dan V., Robert A. Cross, and Takahisa Taguchi. "Protein and cell patterning using bilayer lithography and confocal microscopy." In Smart Materials and MEMS, edited by Alan R. Wilson and Hiroshi Asanuma. SPIE, 2001. http://dx.doi.org/10.1117/12.424413.

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Peterson, Kajsa H., Michael Randen, Richard M. Hays, and Karl-Eric Magnusson. "Lipid and protein distribution in epithelial cells assessed with confocal microscopy." In SPIE/IS&T 1992 Symposium on Electronic Imaging: Science and Technology, edited by Raj S. Acharya, Carol J. Cogswell, and Dmitry B. Goldgof. SPIE, 1992. http://dx.doi.org/10.1117/12.59609.

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McCabe, Eithne M., Christopher Jordan, D. T. Fewer, John F. Donegan, S. Taniguchi, T. Hino, Kazushi Nakano, Akira Ishibashi, Petteri Uusimaa, and Markus Pessa. "Confocal photoluminescense microscopy in II-VI materials: annealing and degradation dynamics." In BiOS '99 International Biomedical Optics Symposium, edited by Dario Cabib, Carol J. Cogswell, Jose-Angel Conchello, Jeremy M. Lerner, and Tony Wilson. SPIE, 1999. http://dx.doi.org/10.1117/12.347591.

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Bezzerides, Vassilios J., and David E. Clapham. "Near-membrane protein dynamics revealed by evanescent field microscopy." In Second International Symposium on Fluctuations and Noise, edited by Derek Abbott, Sergey M. Bezrukov, Andras Der, and Angel Sanchez. SPIE, 2004. http://dx.doi.org/10.1117/12.548399.

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Tao, Xiaodong, Oscar Azucena, Min Fu, Yi Zuo, Diana C. Chen, and Joel Kubby. "Adaptive optics confocal microscopy using fluorescent protein guide-stars for brain tissue imaging." In SPIE MOEMS-MEMS, edited by Scot S. Olivier, Thomas G. Bifano, and Joel Kubby. SPIE, 2012. http://dx.doi.org/10.1117/12.911956.

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Qiu, Le, Edward Vitkin, Hui Fang, Munir M. Zaman, Charlotte Andersson, Saira Salahuddin, Mark D. Modell, et al. "Analyzing cell structure and dynamics with confocal light scattering and absorption spectroscopic microscopy." In Biomedical Optics (BiOS) 2007, edited by Valery V. Tuchin. SPIE, 2007. http://dx.doi.org/10.1117/12.711694.

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Saknite, Inga, Michael Byrne, and Eric R. Tkaczyk. "Characterization of individual cell motion in human skin capillaries by noninvasive reflectance confocal video microscopy (Conference Presentation)." In Dynamics and Fluctuations in Biomedical Photonics XVI, edited by Valery V. Tuchin, Martin J. Leahy, and Ruikang K. Wang. SPIE, 2019. http://dx.doi.org/10.1117/12.2510442.

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Reports on the topic "Protein Dynamics - Confocal Microscopy"

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Or, Dani, Shmulik Friedman, and Jeanette Norton. Physical processes affecting microbial habitats and activity in unsaturated agricultural soils. United States Department of Agriculture, October 2002. http://dx.doi.org/10.32747/2002.7587239.bard.

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experimental methods for quantifying effects of water content and other dynamic environmental factors on bacterial growth in partially-saturated soils. Towards this end we reviewed critically the relevant scientific literature and performed theoretical and experimental studies of bacterial growth and activity in modeled, idealized and real unsaturated soils. The natural wetting-drying cycles common to agricultural soils affect water content and liquid organization resulting in fragmentation of aquatic habitats and limit hydraulic connections. Consequently, substrate diffusion pathways to soil microbial communities become limiting and reduce nutrient fluxes, microbial growth, and mobility. Key elements that govern the extent and manifestation of such ubiquitous interactions include characteristics of diffusion pathways and pore space, the timing, duration, and extent of environmental perturbations, the nature of microbiological adjustments (short-term and longterm), and spatial distribution and properties of EPS clusters (microcolonies). Of these key elements we have chosen to focus on a manageable subset namely on modeling microbial growth and coexistence on simple rough surfaces, and experiments on bacterial growth in variably saturated sand samples and columns. Our extensive review paper providing a definitive “snap-shot” of present scientific understanding of microbial behavior in unsaturated soils revealed a lack of modeling tools that are essential for enhanced predictability of microbial processes in soils. We therefore embarked on two pronged approach of development of simple microbial growth models based on diffusion-reaction principles to incorporate key controls for microbial activity in soils such as diffusion coefficients and temporal variations in soil water content (and related substrate diffusion rates), and development of new methodologies in support of experiments on microbial growth in simple and observable porous media under controlled water status conditions. Experimental efforts led to a series of microbial growth experiments in granular media under variable saturation and ambient conditions, and introduction of atomic force microscopy (AFM) and confocal scanning laser microscopy (CSLM) to study cell size, morphology and multi-cell arrangement at a high resolution from growth experiments in various porous media. The modeling efforts elucidated important links between unsaturated conditions and microbial coexistence which is believed to support the unparallel diversity found in soils. We examined the role of spatial and temporal variation in hydration conditions (such as exist in agricultural soils) on local growth rates and on interactions between two competing microbial species. Interestingly, the complexity of soil spaces and aquatic niches are necessary for supporting a rich microbial diversity and the wide array of microbial functions in unsaturated soils. This project supported collaboration between soil physicists and soil microbiologist that is absolutely essential for making progress in both disciplines. It provided a few basic tools (models, parameterization) for guiding future experiments and for gathering key information necessary for prediction of biological processes in agricultural soils. The project sparked a series of ongoing studies (at DTU and EPFL and in the ARO) into effects of soil hydration dynamics on microbial survival strategy under short term and prolonged desiccation (important for general scientific and agricultural applications).
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Droby, Samir, Michael Wisniewski, Ron Porat, and Dumitru Macarisin. Role of Reactive Oxygen Species (ROS) in Tritrophic Interactions in Postharvest Biocontrol Systems. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7594390.bard.

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To elucidate the role of ROS in the tri-trophic interactions in postharvest biocontrol systems a detailed molecular and biochemical investigation was undertaken. The application of the yeast biocontrol agent Metschnikowia fructicola, microarray analysis was performed on grapefruit surface wounds using an Affymetrix Citrus GeneChip. the data indicated that 1007 putative unigenes showed significant expression changes following wounding and yeast application relative to wounded controls. The expression of the genes encoding Respiratory burst oxidase (Rbo), mitogen-activated protein kinase (MAPK) and mitogen-activated protein kinase kinase (MAPKK), G-proteins, chitinase (CHI), phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS) and 4-coumarate-CoA ligase (4CL). In contrast, three genes, peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT), were down-regulated in grapefruit peel tissue treated with yeast cells. The yeast antagonists, Metschnikowia fructicola (strain 277) and Candida oleophila (strain 182) generate relatively high levels of super oxide anion (O2−) following its interaction with wounded fruit surface. Using laser scanning confocal microscopy we observed that the application of M. fructicola and C. oleophila into citrus and apple fruit wounds correlated with an increase in H2O2 accumulation in host tissue. The present data, together with our earlier discovery of the importance of H₂O₂ production in the defense response of citrus flavedo to postharvest pathogens, indicate that the yeast-induced oxidative response in fruit exocarp may be associated with the ability of specific yeast species to serve as biocontrol agents for the management of postharvest diseases. Effect of ROS on yeast cells was also studied. Pretreatment of the yeast, Candida oleophila, with 5 mM H₂O₂ for 30 min (sublethal) increased yeast tolerance to subsequent lethal levels of oxidative stress (50 mM H₂O₂), high temperature (40 °C), and low pH (pH 4). Suppression subtractive hybridization analysis was used to identify genes expressed in yeast in response to sublethal oxidative stress. Transcript levels were confirmed using semi quantitative reverse transcription-PCR. Seven antioxidant genes were up regulated. Pretreatment of the yeast antagonist Candida oleophila with glycine betaine (GB) increases oxidative stress tolerance in the microenvironment of apple wounds. ROS production is greater when yeast antagonists used as biocontrol agents are applied in the wounds. Compared to untreated control yeast cells, GB-treated cells recovered from the oxidative stress environment of apple wounds exhibited less accumulation of ROS and lower levels of oxidative damage to cellular proteins and lipids. Additionally, GB-treated yeast exhibited greater biocontrol activity against Penicillium expansum and Botrytis cinerea, and faster growth in wounds of apple fruits compared to untreated yeast. The expression of major antioxidant genes, including peroxisomal catalase, peroxiredoxin TSA1, and glutathione peroxidase was elevated in the yeast by GB treatment. A mild heat shock (HS) pretreatment (30 min at 40 1C) improved the tolerance of M. fructicola to subsequent high temperature (45 1C, 20–30 min) and oxidative stress (0.4 mol-¹) hydrogen peroxide, 20–60 min). HS-treated yeast cells showed less accumulation of reactive oxygen species (ROS) than non-treated cells in response to both stresses. Additionally, HS-treated yeast exhibited significantly greater (P≥0.0001) biocontrol activity against Penicillium expansum and a significantly faster (Po0.0001) growth rate in wounds of apple fruits stored at 25 1C compared with the performance of untreated yeast cells. Transcription of a trehalose-6-phosphate synthase gene (TPS1) was up regulated in response to HS and trehalose content also increased.
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