Sample records for auto-luminescent genetically-encoded ratiometric

  1. Auto-luminescent genetically-encoded ratiometric indicator for real-time Ca2+ imaging at the single cell level.

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    Kenta Saito

    Full Text Available BACKGROUND: Efficient bioluminescence resonance energy transfer (BRET from a bioluminescent protein to a fluorescent protein with high fluorescent quantum yield has been utilized to enhance luminescence intensity, allowing single-cell imaging in near real time without external light illumination. METHODOLOGY/PRINCIPAL FINDINGS: We applied BRET to develop an autoluminescent Ca(2+ indicator, BRAC, which is composed of Ca(2+-binding protein, calmodulin, and its target peptide, M13, sandwiched between a yellow fluorescent protein variant, Venus, and an enhanced Renilla luciferase, RLuc8. Adjusting the relative dipole orientation of the luminescent protein's chromophores improved the dynamic range of BRET signal change in BRAC up to 60%, which is the largest dynamic range among BRET-based indicators reported so far. Using BRAC, we demonstrated successful visualization of Ca(2+ dynamics at the single-cell level with temporal resolution at 1 Hz. Moreover, BRAC signals were acquired by ratiometric imaging capable of canceling out Ca(2+-independent signal drifts due to change in cell shape, focus shift, etc. CONCLUSIONS/SIGNIFICANCE: The brightness and large dynamic range of BRAC should facilitate high-sensitive Ca(2+ imaging not only in single live cells but also in small living subjects.

  2. pHlash: a new genetically encoded and ratiometric luminescence sensor of intracellular pH.

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    Yunfei Zhang

    Full Text Available We report the development of a genetically encodable and ratiometic pH probe named "pHlash" that utilizes Bioluminescence Resonance Energy Transfer (BRET rather than fluorescence excitation. The pHlash sensor-composed of a donor luciferase that is genetically fused to a Venus fluorophore-exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H(+ specific; neither Ca(++, Mg(++, Na(+, nor K(+ changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H(+ ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate.

  3. Optimal microscopic systems for long-term imaging of intracellular calcium using a ratiometric genetically-encoded calcium indicator. (United States)

    Miyamoto, Akitoshi; Bannai, Hiroko; Michikawa, Takayuki; Mikoshiba, Katsuhiko


    Monitoring the pattern of intracellular Ca(2+) signals that control many diverse cellular processes is essential for understanding regulatory mechanisms of cellular functions. Various genetically encoded Ca(2+) indicators (GECIs) are used for monitoring intracellular Ca(2+) changes under several types of microscope systems. However, it has not yet been explored which microscopic system is ideal for long-term imaging of the spatiotemporal patterns of Ca(2+) signals using GECIs. We here compared the Ca(2+) signals reported by a fluorescence resonance energy transfer (FRET)-based ratiometric GECI, yellow cameleon 3.60 (YC3.60), stably expressed in DT40 B lymphocytes, using three different imaging systems. These systems included a wide-field fluorescent microscope, a multipoint scanning confocal system, and a single-point scanning confocal system. The degree of photobleaching and the signal-to-noise ratio of YC3.60 in DT40 cells were highly dependent on the fluorescence excitation method, although the total illumination energy was maintained at a constant level within each of the imaging systems. More strikingly, the Ca(2+) responses evoked by B-cell antigen receptor stimulation in YC3.60-expressing DT40 cells were different among the imaging systems, and markedly affected by the illumination power used. Our results suggest that optimization of the imaging system, including illumination and acquisition conditions, is crucial for accurate visualization of intracellular Ca(2+) signals.

  4. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator


    Minderer, M; Liu, W.; Sumanovski, L. T.; Kügler, S; Helmchen, F; Margolis, D. J.


    Abstract  In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal ...

  5. Genetically encoded optical sensors for monitoring of intracellular chloride and chloride-selective channel activity

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    Piotr Bregestovski


    Full Text Available This review briefly discusses the main approaches for monitoring chloride (Cl−, the most abundant physiological anion. Noninvasive monitoring of intracellular Cl− ([Cl−]i is a challenging task owing to two main difficulties: (i the low transmembrane ratio for Cl−, approximately 10:1; and (ii the small driving force for Cl−, as the Cl− reversal potential (ECl is usually close to the resting potential of the cells. Thus, for reliable monitoring of intracellular Cl−, one has to use highly sensitive probes. From several methods for intracellular Cl− analysis, genetically encoded chloride indicators represent the most promising tools. Recent achievements in the development of genetically encoded chloride probes are based on the fact that yellow fluorescent protein (YFP exhibits Cl−-sensitivity. YFP-based probes have been successfully used for quantitative analysis of Cl− transport in different cells and for high-throughput screening of modulators of Cl−-selective channels. Development of a ratiometric genetically encoded probe, Clomeleon, has provided a tool for noninvasive estimation of intracellular Cl− concentrations. While the sensitivity of this protein to Cl− is low (EC50 about 160 mM, it has been successfully used for monitoring intracellular Cl− in different cell types. Recently a CFP–YFP-based probe with a relatively high sensitivity to Cl− (EC50 about 30 mM has been developed. This construct, termed Cl-Sensor, allows ratiometric monitoring using the fluorescence excitation ratio. Of particular interest are genetically encoded probes for monitoring of ion channel distribution and activity. A new molecular probe has been constructed by introducing into the cytoplasmic domain of the Cl−-selective glycine receptor (GlyR channel the CFP–YFP-based Cl-Sensor. This construct, termed BioSensor-GlyR, has been successfully expressed in cell lines. The new genetically encoded chloride probes offer means of screening

  6. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator. (United States)

    Minderer, Matthias; Liu, Wenrui; Sumanovski, Lazar T; Kügler, Sebastian; Helmchen, Fritjof; Margolis, David J


    In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal precision, and furthermore, can be measured repeatedly in separate imaging sessions over multiple weeks. This method opens new possibilities for the longitudinal study of stability and plasticity of cortical sensory representations.

  7. Genetically Encoded Voltage Indicators in Circulation Research. (United States)

    Kaestner, Lars; Tian, Qinghai; Kaiser, Elisabeth; Xian, Wenying; Müller, Andreas; Oberhofer, Martin; Ruppenthal, Sandra; Sinnecker, Daniel; Tsutsui, Hidekazu; Miyawaki, Atsushi; Moretti, Alessandra; Lipp, Peter


    Membrane potentials display the cellular status of non-excitable cells and mediate communication between excitable cells via action potentials. The use of genetically encoded biosensors employing fluorescent proteins allows a non-invasive biocompatible way to read out the membrane potential in cardiac myocytes and other cells of the circulation system. Although the approaches to design such biosensors date back to the time when the first fluorescent-protein based Förster Resonance Energy Transfer (FRET) sensors were constructed, it took 15 years before reliable sensors became readily available. Here, we review different developments of genetically encoded membrane potential sensors. Furthermore, it is shown how such sensors can be used in pharmacological screening applications as well as in circulation related basic biomedical research. Potentials and limitations will be discussed and perspectives of possible future developments will be provided.

  8. Mouse redox histology using genetically encoded probes. (United States)

    Fujikawa, Yuuta; Roma, Leticia P; Sobotta, Mirko C; Rose, Adam J; Diaz, Mauricio Berriel; Locatelli, Giuseppe; Breckwoldt, Michael O; Misgeld, Thomas; Kerschensteiner, Martin; Herzig, Stephan; Müller-Decker, Karin; Dick, Tobias P


    Mapping the in vivo distribution of endogenous oxidants in animal tissues is of substantial biomedical interest. Numerous health-related factors, including diet, physical activity, infection, aging, toxins, or pharmacological intervention, may cause redox changes. Tools are needed to pinpoint redox state changes to particular organs, tissues, cell types, and subcellular organelles. We describe a procedure that preserves the in vivo redox state of genetically encoded redox biosensors within histological tissue sections, thus providing "redox maps" for any tissue and comparison of interest. We demonstrate the utility of the technique by visualizing endogenous redox differences and changes in the context of tumor growth, inflammation, embryonic development, and nutrient starvation.

  9. Illumination of the Spatial Order of Intracellular pH by Genetically Encoded pH-Sensitive Sensors

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    Mojca Benčina


    Full Text Available Fluorescent proteins have been extensively used for engineering genetically encoded sensors that can monitor levels of ions, enzyme activities, redox potential, and metabolites. Certain fluorescent proteins possess specific pH-dependent spectroscopic features, and thus can be used as indicators of intracellular pH. Moreover, concatenated pH-sensitive proteins with target proteins pin the pH sensors to a definite location within the cell, compartment, or tissue. This study provides an overview of the continually expanding family of pH-sensitive fluorescent proteins that have become essential tools for studies of pH homeostasis and cell physiology. We describe and discuss the design of intensity-based and ratiometric pH sensors, their spectral properties and pH-dependency, as well as their performance. Finally, we illustrate some examples of the applications of pH sensors targeted at different subcellular compartments.

  10. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing. (United States)

    Polizzi, Karen M; Kontoravdi, Cleo


    With the current wealth of transcriptomic data, it is possible to design genetically-encoded biosensors for the detection of stress responses and apply these to high-throughput bioprocess development and monitoring of cellular health. Such biosensors can sense extrinsic factors such as nutrient or oxygen deprivation and shear stress, as well as intrinsic stress factors like oxidative damage and unfolded protein accumulation. Alongside, there have been developments in biosensing hardware and software applicable to the field of genetically-encoded biosensors in the near future. This review discusses the current state-of-the-art in biosensors for monitoring cultures during biological manufacturing and the future challenges for the field. Connecting the individual achievements into a coherent whole will enable the application of genetically-encoded biosensors in industry.

  11. Live cell monitoring of glycine betaine by FRET-based genetically encoded nanosensor. (United States)

    Ahmad, Mohammad; Ameen, Seema; Siddiqi, Tariq Omar; Khan, Parvez; Ahmad, Altaf


    Glycine betaine (GB) is one of the key compatible solutes that accumulate in the cell at exceedingly high level under the conditions of high salinity. It plays a crucial role in the maintenance of osmolarity of the cell without affecting the physiological processes. Analysis of stress-induced physiological conditions in living cells, therefore, requires real-time monitoring of cellular GB level. Glycine Betaine Optical Sensor (GBOS), a genetically-encoded FRET-based nanosensor developed in this study, allows the real-time monitoring of GB levels inside living cells. This nanosensor has been developed by sandwiching GB binding protein (ProX) between the Förster resonance energy transfer (FRET) pair, the cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Conformational change in ProX, which was used as sensory domain, reported the change in the level of this compatible solute in in vitro and in vivo conditions. Binding of the GB to the sensory domain fetches close to both the fluorescent moieties that result in the form of increased FRET ratio. So, any change in the concentration of GB is correlated with change in FRET ratio. This sensor also reported the GB cellular dynamics in real-time in Escherichia coli cells after the addition of its precursor, choline. The GBOS was also expressed in yeast and mammalian cells to monitor the intracellular GB. Therefore, the GBOS represents a unique FRET-based nanosensor which allows the non-invasive ratiometric analysis of the GB in living cells.

  12. Toward Better Genetically Encoded Sensors of Membrane Potential. (United States)

    Storace, Douglas; Sepehri Rad, Masoud; Kang, BokEum; Cohen, Lawrence B; Hughes, Thom; Baker, Bradley J


    Genetically encoded optical sensors of cell activity are powerful tools that can be targeted to specific cell types. This is especially important in neuroscience because individual brain regions can include a multitude of different cell types. Optical imaging allows for simultaneous recording from numerous neurons or brain regions. Optical signals of membrane potential are useful because membrane potential changes are a direct sign of both synaptic and action potentials. Here we describe recent improvements in the in vitro and in vivo signal size and kinetics of genetically encoded voltage indicators (GEVIs) and discuss their relationship to alternative sensors of neural activity.

  13. Calibration and functional analysis of three genetically encoded Cl−/pH sensors

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    Marat eMukhtarov


    Full Text Available Monitoring of the intracellular concentrations of Cl− and H+ requires sensitive probes that allow reliable quantitative measurements without perturbation of cell functioning. For these purposes the most promising are genetically encoded fluorescent biosensors, which have become powerful tools for non-invasive intracellular monitoring of ions, molecules and enzymatic activity. A ratiometric CFP/YFP-based construct with a relatively good sensitivity to Cl− has been developed (Markova et al., 2008; Waseem et al., 2010. Recently, a combined Cl−/pH sensor (ClopHensor opened the way for simultaneous ratiometric measurement of these two ions (Arosio et al., 2010. ClopHensor was obtained by fusion of a red-fluorescent protein (DsRed-monomer to the E2GFP variant that contains a specific Cl−-binding site. This construct possesses pKa = 6.8 for H+ and Kd in the 40-50 mM range for Cl− at physiological pH (~7.3 As in the majority of cell types the intracellular Cl− concentration ([Cl−]i is about 10 mM, the development of sensors with higher sensitivity is highly desirable. Here we report the intracellular calibration and functional characterization of ClopHensor and its two derivatives: the membrane targeting PalmPalm-ClopHensor and the H148G/V224L mutant with improved Cl− affinity, reduced pH dependence and pKa shifted to more alkaline values. For functional analysis, constructs were expressed in CHO cells and [Cl−]i was changed by using pipettes with different Cl− concentrations during whole-cell recordings. Kd values for Cl− measured at 33°C and pH ~ 7.3 were, respectively, 39 mM, 47 mM and 21 mM for ClopHensor, PalmPalm-ClopHensor and the H148G/V224L mutant. PalmPalm-ClopHensor resolved responses to activation of Cl−-selective glycine receptor channels better than did ClopHensor. Our observations indicate that these different ClopHensor constructs are promising tools for non-invasive measurement of [Cl−]i in various living

  14. Genetically encoded cleavable protein photo-cross-linker. (United States)

    Lin, Shixian; He, Dan; Long, Teng; Zhang, Shuai; Meng, Rong; Chen, Peng R


    We have developed a genetically encoded, selenium-based cleavable photo-cross-linker that allows for the separation of bait and prey proteins after protein photo-cross-linking. We have further demonstrated the efficient capture of the in situ generated selenenic acid on the cleaved prey proteins. Our strategy involves tagging the selenenic acid with an alkyne-containing dimethoxyaniline molecule and subsequently labeling with an azide-bearing fluorophore or biotin probe. This cleavage-and-capture after protein photo-cross-linking strategy allows for the efficient capture of prey proteins that are readily accessible by two-dimensional gel-based proteomics and mass spectrometry analysis.

  15. Recent Advances in Development of Genetically Encoded Fluorescent Sensors. (United States)

    Sanford, Lynn; Palmer, Amy


    Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.

  16. Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor

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    Potzkei Janko


    Full Text Available Abstract Background Molecular oxygen (O2 is one of the key metabolites of all obligate and facultative aerobic pro- and eukaryotes. It plays a fundamental role in energy homeostasis whereas oxygen deprivation, in turn, broadly affects various physiological and pathophysiological processes. Therefore, real-time monitoring of cellular oxygen levels is basically a prerequisite for the analysis of hypoxia-induced processes in living cells and tissues. Results We developed a genetically encoded Förster resonance energy transfer (FRET-based biosensor allowing the observation of changing molecular oxygen concentrations inside living cells. This biosensor named FluBO (fluorescent protein-based biosensor for oxygen consists of the yellow fluorescent protein (YFP that is sensitive towards oxygen depletion and the hypoxia-tolerant flavin-binding fluorescent protein (FbFP. Since O2 is essential for the formation of the YFP chromophore, efficient FRET from the FbFP donor domain to the YFP acceptor domain only occurs in the presence but not in the absence of oxygen. The oxygen biosensor was used for continuous real-time monitoring of temporal changes of O2 levels in the cytoplasm of Escherichia coli cells during batch cultivation. Conclusions FluBO represents a unique FRET-based oxygen biosensor which allows the non-invasive ratiometric readout of cellular oxygen. Thus, FluBO can serve as a novel and powerful probe for investigating the occurrence of hypoxia and its effects on a variety of (pathophysiological processes in living cells.

  17. Fluorescent proteins as genetically encoded FRET biosensors in life sciences. (United States)

    Hochreiter, Bernhard; Garcia, Alan Pardo; Schmid, Johannes A


    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  18. A genetically encoded, high-signal-to-noise maltose sensor

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    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)


    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  19. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences (United States)

    Hochreiter, Bernhard; Pardo Garcia, Alan; Schmid, Johannes A.


    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them. PMID:26501285

  20. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

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    Bernhard Hochreiter


    Full Text Available Fluorescence- or Förster resonance energy transfer (FRET is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a cleavage; (b conformational-change; (c mechanical force and (d changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  1. Optogenetic Monitoring of Synaptic Activity with Genetically Encoded Voltage Indicators (United States)

    Nakajima, Ryuichi; Jung, Arong; Yoon, Bong-June; Baker, Bradley J.


    The age of genetically encoded voltage indicators (GEVIs) has matured to the point that changes in membrane potential can now be observed optically in vivo. Improving the signal size and speed of these voltage sensors has been the primary driving forces during this maturation process. As a result, there is a wide range of probes using different voltage detecting mechanisms and fluorescent reporters. As the use of these probes transitions from optically reporting membrane potential in single, cultured cells to imaging populations of cells in slice and/or in vivo, a new challenge emerges—optically resolving the different types of neuronal activity. While improvements in speed and signal size are still needed, optimizing the voltage range and the subcellular expression (i.e., soma only) of the probe are becoming more important. In this review, we will examine the ability of recently developed probes to report synaptic activity in slice and in vivo. The voltage-sensing fluorescent protein (VSFP) family of voltage sensors, ArcLight, ASAP-1, and the rhodopsin family of probes are all good at reporting changes in membrane potential, but all have difficulty distinguishing subthreshold depolarizations from action potentials and detecting neuronal inhibition when imaging populations of cells. Finally, we will offer a few possible ways to improve the optical resolution of the various types of neuronal activities. PMID:27547183

  2. A genetically encoded biosensor for visualising hypoxia responses in vivo (United States)

    Misra, Tvisha; Baccino-Calace, Martin; Meyenhofer, Felix; Rodriguez-Crespo, David; Akarsu, Hatice; Armenta-Calderón, Ricardo; Gorr, Thomas A.; Frei, Christian; Cantera, Rafael; Egger, Boris


    ABSTRACT Cells experience different oxygen concentrations depending on location, organismal developmental stage, and physiological or pathological conditions. Responses to reduced oxygen levels (hypoxia) rely on the conserved hypoxia-inducible factor 1 (HIF-1). Understanding the developmental and tissue-specific responses to changing oxygen levels has been limited by the lack of adequate tools for monitoring HIF-1 in vivo. To visualise and analyse HIF-1 dynamics in Drosophila, we used a hypoxia biosensor consisting of GFP fused to the oxygen-dependent degradation domain (ODD) of the HIF-1 homologue Sima. GFP-ODD responds to changing oxygen levels and to genetic manipulations of the hypoxia pathway, reflecting oxygen-dependent regulation of HIF-1 at the single-cell level. Ratiometric imaging of GFP-ODD and a red-fluorescent reference protein reveals tissue-specific differences in the cellular hypoxic status at ambient normoxia. Strikingly, cells in the larval brain show distinct hypoxic states that correlate with the distribution and relative densities of respiratory tubes. We present a set of genetic and image analysis tools that enable new approaches to map hypoxic microenvironments, to probe effects of perturbations on hypoxic signalling, and to identify new regulators of the hypoxia response. PMID:28011628

  3. Genetically encoded tools: bridging the gap between neuronal identity and function. (United States)

    Cho, Yong Ku


    Genetically encoded tools are positioned to serve a unique and critical role in bridging the gap between the genetic identity of neurons and their functional properties. However, the use of these tools is limited by our current understanding of cell-type identity. As we make technological advances that focus on capturing functional aspects of neurons such as connectivity, activity, and metabolic states, our understanding of neuronal identity will deepen and may enable the use of genetically encoded tools for modulating disease-specific circuits for therapeutic purposes.

  4. Genetic encoding of the post-translational modification 2-hydroxyisobutyryl-lysine


    Knight, William A.; Cropp, T.Ashton


    We report the synthesis and genetic encoding of a recently discovered posttranslational modification, 2-hydroxyisobutryl-lysine, to the genetic code of E. coli. The production of homogeneous proteins containing this amino acid will facilitate the study of modification in full-length proteins.

  5. Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry


    Zhang, Wen-Bin; Sun, Fei; Tirrell, David A.; Arnold, Frances H.


    Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag–SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyT...

  6. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction


    Lang, Kathrin; Davis, Lloyd; Torres-Kolbus, Jessica; Chou, Chungjung; Deiters, Alexander; Chin, Jason W.


    The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNACUA pair in Escherichia coli and mammalian cells. We developed a series of tetr...

  7. StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity

    KAUST Repository

    Samodelov, S. L.


    Strigolactones are key regulators of plant development and interaction with symbiotic fungi; however, quantitative tools for strigolactone signaling analysis are lacking. We introduce a genetically encoded hormone biosensor used to analyze strigolactone-mediated processes, including the study of the components involved in the hormone perception/signaling complex and the structural specificity and sensitivity of natural and synthetic strigolactones in Arabidopsis, providing quantitative insights into the stereoselectivity of strigolactone perception. Given the high specificity, sensitivity, dynamic range of activity, modular construction, ease of implementation, and wide applicability, the biosensor StrigoQuant will be useful in unraveling multiple levels of strigolactone metabolic and signaling networks.

  8. FRET-based genetically-encoded sensors for quantitative monitoring of metabolites. (United States)

    Mohsin, Mohd; Ahmad, Altaf; Iqbal, Muhammad


    Neighboring cells in the same tissue can exist in different states of dynamic activities. After genomics, proteomics and metabolomics, fluxomics is now equally important for generating accurate quantitative information on the cellular and sub-cellular dynamics of ions and metabolite, which is critical for functional understanding of organisms. Various spectrometry techniques are used for monitoring ions and metabolites, although their temporal and spatial resolutions are limited. Discovery of the fluorescent proteins and their variants has revolutionized cell biology. Therefore, novel tools and methods targeting sub-cellular compartments need to be deployed in specific cells and targeted to sub-cellular compartments in order to quantify the target-molecule dynamics directly. We require tools that can measure cellular activities and protein dynamics with sub-cellular resolution. Biosensors based on fluorescence resonance energy transfer (FRET) are genetically encoded and hence can specifically target sub-cellular organelles by fusion to proteins or targetted sequences. Since last decade, FRET-based genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of cellular physiology. This review, describing the design and principles of sensors, presents a database of sensors for different analytes/processes, and illustrate examples of application in quantitative live cell imaging.

  9. Optimization of ERK Activity Biosensors for both Ratiometric and Lifetime FRET Measurements

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    Pauline Vandame


    Full Text Available Among biosensors, genetically-encoded FRET-based biosensors are widely used to localize and measure enzymatic activities. Kinases activities are of particular interest as their spatiotemporal regulation has become crucial for the deep understanding of cell fate decisions. This is especially the case for ERK, whose activity is a key node in signal transduction pathways and can direct the cell into various processes. There is a constant need for better tools to analyze kinases in vivo, and to detect even the slightest variations of their activities. Here we report the optimization of the previous ERK activity reporters, EKAR and EKAREV. Those tools are constituted by two fluorophores adapted for FRET experiments, which are flanking a specific substrate of ERK, and a domain able to recognize and bind this substrate when phosphorylated. The latter phosphorylation allows a conformational change of the biosensor and thus a FRET signal. We improved those biosensors with modifications of: (i fluorophores and (ii linkers between substrate and binding domain, resulting in new versions that exhibit broader dynamic ranges upon EGF stimulation when FRET experiments are carried out by fluorescence lifetime and ratiometric measurements. Herein, we characterize those new biosensors and discuss their observed differences that depend on their fluorescence properties.

  10. Organoids and the genetically encoded self-assembly of embryonic stem cells. (United States)

    Turner, David A; Baillie-Johnson, Peter; Martinez Arias, Alfonso


    Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to self-organization, as often suggested, but rather to a process of genetically encoded self-assembly where genetic programs encode and control the emergence of biological structures.

  11. Development and properties of genetically encoded pH sensors in plants.

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    Alexandre eMartinière


    Full Text Available Fluorescent proteins (FPs have given access to a large choice of live imaging techniques and has thereby profoundly modified our view of plant cells. Together with technological improvement of imaging, they have opened the possibility to monitor physico-chemical changes within cells. For this purpose, a new generation of fluorescent proteins has been engineered. For instance, pHluorin, a point mutated version of GFP, allows to get local pH estimates. In this paper, we will describe how genetically encoded sensors can be used to measure pH in the microenvironment of living tissues and subsequently discuss the role of pH in (i exocytosis, (ii ion uptake by plant roots, (iii cell growth and (iv protein trafficking.

  12. A fully genetically encoded protein architecture for optical control of peptide ligand concentration (United States)

    Schmidt, Daniel; Tillberg, Paul W.; Chen, Fei; Boyden, Edward S.


    Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell. Our reagent, which we call a lumitoxin, combines a photoswitch and an ion channel-blocking peptide toxin. Illumination causes the photoswitch to unfold, lowering the toxin's local concentration near the cell surface, and enabling the ion channel to function. We explore lumitoxin modularity by showing operation with peptide toxins that target different voltage-dependent K+ channels. The lumitoxin architecture may represent a new kind of modular protein-engineering strategy for designing light-activated proteins, and thus may enable development of novel tools for modulating cellular physiology.

  13. Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics. (United States)

    Sharma, Vangmayee; Wang, Yane-Shih; Liu, Wenshe R


    Histidine is a unique amino acid with an imidazole side chain in which both of the nitrogen atoms are capable of serving as a proton donor and proton acceptor in hydrogen bonding interactions. In order to probe the functional role of histidine involved in hydrogen bonding networks, fine-tuning the hydrogen bonding potential of the imidazole side chain is required but not feasible through traditional mutagenesis methods. Here, we show that two close mimetics of histidine, 3-methyl-histidine and thiazole alanine, can be genetically encoded using engineered pyrrolysine incorporation machinery. Replacement of the three histidine residues predicted to be involved in an extended charge-relay system in alanine racemase with 3-methyl-histidine or thiazole alanine shows a dramatic loss in the enzyme's catalytic efficiency, implying the role of this extended charge-relay system in activating the active site residue Y265, a general acid/base catalyst in the enzyme.

  14. A genetically encoded toolkit for tracking live-cell histidine dynamics in space and time (United States)

    Hu, Hanyang; Gu, Yanfang; Xu, Lei; Zou, Yejun; Wang, Aoxue; Tao, Rongkun; Chen, Xianjun; Zhao, Yuzheng; Yang, Yi


    High-resolution spatiotemporal imaging of histidine in single living mammalian cells faces technical challenges. Here, we developed a series of ratiometric, highly responsive, and single fluorescent protein-based histidine sensors of wide dynamic range. We used these sensors to quantify subcellular free-histidine concentrations in glucose-deprived cells and glucose-fed cells. Results showed that cytosolic free-histidine concentration was higher and more sensitive to the environment than free histidine in the mitochondria. Moreover, histidine was readily transported across the plasma membrane and mitochondrial inner membrane, which had almost similar transport rates and transport constants, and histidine transport was not influenced by cellular metabolic state. These sensors are potential tools for tracking histidine dynamics inside subcellular organelles, and they will open an avenue to explore complex histidine signaling. PMID:28252043

  15. Controlling enzyme inhibition using an expanded set of genetically encoded amino acids. (United States)

    Zheng, Shun; Kwon, Inchan


    Enzyme inhibition plays an important role in drug development, metabolic pathway regulation, and biocatalysis with product inhibition. When an inhibitor has high structural similarities to the substrate of an enzyme, controlling inhibitor binding without affecting enzyme substrate binding is often challenging and requires fine-tuning of the active site. We hypothesize that an extended set of genetically encoded amino acids can be used to design an enzyme active site that reduces enzyme inhibitor binding without compromising substrate binding. As a model case, we chose murine dihydrofolate reductase (mDHFR), substrate dihydrofolate, and inhibitor methotrexate. Structural models of mDHFR variants containing non-natural amino acids complexed with each ligand were constructed to identify a key residue for inhibitor binding and non-natural amino acids to replace the key residue. Then, we discovered that replacing the key phenylalanine residue with two phenylalanine analogs (p-bromophenylalanine (pBrF) and L-2-naphthylalanine (2Nal)) enhances binding affinity toward the substrate dihydrofolate over the inhibitor by 4.0 and 5.8-fold, respectively. Such an enhanced selectivity is mainly due to a reduced inhibitor binding affinity by 2.1 and 4.3-fold, respectively. The catalytic efficiency of the mDHFR variant containing pBrF is comparable to that of wild-type mDHFR, whereas the mDHFR variant containing 2Nal exhibits a moderate decrease in the catalytic efficiency. The work described here clearly demonstrates the feasibility of selectively controlling enzyme inhibition using an expanded set of genetically encoded amino acids.

  16. Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome (United States)

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.


    Optical imaging of genetically encoded probes has revolutionized biomedical studies by providing valuable information about targeted biological processes. Here, we report a novel imaging technique, termed reversibly switchable photoacoustic tomography (RS-PAT), which exhibits large penetration depth, high detection sensitivity, and super-resolution. RS-PAT combines advanced photoacoustic imaging techniques with, for the first time, a nonfluorescent photoswitchable bacterial phytochrome. This bacterial phytochrome is the most near-infrared shifted genetically encoded probe reported so far. Moreover, this bacterial phytochrome is reversibly photoconvertible between its far-red and near-infrared light absorption states. Taking maximum advantage of the powerful imaging capability of PAT and the unique photochemical properties of the phytochrome, RS-PAT has broken through both the optical diffusion limit for deep-tissue imaging and the optical diffraction limit for super-resolution photoacoustic microscopy. Specifically, with RS-PAT we have achieved an unprecedented detection sensitivity of ~2 μM, or as few as ~20 tumor cells, at a centimeter depth. Such high sensitivity is fully demonstrated in our study by monitoring tumor growth and metastasis at whole-body level with ~100 μm resolution. Moreover, our microscopic implementation of RS-PAT is capable of imaging mammalian cells with a sub-diffraction lateral resolution of ~140 nm and axial resolution of ~400 nm, which are respectively ~2-fold and ~75-fold finer than those of our conventional photoacoustic microscopy. Overall, RS-PAT is a new and promising imaging technology for studying biological processes at different length scales.

  17. Genetic encoding of caged cysteine and caged homocysteine in bacterial and mammalian cells. (United States)

    Uprety, Rajendra; Luo, Ji; Liu, Jihe; Naro, Yuta; Samanta, Subhas; Deiters, Alexander


    We report the genetic incorporation of caged cysteine and caged homocysteine into proteins in bacterial and mammalian cells. The genetic code of these cells was expanded with an engineered pyrrolysine tRNA/tRNA synthetase pair that accepts both light-activatable amino acids as substrates. Incorporation was validated by reporter assays, western blots, and mass spectrometry, and differences in incorporation efficiency were explained by molecular modeling of synthetase-amino acid interactions. As a proof-of-principle application, the genetic replacement of an active-site cysteine residue with a caged cysteine residue in Renilla luciferase led to a complete loss of enzyme activity; however, upon brief exposure to UV light, a >150-fold increase in enzymatic activity was observed, thus showcasing the applicability of the caged cysteine in live human cells. A simultaneously conducted genetic replacement with homocysteine yielded an enzyme with greatly reduced activity, thereby demonstrating the precise probing of a protein active site. These discoveries provide a new tool for the optochemical control of protein function in mammalian cells and expand the set of genetically encoded unnatural amino acids.

  18. Exploring dynamics of molybdate in living animal cells by a genetically encoded FRET nanosensor. (United States)

    Nakanishi, Yoichi; Iida, Syuntaro; Ueoka-Nakanishi, Hanayo; Niimi, Tomoaki; Tomioka, Rie; Maeshima, Masayoshi


    Molybdenum (Mo) is an essential trace element for almost all living organisms including animals. Mo is used as a catalytic center of molybdo-enzymes for oxidation/reduction reactions of carbon, nitrogen, and sulfur metabolism. Whilst living cells are known to import inorganic molybdate oxyanion from the surrounding environment, the in vivo dynamics of cytosolic molybdate remain poorly understood as no appropriate indicator is available for this trace anion. We here describe a genetically encoded Förester-resonance-energy-transfer (FRET)-based nanosensor composed of CFP, YFP and the bacterial molybdate-sensor protein ModE. The nanosensor MolyProbe containing an optimized peptide-linker responded to nanomolar-range molybdate selectively, and increased YFP:CFP fluorescence intensity ratio by up to 109%. By introduction of the nanosensor, we have been able to successfully demonstrate the real-time dynamics of molybdate in living animal cells. Furthermore, time course analyses of the dynamics suggest that novel oxalate-sensitive- and sulfate-resistant- transporter(s) uptake molybdate in a model culture cell.

  19. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.

    Directory of Open Access Journals (Sweden)

    Xiaokun Shu


    Full Text Available Electron microscopy (EM achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce "miniSOG" (for mini Singlet Oxygen Generator, a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy.

  20. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain

    Directory of Open Access Journals (Sweden)

    Yukiko eMishina


    Full Text Available Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviours. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP prototypical design or on the voltage dependent state transitions of microbial opsins.We recently introduced a new VSFP design in which the voltage-sensing domain (VSD is sandwiched between a FRET pair of fluorescent proteins (termed VSFP-Butterflies and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.

  1. Imaging the response of the retina to electrical stimulation with genetically encoded calcium indicators. (United States)

    Weitz, Andrew C; Behrend, Matthew R; Lee, Nan Sook; Klein, Ronald L; Chiodo, Vince A; Hauswirth, William W; Humayun, Mark S; Weiland, James D; Chow, Robert H


    Epiretinal implants for the blind are designed to stimulate surviving retinal neurons, thus bypassing the diseased photoreceptor layer. Single-unit or multielectrode recordings from isolated animal retina are commonly used to inform the design of these implants. However, such electrical recordings provide limited information about the spatial patterns of retinal activation. Calcium imaging overcomes this limitation, as imaging enables high spatial resolution mapping of retinal ganglion cell (RGC) activity as well as simultaneous recording from hundreds of RGCs. Prior experiments in amphibian retina have demonstrated proof of principle, yet experiments in mammalian retina have been hindered by the inability to load calcium indicators into mature mammalian RGCs. Here, we report a method for labeling the majority of ganglion cells in adult rat retina with genetically encoded calcium indicators, specifically GCaMP3 and GCaMP5G. Intravitreal injection of an adeno-associated viral vector targets ∼85% of ganglion cells with high specificity. Because of the large fluorescence signals provided by the GCaMP sensors, we can now for the first time visualize the response of the retina to electrical stimulation in real-time. Imaging transduced retinas mounted on multielectrode arrays reveals how stimulus pulse shape can dramatically affect the spatial extent of RGC activation, which has clear implications in prosthetic applications. Our method can be easily adapted to work with other fluorescent indicator proteins in both wild-type and transgenic mammals.

  2. Imaging Membrane Potential with Two Types of Genetically Encoded Fluorescent Voltage Sensors. (United States)

    Lee, Sungmoo; Piao, Hong Hua; Sepheri-Rad, Masoud; Jung, Arong; Sung, Uhna; Song, Yoon-Kyu; Baker, Bradley J


    Genetically encoded voltage indicators (GEVIs) have improved to the point where they are beginning to be useful for in vivo recordings. While the ultimate goal is to image neuronal activity in vivo, one must be able to image activity of a single cell to ensure successful in vivo preparations. This procedure will describe how to image membrane potential in a single cell to provide a foundation to eventually image in vivo. Here we describe methods for imaging GEVIs consisting of a voltage-sensing domain fused to either a single fluorescent protein (FP) or two fluorescent proteins capable of Förster resonance energy transfer (FRET) in vitro. Using an image splitter enables the projection of images created by two different wavelengths onto the same charge-coupled device (CCD) camera simultaneously. The image splitter positions a second filter cube in the light path. This second filter cube consists of a dichroic and two emission filters to separate the donor and acceptor fluorescent wavelengths depending on the FPs of the GEVI. This setup enables the simultaneous recording of both the acceptor and donor fluorescent partners while the membrane potential is manipulated via whole cell patch clamp configuration. When using a GEVI consisting of a single FP, the second filter cube can be removed allowing the mirrors in the image splitter to project a single image onto the CCD camera.

  3. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening. (United States)

    Doucette, Jaimee; Zhao, Ziyan; Geyer, Rory J; Barra, Melanie M; Balunas, Marcy J; Zweifach, Adam


    Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)-activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.

  4. Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations.

    Directory of Open Access Journals (Sweden)

    Jennifer C Ewald

    Full Text Available Citrate is an intermediate in catabolic as well as biosynthetic pathways and is an important regulatory molecule in the control of glycolysis and lipid metabolism. Mass spectrometric and NMR based metabolomics allow measuring citrate concentrations, but only with limited spatial and temporal resolution. Methods are so far lacking to monitor citrate levels in real-time in-vivo. Here, we present a series of genetically encoded citrate sensors based on Förster resonance energy transfer (FRET. We screened databases for citrate-binding proteins and tested three candidates in vitro. The citrate binding domain of the Klebsiella pneumoniae histidine sensor kinase CitA, inserted between the FRET pair Venus/CFP, yielded a sensor highly specific for citrate. We optimized the peptide linkers to achieve maximal FRET change upon citrate binding. By modifying residues in the citrate binding pocket, we were able to construct seven sensors with different affinities spanning a concentration range of three orders of magnitude without losing specificity. In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation.

  5. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. (United States)

    Michener, Joshua K; Thodey, Kate; Liang, Joe C; Smolke, Christina D


    Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability.

  6. Calcium Signaling throughout the Toxoplasma gondii Lytic Cycle: A STUDY USING GENETICALLY ENCODED CALCIUM INDICATORS. (United States)

    Borges-Pereira, Lucas; Budu, Alexandre; McKnight, Ciara A; Moore, Christina A; Vella, Stephen A; Hortua Triana, Miryam A; Liu, Jing; Garcia, Celia R S; Pace, Douglas A; Moreno, Silvia N J


    Toxoplasma gondii is an obligate intracellular parasite that invades host cells, creating a parasitophorous vacuole where it communicates with the host cell cytosol through the parasitophorous vacuole membrane. The lytic cycle of the parasite starts with its exit from the host cell followed by gliding motility, conoid extrusion, attachment, and invasion of another host cell. Here, we report that Ca(2+) oscillations occur in the cytosol of the parasite during egress, gliding, and invasion, which are critical steps of the lytic cycle. Extracellular Ca(2+) enhances each one of these processes. We used tachyzoite clonal lines expressing genetically encoded calcium indicators combined with host cells expressing transiently expressed calcium indicators of different colors, and we measured Ca(2+) changes in both parasites and host simultaneously during egress. We demonstrated a link between cytosolic Ca(2+) oscillations in the host and in the parasite. Our approach also allowed us to measure two new features of motile parasites, which were enhanced by Ca(2+) influx. This is the first study showing, in real time, Ca(2+) signals preceding egress and their direct link with motility, an essential virulence trait.

  7. EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels. (United States)

    Schmidt, Moritz J; Fedoseev, Artem; Bücker, Dennis; Borbas, Julia; Peter, Christine; Drescher, Malte; Summerer, Daniel


    The genetic encoding of nitroxide amino acids in combination with electron paramagnetic resonance (EPR) distance measurements enables precise structural studies of native proteins, i.e. without the need for mutations to create unique reactive sites for chemical labeling and thus with minimal structural perturbation. We here report on in vitro DEER measurements in native E. coli thioredoxin (TRX) that establish the nitroxide amino acid SLK-1 as a spectroscopic probe that reports distances and conformational flexibilities in the enzyme with nonmutated catalytic centers that are not accessible by the use of the traditional methanethiosulfonate spin label (MTSSL). We generated a rotamer library for SLK-1 that in combination with molecular dynamics (MD) simulation enables predictions of distance distributions between two SLK-1 labels incorporated into a target protein. Toward a routine use of SLK-1 for EPR distance measurements in proteins and the advancement of the approach to intracellular environments, we study the stability of SLK-1 in E. coli cultures and lysates and establish guidelines for protein expression and purification that offer maximal nitroxide stability. These advancements and insights provide new perspectives for facile structural studies of native, endogenous proteins by EPR distance measurements.

  8. Genetically encoded Ca2+ indicators; expanded affinity range, color hue and compatibility with optogenetics

    Directory of Open Access Journals (Sweden)

    Takeharu eNagai


    Full Text Available Fluorescent protein-based indicators are invaluable tools for functional imaging of living cells and organisms. Genetically encoded calcium indicators (GECIs such as derivatives of yellow cameleons (YCs and GCaMPs/pericams (Miyawaki et al., 1997; Nakai et al., 2001; Nagai et al., 2001 are a highly advanced class of indicators. Continued efforts for improvement of the performance of GECIs have resulted in brighter indicators with better photo-stability and expanded dynamic range, thus improving the sensitivity of detection. Fine-tuning of other properties, including Ca2+ affinity and Hill constant, have also contributed to increase the detectability of Ca2+ dynamics. Emerging optogenetic technology has forced the spectrally compatible GECI color variants. In this opinion, we highlight the recent development of GECIs including photo-switchable Ca2+ indicators and bioluminescence-based Ca2+ indicator, mainly invented in our group, focusing especially on the parameters determining their performance in order to provide a guideline for the selection of appropriate GECI for a given experiment.

  9. A highly sensitive colorimetric and ratiometric sensor for fluoride ion

    Institute of Scientific and Technical Information of China (English)

    Zhao Wu Xu; Jin Tang; He Tian


    A new benzoimidazole-naphthalimide derivative 4 was synthesized and its photophysical properties were studied.This compound showed highly selectively and sensitive colorimetric and ratiometric sensing ability for fluoride anion.

  10. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

    Directory of Open Access Journals (Sweden)

    Jasper eAkerboom


    Full Text Available Genetically encoded calcium indicators (GECIs are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, RCaMPs, engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+] and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2 or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

  11. Genetically-encoded tools for cAMP probing and modulation in living systems.

    Directory of Open Access Journals (Sweden)

    Valeriy M Paramonov


    Full Text Available Intracellular 3'-5'-cyclic adenosine monophosphate (cAMP is one of the principal second messengers downstream of a manifold of signal transduction pathways, including the ones triggered by G protein-coupled receptors. Not surprisingly, biochemical assays for cAMP have been instrumental for basic research and drug discovery for decades, providing insights into cellular physiology and guiding pharmaceutical industry. However, despite impressive track record, the majority of conventional biochemical tools for cAMP probing share the same fundamental shortcoming - all the measurements require sample disruption for cAMP liberation. This common bottleneck, together with inherently low spatial resolution of measurements (as cAMP is typically analyzed in lysates of thousands of cells, underpin the ensuing limitations of the conventional cAMP assays: 1 genuine kinetic measurements of cAMP levels over time in a single given sample are unfeasible; 2 inability to obtain precise information on cAMP spatial distribution and transfer at subcellular levels, let alone the attempts to pinpoint dynamic interactions of cAMP and its effectors. At the same time, tremendous progress in synthetic biology over the recent years culminated in drastic refinement of our toolbox, allowing us not only to bypass the limitations of conventional assays, but to put intracellular cAMP life-span under tight control – something, that seemed scarcely attainable before. In this review article we discuss the main classes of modern genetically-encoded tools tailored for cAMP probing and modulation in living systems. We examine the capabilities and weaknesses of these different tools in the context of their operational characteristics and applicability to various experimental set-ups involving living cells, providing the guidance for rational selection of the best tools for particular needs.

  12. Imaging activity in astrocytes and neurons with genetically encoded calcium indicators following in utero electroporation

    Directory of Open Access Journals (Sweden)

    J. Michael eGee


    Full Text Available Complex interactions between networks of astrocytes and neurons are beginning to be appreciated, but remain poorly understood. Transgenic mice expressing fluorescent protein reporters of cellular activity, such as the GCaMP family of genetically encoded calcium indicators, have been used to explore network behavior. However, in some cases, it may be desirable to use long-established rat models that closely mimic particular aspects of human conditions such as Parkinson’s disease and the development of epilepsy following status epilepticus. Methods for expressing reporter proteins in the rat brain are relatively limited. Transgenic rat technologies exist but are fairly immature. Viral-mediated expression is robust but unstable, requires invasive injections, and only works well for fairly small genes (< 5 kb. In utero electroporation offers a valuable alternative. IUE is a proven method for transfecting populations of astrocytes and neurons in the rat brain without the strict limitations on transgene size. We built a toolset of IUE plasmids carrying GCaMP variants 3, 6s or 6f driven by CAG and targeted to the cytosol or the plasma membrane. Because low baseline fluorescence of GCaMP can hinder identification of transfected cells, we included the option of co-expressing a cytosolic tdTomato protein. A binary system consisting of a plasmid carrying a piggyBac inverted terminal repeat-flanked CAG-GCaMP-IRES-tdTomato cassette and a separate plasmid encoding for expression of piggyBac transposase was employed to stably express GCaMP and tdTomato. The plasmids were co-electroporated on embryonic days 13.5-14.5 and astrocytic and neuronal activity was subsequently imaged in acute or cultured brain slices prepared from the cortex or hippocampus. Large spontaneous transients were detected in slices obtained from rats of varying ages up to 127 days. In this report, we demonstrate the utility of this toolset for interrogating astrocytic and neuronal

  13. Targeted silver nanoparticles for ratiometric cell phenotyping (United States)

    Willmore, Anne-Mari A.; Simón-Gracia, Lorena; Toome, Kadri; Paiste, Päärn; Kotamraju, Venkata Ramana; Mölder, Tarmo; Sugahara, Kazuki N.; Ruoslahti, Erkki; Braun, Gary B.; Teesalu, Tambet


    Affinity targeting is used to deliver nanoparticles to cells and tissues. For efficient targeting, it is critical to consider the expression and accessibility of the relevant receptors in the target cells. Here, we describe isotopically barcoded silver nanoparticles (AgNPs) as a tool for auditing affinity ligand receptors in cells. Tumor penetrating peptide RPARPAR (receptor: NRP-1) and tumor homing peptide GKRK (receptor: p32) were used as affinity ligands on the AgNPs. The binding and uptake of the peptide-functionalized AgNPs by cultured PPC-1 prostate cancer and M21 melanoma cells was dependent on the cell surface expression of the cognate peptide receptors. Barcoded peptide-functionalized AgNPs were synthesized from silver and palladium isotopes. The cells were incubated with a cocktail of the barcoded nanoparticles [RPARPAR (R), GKRK (K), and control], and cellular binding and internalization of each type of nanoparticle was assessed by inductively coupled plasma mass spectrometry. The results of isotopic analysis were in agreement with data obtained using optical methods. Using ratiometric measurements, we were able to classify the PPC-1 cell line as mainly NRP-1-positive, with 75 +/- 5% R-AgNP uptake, and the M21 cell line as only p32-positive, with 89 +/- 9% K-AgNP uptake. The isotopically barcoded multiplexed AgNPs are useful as an in vitro ratiometric phenotyping tool and have potential uses in functional evaluation of the expression of accessible homing peptide receptors in vivo.Affinity targeting is used to deliver nanoparticles to cells and tissues. For efficient targeting, it is critical to consider the expression and accessibility of the relevant receptors in the target cells. Here, we describe isotopically barcoded silver nanoparticles (AgNPs) as a tool for auditing affinity ligand receptors in cells. Tumor penetrating peptide RPARPAR (receptor: NRP-1) and tumor homing peptide GKRK (receptor: p32) were used as affinity ligands on the AgNPs. The

  14. Engineering of a Genetically Encodable Fluorescent Voltage Sensor Exploiting Fast Ci-VSP Voltage-Sensing Movements


    Alicia Lundby; Hiroki Mutoh; Dimitar Dimitrov; Walther Akemann; Thomas Knöpfel


    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence re...

  15. Development of an automated fluorescence microscopy system for photomanipulation of genetically encoded photoactivatable proteins (optogenetics) in live cells. (United States)

    Araki, Nobukazu; Ikeda, Yuka; Kato, Takuma; Kawai, Katsuhisa; Egami, Youhei; Miyake, Katsuya; Tsurumaki, Nobuhide; Yamaguchi, Mitsunari


    Photomanipulation of genetically encoded light-sensitive protein activity, also known as optogenetics, is one of the most innovative recent microscopy techniques in the fields of cell biology and neurobiology. Although photomanipulation is usually performed by diverting the photobleaching mode of a confocal laser microscope, photobleaching by the laser scanning unit is not always suitable for photoactivation. We have developed a simple automated wide-field fluorescence microscopy system for the photomanipulation of genetically encoded photoactivatable proteins in live cells. An electrically automated fluorescence microscope can be controlled through MetaMorph imaging software, making it possible to acquire time-lapse, multiwavelength images of live cells. Using the journal (macro recording) function of MetaMorph, we wrote a macro program to change the excitation filter for photoactivation and illumination area during the intervals of image acquisition. When this program was run on the wide-field fluorescence microscope, cells expressing genetically encoded photoactivatable Rac1, which is activated under blue light, showed morphological changes such as lamellipodial extension and cell surface ruffling in the illuminated region. Using software-based development, we successfully constructed a fully automated photoactivation microscopy system for a mercury lamp-based fluorescence microscope.

  16. Engineering of a genetically encodable fluorescent voltage sensor exploiting fast Ci-VSP voltage-sensing movements

    DEFF Research Database (Denmark)

    Lundby, Alicia; Mutoh, Hiroki; Dimitrov, Dimitar


    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a g...... of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence read-outs....

  17. Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo. (United States)

    Bedbrook, Claire N; Kato, Mihoko; Ravindra Kumar, Sripriya; Lakshmanan, Anupama; Nath, Ravi D; Sun, Fei; Sternberg, Paul W; Arnold, Frances H; Gradinaru, Viviana


    Membrane proteins are the main gatekeepers of cellular state, especially in neurons, serving either to maintain homeostasis or instruct response to synaptic input or other external signals. Visualization of membrane protein localization and trafficking in live cells facilitates understanding the molecular basis of cellular dynamics. We describe here a method for specifically labeling the plasma membrane-localized fraction of heterologous membrane protein expression using channelrhodopsins as a case study. We show that the genetically encoded, covalent binding SpyTag and SpyCatcher pair from the Streptococcus pyogenes fibronectin-binding protein FbaB can selectively label membrane-localized proteins in living cells in culture and in vivo in Caenorhabditis elegans. The SpyTag/SpyCatcher covalent labeling method is highly specific, modular, and stable in living cells. We have used the binding pair to develop a channelrhodopsin membrane localization assay that is amenable to high-throughput screening for opsin discovery and engineering.

  18. Ratiometric analysis of in vivo retinal layer thicknesses in multiple sclerosis (United States)

    Bhaduri, Basanta; Nolan, Ryan M.; Shelton, Ryan L.; Pilutti, Lara A.; Motl, Robert W.; Boppart, Stephen A.


    We performed ratiometric analysis of retinal optical coherence tomography images for the first time in multiple sclerosis (MS) patients. The ratiometric analysis identified differences in several retinal layer thickness ratios in the cohort of MS subjects without a history of optic neuritis (ON) compared to healthy control (HC) subjects, and there was no difference in standard retinal nerve fiber layer thickness (RNFLT). The difference in such ratios between HC subjects and those with mild MS-disability, without a difference in RNFLT, further suggests the possibility of using layer ratiometric analysis for detecting early retinal changes in MS. Ratiometric analysis may be useful and potentially more sensitive for detecting disease changes in MS.

  19. ESIPT-Based Photoactivatable Fluorescent Probe for Ratiometric Spatiotemporal Bioimaging

    Directory of Open Access Journals (Sweden)

    Xiaohong Zhou


    Full Text Available Photoactivatable fluorophores have become an important technique for the high spatiotemporal resolution of biological imaging. Here, we developed a novel photoactivatable probe (PHBT, which is based on 2-(2-hydroxyphenylbenzothiazole (HBT, a small organic fluorophore known for its classic luminescence mechanism through excited-state intramolecular proton transfer (ESIPT with the keto form and the enol form. After photocleavage, PHBT released a ratiometric fluorophore HBT, which showed dual emission bands with more than 73-fold fluorescence enhancement at 512 nm in buffer and more than 69-fold enhancement at 452 nm in bovine serum. The probe displayed a high ratiometric imaging resolution and is believed to have a wide application in biological imaging.

  20. A genetically encoded reporter for real-time imaging of cofilin-actin rods in living neurons.

    Directory of Open Access Journals (Sweden)

    Jianjie Mi

    Full Text Available Filament bundles (rods of cofilin and actin (1:1 form in neurites of stressed neurons where they inhibit synaptic function. Live-cell imaging of rod formation is hampered by the fact that overexpression of a chimera of wild type cofilin with a fluorescent protein causes formation of spontaneous and persistent rods, which is exacerbated by the photostress of imaging. The study of rod induction in living cells calls for a rod reporter that does not cause spontaneous rods. From a study in which single cofilin surface residues were mutated, we identified a mutant, cofilinR21Q, which when fused with monomeric Red Fluorescent Protein (mRFP and expressed several fold above endogenous cofilin, does not induce spontaneous rods even during the photostress of imaging. CofilinR21Q-mRFP only incorporates into rods when they form from endogenous proteins in stressed cells. In neurons, cofilinR21Q-mRFP reports on rods formed from endogenous cofilin and induced by all modes tested thus far. Rods have a half-life of 30-60 min upon removal of the inducer. Vesicle transport in neurites is arrested upon treatments that form rods and recovers as rods disappear. CofilinR21Q-mRFP is a genetically encoded rod reporter that is useful in live cell imaging studies of induced rod formation, including rod dynamics, and kinetics of rod elimination.

  1. Redesign of genetically encoded biosensors for monitoring mitochondrial redox status in a broad range of model eukaryotes. (United States)

    Albrecht, Simone C; Sobotta, Mirko C; Bausewein, Daniela; Aller, Isabel; Hell, Rüdiger; Dick, Tobias P; Meyer, Andreas J


    The development of genetically encoded redox biosensors has paved the way toward chemically specific, quantitative, dynamic, and compartment-specific redox measurements in cells and organisms. In particular, redox-sensitive green fluorescent proteins (roGFPs) have attracted major interest as tools to monitor biological redox changes in real time and in vivo. Most recently, the engineering of a redox relay that combines glutaredoxin (Grx) with roGFP2 as a translational fusion (Grx1-roGFP2) led to a biosensor for the glutathione redox potential (EGSH ). The expression of this probe in mitochondria is of particular interest as mitochondria are the major source of oxidants, and their redox status is closely connected to cell fate decisions. While Grx1-roGFP2 can be expressed in mammalian mitochondria, it fails to enter mitochondria in various nonmammalian model organisms. Here we report that inversion of domain order from Grx1-roGFP2 to roGFP2-Grx1 yields a biosensor with perfect mitochondrial targeting while fully maintaining its biosensor capabilities. The redesigned probe thus allows extending in vivo observations of mitochondrial redox homeostasis to important nonmammalian model organisms, particularly plants and insects.

  2. Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity

    Directory of Open Access Journals (Sweden)

    Alexander S. Goryashchenko


    Full Text Available This article describes the genetically encoded caspase-3 FRET-sensor based on the terbium-binding peptide, cleavable linker with caspase-3 recognition site, and red fluorescent protein TagRFP. The engineered construction performs two induction-resonance energy transfer processes: from tryptophan of the terbium-binding peptide to Tb3+ and from sensitized Tb3+ to acceptor—the chromophore of TagRFP. Long-lived terbium-sensitized emission (microseconds, pulse excitation source, and time-resolved detection were utilized to eliminate directly excited TagRFP fluorescence and background cellular autofluorescence, which lasts a fraction of nanosecond, and thus to improve sensitivity of analyses. Furthermore the technique facilitates selective detection of fluorescence, induced by uncleaved acceptor emission. For the first time it was shown that fluorescence resonance energy transfer between sensitized terbium and TagRFP in the engineered construction can be studied via detection of microsecond TagRFP fluorescence intensities. The lifetime and distance distribution between donor and acceptor were calculated using molecular dynamics simulation. Using this data, quantum yield of terbium ions with binding peptide was estimated.

  3. Use of genetically-encoded calcium indicators for live cell calcium imaging and localization in virus-infected cells. (United States)

    Perry, Jacob L; Ramachandran, Nina K; Utama, Budi; Hyser, Joseph M


    Calcium signaling is a ubiquitous and versatile process involved in nearly every cellular process, and exploitation of host calcium signals is a common strategy used by viruses to facilitate replication and cause disease. Small molecule fluorescent calcium dyes have been used by many to examine changes in host cell calcium signaling and calcium channel activation during virus infections, but disadvantages of these dyes, including poor loading and poor long-term retention, complicate analysis of calcium imaging in virus-infected cells due to changes in cell physiology and membrane integrity. The recent expansion of genetically-encoded calcium indicators (GECIs), including blue and red-shifted color variants and variants with calcium affinities appropriate for calcium storage organelles like the endoplasmic reticulum (ER), make the use of GECIs an attractive alternative for calcium imaging in the context of virus infections. Here we describe the development and testing of cell lines stably expressing both green cytoplasmic (GCaMP5G and GCaMP6s) and red ER-targeted (RCEPIAer) GECIs. Using three viruses (rotavirus, poliovirus and respiratory syncytial virus) previously shown to disrupt host calcium homeostasis, we show the GECI cell lines can be used to detect simultaneous cytoplasmic and ER calcium signals. Further, we demonstrate the GECI expression has sufficient stability to enable long-term confocal imaging of both cytoplasmic and ER calcium during the course of virus infections.

  4. Imaging intracellular Ca²⁺ signals in striatal astrocytes from adult mice using genetically-encoded calcium indicators. (United States)

    Jiang, Ruotian; Haustein, Martin D; Sofroniew, Michael V; Khakh, Baljit S


    Astrocytes display spontaneous intracellular Ca(2+) concentration fluctuations ([Ca(2+)]i) and in several settings respond to neuronal excitation with enhanced [Ca(2+)]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca(2+)]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca(2+)]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca(2+)]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca(2+)]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca(2+)]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca(2+)]i signals in the striatal microcircuitry.

  5. Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo. (United States)

    Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T


    All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pH(cyto)) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pH(cyto) shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2,7-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pH(cyto). Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤ 4 s) trains of action potentials but did buffer slow (~60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca(2+) increase upon stimulation, and partial inhibition of the plasma membrane Ca(2+)-ATPase, a Ca(2+)/H(+) exchanger, attenuated pH(cyto) shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (~0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pH(cyto) shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pH(cyto) shifts cannot be dismissed as artifacts of ex vivo preparations.

  6. Optical recording of neuronal activity with a genetically-encoded calcium indicator in anesthetized and freely moving mice

    Directory of Open Access Journals (Sweden)

    Henry Lütcke


    Full Text Available Fluorescent calcium (Ca2+ indicator proteins (FCIPs are promising tools for functional imaging of cellular activity in living animals. However, they have still not reached their full potential for in vivo imaging of neuronal activity due to limitations in expression levels, dynamic range, and sensitivity for reporting action potentials. Here, we report that viral expression of the ratiometric Ca2+ sensor yellow cameleon 3.60 (YC3.60 in pyramidal neurons of mouse barrel cortex enables in vivo measurement of neuronal activity with high dynamic range and sensitivity across multiple spatial scales. By combining juxtacellular recordings and two-photon imaging in vitro and in vivo, we demonstrate that YC3.60 can resolve single action potential (AP-evoked Ca2+ transients and reliably reports bursts of APs with negligible saturation. Spontaneous and whisker-evoked Ca2+ transients were detected in individual apical dendrites and somata as well as in local neuronal populations. Moreover, bulk measurements using wide-field imaging or fiber-optics revealed sensory-evoked YC3.60 signals in large areas of the barrel field. Fiber-optic recordings in particular enabled measurements in awake, freely moving mice and revealed complex Ca2+ dynamics, possibly reflecting different behavior-related brain states. Viral expression of YC3.60 - in combination with various optical techniques - thus opens a multitude of opportunities for functional studies of the neural basis of animal behavior, from dendrites to the levels of local and large-scale neuronal populations.

  7. Genetically-encoded yellow fluorescent cAMP indicator with an expanded dynamic range for dual-color imaging.

    Directory of Open Access Journals (Sweden)

    Haruki Odaka

    Full Text Available Cyclic AMP is a ubiquitous second messenger, which mediates many cellular responses mainly initiated by activation of cell surface receptors. Various Förster resonance energy transfer-based ratiometric cAMP indicators have been created for monitoring the spatial and temporal dynamics of cAMP at the single-cell level. However, single fluorescent protein-based cAMP indicators have been poorly developed, with improvement required for dynamic range and brightness. Based on our previous yellow fluorescent protein-based cAMP indicator, Flamindo, we developed an improved yellow fluorescent cAMP indicator named Flamindo2. Flamindo2 has a 2-fold expanded dynamic range and 8-fold increased brightness compared with Flamindo by optimization of linker peptides in the vicinity of the chromophore. We found that fluorescence intensity of Flamindo2 was decreased to 25% in response to cAMP. Live-cell cAMP imaging of the cytosol and nucleus in COS7 cells using Flamindo2 and nlsFlamindo2, respectively, showed that forskolin elevated cAMP levels in each compartment with different kinetics. Furthermore, dual-color imaging of cAMP and Ca2+ with Flamindo2 and a red fluorescent Ca2+ indicator, R-GECO, showed that cAMP and Ca2+ elevation were induced by noradrenaline in single HeLa cells. Our study shows that Flamindo2, which is feasible for multi-color imaging with other intracellular signaling molecules, is useful and is an alternative tool for live-cell imaging of intracellular cAMP dynamics.

  8. Genetically-Encoded Yellow Fluorescent cAMP Indicator with an Expanded Dynamic Range for Dual-Color Imaging (United States)

    Odaka, Haruki; Arai, Satoshi; Inoue, Takafumi; Kitaguchi, Tetsuya


    Cyclic AMP is a ubiquitous second messenger, which mediates many cellular responses mainly initiated by activation of cell surface receptors. Various Förster resonance energy transfer-based ratiometric cAMP indicators have been created for monitoring the spatial and temporal dynamics of cAMP at the single-cell level. However, single fluorescent protein-based cAMP indicators have been poorly developed, with improvement required for dynamic range and brightness. Based on our previous yellow fluorescent protein-based cAMP indicator, Flamindo, we developed an improved yellow fluorescent cAMP indicator named Flamindo2. Flamindo2 has a 2-fold expanded dynamic range and 8-fold increased brightness compared with Flamindo by optimization of linker peptides in the vicinity of the chromophore. We found that fluorescence intensity of Flamindo2 was decreased to 25% in response to cAMP. Live-cell cAMP imaging of the cytosol and nucleus in COS7 cells using Flamindo2 and nlsFlamindo2, respectively, showed that forskolin elevated cAMP levels in each compartment with different kinetics. Furthermore, dual-color imaging of cAMP and Ca2+ with Flamindo2 and a red fluorescent Ca2+ indicator, R-GECO, showed that cAMP and Ca2+ elevation were induced by noradrenaline in single HeLa cells. Our study shows that Flamindo2, which is feasible for multi-color imaging with other intracellular signaling molecules, is useful and is an alternative tool for live-cell imaging of intracellular cAMP dynamics. PMID:24959857

  9. An easy ratiometric compensation for the extracellular Ca2+ indicator-caused fluorescence artifact. (United States)

    Kukkonen, Jyrki P


    Measurement of intracellular Ca(2+) dynamics is one of the most central real-time assays for cellular signaling. Ratiometric methods reduce the need for internal calibration and also effectively compensate for most artifacts when used in imaging. However, ratiometric calculation cannot compensate for extracellularly leaked (and fluorescent) Ca(2+) indicator and will instead indicate erroneous Ca(2+) concentration. This frequently occurs in systems where extracellular indicator is accumulated such as fluorescence spectrophotometers and plate readers. Here I present a method that, for the first time, fully compensates for this phenomenon. The method uses a single-step internal calibration together with a predefined ratiometric calibration protocol.

  10. Facile synthesis of a ratiometric oxygen nanosensor for cellular imaging. (United States)

    Lu, Sisi; Xu, Wei; Zhang, Jinliang; Chen, Yiying; Xie, Lei; Yao, Qiuhong; Jiang, Yaqi; Wang, Yiru; Chen, Xi


    A new type of cell-penetrating ratiometric fluorescence oxygen sensing nanoparticle was prepared through a facile co-precipitation method. Amphiphilic polymer poly (styrene-co-maleic anhydride) (PSMA) was firstly cooperated with polystyrene (PS) to envelop the highly photostable phosphorescent oxygen indicator, platinum(II)-tetrakis(pentafluorophenyl)porphyrin (PtTFPP, emission at 648nm), and the reference fluorophore, poly(9, 9-dioctylfluorene) (PFO, emission at 440nm ), via hydrophobic interaction in aqueous solution. To improve the sensor biocompatibility, the biomacromolecule poly-l-lysine (PLL) was selected to act as a shell via electrostatic forces. The as-prepared PtTFPP doped core-shell nanoparticles (called PPMA/PLL NPs) exhibited an excellent ratiometric luminescence response to O2 content with high quenching efficiency and full reversibility in the oxygen sensing. More importantly, these oxygen nanosensors passed across the cell membrane after co-incubation without external force. Labeled cells exhibited high brightness in the matching blue and red channels of a digital camera. And most nanosensors were found locating in cytoplasm rather than being trapped in endosomes.

  11. Ratiometric Photoacoustic Molecular Imaging for Methylmercury Detection in Living Subjects. (United States)

    Liu, Yi; Wang, Sheng; Ma, Ying; Lin, Jing; Wang, Hai-Yan; Gu, Yueqing; Chen, Xiaoyuan; Huang, Peng


    Photoacoustic molecular imaging is an emerging and promising diagnostic tool for heavy metal ions detection. Methylmercury (MeHg(+) ) is one of the most potent neurotoxins, which damages the brain and nervous system of human beings through fish consumption. The development of a selective and sensitive method for MeHg(+) detection is highly desirable. In this Communication, we develope a chemoselective photoacoustic sensor (LP-hCy7) composed of the liposome (LP) and MeHg(+) -responsive near-infrared (NIR) cyanine dye (hCy7) for MeHg(+) detection within living subjects, such as zebrafish and mouse. The as-prepared LP-hCy7 nanoprobe displays unique dual-shift NIR absorbance peaks and produces a normalized turn-on response after the reaction of MeHg(+) and hCy7 through a mercury-promoted cyclization reaction. The absorbance intensities of LP-hCy7 nanoprobe at 690 and 860 nm are decreased and increased, respectively. The ratiometric photoacoustic signal (PA860/PA690) is noticeably increased in the presence of MeHg(+) . These findings not only provide a ratiometric photoacoustic molecular imaging probe for the detection of metal ions in vivo, but also provides a tool for spectroscopic photoacoustic molecular imaging.

  12. Synthesis of a new ratiometric emission Ca2+ indicator for in vivo bioimaging

    Institute of Scientific and Technical Information of China (English)

    Qiao-Ling Liu; Meng Fan; Wei Bian; Shao-Min Shuang; Chuan Dong


    A novel fluorescent calcium indicator with a 490/582 nm ratiometric emission has been designed and synthesized.The indicator exhibits a highly selective ratiometric emission response to Ca2+ over other metal cations and a large Stokes shift of 202 nm.Moreover,its practical cell imaging capability for intracellular Ca2+ in the resting-and dynamic-state has been demonstrated in human umbilical vein endothelial cells using a confocal laser scanning microscope.

  13. Ratiometric fluorescence signalling of fluoride ions by an amidophthalimide derivative

    Indian Academy of Sciences (India)

    Moloy Sarkar; Raghavendra Yellampalli; Bhaswati Bhattacharya; Ravi Kumar Kanaparthi; Anunay Samanta


    Fluorescence behaviour of 4-benzoylamido-N-methylphthalimide (1), designed and developed for selective detection of fluoride ions, is reported. 1 displays F--induced colour change that allows its detection with the naked eye. The F- specificity of the sensor system is evident from the fact that unlike F-, other halides do not affect the absorption characteristics of 1. Apart from the colorimetric response, the fluorescence output of 1 is also modulated by F- in a manner that permits ratiometric fluorescence signalling of F- as well. It is found that the system can detect F- in the concentration range of 10- 60 M. The results of the experiments and theoretical calculations unambiguously suggest that the changes of the electronic absorption and fluorescence behaviour of 1, which have been exploited for signalling purpose, are due to F--induced deprotonation of the 4-amido moiety of the sensor system.

  14. Ratiometric Imaging of Extracellular pH in Dental Biofilms. (United States)

    Schlafer, Sebastian; Dige, Irene


    The pH in bacterial biofilms on teeth is of central importance for dental caries, a disease with a high worldwide prevalence. Nutrients and metabolites are not distributed evenly in dental biofilms. A complex interplay of sorption to and reaction with organic matter in the biofilm reduces the diffusion paths of solutes and creates steep gradients of reactive molecules, including organic acids, across the biofilm. Quantitative fluorescent microscopic methods, such as fluorescence life time imaging or pH ratiometry, can be employed to visualize pH in different microenvironments of dental biofilms. pH ratiometry exploits a pH-dependent shift in the fluorescent emission of pH-sensitive dyes. Calculation of the emission ratio at two different wavelengths allows determining local pH in microscopic images, irrespective of the concentration of the dye. Contrary to microelectrodes the technique allows monitoring both vertical and horizontal pH gradients in real-time without mechanically disturbing the biofilm. However, care must be taken to differentiate accurately between extra- and intracellular compartments of the biofilm. Here, the ratiometric dye, seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) is employed to monitor extracellular pH in in vivo grown dental biofilms of unknown species composition. Upon exposure to glucose the dye is up-concentrated inside all bacterial cells in the biofilms; it is thus used both as a universal bacterial stain and as a marker of extracellular pH. After confocal microscopic image acquisition, the bacterial biomass is removed from all pictures using digital image analysis software, which permits to exclusively calculate extracellular pH. pH ratiometry with the ratiometric dye is well-suited to study extracellular pH in thin biofilms of up to 75 µm thickness, but is limited to the pH range between 4.5 and 7.0.

  15. Towards PDT with Genetically Encoded Photosensitizer KillerRed: A Comparison of Continuous and Pulsed Laser Regimens in an Animal Tumor Model.

    Directory of Open Access Journals (Sweden)

    Marina Shirmanova

    Full Text Available The strong phototoxicity of the red fluorescent protein KillerRed allows it to be considered as a potential genetically encoded photosensitizer for the photodynamic therapy (PDT of cancer. The advantages of KillerRed over chemical photosensitizers are its expression in tumor cells transduced with the appropriate gene and direct killing of cells through precise damage to any desired cell compartment. The ability of KillerRed to affect cell division and to induce cell death has already been demonstrated in cancer cell lines in vitro and HeLa tumor xenografts in vivo. However, the further development of this approach for PDT requires optimization of the method of treatment. In this study we tested the continuous wave (593 nm and pulsed laser (584 nm, 10 Hz, 18 ns modes to achieve an antitumor effect. The research was implemented on CT26 subcutaneous mouse tumors expressing KillerRed in fusion with histone H2B. The results showed that the pulsed mode provided a higher rate of photobleaching of KillerRed without any temperature increase on the tumor surface. PDT with the continuous wave laser was ineffective against CT26 tumors in mice, whereas the pulsed laser induced pronounced histopathological changes and inhibition of tumor growth. Therefore, we selected an effective regimen for PDT when using the genetically encoded photosensitizer KillerRed and pulsed laser irradiation.

  16. Estimating weak ratiometric signals in imaging data. II. Meta-analysis with multiple, dual-channel datasets. (United States)

    Sornborger, Andrew; Broder, Josef; Majumder, Anirban; Srinivasamoorthy, Ganesh; Porter, Erika; Reagin, Sean S; Keith, Charles; Lauderdale, James D


    Ratiometric fluorescent indicators are used for making quantitative measurements of a variety of physiological variables. Their utility is often limited by noise. This is the second in a series of papers describing statistical methods for denoising ratiometric data with the aim of obtaining improved quantitative estimates of variables of interest. Here, we outline a statistical optimization method that is designed for the analysis of ratiometric imaging data in which multiple measurements have been taken of systems responding to the same stimulation protocol. This method takes advantage of correlated information across multiple datasets for objectively detecting and estimating ratiometric signals. We demonstrate our method by showing results of its application on multiple, ratiometric calcium imaging experiments.

  17. Ratiometric artifact reduction in low power reflective photoplethysmography. (United States)

    Patterson, J A C; Guang-Zhong Yang


    This paper presents effective signal-processing techniques for the compensation of motion artifacts and ambient light offsets in a reflective photoplethysmography sensor suitable for wearable applications. A ratiometric comparison of infrared (IR) and red absorption characteristics cancels out noise that is multiplicative in nature and amplitude modulation of pulsatile absorption signals enables rejection of additive noise. A low-power, discrete-time pulse-oximeter platform is used to capture IR and red photoplethysmograms so that the data used for analysis have noise levels representative of what a true body sensor network device would experience. The proposed artifact rejection algorithm is designed for real-time implementation with a low-power microcontroller while being robust enough to compensate for varying levels in ambient light as well as reducing the effects of motion-induced artifacts. The performance of the system is illustrated by its ability to extract a typical plethysmogram heart-rate waveform since the sensor is subjected to a range of physical disturbances.

  18. Cell Permeable Ratiometric Fluorescent Sensors for Imaging Phosphoinositides. (United States)

    Mondal, Samsuzzoha; Rakshit, Ananya; Pal, Suranjana; Datta, Ankona


    Phosphoinositides are critical cell-signal mediators present on the plasma membrane. The dynamic change of phosphoinositide concentrations on the membrane including clustering and declustering mediates signal transduction. The importance of phosphoinositides is scored by the fact that they participate in almost all cell-signaling events, and a defect in phosphoinositide metabolism is linked to multiple diseases including cancer, bipolar disorder, and type-2 diabetes. Optical sensors for visualizing phosphoinositide distribution can provide information on phosphoinositide dynamics. This exercise will ultimately afford a handle into understanding and manipulating cell-signaling processes. The major requirement in phosphoinositide sensor development is a selective, cell permeable probe that can quantify phosphoinositides. To address this requirement, we have developed short peptide-based ratiometric fluorescent sensors for imaging phosphoinositides. The sensors afford a selective response toward two crucial signaling phosphoinositides, phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol-4-phosphate (PI4P), over other anionic membrane phospholipids and soluble inositol phosphates. Dissociation constant values indicate up to 4 times higher probe affinity toward PI(4,5)P2 when compared to PI4P. Significantly, the sensors are readily cell-permeable and enter cells within 15 min of incubation as indicated by multiphoton excitation confocal microscopy. Furthermore, the sensors light up signaling phosphoinositides present both on the cell membrane and on organelle membranes near the perinuclear space, opening avenues for quantifying and monitoring phosphoinositide signaling.

  19. Real-time and high-throughput analysis of mitochondrial metabolic states in living cells using genetically encoded NAD(+)/NADH sensors. (United States)

    Zhao, Yuzheng; Yang, Yi


    Mitochondria are central organelles that regulate cellular bioenergetics, biosynthesis, and signaling processes. NADH, a key player in cell metabolism, is often considered as a marker of mitochondrial function. However, traditional methods for NADH measurements are either destructive or unable to distinguish between NADH and NADPH. In contrast to traditional methods, genetically encoded NADH sensors can be used for the real-time tracking and quantitative measurement of subcellular NADH levels in living cells. Therefore, these sensors provide innovative tools and address the limitations of current techniques. We herein summarize the properties of different types of recently developed NADH biosensors, discuss their advantages and disadvantages, and focus on the high-throughput analysis of mitochondrial function by using highly responsive NAD(+)/NADH sensors.

  20. Synthesis and evaluation of a new colorimetric and ratiometric fluorescence probe for copper ions

    Energy Technology Data Exchange (ETDEWEB)

    Chawla, Har Mohindra, E-mail:; Munjal, Priyanka; Goel, Preeti


    Synthesis and spectroscopic evaluation of compounds 3a, 3b and 4 reveal that cone conformer of 25,27-bis(o-aminothiophenyl propyloxy) -tetra-p-tert-butylcalix[4]arene 3a can function as a highly selective ratiometric and colorimetric fluorescence probe for copper ions. - Highlights: • We have synthesized a new calixarene based receptor 3 for Cu{sup 2+}. • 3 Showed ratiometric changes with Cu{sup 2+} in emission spectrum. • Reference compound 4 showed quenching with Cu{sup 2+} in emission spectrum. • Importance of calix[4]arene platform in ion recognition.

  1. Development of microscopic systems for high-speed dual-excitation ratiometric Ca2+ imaging. (United States)

    Fukano, Takashi; Shimozono, Satoshi; Miyawaki, Atsushi


    For quantitative measurements of Ca(2+) concentration ([Ca(2+)]), ratiometric dyes are preferable, because the use of such dyes allows for correction of uneven loading or partitioning of dye within the cell as well as variations in cell thickness. Although dual-excitation ratiometric dyes for measuring [Ca(2+)], such as Fura-2, Fura-Red, and ratiometric-pericam, are widely used for a variety of applications, it has been difficult to use them for monitoring very fast Ca(2+) dynamics or Ca(2+) changes in highly motile cells. To overcome this problem, we have developed three new dual-excitation ratiometry systems. (1) A system in which two laser beams are alternated on every scanning line, allowing us to obtain confocal images using dual-excitation ratiometric dyes. This system increases the rate at which ratio measurements can be made to 200 Hz and provides confocal images at 1-10 Hz depending on the image size. (2) A truly simultaneous dual-excitation ratiometry system that used linearly polarized excitation light and polarization detection, allowing us to obtain ratiometric images without any time lag. This system, however, is based on statistical features of the fluorescence polarization and is limited to samples that contain a large number of fluorophores. In addition, this method requires complicated calculations. (3) An efficient, nearly simultaneous dual-excitation ratiometry system that allows us to rapidly switch between two synchronized excitation-detection components by employing two high-power light-emitting diodes (LEDs) and two high-speed liquid crystal shutters. The open/close operation of the two shutters is synchronized with the on/off switching of the two LEDs. This system increases the rate at which ratio measurements are made to 1 kHz, and provides ratio images at 10-100 Hz depending on the signal intensity.

  2. Ratiometric fluorescence sensing of sugars via a reversible disassembly and assembly of the peptide aggregates mediated by sugars. (United States)

    Neupane, Lok Nath; Han, Song Yee; Lee, Keun-Hyeung


    An amphiphilic dipeptide (1) bearing pyrene and phenylboronic acid was demonstrated as a unique example of a ratiometric sensing system for sugars by reversibly converting the peptide aggregates into the monomer form of the complex with sugars in aqueous solutions.

  3. Combinatorial mutagenesis of the voltage-sensing domain enables the optical resolution of action potentials firing at 60 Hz by a genetically encoded fluorescent sensor of membrane potential. (United States)

    Piao, Hong Hua; Rajakumar, Dhanarajan; Kang, Bok Eum; Kim, Eun Ha; Baker, Bradley J


    ArcLight is a genetically encoded fluorescent voltage sensor using the voltage-sensing domain of the voltage-sensing phosphatase from Ciona intestinalis that gives a large but slow-responding optical signal in response to changes in membrane potential (Jin et al., 2012). Fluorescent voltage sensors using the voltage-sensing domain from other species give faster yet weaker optical signals (Baker et al., 2012; Han et al., 2013). Sequence alignment of voltage-sensing phosphatases from different species revealed conserved polar and charged residues at 7 aa intervals in the S1-S3 transmembrane segments of the voltage-sensing domain, suggesting potential coil-coil interactions. The contribution of these residues to the voltage-induced optical signal was tested using a cassette mutagenesis screen by flanking each transmembrane segment with unique restriction sites to allow for the testing of individual mutations in each transmembrane segment, as well as combinations in all four transmembrane segments. Addition of a counter charge in S2 improved the kinetics of the optical response. A double mutation in the S4 domain dramatically reduced the slow component of the optical signal seen in ArcLight. Combining that double S4 mutant with the mutation in the S2 domain yielded a probe with kinetics voltage-sensing domain could potentially lead to fluorescent sensors capable of optically resolving neuronal inhibition and subthreshold synaptic activity.

  4. Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag. (United States)

    Hirabayashi, Ai; Fukunaga, Yuko; Miyazawa, Atsuo


    Postsynaptic density-95 (PSD-95) accumulates at excitatory postsynapses and plays important roles in the clustering and anchoring of numerous proteins at the PSD. However, a detailed ultrastructural analysis of clusters exclusively consisting of PSD-95 has never been performed. Here, we employed a genetically encoded tag, three tandem repeats of metallothionein (3MT), to study the structure of PSD-95 clusters in cells by electron tomography and cryo-electron microscopy of vitreous sections. We also performed conventional transmission electron microscopy (TEM). Cultured hippocampal neurons expressing a fusion protein of PSD-95 coupled to 3MT (PDS-95-3MT) were incubated with CdCl2 to result in the formation of Cd-bound PSD-95-3MT. Two types of electron-dense deposits composed of Cd-bound PSD-95-3MT were observed in these cells by TEM, as reported previously. Electron tomography revealed the presence of membrane-shaped structures representing PSD-95 clusters at the PSD and an ellipsoidal structure located in the non-synaptic cytoplasm. By TEM, the PSD-95 clusters appeared to be composed of a number of dense cores. In frozen hydrated sections, these dense cores were also found beneath the postsynaptic membrane. Taken together, our findings suggest that dense cores of PSD-95 aggregate to form the larger clusters present in the PSD and the non-synaptic cytoplasm.

  5. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. (United States)

    Guntas, Gurkan; Lewis, Steven M; Mulvaney, Kathleen M; Cloer, Erica W; Tripathy, Ashutosh; Lane, Thomas R; Major, Michael B; Kuhlman, Brian


    In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1-NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1-NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.

  6. A naked-eye and ratiometric near-infrared probe for palladium via modulation of a π-conjugated system of cyanines. (United States)

    Wang, Xiaohang; Guo, Zhiqian; Zhu, Shiqin; Tian, He; Zhu, Weihong


    A ratiometric and colorimetric cyanine-based palladium sensor with an excellent selectivity and sensitivity has been designed. Notably, the modulation of π-conjugated electrons in cyanine dyes can result in a ratiometric fluorescence change with a large Stokes shift (270 nm), especially for realizing palladium detection in aqueous samples using indicator paper and in living cells by ratiometric mode. The limit of detection is as low as 0.3 ppb.

  7. Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Xiu-Fang; Chen, Zeng-Ping, E-mail:; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin


    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFM{sub GRP}) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFM{sub GRP} has been tested on the quantitative determination of free Ca{sup 2+} in both simulated and real turbid media using a Ca{sup 2+} sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFM{sub GRP} could realize precise and accurate quantification of free Ca{sup 2+} in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca{sup 2+} bound Rhod-2. The average relative predictive error value of QFM{sub GRP} for the test simulated turbid samples was 5.9%, about 2–4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca{sup 2+} bound Rhod-2 and eosin B. The recovery rates of QFM{sub GRP} for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. - Highlights: • An advanced model was derived for generalized wavelength-ratiometric PEBBLEs. • The model can simplify the design of generalized wavelength-ratiometric

  8. A General Strategy for the Semisynthesis of Ratiometric Fluorescent Sensor Proteins with Increased Dynamic Range. (United States)

    Xue, Lin; Prifti, Efthymia; Johnsson, Kai


    We demonstrate how a combination of self-labeling protein tags and unnatural amino acid technology permits the semisynthesis of ratiometric fluorescent sensor proteins with unprecedented dynamic range in vitro and on live cells. To generate such a sensor, a binding protein is labeled with a fluorescent competitor of the analyte using SNAP-tag in conjugation with a second fluorophore that is positioned in vicinity of the binding site of the binding protein using unnatural amino acid technology. Binding of the analyte by the sensor displaces the tethered fluorescent competitor from the binding protein and disrupts fluorescence resonance energy transfer between the two fluorophores. Using this design principle, we generate a ratiometric fluorescent sensor protein for methotrexate that exhibits large dynamic ranges both in vitro (ratio changes up to 32) and on cell surfaces (ratio change of 13). The performance of these semisynthetic sensor proteins makes them attractive for applications in basic research and diagnostics.

  9. Ratiometric and near-infrared molecular probes for the detection and imaging of zinc ions. (United States)

    Carol, Priya; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai


    The detection and imaging of Zn2+ in biological samples are of paramount interest owing to the role of this cation in physiological functions. This is possible only with molecular probes that specifically bind to Zn2+ and result in changes in emission properties. A "turn-on" emission or shift in the emission color upon binding to Zn2+ should be ideal for in vivo imaging. In this context, ratiometric and near-IR probes are of particular interest. Therefore, in the area of chemosensors or molecular probes, the design of fluorophores that allow ratiometric sensing or imaging in the near-IR region is attracting the attention of chemists. The purpose of this Focus Review is to highlight recent developments in this area and stress the importance of further research for future applications.

  10. A ratiometric fluorescent probe for gasotransmitter hydrogen sulfide based on a coumarin-benzopyrylium platform. (United States)

    Duan, Yu-Wei; Yang, Xiao-Feng; Zhong, Yaogang; Guo, Yuan; Li, Zheng; Li, Hua


    A ratiometric fluorescent probe for H2S was developed based on a coumarin- benzopyrylium platform. The ratiometric sensing is realized by a selective conversion of acyl azide to the corresponding amide, which subsequently undergoes an intramolecular spirocyclization to alter the large π-conjugated system of CB fluorophore. Compared with the traditional azide-based H2S probes, the proposed probe utilizes the acyl azide as the recognition moiety and exhibits a rapid response (∼1min) towards H2S, which is superior to most of the azide-based H2S probes. Preliminary fluorescence imaging experiments show that probe 1 has potential to track H2S in living cells.

  11. An ICT-based approach to ratiometric fluorescence imaging of hydrogen peroxide produced in living cells. (United States)

    Srikun, Duangkhae; Miller, Evan W; Domaille, Dylan W; Chang, Christopher J


    We present the synthesis, properties, and biological applications of Peroxy Lucifer 1 (PL1), a new fluorescent probe for imaging hydrogen peroxide produced in living cells by a ratiometric response. PL1 utilizes a chemoselective boronate-based switch to detect hydrogen peroxide by modulation of internal charge transfer (ICT) within a 1,8-naphthalimide dye. PL1 features high selectivity for hydrogen peroxide over similar reactive oxygen species, including superoxide, and nitric oxide, and a 65 nm shift in emission from blue-colored fluorescence to green-colored fluorescence upon reaction with peroxide. Two-photon confocal microscopy experiments in live macrophages show that PL1 can ratiometrically visualize localized hydrogen peroxide bursts generated in living cells at immune response levels.

  12. Biosynthesis of the 22nd Genetically Encoded Amino Acid Pyrrolysine: Structure and Reaction Mechanism of PylC at 1.5Å Resolution

    KAUST Repository

    Quitterer, Felix


    The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide l-lysine-Nε-3R-methyl-d-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5′-adenylyl-β-γ-imidodiphosphate, ADP, d-ornithine (d-Orn), l-lysine (Lys), phosphorylated d-Orn, l-lysine-Nε-d-ornithine, inorganic phosphate, carbonate, and Mg2 +. The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of d-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an SN2 reaction resulting in l-lysine-Nε-d-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis. © 2012 Elsevier Ltd.

  13. Dual optical recordings for action potentials and calcium handling in induced pluripotent stem cell models of cardiac arrhythmias using genetically encoded fluorescent indicators. (United States)

    Song, LouJin; Awari, Daniel W; Han, Elizabeth Y; Uche-Anya, Eugenia; Park, Seon-Hye E; Yabe, Yoko A; Chung, Wendy K; Yazawa, Masayuki


    Reprogramming of human somatic cells to pluripotency has been used to investigate disease mechanisms and to identify potential therapeutics. However, the methods used for reprogramming, in vitro differentiation, and phenotyping are still complicated, expensive, and time-consuming. To address the limitations, we first optimized a protocol for reprogramming of human fibroblasts and keratinocytes into pluripotency using single lipofection and the episomal vectors in a 24-well plate format. This method allowed us to generate multiple lines of integration-free and feeder-free induced pluripotent stem cells (iPSCs) from seven patients with cardiac diseases and three controls. Second, we differentiated human iPSCs derived from patients with Timothy syndrome into cardiomyocytes using a monolayer differentiation method. We found that Timothy syndrome cardiomyocytes showed slower, irregular contractions and abnormal calcium handling compared with the controls. The results are consistent with previous reports using a retroviral method for reprogramming and an embryoid body-based method for cardiac differentiation. Third, we developed an efficient approach for recording the action potentials and calcium transients simultaneously in control and patient cardiomyocytes using genetically encoded fluorescent indicators, ArcLight and R-GECO1. The dual optical recordings enabled us to observe prolonged action potentials and abnormal calcium handling in Timothy syndrome cardiomyocytes. We confirmed that roscovitine rescued the phenotypes in Timothy syndrome cardiomyocytes and that these findings were consistent with previous studies using conventional electrophysiological recordings and calcium imaging with dyes. The approaches using our optimized methods and dual optical recordings will improve iPSC applicability for disease modeling to investigate mechanisms underlying cardiac arrhythmias and to test potential therapeutics.

  14. Application of a genetically encoded biosensor for live cell imaging of L-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains. (United States)

    Mustafi, Nurije; Grünberger, Alexander; Mahr, Regina; Helfrich, Stefan; Nöh, Katharina; Blombach, Bastian; Kohlheyer, Dietrich; Frunzke, Julia


    The majority of biotechnologically relevant metabolites do not impart a conspicuous phenotype to the producing cell. Consequently, the analysis of microbial metabolite production is still dominated by bulk techniques, which may obscure significant variation at the single-cell level. In this study, we have applied the recently developed Lrp-biosensor for monitoring of amino acid production in single cells of gradually engineered L-valine producing Corynebacterium glutamicum strains based on the pyruvate dehydrogenase complex-deficient (PDHC) strain C. glutamicum ΔaceE. Online monitoring of the sensor output (eYFP fluorescence) during batch cultivation proved the sensor's suitability for visualizing different production levels. In the following, we conducted live cell imaging studies on C. glutamicum sensor strains using microfluidic chip devices. As expected, the sensor output was higher in microcolonies of high-yield producers in comparison to the basic strain C. glutamicum ΔaceE. Microfluidic cultivation in minimal medium revealed a typical Gaussian distribution of single cell fluorescence during the production phase. Remarkably, low amounts of complex nutrients completely changed the observed phenotypic pattern of all strains, resulting in a phenotypic split of the population. Whereas some cells stopped growing and initiated L-valine production, others continued to grow or showed a delayed transition to production. Depending on the cultivation conditions, a considerable fraction of non-fluorescent cells was observed, suggesting a loss of metabolic activity. These studies demonstrate that genetically encoded biosensors are a valuable tool for monitoring single cell productivity and to study the phenotypic pattern of microbial production strains.

  15. A quinoline based pH sensitive ratiometric fluorescent sensor: Structure and spectroscopy

    Indian Academy of Sciences (India)

    Soma Mukherjee; Amit Kumar Paul; Helen Stoeckli-Evans


    A new quinoline based hydrazone was synthesized via a condensation reaction and characterized by NMR, mass and single crystal X-ray diffraction studies. It was investigated for suitability as a reversible ratiometric fluorescent pH sensor in acidic pH region. The sensor exhibits intramolecular charge transfer (ICT) type photophysical changes upon protonation of the quinoline ring. No significant interference on emission behavior was observed in the presence of various metal ions.

  16. A Ratiometric Luminescent Thermometer Co-doped with Lanthanide and Transition Metals. (United States)

    Li, Zhiqiang; Hou, Zhaohui; Ha, Denghui; Li, Huanrong


    Herein, we report the fabrication of a sensitive ratiometric and colorimetric luminescent thermometer with a wide operating-temperature range, from cryogenic temperatures up to high temperatures, through the combination of lanthanide and transition metal complexes. Benefiting from the transition metal complex as a self-reference, the lanthanide content in the mixed-coordination complex, Eu0.05(Mebip-mim bromine)0.15Zn0.95(Mebip-mim bromine)1.9, was lowered to 5%.

  17. Ratiometric activatable cell-penetrating peptides provide rapid in vivo readout of thrombin activation. (United States)

    Whitney, Michael; Savariar, Elamprakash N; Friedman, Beth; Levin, Rachel A; Crisp, Jessica L; Glasgow, Heather L; Lefkowitz, Roy; Adams, Stephen R; Steinbach, Paul; Nashi, Nadia; Nguyen, Quyen T; Tsien, Roger Y


    In real time: thrombin activation in vivo can be imaged in real time with ratiometric activatable cell penetrating peptides (RACPPs). RACPPs are designed to combine 1) dual-emission ratioing, 2) far red to infrared wavelengths for in vivo mammalian imaging, and 3) cleavage-dependent spatial localization. The most advanced RACPP uses norleucine (Nle)-TPRSFL as a linker that increases sensitivity to thrombin by about 90-fold.

  18. Trihydroxytrioxatriangulene - An Extended Fluorescein and a Ratiometric pH Sensor

    DEFF Research Database (Denmark)

    Westerlund, Fredrik; Hildebrandt, Christoffer Boli; Sørensen, Thomas Just


    Fluorescein ver. 2.0: A new, highly fluorescent, pH-sensitive trihydroxytrioxatriangulenium dye (H-TOTA) has been synthesised and characterised. The dye is closely related to fluorescein and may be considered to be a two-dimensional extended version. This new dye can exist in four different proto...... protonation states (see graphic) depending on the pH, and its use as a sensitive fluorescent ratiometric pH probe in a physiological buffer is demonstrated....

  19. Errors in confocal fluorescence ratiometric imaging microscopy due to chromatic aberration. (United States)

    Lin, Yuxiang; Gmitro, Arthur F


    Confocal fluorescence ratiometric imaging is an optical technique used to measure a variety of important biological parameters. A small amount of chromatic aberration in the microscope system can introduce a variation in the signal ratio dependent on the fluorophore concentration gradient along the optical axis and lead to bias in the measurement. We present a theoretical model of this effect. Experimental results and simulations clearly demonstrate that this error can be significant and should not be ignored.

  20. An FITC-BODIPY FRET couple: application to selective, ratiometric detection and bioimaging of cysteine. (United States)

    Ma, Dong Hee; Kim, Dokyoung; Akisawa, Takuya; Lee, Kyung-Ha; Kim, Kyong-Tai; Ahn, Kyo Han


    A novel FRET couple of fluorescein is disclosed, and it was readily constructed by conjugating an amino-BODIPY dye, a new FRET donor, with fluorescein isocyanate. Its potential was demonstrated by a fluorescence sensing system for cysteine, which was prepared by introducing acryloyl groups to the fluorescein moiety. The FRET probe exhibited promising ratiometric response to cysteine with high selectivity and sensitivity in a buffer solution containing acetonitrile at a physiological pH of 7.4, but showed slow reactivity. This slow response was solved by addition of a surfactant, thus allowing ratiometric imaging and determination of the endogenous level of cysteine in cells in HEPES buffer, by confocal fluorescence microscopy. Imaging experiments toward various cells suggested that such aryl acrylate type probes are vulnerable to the ubiquitous esterase activity. For the selected C6 cell line, in which the esterase activity was minimal, the ratiometric quantification of cysteine level was demonstrated. The FRET probe was also applied to determine the level of cysteine in human blood plasma.

  1. A novel, cell-permeable, fluorescent probe for ratiometric imaging of zinc ion. (United States)

    Maruyama, Satoko; Kikuchi, Kazuya; Hirano, Tomoya; Urano, Yasuteru; Nagano, Tetsuo


    Zn(2+) plays important roles in various biological systems; as a result, the development of tools that can visualize chelatable Zn(2+) has attracted much attention recently. We report here newly synthesized fluorescent sensors for Zn(2+), ZnAF-Rs, whose excitation maximum is shifted by Zn(2+) under physiological conditions. Thus, these sensors enable ratiometric imaging, which is a technique to reduce artifacts by minimizing the influence of extraneous factors on the fluorescence of a probe. Ratiometric measurement can provide precise data, and some probes allow quantitative detection. ZnAF-Rs are the first ratiometric fluorescent sensors for Zn(2+) that enable quantitative analysis under physiological conditions. ZnAF-Rs also possess suitable K(d) for applications, and high selectivity against other biologically relevant cations, especially Ca(2+). Using these probes, changes of intracellular Zn(2+) concentration in cultured cells were monitored successfully. We believe that these probes will be extremely useful in studies on the biological functions of Zn(2+).

  2. An effective colorimetric and ratiometric fluorescent probe for bisulfite in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Xi [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Zhang, Tao [Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100 (China); Du, Zhi-Fang; Cao, Xiang-Jian; Chen, Ming-Yu [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Taishan College, Shandong University, Jinan 250100 (China); Hu, Sheng-Wen [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Miao, Jun-Ying, E-mail: [Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100 (China); Zhao, Bao-Xiang, E-mail: [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)


    We have developed the first two-photon colorimetric and ratiometric fluorescent probe, BICO, for the detection of bisulfite (HSO{sub 3}{sup −}) in aqueous solution. The probe contains coumarin and benzimidazole moieties and can detect HSO{sub 3}{sup −} based on the Michael addition reaction with a limit of detection 5.3 × 10{sup −8} M in phosphate-buffered saline solution. The probe was used to detect bisulfite in tap water, sugar and dry white wine. Moreover, test strips were made and used easily. We successfully applied the probe to image living cells, using one-photon fluorescence imaging. BICO overcomes the limitations in sensitivity of previously reported probes and the solvation effect of bisulfite, which demonstrates its excellent value in practical application. - Highlights: • A colorimetric and ratiometric fluorescent probe was developed. • The probe could detect bisulfite in PBS buffer solution and real samples. • Bisulfite test paper was made to naked-eye detect bisulfite. • This probe successfully used to living cell imaging in ratiometric manner.

  3. Ratiometric fluorescence imaging of cellular polarity: decrease in mitochondrial polarity in cancer cells. (United States)

    Jiang, Na; Fan, Jiangli; Xu, Feng; Peng, Xiaojun; Mu, Huiying; Wang, Jingyun; Xiong, Xiaoqing


    Mitochondrial polarity strongly influences the intracellular transportation of proteins and interactions between biomacromolecules. The first fluorescent probe capable of the ratiometric imaging of mitochondrial polarity is reported. The probe, termed BOB, has two absorption maxima (λabs = 426 and 561 nm) and two emission maxima--a strong green emission (λem = 467 nm) and a weak red emission (642 nm in methanol)--when excited at 405 nm. However, only the green emission is markedly sensitive to polarity changes, thus providing a ratiometric fluorescence response with a good linear relationship in both extensive and narrow ranges of solution polarity. BOB possesses high specificity to mitochondria (Rr =0.96) that is independent of the mitochondrial membrane potential. The mitochondrial polarity in cancer cells was found to be lower than that of normal cells by ratiometric fluorescence imaging with BOB. The difference in mitochondrial polarity might be used to distinguish cancer cells from normal cells.

  4. Imaging of Fluoride Ion in Living Cells and Tissues with a Two-Photon Ratiometric Fluorescence Probe

    Directory of Open Access Journals (Sweden)

    Xinyue Zhu


    Full Text Available A reaction-based two-photon (TP ratiometric fluorescence probe Z2 has been developed and successfully applied to detect and image fluoride ion in living cells and tissues. The Z2 probe was designed designed to utilize an ICT mechanism between n-butylnaphthalimide as a fluorophore and tert-butyldiphenylsilane (TBDPS as a response group. Upon addition of fluoride ion, the Si-O bond in the Z2 would be cleaved, and then a stronger electron-donating group was released. The fluorescent changes at 450 and 540 nm, respectively, made it possible to achieve ratiometric fluorescence detection. The results indicated that the Z2 could ratiometrically detect and image fluoride ion in living cells and tissues in a depth of 250 μm by two-photon microscopy (TPM.

  5. Upconversion ratiometric fluorescence and colorimetric dual-readout assay for uric acid. (United States)

    Fang, Aijin; Wu, Qiongqiong; Lu, Qiujun; Chen, Hongyu; Li, Haitao; Liu, Meiling; Zhang, Youyu; Yao, Shouzhuo


    A new upconversion colorimetric and ratiometric fluorescence detection method for uric acid (UA) has been designed. Yb(3+), Er(3+) and Tm(3+) co-doped NaYF4 nanoparticles (UCNPs) was synthesized. The co-doped NaYF4 nanoparticles, emit upconversion fluorescence with four typical emission peaks centered at 490nm, 557nm, 670nm and 705nm under the 980nm near-infrared (NIR) irradiation. The ZnFe2O4 magnetic nanoparticles (MNPs) possessing excellent peroxidase-like activity was prepared and used to catalyze oxidation the coupling of N-ethyl-N-(3-sulfopropyl)-3-methylaniline sodium salt (TOPS) and 4-amino-antipyrine (4-AAP) in the presence of H2O2 to form purple products (compound 1) which has a characteristic absorption peak located at 550nm. The upconversion fluorescence at 557nm was quenched by the compound 1 while the upconversion emission at 705nm was essentially unchanged, the fluorescence ratio ((I557/I705)0/(I557/I705)) is positively proportional to UA concentration in existence of uricase. More importantly, colorimetric signal can be easily observed and applied to directly distinguish the concentration of UA by the naked eye. Under the optimized conditions, the linear range of colorimetric and ratiometric fluorescence sensing towards UA was 0.01-1mM, the detection limits were as low as 5.79μM and 2.86μM (S/N=3), respectively. The proposed method has been successfully applied to the analysis of UA in human serum. These results indicate that the colorimetric and ratiometric fluorescence dual-readout assay method has great potential for applications in physiological and pathological diagnosis.

  6. A Three-Photon Active Organic Fluorophore for Deep Tissue Ratiometric Imaging of Intracellular Divalent Zinc. (United States)

    Philips, Divya Susan; Sreejith, Sivaramapanicker; He, Tingchao; Menon, Nishanth Venugopal; Anees, Palapuravan; Mathew, Jomon; Sajikumar, Sreedharan; Kang, Yuejun; Stuparu, Mihaiela Corina; Sun, Handong; Zhao, Yanli; Ajayaghosh, Ayyappanpillai


    Deep tissue bioimaging with three-photon (3P) excitation using near-infrared (NIR) light in the second IR window (1.0-1.4 μm) could provide high resolution images with an improved signal-to-noise ratio. Herein, we report a photostable and nontoxic 3P excitable donor-π-acceptor system (GMP) having 3P cross-section (σ3 ) of 1.78×10(-80)  cm(6)  s(2)  photon(-2) and action cross-section (σ3 η3 ) of 2.31×10(-81)  cm(6)  s(2)  photon(-2) , which provides ratiometric fluorescence response with divalent zinc ions in aqueous conditions. The probe signals the Zn(2+) binding at 530 and 600 nm, respectively, upon 1150 nm excitation with enhanced σ3 of 1.85×10(-80)  cm(6)  s(2)  photon(-2) and σ3 η3 of 3.33×10(-81)  cm(6)  s(2)  photon(-2) . The application of this probe is demonstrated for ratiometric 3P imaging of Zn(2+) in vitro using HuH-7 cell lines. Furthermore, the Zn(2+) concentration in rat hippocampal slices was imaged at 1150 nm excitation after incubation with GMP, illustrating its potential as a 3P ratiometric probe for deep tissue Zn(2+) ion imaging.

  7. Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients (United States)

    Castelló Serrano, Iván; Stoica, Georgiana; Matas Adams, Alba; Palomares, Emilio


    We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for

  8. A Nanocrystal-based Ratiometric pH Sensor for Natural pH Ranges. (United States)

    Somers, Rebecca C; Lanning, Ryan M; Snee, Preston T; Greytak, Andrew B; Jain, Rakesh K; Bawendi, Moungi G; Nocera, Daniel G

    A ratiometric fluorescent pH sensor based on CdSe/CdZnS nanocrystal quantum dots (NCs) has been designed for biological pH ranges. The construct is formed from the conjugation of a pH dye (SNARF) to NCs coated with a poly(amido amine) (PAMAM) dendrimer. The sensor exhibits a well-resolved ratio response at pH values between 6 and 8 under linear or two-photon excitation, and in the presence of a 4% bovine serum albumin (BSA) solution.

  9. Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis. (United States)

    Kumar, Srividya; Verma, Taru; Mukherjee, Ria; Ariese, Freek; Somasundaram, Kumaravel; Umapathy, Siva


    Biomolecular structure elucidation is one of the major techniques for studying the basic processes of life. These processes get modulated, hindered or altered due to various causes like diseases, which is why biomolecular analysis and imaging play an important role in diagnosis, treatment prognosis and monitoring. Vibrational spectroscopy (IR and Raman), which is a molecular bond specific technique, can assist the researcher in chemical structure interpretation. Based on the combination with microscopy, vibrational microspectroscopy is currently emerging as an important tool for biomedical research, with a spatial resolution at the cellular and sub-cellular level. These techniques offer various advantages, enabling label-free, biomolecular fingerprinting in the native state. However, the complexity involved in deciphering the required information from a spectrum hampered their entry into the clinic. Today with the advent of automated algorithms, vibrational microspectroscopy excels in the field of spectropathology. However, researchers should be aware of how quantification based on absolute band intensities may be affected by instrumental parameters, sample thickness, water content, substrate backgrounds and other possible artefacts. In this review these practical issues and their effects on the quantification of biomolecules will be discussed in detail. In many cases ratiometric analysis can help to circumvent these problems and enable the quantitative study of biological samples, including ratiometric imaging in 1D, 2D and 3D. We provide an extensive overview from the recent scientific literature on IR and Raman band ratios used for studying biological systems and for disease diagnosis and treatment prognosis.

  10. A Two-Photon Ratiometric Fluorescent Probe for Imaging Carboxylesterase 2 in Living Cells and Tissues. (United States)

    Jin, Qiang; Feng, Lei; Wang, Dan-Dan; Dai, Zi-Ru; Wang, Ping; Zou, Li-Wei; Liu, Zhi-Hong; Wang, Jia-Yue; Yu, Yang; Ge, Guang-Bo; Cui, Jing-Nan; Yang, Ling


    In this study, a two-photon ratiometric fluorescent probe NCEN has been designed and developed for highly selective and sensitive sensing of human carboxylesterase 2 (hCE2) based on the catalytic properties and substrate preference of hCE2. Upon addition of hCE2, the probe could be readily hydrolyzed to release 4-amino-1,8-naphthalimide (NAH), which brings remarkable red-shift in fluorescence (90 nm) spectrum. The newly developed probe exhibits good specificity, ultrahigh sensitivity, and has been successfully applied to determine the real activities of hCE2 in complex biological samples such as cell and tissue preparations. NCEN has also been used for two-photon imaging of intracellular hCE2 in living cells as well as in deep-tissues for the first time, and the results showed that the probe exhibited high ratiometric imaging resolution and deep-tissue imaging depth. All these findings suggested that this probe holds great promise for applications in bioimaging of endogenous hCE2 in living cells and in exploring the biological functions of hCE2 in complex biological systems.

  11. A ratiometric nanosensor based on conjugated polyelectrolyte-stabilized AgNPs for ultrasensitive fluorescent and colorimetric sensing of melamine. (United States)

    Zhu, Xixi; Xiao, Yi; Jiang, Xiaoying; Li, Jiahui; Qin, Hongling; Huang, Hongmei; Zhang, Youyu; He, Xiaoxiao; Wang, Kemin


    A new ratiometric nanosensor is developed for selective and ultrasensitive detection of melamine based on conjugated polyelectrolyte (CPE)-stabilized silver nanoparticles (P1-AgNPs) by perfectly combining the advantages of CPE and AgNPs. P1 featuring a π-delocalized backbone bearing pyridinyl groups can act as an excellent dual-emission fluorescent probe as well as a polymer localizer for AgNPs. In the presence of melamine, the fluorescence intensity at 386nm increases owing to the turn-on of the fluorescence of P1, whereas FL intensity at 488nm decreases due to the melamine-induced aggregation and subsequent aggregation-enhanced emission quenching of P1-AgNPs, therefore leading to the ratiometric fluorescent sensing of analyte. Moreover, analyte-induced aggregation of P1-AgNPs also allows the ratiometric colorimetric measurement of melamine. Under the optimum conditions, this facile ratiometric nanosensor favors the fluorescent and colorimetric determination of melamine in liquid milk products with the detection limit as low as 0.1 and 0.45nM, respectively.

  12. A cyclization-induced emission enhancement (CIEE)-based ratiometric fluorogenic and chromogenic probe for the facile detection of a nerve agent simulant DCP. (United States)

    Mahapatra, Ajit Kumar; Maiti, Kalipada; Manna, Saikat Kumar; Maji, Rajkishor; Mondal, Sanchita; Das Mukhopadhyay, Chitrangada; Sahoo, Prithidipa; Mandal, Debasish


    The first ratiometric fluorescent probe for the detection of a nerve agent simulant was developed based on tandem phosphorylation and intramolecular cyclization, by which high sensitivity as well as large emission shift could be achieved.

  13. DNA-encapsulated silver nanodots as ratiometric luminescent probes for hypochlorite detection (United States)

    Park, Soonyoung; Choi, Sungmoon; Yu, Junhua


    DNA-encapsulated silver nanodots are noteworthy candidates for bio-imaging probes, thanks to their excellent photophysical properties. The spectral shift of silver nanodot emitters from red to blue shows excellent correlations with the concentration of reactive oxygen species, which makes it possible to develop new types of probes for reactive oxygen species (ROS), such as hypochlorous acid (HOCl), given the outstanding stability of the blue in oxidizing environments. HOCl plays a role as a microbicide in immune systems but, on the other hand, is regarded as a disease contributor. Moreover, it is a common ingredient in household cleaners. There are still great demands to detect HOCl fluxes and their physiological pathways. We introduce a new ratiometric luminescence imaging method based on silver nanodots to sensitively detect hypochlorite. The factors that influence the accuracy of the detection are investigated. Its availability has also been demonstrated by detecting the active component in cleaners.

  14. Fabrication strategies, sensing modes and analytical applications of ratiometric electrochemical biosensors. (United States)

    Jin, Hui; Gui, Rijun; Yu, Jianbo; Lv, Wei; Wang, Zonghua


    Previously developed electrochemical biosensors with single-electric signal output are probably affected by intrinsic and extrinsic factors. In contrast, the ratiometric electrochemical biosensors (RECBSs) with dual-electric signal outputs have an intrinsic built-in correction to the effects from system or background electric signals, and therefore exhibit a significant potential to improve the accuracy and sensitivity in electrochemical sensing applications. In this review, we systematically summarize the fabrication strategies, sensing modes and analytical applications of RECBSs. First, the different fabrication strategies of RECBSs were introduced, referring to the analytes-induced single- and dual-dependent electrochemical signal strategies for RECBSs. Second, the different sensing modes of RECBSs were illustrated, such as differential pulse voltammetry, square wave voltammetry, cyclic voltammetry, alternating current voltammetry, electrochemiluminescence, and so forth. Third, the analytical applications of RECBSs were discussed based on the types of target analytes. Finally, the forthcoming development and future prospects in the research field of RECBSs were also highlighted.

  15. Ratiometric FRET-based detection of DNA and micro-RNA in solution

    Energy Technology Data Exchange (ETDEWEB)

    Matveeva, Evgenia G., E-mail: ematveev@hsc.unt.ed [Center for Commercialization of Fluorescence Technologies, University of North Texas Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107 (United States); Gryczynski, Zygmunt [Center for Commercialization of Fluorescence Technologies, University of North Texas Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107 (United States); Stewart, Donald R. [Omm Scientific, Inc., 2600 N. Stemmons Freeway, Suite 129, Dallas, TX 75207 (United States); Gryczynski, Ignacy [Center for Commercialization of Fluorescence Technologies, University of North Texas Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107 (United States)


    A ratiometric method for detecting DNA oligomers in bulk solution based on Foerster resonance energy transfer (FRET) is described. The two fluorescence signals (green and red), originating from Cy3 (donor, green) and Cy5 (acceptor, red) labels, are simultaneously detected from the pre-hybridized Cy3oligomerY:Cy5oligomerX system. The ratio of red to green intensities is sensitive to the presence of the single-stranded complimentary oligomer, which replaces single-stranded Cy3oligomerY in the donor:acceptor complex and perturbs the FRET. The detection scheme is generally applicable to the detection of DNA and RNA, and particularly micro-RNA. The proposed method is applicable to various double-stranded various lengths targets (manipulation of the sample preparation conditions, such as temperature, incubation time, denaturizing agent, may be needed).

  16. Measurement of intracellular Ca2+ concentration in single cells using ratiometric calcium dyes. (United States)

    Srikanth, Sonal; Gwack, Yousang


    Measurement of intracellular Ca(2+) concentration ([Ca(2+)](i)) is useful to study the upstream and downstream events of Ca(2+) signaling. Ca(2+)-binding proteins including EF-hand-containing proteins are important downstream effector molecules after an increase of [Ca(2+)](i). Conversely, these proteins can also act as key modulators for regulation of [Ca(2+)](i) by sensing the Ca(2+) levels in the intracellular organelles and cytoplasm. Here we describe a single-cell Ca(2+) imaging technique that was used to measure the intracellular Ca(2+) levels to examine the function of Ca(2+)-binding proteins, STIM1 and Calcium release-activated Calcium channel regulator 2A (CRACR2A), using ratiometric Ca(2+) dye Fura-2 in adherent and non-adherent cells.

  17. Preparation of Gold-Carbon Dots and Ratiometric Fluorescence Cellular Imaging. (United States)

    Zhang, Lingyang; Wang, Donghui; Huang, Haowen; Liu, Lanfang; Zhou, Yuan; Xia, Xiaodong; Deng, Keqin; Liu, Xuanyong


    In this study, we synthesized novel gold-carbon dots (GCDs) with unique properties by microwave-assisted method. The characterization of high-resolution transmission electron microscope (HRTEM), XRD, high-angle annular dark field scanning transmission electron microscope (HAADF-STEM), and energy dispersive spectrometer demonstrates that GCDs are composed of carbon and Au. Tiny Au clusters are dispersed in a 2 nm-size carbon skeleton, which integrates the properties of typical CDs and gold nanoclusters (AuNCs), displaying fascinating peroxidase-like activity and single excitation/dual emission. Dual emission of the GCDs exhibits different fluorescent response to the target species and enables the GCDs to be exploited for sensing and bioimaging. The highly photostable and biocompatible GCDs were applied to dual fluorescent imaging for breast cancer cells and normal rat osteoblast cells under a single excitation. Moreover, ratiometric fluorescence imaging was used to monitor Fe(3+) level in normal rat osteoblast cells.

  18. New Azobenzene Dye Colorimetric and Ratiometric Chemosensors for Mercury(Ⅱ)Ion

    Institute of Scientific and Technical Information of China (English)

    GUO Min; XUE wei; GUAN Mingyun; SUN Jianhua; YIN Gui


    A new series of azobenzene dyes,which possessed colorimetric and ratiometric recognition to Hg2+ based on the mechanism of internal charge transfer(ICT),was developed and characterized.The molecules involving azo and imino functional groups can coordinate with Hg2+ to result in a large blue shift from 453 to 363 nm corresponding to a notable color change from orange to pale yellow in aqueous methanol solution(H2O/CH3OH = 1/4,V/V),which can be applied to naked eye detection of Hg2+.The sensitivity,selectivity and binding mode of the sensors to Hg2+ were investigated by UV-Vis spectroscopy.

  19. Dansyl-anthracene dyads for ratiometric fluorescence recognition of Cu2+. (United States)

    Kaur, Kuljit; Kumar, Subodh


    Dansyl-anthracene dyads 1 and 2 in CH(3)CN-H(2)O (7:3) selectively recognize Cu(2+) ions amongst alkali, alkaline earth and other heavy metal ions using both absorbance and fluorescence spectroscopy. In absorbance, the addition of Cu(2+) to the solution of dyads 1 or 2 results in appearance of broad absorption band from 200 nm to 725 nm for dyad 1 and from 200 nm to 520 nm for dyad 2. This is associated with color change from colorless to blue (for 1) and fluorescent green (for 2). This bathochromic shift of the spectrum could be assigned to internal charge transfer from sulfonamide nitrogen to anthracene moiety. In fluorescence, under similar conditions dyads 1 and 2 on addition of Cu(2+) selectively quench fluorescence due to dansyl moiety between 520-570 nm (for 1)/555-650 nm (for 2) with simultaneous fluorescence enhancement at 470 nm and 505 nm for dyads 1 and 2, respectively. Hence these dyads provide opportunity for ratiometric analysis of 1-50 μM Cu(2+). The other metal ions viz. Fe(3+), Co(2+), Ni(2+), Cd(2+), Zn(2+), Hg(2+), Ag(+), Pb(2+), Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ba(2+) do not interfere in the estimation of Cu(2+) except Cr(3+) in case of dyad 1. The coordination of dimethylamino group of dansyl unit with Cu(2+) causes quenching of fluorescence due to dansyl moiety between 520-600 nm and also restricts the photoinduced electron transfer from dimethylamino to anthracene moiety to release fluorescence between 450-510 nm. This simultaneous quenching and release of fluorescence respectively due to dansyl and anthracene moieties emulates into Cu(2+) induced ratiometric change.

  20. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe (United States)

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui


    Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0–7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.

  1. Ratiometric high-resolution imaging of JC-1 fluorescence reveals the subcellular heterogeneity of astrocytic mitochondria. (United States)

    Keil, Vera C; Funke, Frank; Zeug, Andre; Schild, Detlev; Müller, Michael


    Using the mitochondrial potential (ΔΨ(m)) marker JC-1 (5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine iodide) and high-resolution imaging, we functionally analyzed mitochondria in cultured rat hippocampal astrocytes. Ratiometric detection of JC-1 fluorescence identified mitochondria with high and low ΔΨ(m). Mitochondrial density was highest in the perinuclear region, whereas ΔΨ(m) tended to be higher in peripheral mitochondria. Spontaneous ΔΨ(m) fluctuations, representing episodes of increased energization, appeared in individual mitochondria or synchronized in mitochondrial clusters. They continued upon withdrawal of extracellular Ca(2+), but were antagonized by dantrolene or 2-aminoethoxydiphenylborate (2-APB). Fluo-3 imaging revealed local cytosolic Ca(2+) transients with similar kinetics that also were depressed by dantrolene and 2-APB. Massive cellular Ca(2+) load or metabolic impairment abolished ΔΨ(m) fluctuations, occasionally evoking heterogeneous mitochondrial depolarizations. The detected diversity and ΔΨ(m) heterogeneity of mitochondria confirms that even in less structurally polarized cells, such as astrocytes, specialized mitochondrial subpopulations coexist. We conclude that ΔΨ(m) fluctuations are an indication of mitochondrial viability and are triggered by local Ca(2+) release from the endoplasmic reticulum. This spatially confined organelle crosstalk contributes to the functional heterogeneity of mitochondria and may serve to adapt the metabolism of glial cells to the activity and metabolic demand of complex neuronal networks. The established ratiometric JC-1 imaging-especially combined with two-photon microscopy-enables quantitative functional analyses of individual mitochondria as well as the comparison of mitochondrial heterogeneity in different preparations and/or treatment conditions.

  2. A novel ratiometric fluorescent probe based on 1, 8-naphthalimide for the detection of Ho3 + and its bioimaging (United States)

    Zhang, Huifang; Liu, Tao; Yin, Caixia; Wen, Yin; Chao, Jianbin; Zhang, Yongbin; Huo, Fangjun


    A ratiometric fluorescent probe for the detection of Ho3 + in DMSO-aqueous medium was designed and synthesized based on 1, 8-naphthalimide. The probe displayed response to Ho3 + with a fluorescence decrease at 512 nm and enhancement at 480 nm, accompanying with a distinct fluorescence change from bright yellow-green to cyan. Besides, the probe exhibited a lower detection limit (6 × 10- 8 M) and could be used in intracellular fluorescence imaging. To the best of the knowledge, it was the first ratiometric fluorescent probe for Ho3 + detection. This probe was expected to be a useful tool for further elucidating the roles of Ho3 + in materials, biology and environment.

  3. A FRET-based ratiometric fluorescent and colorimetric probe for the facile detection of organophosphonate nerve agent mimic DCP. (United States)

    Xuan, Weimin; Cao, Yanting; Zhou, Jiahong; Wang, Wei


    A FRET ratiometric fluorescent probe enabling a fast and highly sensitive response to OP nerve agent mimic DCP within 1 min and with as low as 0.17 ppm concentration detection limit has been developed. Moreover, the probe exhibits noticeable color changes under UV light and even with the naked eye. It is also demonstrated that it can detect both liquid and gas nerve agents.

  4. A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids. (United States)

    Maity, Debabrata; Jiang, Juanjuan; Ehlers, Martin; Wu, Junchen; Schmuck, Carsten


    A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.

  5. Design of Modular DNA Triangular-Prism Sensor Enabling Ratiometric and Multiplexed Biomolecule Detection on Single Microbead. (United States)

    Liu, Yu; Chen, Qiaoshu; Liu, Jianbo; Yang, Xiaohai; Guo, Qiuping; Li, Li; Liu, Wei; Wang, Kemin


    DNA nanostructures have emerged as powerful and versatile building blocks for the construction of programmable nanoscale structures and functional sensors for biomarker detection, disease diagnostics and therapy. Here we integrated multiple sensing modules into a single DNA 3D nanoarchitecture with a triangular-prism (TP) structure for ratiometric and multiplexed biomolecule detection on single microbead. In our design, the complementary hybridization of three clip sequences formed TP nanoassemblies in which the six single-strand regions in the top and bottom faces act as binding sites for different sensing modules, including an anchor module, reference sequence module and capture sequence module. The multifunctional modular TP nanostructures were thus exploited for ratiometric and multiplexed biomolecule detection on microbeads. Microbead imaging demonstrated that after ratiometric self-calibration analysis, the imaging deviations resulting from uneven fluorescent intensity distribution and differing probe concentrations were greatly reduced. The rigid nanostructure also conferred the TP as a framework for geometric positioning of different capture sequences. The inclusion of multiple targets led to the formation of sandwich hybridization structures that gave a readily detectable optical response at different fluorescent channels and distinct fingerprint-like pattern arrays. This approach allowed us to discriminate multiplexed biomolecule targets in a simple and efficient fashion. In this module-designed strategy, the diversity of the controlled DNA assembly coupled with the geometrically well-defined rigid nanostructures of the TP assembly provides a flexible and reliable biosensing approach that shows great promise for biomedical applications.

  6. A tautomeric zinc sensor for ratiometric fluorescence imaging: application to nitric oxide-induced release of intracellular zinc. (United States)

    Chang, Christopher J; Jaworski, Jacek; Nolan, Elizabeth M; Sheng, Morgan; Lippard, Stephen J


    Zinc is an essential metal ion for human growth and development, the disruption of cellular Zn(2+) homeostasis being implicated in several major disorders including Alzheimer's disease, diabetes, and cancer. The molecular mechanisms of Zn(2+) physiology and pathology are insufficiently understood, however, owing in part to the lack of tools for measuring changes in intracellular Zn(2+) concentrations with high spatial and temporal fidelity. To address this critical need, we have synthesized, characterized, and applied an intracellular fluorescent probe for the ratiometric imaging of Zn(2+) based on a tautomeric seminaphthofluorescein platform. Zin-naphthopyr 1 (ZNP1) affords single-excitation, dual-emission ratiometric detection of intracellular Zn(2+) through Zn(2+)-controlled switching between fluorescein and naphthofluorescein tautomeric forms. The probe features visible excitation and emission profiles, excellent selectivity responses for Zn(2+) over competing Ca(2+) and Mg(2+) ions at intracellular concentrations, a dissociation constant (K(d)) for Zn(2+) of zinc binding. We demonstrate the value of the ZNP1 platform for biological applications by imaging changes in intracellular [Zn(2+)] in living mammalian cells. Included is the ratiometric detection of endogenous pools of intracellular Zn(2+) after NO-induced release of Zn(2+) from cellular metalloproteins. We anticipate that ZNP1 and related probes should find utility for interrogating the biology of Zn(2+).

  7. A general strategy to facilely design ratiometric electrochemical sensors in electrolyte solution by directly using a bare electrode for dual-signal sensing of analytes. (United States)

    Yu, Jianbo; Jin, Hui; Gui, Rijun; Wang, Zonghua; Ge, Feng


    In this paper, we have described a general strategy to facilely design ratiometric electrochemical sensors in electrolyte solutions, directly using a bare electrode for dual-signal sensing of analytes. Two types of substances (methylene blue/MB, doxorubicin/DOX) with different electrochemical signal peaks were added into electrolyte solutions (phosphate buffered saline, NaCl), where one was the analyte (DOX) and the other was used as a reference (MB). A linear plotting of DOX concentration [DOX] versus ratiometric electrochemical signal peak intensity (IDOX/IMB) was achieved, with a good linear coefficient and low detection limit of DOX (0.4nM). Experimental results implied that this ratiometric electrochemical sensor (ECS) of DOX enabled highly selective and sensitive detection of DOX in real samples, with high detection recoveries. In comparison with previous reports about ratiometric ECS, this as-proposed strategy can directly fabricate a ratiometric ECS in electrolyte solution (not on electrode), only using a bare electrode for dual- signal sensing of analytes. This strategy is not only novel and facile, but also flexible and general, as adequately confirmed in experiments, which would facilitate a further development in the facile fabrication and efficient applications of electrochemical sensors.

  8. A selective colorimetric and ratiometric fluorescent chemosensor for detection of Al{sup 3+} ion

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Pei-Ju; Chir, Jiun-Ly; Ting, Wei; Wu, An-Tai, E-mail:


    A simple Schiff-base fluorescent receptor 1 was synthesized in an one step procedure. Receptor 1 displayed a selective colorimetric change (from light yellow to light green) and high ratiometric signals upon binding to Al{sup 3+} in EtOH solution. The association constant for 1–Al{sup 3+} in EtOH was determined as 2.08×10{sup 6} M{sup −2} and the detection limit for Al{sup 3+} was determined as 5.21×10{sup −7} M. The detection limit was sufficiently low to detect submicromolar concentration of the Al{sup 3+}. - Highlights: • A new Al{sup 3+} receptor can be easily prepared. • The receptor exhibits an “off-on-type” mode with high selectivity in the presence of Al{sup 3+}. • Receptor 1 could serve as selective and efficient colorimetric sensor for the detection of Al{sup 3+} by naked eye method.

  9. Optical tweezers and non-ratiometric fluorescent-dye-based studies of respiration in sperm mitochondria (United States)

    Chen, Timothy; Shi, Linda Z.; Zhu, Qingyuan; Chandsawangbhuwana, Charlie; Berns, Michael W.


    The purpose of this study is to investigate how the mitochondrial membrane potential affects sperm motility using laser tweezers and a non-ratiometric fluorescent probe, DiOC6(3). A 1064 nm Nd:YVO4 continuous wave laser was used to trap motile sperm at a power of 450 mW in the trap spot. Using customized tracking software, the curvilinear velocity (VCL) and the escape force from the laser tweezers were measured. Human (Homo sapiens), dog (Canis lupis familiaris) and drill (Mandrillus leucophaeus) sperm were treated with DiOC6(3) to measure the membrane potential in the mitochondria-rich sperm midpieces. Sperm from all three species exhibited an increase in fluorescence when treated with the DiOC6(3). When a cyanide inhibitor (CCCP) of aerobic respiration was applied, sperm of all three species exhibited a reduction in fluorescence to pre-dye levels. With respect to VCL and escape force, the CCCP had no effect on dog or human sperm, suggesting a major reliance upon anaerobic respiration (glycolysis) for ATP in these two species. Based on the preliminary study on drill sperm, CCCP caused a drop in the VCL, suggesting potential reliance on both glycolysis and aerobic respiration for motility. The results demonstrate that optical trapping in combination with DiOC6(3) is an effective way to study sperm motility and energetics.

  10. Quadruple labelled dual oxygen and pH-sensitive ratiometric nanosensors

    Directory of Open Access Journals (Sweden)

    Veeren M. Chauhan


    Full Text Available Nanosensors capable of simultaneously measuring dissolved oxygen concentrations from 0 to 100% saturation and pH over the full physiological range, from pH 3.5 to 7.5, that advance the methods towards understanding of key biological gradients, were synthesised. A library of water soluble oxygen-sensitive porphyrins, with three substituted charged functional groups and a chemically flexible carboxylate functional group were spectroscopically analysed to assess their sensitivity to changes in dissolved oxygen concentrations as free species in solution and in suspension as nanoparticle conjugates. A platinum cationic porphyrin was taken forward to fabricate ratiometric oxygen-sensitive nanosensors, using 5-(and-6-carboxytetramethylrhodamine (TAMRA as internal standard. In addition, quadruple labelled dual oxygen and pH-sensitive nanosensors were synthesised using the cationic Pt porphyrin, pH-sensitive fluorescein dyes, carboxyfluorescein (FAM and Oregon Green (OG, in a 1:1 ratio, and TAMRA. We envisage the dual oxygen and pH nanosensors will find broad utility in the characterisation of diverse microenvironments, where there are complex interactions between molecular oxygen and pH.

  11. Dual wavelength fluorescent ratiometric pH measurement by scanning near-field optical microscopy (United States)

    Li, Yongbo; Shinohara, Ryosuke; Iwami, Kentaro; Ohta, Yoshihiro; Umeda, Norihiro


    A novel method to observe pH distribution by dual wavelength fluorescent ratiometric pH measurement by scanning near-field optical microscopy (SNOM) is developed. In this method, in order to investigate not only the pH of mitochondrial membrane but also its distribution in the vicinity, a pH sensitive fluorescent reagent covers mitochondria instead of injecting it to mitochondria. This method utilizes a dual-emission pH sensitive dye and SNOM with a themally-pulled and metal-coated optical fiber to improve the spatial resolution. Time-dependence of Fluorescent intensity ratio (FIR) under acid addition is investigated. As the distances between the dropped point and the SNOM probe becomes closer, the time when FIR changes becomes earlier. The response of mitochondria under supplement of nutrition is studied by using this method. While the probe is near to mitochondria, the ratio quickly becomes to increase. In conclusion, it was confirmed that the temporal variation of pH can be detected by this method, and pH distribution in the vicinity of mitochondria is able to be measured by this method.

  12. Polycation-induced benzoperylene probe excimer formation and the ratiometric detection of heparin and heparinase. (United States)

    Yang, Meiding; Chen, Jian; Zhou, Huipeng; Li, Wenying; Wang, Yan; Li, Juanmin; Zhang, Cuiyun; Zhou, Chuibei; Yu, Cong


    A benzoperylene probe excimer emission in an aqueous buffer solution is observed for the first time, and a novel ratiometric fluorescence method based on the probe excimer emission for the sensitive detection of heparin and heparinase is demonstrated. A negatively charged benzoperylene derivative, 6-(benzo[ghi]perylene-1,2-dicarboxylic imide-yl)hexanoic acid (BPDI), was employed. A polycation, poly(diallyldimethylammonium) chloride (poly-DDA), could induce aggregation of BPDI through noncovalent interactions. A decrease of BPDI monomer emission and a simultaneous increase of BPDI excimer emission were observed. Upon the addition of heparin, the strong binding between heparin and poly-DDA caused release of BPDI monomer molecules, and an excimer-monomer emission signal transition was detected. However, after the enzymatic hydrolysis of heparin by heparinase, heparin was hydrolyzed into small fragments, which weakened the competitive binding of heparin to poly-DDA. Poly-DDA induced aggregation of BPDI, and a monomer-excimer emission signal transition was detected. Our assay is simple, rapid, inexpensive, sensitive and selective, which could facilitate the heparin and heparinase related biochemical and biomedical research.

  13. A novel, rapid method to quantify intraplatelet calcium dynamics by ratiometric flow cytometry.

    Directory of Open Access Journals (Sweden)

    Alice Assinger

    Full Text Available Cytosolic free calcium ions represent important second-messengers in platelets. Therefore, quantitative measurement of intraplatelet calcium provides a popular and very sensitive tool to evaluate platelet activation and reactivity. Current protocols for determination of intracellular calcium concentrations in platelets have a number of limitations. Cuvette-based methods do not allow measurement of calcium flux in complex systems, such as whole blood, and therefore require isolation steps that potentially interfere with platelet activation. Flow cytometry has the potential to overcome this limitation, but to date the application of calibrated, quantitative readout of calcium kinetics has only been described for Indo-1. As excitation of Indo-1 requires a laser in the ultraviolet range, such measurements cannot be performed with a standard flow cytometer. Here, we describe a novel, rapid calibration method for ratiometric calcium measurement in platelets using both Ar(+-laser excited fluorescence dyes Fluo-4 and Fura Red. We provide appropriate equations that allow rapid quantification of intraplatelet calcium fluxes by measurement of only two standardisation buffers. We demonstrate that this method allows quantitative calcium measurement in platelet rich plasma as well as in whole blood. Further, we show that this method prevents artefacts due to platelet aggregate formation and is therefore an ideal tool to determine basal and agonist induced calcium kinetics.

  14. Colorimetric sensing of anions in water using ratiometric indicator-displacement assay. (United States)

    Feng, Liang; Li, Hui; Li, Xiao; Chen, Liang; Shen, Zheng; Guan, Yafeng


    The analysis of anions in water presents a difficult challenge due to their low charge-to-radius ratio, and the ability to discriminate among similar anions often remains problematic. The use of a 3×6 ratiometric indicator-displacement assay (RIDA) array for the colorimetric detection and identification of ten anions in water is reported. The sensor array consists of different combinations of colorimetric indicators and metal cations. The colorimetric indicators chelate with metal cations, forming the color changes. Upon the addition of anions, anions compete with the indicator ligands according to solubility product constants (K(sp)). The indicator-metal chelate compound changes color back dramatically when the competition of anions wins. The color changes of the RIDA array were used as a digital representation of the array response and analyzed with standard statistical methods, including principal component analysis and hierarchical clustering analysis. No confusion or errors in classification by hierarchical clustering analysis were observed in 44 trials. The limit of detection was calculated approximately, and most limits of detections of anions are well below μM level using our RIDA array. The pH effect, temperature influence, interfering anions were also investigated, and the RIDA array shows the feasibility of real sample testing.

  15. A fluorescence ratiometric sensor for hypochlorite based on a novel dual-fluorophore response approach. (United States)

    Long, Lingliang; Zhang, Dongdong; Li, Xiufen; Zhang, Jinfang; Zhang, Chi; Zhou, Liping


    A fluorescence ratiometric sensor for OCl(-) has been developed based on a novel dual fluorophore response approach. The sensor molecule contains a coumarin fluorophore and a rhodamine fluorophore, and the two fluorophores are directly linked to an OCl(-) recognition group. The structure of the sensor was characterized by ESI-MS, NMR, and X-ray crystallographic analysis. Upon treatment with OCl(-), both fluorophores in the sensor responded simultaneously at two separate optical windows, with large enhancement of the fluorescence ratio (I578/I501) from 0.01 to 39.55. The fluorescence ratios for the sensor showed a good linearity with the concentration of OCl(-) in the range of 0.2-40 μM and the detection limits is 0.024 μM (SN(-1)=3). Investigation of reaction products indicated that the sensor reaction with OCl(-) produced two new fluorescent molecules, which were responsible for the fluorescence changes in two optical windows. In addition, the sensor showed high selectivity to OCl(-) over other reactive oxygen species, reactive nitrogen species, cations, and anions. The sensor has also been successfully applied to detection of OCl(-) in natural water samples with satisfactory recovery.

  16. Laser Induced Dual Fluorescence Ratiometric Technique for Mixing Characterization in Microfluidic Systems (United States)

    Bedding, David; Hidrovo, Carlso


    Increasing the rate of mixing within microfluidic systems is vitally important in understanding biological and chemical reaction kinetics and mechanisms. The small length scales characteristic of these systems which translate into highly viscous, Stokes flows result in mixing that is primarily dominated by diffusion. In order to counteract this, an approach that utilizes inertial droplet collisions to promote chaotic advection between two mixing species has been developed. A Laser-Induced Dual Fluorescence (LIDF) system in conjunction with a high-speed camera and appropriate optics are used to capture two intensity fields providing information about the mixing process as well as the excitation intensity field over the volume of interest. The rate of mixing for the coalescing droplets was quantified by taking the standard deviation of the first intensity field over time, while the second intensity field provides information about the intensity field. A ratiometric imaging approach allows removal of mixing fluorescence signal noise in the form of variation in excitation intensity, primarily from the lasing patterns and lensing effects within the interrogation volume. NSF CAREER Award Grant CBET - 1151091.

  17. Ratiometric Imaging of Extracellular pH in Dental Biofilms Using C-SNARF-4

    DEFF Research Database (Denmark)

    Dige, Irene

    H-sensitive ratiometric dye and as a bacterial stain. We tested the method on natural 48-h in-situ-grown dental biofilms from two individuals. Four biofilms per person were collected on standardized glass slabs mounted in intra-oral appliances. Digital image analysis was employed to remove the bacterial biomass from...... the microscopic images in order to exclusively determine extracellular pH. We monitored the pH drop at the biofilm-substratum interface in six microscopic fields of view per biofilm for 1h after exposure to 0.4% glucose. Results: Extracellular pH dropped rapidly in all specimens. In both individuals, analysis...... with C-SNARF-4 and digital image analysis allows monitoring of extracellular pH in in-situ biofilms without destroying the complex three-dimensional biofilm architecture. Within the limitations of this study using young biofilms and only two individuals the data suggest that biofilm pH differs more...

  18. Peptide-based, two-fluorophore, ratiometric probe for quantifying mobile zinc in biological solutions. (United States)

    Zhang, Daniel Y; Azrad, Maria; Demark-Wahnefried, Wendy; Frederickson, Christopher J; Lippard, Stephen J; Radford, Robert J


    Small-molecule fluorescent sensors are versatile agents for detecting mobile zinc in biology. Capitalizing on the abundance of validated mobile zinc probes, we devised a strategy for repurposing existing intensity-based sensors for quantitative applications. Using solid-phase peptide synthesis, we conjugated a zinc-sensitive Zinpyr-1 derivative and a zinc-insensitive 7-hydroxycoumarin derivative onto opposite ends of a rigid P9K peptide scaffold to create HcZ9, a ratiometric fluorescent probe for mobile zinc. A plate reader-based assay using HcZ9 was developed, the accuracy of which is comparable to that of atomic absorption spectroscopy. We investigated zinc accumulation in prostatic cells and zinc levels in human seminal fluid. When normal and tumorigenic cells are bathed in zinc-enriched media, cellular mobile zinc is buffered and changes slightly, but total zinc levels increase significantly. Quantification of mobile and total zinc levels in human seminal plasma revealed that the two are positively correlated with a Pearson's coefficient of 0.73.

  19. A ratiometric fluorescence probe for selective visual sensing of Zn2+. (United States)

    Ajayaghosh, Ayyappanpillai; Carol, Priya; Sreejith, Sivaramapanicker


    A simple ratiometric fluorescence probe based on vinylpyrrole end-capped bipyridine for the visual sensing of Zn2+ under aqueous physiological pH (6.8-7.4) is described. The fluorophores 3a-c showed strong emission around 537 nm in acetonitrile with a quantum yield of 0.4. In buffered (HEPES, pH 7.2) acetonitrile-water mixture (9:1 v/v), titration of transition metal salts to 3c showed strong quenching of the emission at 547 nm except in the case of Zn2+, which resulted in a red-shifted emission at 637 nm. Alkali and alkaline earth metal salts could not induce any considerable changes to the emission behavior of 3a-c. The binding of Zn2+ was highly selective in the presence of a variety of other metal ions. Though Cu2+ quenches the emission of 3c, in the presence of Zn2+, a red emission prevails, indicating the preference of 3c toward Zn2+. Job plot and Benesi-Hildebrand analysis revealed a 1:1 complexation between the probe and the metal ion. The selective visual sensing of Zn2+ with a red emission is ideally suited for the imaging of biological specimens.

  20. UV-Vis Ratiometric Resonance Synchronous Spectroscopy for Determination of Nanoparticle and Molecular Optical Cross Sections. (United States)

    Nettles, Charles B; Zhou, Yadong; Zou, Shengli; Zhang, Dongmao


    Demonstrated herein is a UV-vis Ratiometric Resonance Synchronous Spectroscopic (R2S2, pronounced as "R-two-S-two" for simplicity) technique where the R2S2 spectrum is obtained by dividing the resonance synchronous spectrum of a NP-containing solution by the solvent resonance synchronous spectrum. Combined with conventional UV-vis measurements, this R2S2 method enables experimental quantification of the absolute optical cross sections for a wide range of molecular and nanoparticle (NP) materials that range optically from pure photon absorbers or scatterers to simultaneous photon absorbers and scatterers, simultaneous photon absorbers and emitters, and all the way to simultaneous photon absorbers, scatterers, and emitters in the UV-vis wavelength region. Example applications of this R2S2 method were demonstrated for quantifying the Rayleigh scattering cross sections of solvents including water and toluene, absorption and resonance light scattering cross sections for plasmonic gold nanoparticles, and absorption, scattering, and on-resonance fluorescence cross sections for semiconductor quantum dots (Qdots). On-resonance fluorescence quantum yields were quantified for the model molecular fluorophore Eosin Y and fluorescent Qdots CdSe and CdSe/ZnS. The insights and methodology presented in this work should be of broad significance in physical and biological science research that involves photon/matter interactions.

  1. Chemosensitivity assay in mice prostate tumor: Preliminary report of flow cytometry, DNA fragmentation, ion ratiometric methods of anti-neoplastic drug monitoring

    Directory of Open Access Journals (Sweden)

    Kline Richard


    Full Text Available Abstract Flow cytometry, DNA fragmentation, ion ratiomateric analysis and NMR peaks characterized drug chemosensitivity of antineoplastic drugs. Hypotheses were: 1. The chemosensitive effect of different cancer cell lines is characteristic; 2. DNA fragmentation, ion ratiometric analysis suggest apoptosis status of tumor cells. Methods PC-3 cell lines were compared with DU-145, LNCaP cell lines in culture for the [Na]i and [Ca]i ion sensing dyes, cell death, NMR peaks and apoptosis staining for chemotherapeutic action of different drugs. Results DNA fragmentation, ratiometric ions and fluorescence endlabelling plots were characteristic for cell lines and drug response. 31P-23Na NMR spectra showed characteristic high phospho-choline and sodium peaks. Conclusion Flow cytometry, DNA fragmentation, ion ratiometric methods and NMR peaks indicated apoptosis and offered in vivo drug monitoring method.

  2. Dual-Modal Colorimetric/Fluorescence Molecular Probe for Ratiometric Sensing of pH and Its Application. (United States)

    Wu, Luling; Li, Xiaolin; Huang, Chusen; Jia, Nengqin


    As traditional pH meters cannot work well for minute regions (such as subcellular organelles) and in harsh media, molecular pH-sensitive devices for monitoring pH changes in diverse local heterogeneous environments are urgently needed. Here, we report a new dual-modal colorimetric/fluorescence merocyanine-based molecular probe (CPH) for ratiometric sensing of pH. Compared with previously reported pH probes, CPH bearing the benzyl group at the nitrogen position of the indolium group and the phenol, which is used as the acceptor for proton, could respond to pH changes immediately through both the ratiometric fluorescence signal readout and naked-eye colorimetric observation. The sensing process was highly stable and reversible. Most importantly, the suitable pKa value (6.44) allows CPH to presumably accumulate in lysosomes and become a lysosome-target fluorescent probe. By using CPH, the intralysosomal pH fluctuation stimulated by antimalaria drug chloroquine was successfully tracked in live cells through the ratiometric fluorescence images. Additionally, CPH could be immobilized on test papers, which exhibited a rapid and reversible colorimetric response to acid/base vapor through the naked-eye colorimetric analysis. This proof-of-concept study presents the potential application of CPH as a molecular tool for monitoring intralysosomal pH fluctuation in live cells, as well as paves the way for developing the economic, reusable, and fast-response optical pH meters for colorimetric sensing acid/base vapor with direct naked-eye observation.

  3. FITC Doped Rattle-Type Silica Colloidal Particle-Based Ratiometric Fluorescent Sensor for Biosensing and Imaging of Superoxide Anion. (United States)

    Zhou, Ying; Ding, Jie; Liang, Tingxizi; Abdel-Halim, E S; Jiang, Liping; Zhu, Jun-Jie


    Fluorescent nanosensors have been widely applied in recognition and imaging of bioactive small molecules; however, the complicated surface modification process and background interference limit their applications in practical biological samples. Here, a simple, universal method was developed for ratiometric fluorescent determination of general small molecules. Taking superoxide anion (O2(•-)) as an example, the designed sensor was composed of three main moieties: probe carrier, rattle-type silica colloidal particles (mSiO2@hmSiO2 NPs); reference fluorophore doped into the core of NPs, fluorescein isothiocyanate (FITC); fluorescent probe for superoxide anion, hydroethidine (HE). In the absence of O2(•-), the sensor just emitted green fluorescence of FITC at 518 nm. When released HE was oxidized by O2(•-), the oxidation product exhibited red fluorescence at 570 nm and the intensity was linearly associated with the concentration of O2(•-), while that of reference element remained constant. Accordingly, ratiometric determination of O2(•-) was sensitively and selectively achieved with a linear range of 0.2-20 μM, and the detection limit was calculated as low as 80 nM. Besides, the technique was also successfully applied for dual-emission imaging of O2(•-) in live cells and realized visual recognition with obvious fluorescence color change in normal conditions or under oxidative stress. As long as appropriate reference dyes and sensing probes are selected, ratiometric biosensing and imaging of bioactive small molecules would be achieved. Therefore, the design could provide a simple, accurate, universal platform for biological applications.

  4. Genetically encoded fluorescent coumarin amino acids (United States)

    Wang, Jiangyun; Xie, Jianming; Schultz, Peter G.


    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl) ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  5. Genetically encoded fluorescent coumarin amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jiangyun [San Diego, CA; Xie, Jianming [San Diego, CA; Schultz, Peter G [La Jolla, CA


    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  6. Magnetic core-shell fluorescent pH ratiometric nanosensor using a Stoeber coating method

    Energy Technology Data Exchange (ETDEWEB)

    Lapresta-Fernandez, A., E-mail: [Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Lessingstrasse 10, 07743 Jena (Germany); Instituto de Ciencia de Materiales de Sevilla, centro mixto CSIC-Univ. Sevilla, Avda. Americo Vespucio 49, 41092 Sevilla (Spain); Doussineau, T. [Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Lessingstrasse 10, 07743 Jena (Germany); Universite Lyon 1, CNRS, UMR 5579, LASIM, F-69622 Villeurbanne (France); Moro, A.J. [Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Lessingstrasse 10, 07743 Jena (Germany); REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Dutz, S. [Institute of Photonic Technology, Department of Nano Biophotonics, Jena (Germany); Steiniger, F. [Center for Electron Microscopy of the Medical Faculty, Jena (Germany); Mohr, G.J. [Fraunhofer Research Institution for Modular Solid State Technologies, Department of Polytronic Systems, Workgroup Sensor Materials, Josef-Engert-Strasse 13, D-93053 Regensburg (Germany)


    Highlights: Black-Right-Pointing-Pointer Architecture combination of magnetic core with two fluorescence silica shells. Black-Right-Pointing-Pointer Both shells properly functionalized which develops ratiometric pH measurements. Black-Right-Pointing-Pointer Reference dye does not change significantly ({approx}1.9%) by modifying the pH. Black-Right-Pointing-Pointer Sensitivity range between 2.0% and 4.9% and a few seconds of response time. Black-Right-Pointing-Pointer One month stability with a signal variation of 4.3%. - Abstract: We describe the use of a modified Stoeber method for coating maghemite ({gamma}-Fe{sub 2}O{sub 3}) nanocrystals with silica shells in order to built magnetic fluorescent sensor nanoparticles in the 50-70 nm diameter range. In detail, the magnetic cores were coated by two successive silica shells embedding two fluorophores (two different silylated dye derivatives), which allows for ratiometric pH-measurements in the pH range 5-8. Silica coated magnetic nanoparticles were prepared using maghemite nanocrystals as cores (5-10 nm in diameter) coated by tetraethoxyorthosilicate via hydrolysis/condensation in ethanol, catalyzed by ammonia. In the inner shell was covalently attached a sulforhodamine B, which was used as a reference dye; while a pH-sensitive fluorescein was incorporated into the outer shell. Once synthesized, the particles were characterized in terms of morphology, size, composition and magnetization, using dynamic light scattering (DLS), transmission electron microscopy (TEM), X-ray diffraction (XRD) and vibrating sample magnetometry (VSM). TEM analysis showed the nanoparticles to be very uniform in size. Wide-angle X-ray diffractograms showed, for uncoated as well as coated nanoparticles, typical peaks for the spinel structure of maghemite at the same diffraction angle, with no structural changes after coating. When using VSM, we obtained the magnetization curves of the resulting nanoparticles and the typical magnetization

  7. Magnetic and fluorescent core-shell nanoparticles for ratiometric pH sensing. (United States)

    Lapresta-Fernández, Alejandro; Doussineau, Tristan; Dutz, Silvio; Steiniger, Frank; Moro, Artur J; Mohr, Gerhard J


    This paper describes the preparation of nanoparticles composed of a magnetic core surrounded by two successive silica shells embedding two fluorophores, showing uniform nanoparticle size (50-60 nm in diameter) and shape, which allow ratiometric pH measurements in the pH range 5-8. Uncoated iron oxide magnetic nanoparticles (∼10 nm in diameter) were formed by the coprecipitation reaction of ferrous and ferric salts. Then, they were added to a water-in-oil microemulsion where the hydrophilic silica shells were obtained through hydrolysis and condensation of tetraethoxyorthosilicate together with the corresponding silylated dye derivatives-a sulforhodamine was embedded in the inner silica shell and used as the reference dye while a pH-sensitive fluorescein was incorporated in the outer shell as the pH indicator. The magnetic nanoparticles were characterized using vibrating sample magnetometry, dynamic light scattering, transmission electron microscopy, x-ray diffraction and Fourier transform infrared spectroscopy. The relationship between the analytical parameter, that is, the ratio of fluorescence between the sensing and reference dyes versus the pH was adjusted to a sigmoidal fit using a Boltzmann type equation giving an apparent pK(a) value of 6.8. The fluorescence intensity of the reference dye did not change significantly (∼3.0%) on modifying the pH of the nanoparticle dispersion. Finally, the proposed method was statistically validated against a reference procedure using samples of water and physiological buffer with 2% of horse serum, indicating that there are no significant statistical differences at a 95% confidence level.

  8. Magnetically assisted fluorescence ratiometric assays for adenosine deaminase using water-soluble conjusated polymers

    Institute of Scientific and Technical Information of China (English)

    HE Fang; YU MingHui; WANG Shu


    A magnetically assisted fluorescence ratiometric technique has been developed for adenosine deami-nase assays with high sensitivity using water-soluble cationic conjugated polymers (CCPs).The assay contains three elements:a biotin-labeled aptamer of adenosine (biotin-aptamer),a signaling probe single-stranded DNA-tagged fiuorescein at terminus (ssDNA-FI) and a CCP.The specific binding of adenosine to biotin-aptamer makes biotin-aptamer and ssDNA-FI unhybridized,and the ssDNA-FI is washed out after streptavidin-coated magnetic beads are added and separated from the assay solution under magnetic field.In this case,after the addition of CCP to the magnetic beads solution,the fluo-rescence resonance energy transfer (FRET) from CCP to fluorescein is inefficient.Upon adding adenosine deaminase,the adenosine is converted into inosine,and the biotin-aptamer is hybridized with ssDNA-FI to form doubled stranded DNA (biotin-dsDNA-FI).The ssONA-FI is attached to the mag-netic beads at the separation step,and the addition of CCP to the magnetic beads solution leads to efficient FRET from CCP to fluorescein.Thus the adenosine deaminase activity can be monitored by fluorescence spectra in view of the intensity decrease of CCP emission or the increase of fluorescein emission in aqueous solutions.The assay integrates surface-functionalized magnetic particles with significant amplification of detection signal of water-soluble cationic conjugated polymers.

  9. Low-Cost Ratiometric Front-End for Industrial PRT Applications (United States)

    Smorgon, D.; Fernicola, V. C.; Coslovi, L.


    Cost, size, speed, and measurement range limitations make the resistance bridge not always suitable for temperature measurements with platinum resistance thermometers (PRTs) in industrial applications. However, high-accuracy resistance thermometer systems are often needed in many industrial applications, where measurement performances comparable to resistance bridges are often needed at a lower cost and size. A tiny, portable, ratiometric front-end exploiting a 24-bit analog-to-digital converter (ADC) with Σ Δ modulator is described. It was designed to measure the resistance ratio between a 100 Ω industrial PRT (IPRT) and a reference resistor with repeatability to within a few parts in 106. Its small size makes it ideal for integration in the stem-handle assembly of a thermometric probe, enabling an early transmission of measurement data in digital form. The ADC-based system design, development, and performance testing are discussed. The system was investigated in the resistance ratio range from about 4 × 10-3 to 5 × 10-2. Furthermore, a comparison between the system performance and a commercial AC resistance bridge was carried out and the results reported in this paper. An accurate thermometer for industrial applications resulted from the above developments. The compactness of the devices enabled an implementation of the `smart sensor' concept in the measurement chain, where the front-end electronics was placed inside the IPRT handle together with an integrated memory to hold device identification, calibration coefficients, and the associated uncertainty. All data are transmitted to the readout module and are available to the user at a 5 Hz update rate for further analysis.

  10. Magnetic and fluorescent core-shell nanoparticles for ratiometric pH sensing

    Energy Technology Data Exchange (ETDEWEB)

    Lapresta-Fernandez, Alejandro; Doussineau, Tristan; Moro, Artur J [Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Lessingstrasse 10, 07743 Jena (Germany); Dutz, Silvio [Institute of Photonic Technology, Department of Nano-Biophotonics, Jena (Germany); Steiniger, Frank [Centre for Electron Microscopy of the Medical Faculty, Jena (Germany); Mohr, Gerhard J, E-mail: [Fraunhofer Research Institution for Modular Solid State Technologies, Department of Polytronic Systems, Workgroup Sensor Materials, Josef-Engert-Strasse 9, D-93053 Regensburg (Germany)


    This paper describes the preparation of nanoparticles composed of a magnetic core surrounded by two successive silica shells embedding two fluorophores, showing uniform nanoparticle size (50-60 nm in diameter) and shape, which allow ratiometric pH measurements in the pH range 5-8. Uncoated iron oxide magnetic nanoparticles ({approx}10 nm in diameter) were formed by the coprecipitation reaction of ferrous and ferric salts. Then, they were added to a water-in-oil microemulsion where the hydrophilic silica shells were obtained through hydrolysis and condensation of tetraethoxyorthosilicate together with the corresponding silylated dye derivatives-a sulforhodamine was embedded in the inner silica shell and used as the reference dye while a pH-sensitive fluorescein was incorporated in the outer shell as the pH indicator. The magnetic nanoparticles were characterized using vibrating sample magnetometry, dynamic light scattering, transmission electron microscopy, x-ray diffraction and Fourier transform infrared spectroscopy. The relationship between the analytical parameter, that is, the ratio of fluorescence between the sensing and reference dyes versus the pH was adjusted to a sigmoidal fit using a Boltzmann type equation giving an apparent pK{sub a} value of 6.8. The fluorescence intensity of the reference dye did not change significantly ({approx}3.0%) on modifying the pH of the nanoparticle dispersion. Finally, the proposed method was statistically validated against a reference procedure using samples of water and physiological buffer with 2% of horse serum, indicating that there are no significant statistical differences at a 95% confidence level.

  11. Ratiometric imaging of extracellular pH in bacterial biofilms with C-SNARF-4. (United States)

    Schlafer, Sebastian; Garcia, Javier E; Greve, Matilde; Raarup, Merete K; Nyvad, Bente; Dige, Irene


    pH in the extracellular matrix of bacterial biofilms is of central importance for microbial metabolism. Biofilms possess a complex three-dimensional architecture characterized by chemically different microenvironments in close proximity. For decades, pH measurements in biofilms have been limited to monitoring bulk pH with electrodes. Although pH microelectrodes with a better spatial resolution have been developed, they do not permit the monitoring of horizontal pH gradients in biofilms in real time. Quantitative fluorescence microscopy can overcome these problems, but none of the hitherto employed methods differentiated accurately between extracellular and intracellular microbial pH and visualized extracellular pH in all areas of the biofilms. Here, we developed a method to reliably monitor extracellular biofilm pH microscopically with the ratiometric pH-sensitive dye C-SNARF-4, choosing dental biofilms as an example. Fluorescent emissions of C-SNARF-4 can be used to calculate extracellular pH irrespective of the dye concentration. We showed that at pH values of biofilm and visualized the entire bacterial biomass in in vivo-grown dental biofilms with unknown species composition. We then employed digital image analysis to remove the bacterial biomass from the microscopic images and adequately calculate extracellular pH values. As a proof of concept, we monitored the extracellular pH drop in in vivo-grown dental biofilms fermenting glucose. The combination of pH ratiometry with C-SNARF-4 and digital image analysis allows the accurate monitoring of extracellular pH in bacterial biofilms in three dimensions in real time and represents a significant improvement to previously employed methods of biofilm pH measurement.

  12. Monitoring cytosolic and ER Zn2+ in stimulated breast cancer cells using genetically encoded FRET sensors† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5mt00257e Click here for additional data file. (United States)

    Hessels, Anne M.; Taylor, Kathryn M.


    The Zn2+-specific ion channel ZIP7 has been implicated to play an important role in releasing Zn2+ from the ER. External stimulation of breast cancer cells has been proposed to induce phosphorylation of ZIP7 by CK2α, resulting in ZIP7-mediated Zn2+ release from the ER into the cytosol. Here, we examined whether changes in cytosolic and ER Zn2+ concentrations can be detected upon such external stimuli. Two previously developed FRET sensors for Zn2+, eZinCh-2 (K d = 1 nM at pH 7.1) and eCALWY-4 (K d = 0.63 nM at pH 7.1), were expressed in both the cytosol and the ER of wild-type MCF-7 and TamR cells. Treatment of MCF-7 and TamR cells with external Zn2+ and pyrithione, one of the previously used triggers, resulted in an immediate increase in free Zn2+ in both cytosol and ER, suggesting that Zn2+ was directly transferred across the cellular membranes by pyrithione. Cells treated with a second trigger, EGF/ionomycin, showed no changes in intracellular Zn2+ levels, neither in multicolor imaging experiments that allowed simultaneous imaging of cytosolic and ER Zn2+, nor in experiments in which cytosolic and ER Zn2+ were monitored separately. In contrast to previous work using small-molecule fluorescent dyes, these results indicate that EGF–ionomycin treatment does not result in significant changes in cytosolic Zn2+ levels as a result from Zn2+ release from the ER. These results underline the importance of using genetically encoded fluorescent sensors to complement and verify intracellular imaging experiments with synthetic fluorescent Zn2+ dyes. PMID:26739447

  13. A Simple and Effective Ratiometric Fluorescent Probe for the Selective Detection of Cysteine and Homocysteine in Aqueous Media

    Directory of Open Access Journals (Sweden)

    Risong Na


    Full Text Available Biothiols such as cysteine (Cys and homocysteine (Hcy are essential biomolecules participating in molecular and physiological processes in an organism. However, their selective detection remains challenging. In this study, ethyl 2-(3-formyl-4-hydroxyphenyl-4-methylthiazole-5-carboxylate (NL was synthesized as a ratiometric fluorescent probe for the rapid and selective detection of Cys and Hcy over glutathione (GSH and other amino acids. The fluorescence intensity of the probe in the presence of Cys/Hcy increased about 3-fold at a concentration of 20 equiv. of the probe, compared with that in the absence of these chemicals in aqueous media. The limits of detection of the fluorescent assay were 0.911 μM and 0.828 μM of Cys and Hcy, respectively. 1H-NMR and MS analyses indicated that an excited-state intramolecular proton transfer is the mechanism of fluorescence sensing. This ratiometric probe is structurally simple and highly selective. The results suggest that it has useful applications in analytical chemistry and diagnostics.

  14. FRET ratiometric probes reveal the chiral-sensitive cysteine-dependent H2S production and regulation in living cells (United States)

    Wei, Lv; Yi, Long; Song, Fanbo; Wei, Chao; Wang, Bai-Fan; Xi, Zhen


    Hydrogen sulfide (H2S) is an endogenously produced gaseous signalling molecule with multiple biological functions. In order to visualize and quantify the endogenous in situ production of H2S in living cells, here we developed two new sulphide ratiometric probes (SR400 and SR550) based on fluorescence resonance energy transfer (FRET) strategy for live capture of H2S. The FRET-based probes show excellent selectivity toward H2S in a high thiol background under physiological buffer. The probe can be used to in situ visualize cysteine-dependent H2S production in a chiral-sensitive manner in living cells. The ratiometric imaging studies indicated that D-Cys induces more H2S production than that of L-Cys in mitochondria of human embryonic kidney 293 cells (HEK293). The cysteine mimics propargylglycine (PPG) has also been found to inhibit the cysteine-dependent endogenous H2S production in a chiral-sensitive manner in living cells. D-PPG inhibited D-Cys-dependent H2S production more efficiently than L-PPG, while, L-PPG inhibited L-Cys-dependent H2S production more efficiently than D-PPG. Our bioimaging studies support Kimura's discovery of H2S production from D-cysteine in mammalian cells and further highlight the potential of D-cysteine and its derivatives as an alternative strategy for classical H2S-releasing drugs.

  15. Combined SERS biotags (SBTs) and microfluidic platform for the quantitative ratiometric discrimination between noncancerous and cancerous cells in flow (United States)

    Pallaoro, Alessia; Hoonejani, Mehran R.; Braun, Gary B.; Meinhart, Carl; Moskovits, Martin


    SERS biotags are made from polymer-encapsulated silver nanoparticle dimers infused with unique Raman reporter molecules, and carry peptides as cell recognition moieties. We demonstrate their potential use for early and rapid identification of malignant cells, a central goal in cancer research. SERS biotags (SBTs) can be routinely synthesized and simultaneously excited with a single, low intensity laser source, making the determination of the relative contribution of the individual SBTs to the overall spectrum tractable. Importantly for biomedical applications, SERS employs tissuepenetrating lasers in the red to near-infrared range resulting in low autofluorescence. We have previously described a multiplexed, ratiometric method that can confidently distinguish between cancerous and noncancerous epithelial prostate cells in vitro based on receptor overexpression. Here we present the progress towards the application of this quantitative methodology for the identification of cancer cells in a microfluidic flow-focusing device. Beads are used as cell mimics to characterize the devices. Cells (and beads) are simultaneously incubated with two sets of SBTs while in suspension (simulating cells' capture from blood), then injected into the device for laser interrogation under flow. Each cell event is characterized by a composite Raman spectrum, deconvoluted into its single components to ultimately determine their relative contribution. We show that using SBTs ratiometrically can provide cell identification insensitive to normal causes of uncertainty in optical measurements such as variations in focal plane, cell concentration, autofluorescence, and turbidity.

  16. Microscopic imaging of intracellular calcium in live cells using lifetime-based ratiometric measurements of Oregon Green BAPTA-1. (United States)

    Lattarulo, Carli; Thyssen, Diana; Kuchibholta, Kishore V; Hyman, Bradley T; Bacskaiq, Brian J


    Calcium is a ubiquitous intracellular messenger that has important functions in normal neuronal function. The pathology of Alzheimer's disease has been shown to alter calcium homeostasis in neurons and astrocytes. Several calcium dye indicators are available to measure intracellular calcium within cells, including Oregon Green BAPTA-1 (OGB-1). Using fluorescence lifetime imaging microscopy, we adapted this single wavelength calcium dye into a ratiometric dye to allow quantitative imaging of cellular calcium. We used this approach for in vitro calibrations, single-cell microscopy, high-throughput imaging in automated plate readers, and in single cells in the intact living brain. While OGB is a commonly used fluorescent dye for imaging calcium qualitatively, there are distinct advantages to using a ratiometric approach, which allows quantitative determinations of calcium that are independent of dye concentration. Taking advantage of the distinct lifetime contrast of the calcium-free and calcium-bound forms of OGB, we used time-domain lifetime measurements to generate calibration curves for OGB lifetime ratios as a function of calcium concentration. In summary, we demonstrate approaches using commercially available tools to measure calcium concentrations in live cells at multiple scales using lifetime contrast. These approaches are broadly applicable to other fluorescent readouts that exhibit lifetime contrast and serve as powerful alternatives to spectral or intensity readouts in multiplexing experiments.

  17. Ratiometric fluorescent paper sensor utilizing hybrid carbon dots-quantum dots for the visual determination of copper ions. (United States)

    Wang, Yahui; Zhang, Cheng; Chen, Xiaochun; Yang, Bo; Yang, Liang; Jiang, Changlong; Zhang, Zhongping


    A simple and effective ratiometric fluorescence nanosensor for the selective detection of Cu(2+) has been developed by covalently connecting the carboxyl-modified red fluorescent cadmium telluride (CdTe) quantum dots (QDs) to the amino-functionalized blue fluorescent carbon nanodots (CDs). The sensor exhibits the dual-emissions peaked at 437 and 654 nm, under a single excitation wavelength of 340 nm. The red fluorescence can be selectively quenched by Cu(2+), while the blue fluorescence is a internal reference, resulting in a distinguishable fluorescence color change from pink to blue under a UV lamp. The detection limit of this highly sensitive ratiometric probe is as low as 0.36 nM, which is lower than the U.S. Environmental Protection Agency (EPA) defined limit (20 μM). Moreover, a paper-based sensor has been prepared by printing the hybrid carbon dots-quantum dots probe on a microporous membrane, which provides a convenient and simple approach for the visual detection of Cu(2+). Therefore, the as-synthesized probe shows great potential application for the determination of Cu(2+) in real samples.

  18. A high-resolution mitochondria-targeting ratiometric fluorescent probe for detection of the endogenous hypochlorous acid (United States)

    Zhou, Liyi; Lu, Dan-Qing; Wang, Qianqian; Hu, Shunqin; Wang, Haifei; Sun, Hongyan; Zhang, Xiaobing


    Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (Cdbnd C) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210 nm) and the two well-resolved emission peaks separated by 140 nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50 s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

  19. Selective detection of endogenous H2S in living cells and the mouse hippocampus using a ratiometric fluorescent probe (United States)

    Zhang, Ling; Meng, Wen-Qi; Lu, Liang; Xue, Yun-Sheng; Li, Cheng; Zou, Fang; Liu, Yi; Zhao, Jing


    As one of three gasotransmitters, the fundamental signalling roles of hydrogen sulphide are receiving increasing attention. New tools for the accurate detection of hydrogen sulphide in cells and tissues are in demand to probe its biological functions. We report the p-nitrobenzyl-based ratiometric fluorescent probe RHP-2, which features a low detection limit, high selectivity and good photostability. The emission intensity ratios had a good linear relationship with the sulphide concentrations in PBS buffer and bovine serum. Our probe was applied to the ratiometric determination and imaging of endogenous H2S in living cells. Furthermore, RHP-2 was used as an effective tool to measure endogenous H2S in the mouse hippocampus. We observed a significant reduction in sulphide concentrations and downregulated expression of cystathionine β-synthetase (CBS) mRNA and CBS protein in the mouse hippocampus in a chronic unpredictable mild stress (CUMS)-induced depression model. These data suggested that decreased concentrations of endogenous H2S may be involved in the pathogenesis of chronic stress depression.

  20. Rapid and facile ratiometric detection of an anthrax biomarker by regulating energy transfer process in bio-metal-organic framework. (United States)

    Zhang, Yihe; Li, Bin; Ma, Heping; Zhang, Liming; Zheng, Youxuan


    A ratiometric fluorescent sensor based on luminescent bio-metal-organic framework was prepared by exchanging both Tb(3+) and Eu(3+) cations into anionic bio-MOF-1. Due to a highly efficient energy transfer from Tb(3+) to Eu(3+) (>89%), emission color of Tb/Eu@bio-MOF-1 was orange-red even though Tb(3+) was the dominant content in this Tb/Eu co-doping material. More interestingly, this energy transfer process could be modulated by dipicolinic acid (DPA), an unique biomarker for bacillus spores. With DPA addition, corresponding DPA-to-Tb(3+) energy transfer was gradually enhanced while the energy transfer from Tb(3+) to Eu(3+) was significantly weakened. By regulating the energy transfer process in Tb/Eu@bio-MOF-1, visual colorimetric sensing of DPA in porous MOF was realized for the first time. Detection limit of Tb/Eu@bio-MOF-1 for DPA was 34nM, which was much lower than an infectious dosage of Bacillus anthracis spores (60μM) for human being. Besides, Tb/Eu@bio-MOF-1 showed a remarkable selectivity over other aromatic ligands and amino acids. More importantly, this porous ratiometric sensor worked equally well in human serum. These particularly attractive features of Tb/Eu@bio-MOF-1 made the direct, rapid and naked-eye detection of DPA for practical application possible.

  1. Label-free silicon nanodots featured ratiometric fluorescent aptasensor for lysosomal imaging and pH measurement. (United States)

    Zhang, Yanan; Guo, Shan; Cheng, Shibo; Ji, Xinghu; He, Zhike


    The homeostasis of lysosomal pH is crucial in cell physiology. Developing small fluorescent nanosensors for lysosome imaging and ratiometric measurement of pH is highly demanded yet challenging. Herein, a pH-sensitive fluorescein tagged aptamer AS1411 has been utilized to covalently modify the label-free fluorescent silicon nanodots via a crosslinker for construction of a ratiometric pH biosensor. The established aptasensor exhibits the advantages of ultrasmall size, hypotoxicity, excellent pH reversibility and good photostability, which favors its application in an intracellular environment. Using human breast MCF-7 cancer cells and MCF-10A normal cells as the model, this aptasensor shows cell specificity for cancer cells and displays a wide pH response range of 4.5-8.0 in living cells. The results demonstrate that the pH of MCF-7 cells is 5.1, which is the expected value for acidic organelles. Lysosome imaging and accurate measurement of pH in MCF-7 cells have been successfully conducted based on this nanosensor via fluorescent microscopy and flow cytometry.

  2. Ratiometric Molecular Probes Based on Dual Emission of a Blue Fluorescent Coumarin and a Red Phosphorescent Cationic Iridium(III) Complex for Intracellular Oxygen Sensing. (United States)

    Yoshihara, Toshitada; Murayama, Saori; Tobita, Seiji


    Ratiometric molecular probes RP1 and RP2 consisting of a blue fluorescent coumarin and a red phosphorescent cationic iridium complex connected by a tetra- or octaproline linker, respectively, were designed and synthesized for sensing oxygen levels in living cells. These probes exhibited dual emission with good spectral separation in acetonitrile. The photorelaxation processes, including intramolecular energy transfer, were revealed by emission quantum yield and lifetime measurements. The ratios (R(I) = (I(p)/I(f))) between the phosphorescence (I(p)) and fluorescence (I(f)) intensities showed excellent oxygen responses; the ratio of R(I) under degassed and aerated conditions ( R(I)(0) was 20.3 and 19.6 for RP1 and RP2. The introduction of the cationic Ir (III) complex improved the cellular uptake efficiency compared to that of a neutral analogue with a tetraproline linker. The emission spectra of the ratiometric probes internalized into living HeLa or MCF-7 cells could be obtained using a conventional microplate reader. The complex RP2 with an octaproline linker provided ratios comparable to the ratiometric measurements obtained using a microplate reader: the ratio of the R(I)) value of RP2 under hypoxia (2.5% O2) to that under normoxia (21% O2) was 1.5 and 1.7 for HeLa and MCF-7 cells, respectively. Thus, the intracellular oxygen levels of MCF-7 cells could be imaged by ratiometric emission measurements using the complex RP2.

  3. Real-Time Tracking and In Vivo Visualization of β-Galactosidase Activity in Colorectal Tumor with a Ratiometric Near-Infrared Fluorescent Probe. (United States)

    Gu, Kaizhi; Xu, Yisheng; Li, Hui; Guo, Zhiqian; Zhu, Shaojia; Zhu, Shiqin; Shi, Ping; James, Tony D; Tian, He; Zhu, Wei-Hong


    Development of "smart" noninvasive bioimaging probes for trapping specific enzyme activities is highly desirable for cancer therapy in vivo. Given that β-galactosidase (β-gal) is an important biomarker for cell senescence and primary ovarian cancers, we design an enzyme-activatable ratiometric near-infrared (NIR) probe (DCM-βgal) for the real-time fluorescent quantification and trapping of β-gal activity in vivo and in situ. DCM-βgal manifests significantly ratiometric and turn-on NIR fluorescent signals simultaneously in response to β-gal concentration, which makes it favorable for monitoring dynamic β-gal activity in vivo with self-calibration in fluorescent mode. We exemplify DCM-βgal for the ratiometric tracking of endogenously overexpressed β-gal distribution in living 293T cells via the lacZ gene transfection method and OVCAR-3 cells, and further realize real-time in vivo bioimaging of β-gal activity in colorectal tumor-bearing nude mice. Advantages of our system include light-up ratiometric NIR fluorescence with large Stokes shift, high photostability, and pH independency under the physiological range, allowing for the in vivo real-time evaluation of β-gal activity at the tumor site with high-resolution three-dimensional bioimaging for the first time. Our work provides a potential tool for in vivo real-time tracking enzyme activity in preclinical applications.

  4. Ratiometric FRET-based detection of DNA and micro-RNA on the surface using TIRF detection

    Energy Technology Data Exchange (ETDEWEB)

    Matveeva, Evgenia G., E-mail: [Center for Commercialization of Fluorescence Technologies, University of North Texas, Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States); Gryczynski, Zygmunt [Center for Commercialization of Fluorescence Technologies, University of North Texas, Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States); Stewart, Donald R. [Omm Scientific, Inc., 2600 N. Stemmons Freeway, Suite 129, Dallas, TX 75207 (United States); Gryczynski, Ignacy [Center for Commercialization of Fluorescence Technologies, University of North Texas, Health Science Center, Department of Molecular Biology and Immunology and Department of Cell Biology and Genetics, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 (United States)


    A new FRET-based method for the ratiometric detection of DNA oligomers on a surface using TIRF detection mode is reported. The dual-labeled system consisting of two hybridized oligomers, Cy3oligoY:Cy5oligoX was immobilized on the surface, and the total internal reflection fluorescence (TIRF) was used to detect emission signals from the surface. Two signals, green and red, which originated from the green donor Cy3 and the red acceptor Cy5, have been simultaneously detected. When the target single-stranded complimentary oligomer was present in the solution, this oligomer replaced the Cy3oligoY in the donor:acceptor complex on the surface and the ratio of red-to-green signal was dramatically changed. This detection scheme is generally applicable to the detection of DNA or RNA on a surface.

  5. A triterpene oleanolic acid conjugate with 3-hydroxyflavone derivative as a new membrane probe with two-color ratiometric response. (United States)

    Turkmen, Zeynep; Klymchenko, Andrey S; Oncul, Sule; Duportail, Guy; Topcu, Gulacti; Demchenko, Alexander P


    We report on the synthesis by coupling of a triterpenoid oleanolic acid with 4'-diethylamino-3-hydroxyflavone (FE) to produce an environment-sensitive biomembrane probe with two-band ratiometric response in fluorescence emission. The synthesized compound (probe FOT) was tested in a series of model solvents and demonstrated the response to solvent polarity and intermolecular hydrogen bonding very similar to that of parent probe FE. Meantime when incorporated into lipid bilayer membranes, it showed new features differing in response between lipids of different surface charges as well as between glycerophospholipids and sphingomyelin. We observed that in the conditions of coexistence of rafts and non-raft structures the probe is excluded from the rafts.

  6. Theoretical investigation on ratiometric two-photon fluorescent probe for Zn2+ detection based on ICT mechanism (United States)

    Huang, Shuang; Yang, Bao-Zhu; Ren, Ai-Min


    OPA (one-photon absorption), TPA (two-photon absorption) and fluorescence properties of a free ligand L upon coordination with Zn2+, and the regeneration with CN- were investigated in theory. According to our research, OPA spectra of ligand L show red-shift binding with Zn2+ while blue-shift with CN-. The fluorescence spectra and TPA wavelength are shifted in the same situation as those of OPA spectra. The value of TPA cross-section decreased at first, and then increased to 1813 GM for [L-Zn(CN)4]2-. Intramolecular charge transfer (ICT) mechanism was investigated by natural bond orbital (NBO) analysis. It demonstrates that L is hopeful to be a good ratiometric fluorescent probe for zinc ion detection in solution, and it can regenerate after CN- was introduced.

  7. An Interactive Quantum Dot and Carbon Dot Conjugate for pH-Sensitive and Ratiometric Cu(2+) Sensing. (United States)

    Ahmad, Kafeel; Gogoi, Sonit Kumar; Begum, Raihana; Sk, Md Palashuddin; Paul, Anumita; Chattopadhyay, Arun


    Herein we report the photoinduced electron transfer from Mn(2+) -doped ZnS quantum dots (Qdots) to carbon dots (Cdots) in an aqueous dispersion. We also report that the electron transfer was observed for low pH values, at which the oppositely charged nanoparticles (NPs) interacted with each other. Conversely, at higher pH values the NPs were both negatively charged and thus not in contact with each other, so the electron transfer was absent. Steady-state and time-resolved photoluminescence studies revealed that interacting particle conjugates were responsible for the electron transfer. The phenomenon could be used to detect the presence of Cu(2+) ions, which preferentially, ratiometrically, and efficiently quenched the luminescence of the Qdots.

  8. Ratiometric biosensor array for multiplexed detection of microRNAs based on electrochemiluminescence coupled with cyclic voltammetry. (United States)

    Feng, Xiaobin; Gan, Ning; Zhang, Huairong; Li, Tianhua; Cao, Yuting; Hu, Futao; Jiang, Qianli


    A novel multiplexed ratiometric biosensor array was fabricated on a homemade screen-printed carbon electrode (SPCE) for near-simultaneous detection of microRNA (miRNA)-21 and miRNA-141 based on electrochemiluminescence (ECL) coupled with cyclic voltammetry (CV) method. In the detection system, the ECL signal tags (Ru-SiO2@PLL-Au) were fabricated using poly-l-lysine (PLL) as bridging agent and co-reactant to connect Ru-SiO2 (Ru(bpy)3(2+)-doped silica) and gold nanoparticles (Au NPs), which were respectively modified on two spatial resolved working electrodes (WE1 and WE2) of SPCE. Then the ferrocene (Fc)-labeled hairpin DNA (Fc-HDNA1 and Fc-HDNA2) as CV signal tags and ECL quenching material were immobilized on Ru-SiO2@PLL-Au. Upon miRNA-21 and miRNA-141 adding, the target miRNAs could hybridize with corresponding Fc-HDNA, which could lead to Fc away from Ru-SiO2@PLL-Au. Such conformational changes could recover the ECL of Ru-SiO2@PLL-Au and decreased the CV current of Fc, respectively. This "signal-on" of ECL and "signal-off" of CV were employed for dual-signal ratiometric readout. With the help of a multiplexed switch, two dual-signals from WE1 and WE2 were used for multiplexed detection of miRNA-21 and miRNA-141 down to 6.3 and 8.6fM, respectively. This approach was used in real sample analysis and has significant potential for miRNA biomarkers detection in a clinical laboratory setting.

  9. Ratiometric and colorimetric near-infrared sensors for multi-channel detection of cyanide ion and their application to measure β-glucosidase (United States)

    Xing, Panfei; Xu, Yongqian; Li, Hongjuan; Liu, Shuhui; Lu, Aiping; Sun, Shiguo


    A near-infrared sensor for cyanide ion (CN-) was developed via internal charge transfer (ICT). This sensor can selectively detect CN- either through dual-ratiometric fluorescence (logarithm of I414/I564 and I803/I564) or under various absorption (356 and 440 nm) and emission (414, 564 and 803 nm) channels. Especially, the proposed method can be employed to measure β-glucosidase by detecting CN- traces in commercial amygdalin samples.

  10. Chemosensitivity assay in mice prostate tumor: Preliminary report of flow cytometry, DNA fragmentation, ion ratiometric methods of anti-neoplastic drug monitoring



    Abstract Flow cytometry, DNA fragmentation, ion ratiomateric analysis and NMR peaks characterized drug chemosensitivity of antineoplastic drugs. Hypotheses were: 1. The chemosensitive effect of different cancer cell lines is characteristic; 2. DNA fragmentation, ion ratiometric analysis suggest apoptosis status of tumor cells. Methods PC-3 cell lines were compared with DU-145, LNCaP cell lines in culture for the [Na]i and [Ca]i ion sensing dyes, cell death, NMR peaks and apoptosis staining fo...

  11. A Novel Ratiometric Probe Based on Nitrogen-Doped Carbon Dots and Rhodamine B Isothiocyanate for Detection of Fe3+ in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Lin Liu


    Full Text Available A ratiometric probe for determining ferric ions (Fe3+ was developed based on nitrogen-doped carbon dots (CDs and rhodamine B isothiocyanate (RhB, which was then applied to selective detection of Fe3+ in PB buffer solution, lake water, and tap water. In the sensing system, FePO4 particles deposit on the surface of CDs, resulting in larger particles and surface passivation. The fluorescence (FL intensity and the light scattering (LS intensity of CDs can be gradually enhanced with the addition of Fe3+, while the FL intensity of RhB remains constant. The ratiometric light intensity of CDs LS and RhB FL was quantitatively in response to Fe3+ concentrations in a dynamic range of 0.01–1.2 μM, with a detection limit as low as 6 nM. Other metal ions, such as Fe2+, Al3+, K+, Ca2+, and Co2+, had no significant interference on the determination of Fe3+. Compared with traditional probes based on single-signal probe for Fe3+ detection, this dual-signal-based ratiometric probe exhibits a more reliable and stable response on target concentration and is characterized by easy operation in a simple fluorescence spectrophotometer.

  12. Development of a ratiometric time-resolved luminescence sensor for pH based on lanthanide complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu Mingjing [State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024 (China); Ye Zhiqiang, E-mail: [State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024 (China); Xin Chenglong [State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024 (China); Yuan Jingli, E-mail: [State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024 (China)


    Highlights: Black-Right-Pointing-Pointer A lanthanide complex-based ratiometric luminescent pH sensor was developed. Black-Right-Pointing-Pointer The sensor can luminously respond to pH in weakly acidic to neutral media. Black-Right-Pointing-Pointer The sensor can be used for monitoring pH with time-resolved luminescence mode. Black-Right-Pointing-Pointer The sensor can be also used for monitoring pH with absorbance mode. Black-Right-Pointing-Pointer The utility of the sensor for the luminescent cell imaging was demonstrated. - Abstract: Time-resolved luminescence bioassay technique using lanthanide complexes as luminescent probes/sensors has shown great utilities in clinical diagnostics and biotechnology discoveries. In this work, a novel terpyridine polyacid derivative that can form highly stable complexes with lanthanide ions in aqueous media, (4 Prime -hydroxy-2,2 Prime :6 Prime ,2 Prime Prime -terpyridine-6,6 Prime Prime -diyl) bis(methylenenitrilo) tetrakis(acetic acid) (HTTA), was designed and synthesized for developing time-resolved luminescence pH sensors based on its Eu{sup 3+} and Tb{sup 3+} complexes. The luminescence characterization results reveal that the luminescence intensity of HTTA-Eu{sup 3+} is strongly dependent on the pH values in weakly acidic to neutral media (pK{sub a} = 5.8, pH 4.8-7.5), while that of HTTA-Tb{sup 3+} is pH-independent. This unique luminescence response allows the mixture of HTTA-Eu{sup 3+} and HTTA-Tb{sup 3+} (the HTTA-Eu{sup 3+}/Tb{sup 3+} mixture) to be used as a ratiometric luminescence sensor for the time-resolved luminescence detection of pH with the intensity ratio of its Tb{sup 3+} emission at 540 nm to its Eu{sup 3+} emission at 610 nm, I{sub 540nm}/I{sub 610nm}, as a signal. Moreover, the UV absorption spectrum changes of the HTTA-Eu{sup 3+}/Tb{sup 3+} mixture at different pHs (pH 4.0-7.0) also display a ratiometric response to the pH changes with the ratio of absorbance at 290 nm to that at 325 nm, A{sub 290nm

  13. Ratiometric bioluminescence indicators for monitoring cyclic adenosine 3',5'-monophosphate in live cells based on luciferase-fragment complementation. (United States)

    Takeuchi, Masaki; Nagaoka, Yasutaka; Yamada, Toshimichi; Takakura, Hideo; Ozawa, Takeaki


    Bioluminescent indicators for cyclic 3',5'-monophosphate AMP (cAMP) are powerful tools for noninvasive detection with high sensitivity. However, the absolute photon counts are affected substantially by adenosine 5'-triphosphate (ATP) and d-luciferin concentrations, limiting temporal analysis in live cells. This report describes a genetically encoded bioluminescent indicator for detecting intracellular cAMP based on complementation of split fragments of two-color luciferase mutants originated from click beetles. A cAMP binding domain of protein kinase A was connected with an engineered carboxy-terminal fragment of luciferase, of which ends were connected with amino-terminal fragments of green luciferase and red luciferase. We demonstrated that the ratio of green to red bioluminescence intensities was less influenced by the changes of ATP and d-luciferin concentrations. We also showed an applicability of the bioluminescent indicator for time-course and quantitative assessments of intracellular cAMP in living cells and mice. The bioluminescent indicator will enable quantitative analysis and imaging of spatiotemporal dynamics of cAMP in opaque and autofluorescent living subjects.

  14. Ratiometric Optical Temperature Sensor Using Two Fluorescent Dyes Dissolved in an Ionic Liquid Encapsulated by Parylene Film

    Directory of Open Access Journals (Sweden)

    Isao Shimoyama


    Full Text Available A temperature sensor that uses temperature-sensitive fluorescent dyes is developed. The droplet sensor has a diameter of 40 µm and uses 1 g/L of Rhodamine B (RhB and 0.5 g/L of Rhodamine 110 (Rh110, which are fluorescent dyes that are dissolved in an ionic liquid (1-ethyl-3-methylimidazolium ethyl sulfate to function as temperature indicators. This ionic liquid is encapsulated using vacuum Parylene film deposition (which is known as the Parylene-on-liquid-deposition (PoLD method. The droplet is sealed by the chemically stable and impermeable Parylene film, which prevents the dye from interacting with the molecules in the solution and keeps the volume and concentration of the fluorescent material fixed. The two fluorescent dyes enable the temperature to be measured ratiometrically such that the droplet sensor can be used in various applications, such as the wireless temperature measurement of microregions. The sensor can measure the temperature of such microregions with an accuracy of 1.9 °C, a precision of 3.7 °C, and a fluorescence intensity change sensitivity of 1.0%/K. The sensor can measure temperatures at different sensor depths in water, ranging from 0 to 850 µm. The droplet sensor is fabricated using microelectromechanical system (MEMS technology and is highly applicable to lab-on-a-chip devices.

  15. Ratiometric optical temperature sensor using two fluorescent dyes dissolved in an ionic liquid encapsulated by Parylene film. (United States)

    Kan, Tetsuo; Aoki, Hironori; Binh-Khiem, Nguyen; Matsumoto, Kiyoshi; Shimoyama, Isao


    A temperature sensor that uses temperature-sensitive fluorescent dyes is developed. The droplet sensor has a diameter of 40 µm and uses 1 g/L of Rhodamine B (RhB) and 0.5 g/L of Rhodamine 110 (Rh110), which are fluorescent dyes that are dissolved in an ionic liquid (1-ethyl-3-methylimidazolium ethyl sulfate) to function as temperature indicators. This ionic liquid is encapsulated using vacuum Parylene film deposition (which is known as the Parylene-on-liquid-deposition (PoLD) method). The droplet is sealed by the chemically stable and impermeable Parylene film, which prevents the dye from interacting with the molecules in the solution and keeps the volume and concentration of the fluorescent material fixed. The two fluorescent dyes enable the temperature to be measured ratiometrically such that the droplet sensor can be used in various applications, such as the wireless temperature measurement of microregions. The sensor can measure the temperature of such microregions with an accuracy of 1.9 °C, a precision of 3.7 °C, and a fluorescence intensity change sensitivity of 1.0%/K. The sensor can measure temperatures at different sensor depths in water, ranging from 0 to 850 µm. The droplet sensor is fabricated using microelectromechanical system (MEMS) technology and is highly applicable to lab-on-a-chip devices.

  16. Facile and high spatial resolution ratio-metric luminescence thermal mapping in microfluidics by near infrared excited upconversion nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yu; Li, Shunbo; Wen, Weijia, E-mail: [Department of Physics, KAUST-HKUST Joint Micro/Nanofluidic Laboratory, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Cao, Wenbin [Nano Science and Technology Program, Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong)


    A local area temperature monitor is important for precise control of chemical and biological processes in microfluidics. In this work, we developed a facile method to realize micron spatial resolution of temperature mapping in a microfluidic channel quickly and cost effectively. Based on the temperature dependent fluorescence emission of NaYF{sub 4}:Yb{sup 3+}, Er{sup 3+} upconversion nanoparticles (UCNPs) under near-infrared irradiation, ratio-metric imaging of UCNPs doped polydimethylsiloxane can map detailed temperature distribution in the channel. Unlike some reported strategies that utilize temperature sensitive organic dye (such as Rhodamine) to achieve thermal sensing, our method is highly chemically inert and physically stable without any performance degradation in long term operation. Moreover, this method can be easily scaled up or down, since the spatial and temperature resolution is determined by an optical imaging system. Our method supplied a simple and efficient solution for temperature mapping on a heterogeneous surface where usage of an infrared thermal camera was limited.

  17. Ratiometric analysis of fura red by flow cytometry: a technique for monitoring intracellular calcium flux in primary cell subsets.

    Directory of Open Access Journals (Sweden)

    Emily R Wendt

    Full Text Available Calcium flux is a rapid and sensitive measure of cell activation whose utility could be enhanced with better techniques for data extraction. We describe a technique to monitor calcium flux by flow cytometry, measuring Fura Red calcium dye by ratiometric analysis. This technique has several advantages: 1 using a single calcium dye provides an additional channel for surface marker characterization, 2 allows robust detection of calcium flux by minority cell populations within a heterogeneous population of primary T cells and monocytes 3 can measure total calcium flux and additionally, the proportion of responding cells, 4 can be applied to studying the effects of drug treatment, simultaneously stimulating and monitoring untreated and drug treated cells. Using chemokine receptor activation as an example, we highlight the utility of this assay, demonstrating that only cells expressing a specific chemokine receptor are activated by cognate chemokine ligand. Furthermore, we describe a technique for simultaneously stimulating and monitoring calcium flux in vehicle and drug treated cells, demonstrating the effects of the Gαi inhibitor, pertussis toxin (PTX, on chemokine stimulated calcium flux. The described real time calcium flux assay provides a robust platform for characterizing cell activation within primary cells, and offers a more accurate technique for studying the effect of drug treatment on receptor activation in a heterogeneous population of primary cells.

  18. Fluorescence Ratiometric Assay Strategy for Chemical Transmitter of Living Cells Using H2O2-Sensitive Conjugated Polymers. (United States)

    Wang, Yunxia; Li, Shengliang; Feng, Liheng; Nie, Chenyao; Liu, Libing; Lv, Fengting; Wang, Shu


    A new water-soluble conjugated poly(fluorene-co-phenylene) derivative (PFP-FB) modified with boronate-protected fluorescein (peroxyfluor-1) via PEG linker has been designed and synthesized. In the presence of H2O2, the peroxyfluor-1 group can transform into green fluorescent fluorescein by deprotecting the boronate protecting groups. In this case, upon selective excitation of PFP-FB backbone at 380 nm, efficient fluorescence resonance energy transfer (FRET) from PFP-FB backbone to fluorescein occurs, and accordingly, the fluorescence color of PFP-FB changes from blue to green. Furthermore, the emission color of PFP-FB and the FRET ratio change in a concentration-dependent manner. By taking advantage of PFP-FB, ratiometric detection of choline and acetylcholine (ACh) through cascade enzymatic reactions and further dynamic monitoring of the choline consumption process of cancer cells have been successfully realized. Thus, this new polymer probe promotes the development of enzymatic biosensors and provides a simpler and more effective way for detecting the chemical transmitter of living cells.

  19. A triphenyl amine-based solvatofluorochromic dye for the selective and ratiometric sensing of OCl- in human blood cells. (United States)

    Goswami, Shyamaprosad; Aich, Krishnendu; Das, Sangita; Pakhira, Bholanath; Ghoshal, Kakali; Quah, Ching Kheng; Bhattacharyya, Maitree; Fun, Hoong-Kun; Sarkar, Sabyasachi


    A new visible-light-excitable fluorescence ratiometric probe for OCl(-) has been developed based on a triphenylamine-diamiomaleonitrile (TAM) moiety. The structure of the dye was confirmed by single-crystal X-ray analysis. It behaves as a highly selective and sensitive probe for OCl(-) over other analytes with a fast response time (∼100 s). OCl(-) reacts with the probe leading to the formation of the corresponding aldehyde in a mixed-aqueous system. The detection limit of the probe is in the 10(-8) M range. The probe (TAM) also exhibits solvatofluorochromism. Changing the solvent from non-polar to polar, the emission band of TAM largely red-shifted. Moreover, the probe shows an excellent performance in real-life application in detecting OCl(-) in human blood cells. The experimentally observed changes in the structure and electronic properties of the probe after reaction with OCl(-) were studied by DFT and TDDFT computational calculations.

  20. Two-dimensional Oxygen Distribution in a Surface Sediment Layer Measured Using an RGB Color Ratiometric Oxygen Planar Optode

    Directory of Open Access Journals (Sweden)

    Jae Seong Lee


    Full Text Available We measured two-dimensional (2-D oxygen distribution in the surface sediment layer of intertidal sediment using a simple and inexpensive planar oxygen optode, which is based on a color ratiometric image approach. The recorded emission intensity of red color luminophore light significantly changed with oxygen concentration by O2 quenching of platinum(IIoctaethylporphyrin (PtOEP. The ratios between the intensity of red and green emissions with oxygen concentration variation demonstrated the Stern-Volmer relationship. The 2-D oxygen distribution image showed microtopographic structure, diffusivity boundary layer and burrow in surface sediment layer. The oxygen penetration depth (OPD was about 2 mm and the one-dimensional vertical diffusive oxygen uptake (DOU was 12.6 mmol m−2 d−1 in the undisturbed surface sediment layer. However, those were enhanced near burrow by benthic fauna, and the OPD was two times deeper and DOU was increased by 34%. The simple and inexpensive oxygen planar optode has great application potential in the study of oxygen dynamics with high spatiotemporal resolution, in benthic boundary layers.

  1. Ionic selectivity of low-affinity ratiometric calcium indicators: mag-Fura-2, Fura-2FF and BTC. (United States)

    Hyrc, K L; Bownik, J M; Goldberg, M P


    Accurate measurement of elevated intracellular calcium levels requires indicators with low calcium affinity and high selectivity. We examined fluorescence spectral properties and ionic specificity of three low-affinity, ratiometric indicators structurally related to Fura-2: mag-Fura-2 (furaptra), Fura-2FF, and BTC. The indicators differed in respect to their excitation wavelengths, affinity for Ca2+ (Kd approximately 20 microM, 6 microM and 12 microM respectively) and selectivity over Mg2+ (Kd approximately 2 mM for mag-Fura-2, > 10 mM for Fura-2FF and BTC). Among the tested indicators, BTC was limited by a modest dynamic range upon Ca2+ binding, susceptibility to photodamage, and sensitivity to alterations in pH. All three indicators bound other metal ions including Zn2+, Cd2+ and Gd3+. Interestingly, only in the case of BTC were spectral differences apparent between Ca2+ and other metal ions. For example, the presence of Zn2+ increased BTC fluorescence 6-fold at the Ca2+ isosbestic point, suggesting that this dye may be used as a fluorescent Zn2+ indicator. Fura-2FF has high specificity, wide dynamic range, and low pH sensitivity, and is an optimal low-affinity Ca2+ indicator for most imaging applications. BTC may be useful if experimental conditions require visible wavelength excitation or sensitivity to other metal ions including Zn2+.

  2. Zinc(II)-selective ratiometric fluorescent sensors based on inhibition of excited-state intramolecular proton transfer. (United States)

    Henary, Maged M; Wu, Yonggang; Fahrni, Christoph J


    To develop a zinc(II)-selective emission ratiometric probe suitable for biological applications, we explored the cation-induced inhibition of excited-state intramolecular proton transfer (ESIPT) with a series of 2-(2'-benzenesulfonamidophenyl)benzimidazole derivatives. In the absence of Zn(II) at neutral pH, the fluorophores undergo ESIPT to yield a highly Stokes' shifted emission from the proton-transfer tautomer. Coordination of Zn(II) inhibits the ESIPT process and yields a significant hypsochromic shift of the fluorescence emission maximum. Whereas the paramagnetic metal cations Cu(II), Fe(II), Ni(II), Co(II), and Mn(II) result in fluorescence quenching, the emission response is not altered by millimolar concentrations of Ca(II) or Mg(II), rendering the sensors selective for Zn(II) among all biologically important metal cations. Due to the modular architecture of the fluorophore, the Zn(II) binding affinity can be readily tuned by implementing simple structural modifications. The synthesized probes are suitable to gauge free Zn(II) concentrations in the micromolar to picomolar range under physiological conditions.

  3. Mapping of healthy oral mucosal tissue using diffuse reflectance spectroscopy: ratiometric-based total hemoglobin comparative study. (United States)

    Hafez, Razan; Hamadah, Omar; Bachir, Wesam


    The objective of this study is to clinically evaluate the diffuse reflectance spectroscopy (DRS) ratiometric method for differentiation of normal oral mucosal tissues with different histological natures and vascularizations in the oral cavity. Twenty-one healthy patients aged 20-44 years were diagnosed as healthy and probed with a portable DRS system. Diffuse reflectance spectra were recorded in vivo in the range (450-650 nm). In this study, the following three oral mucosal tissues were considered: masticatory mucosa, lining mucosa, and specialized mucosa. Spectral features based on spectral intensity ratios were determined at five specific wavelengths (512, 540, 558, 575, and 620 nm). Total hemoglobin based on spectral ratios for the three anatomical regions have also been evaluated. The three studied groups representing different anatomical regions in the oral cavity were compared using analysis of variance and post hoc least significant difference tests. Statistical analysis showed a significant difference in the mean of diffuse spectral ratios between the groups (P spectroscopy might be used for creating a DRS databank of normal oral mucosal tissue with specific spectral ratios featuring the total hemoglobin concentrations. That would further enhance the discrimination of oral tissue for examining the histological nature of oral mucosa and diagnosis of early precancerous changes in the oral cavity based on non-invasive monitoring of neovascularization.

  4. A highly selective ratiometric fluorescent pH probe based on a PAMAM wavelength-shifting bichromophoric system (United States)

    Alamry, Khalid A.; Georgiev, Nikolai I.; El-Daly, Samy Abdullah; Taib, Layla A.; Bojinov, Vladimir B.


    A novel PAMAM wavelength-shifting bichromophoric system has been successfully developed. Novel compound was configured as a light harvesting antenna where the system surface is labeled with yellow-green emitting 4-(N,N-dimethylamino)ethylamino-1,8-naphthalimide "donor" units capable of absorbing light and efficiently transferring the energy to a focal Rhodamine 6G "acceptor". The periphery of the system was designed on the "fluorophore-spacer-receptor" format, capable of acting as a molecular fluorescence photoinduced electron transfer based probe. Due to the both effects, photoinduced electron transfer in the periphery of the system and pH dependent rhodamine core absorption, novel antenna is able to act as a selective ratiometric pH fluorescence probe in aqueous medium. Thus, the distinguishing features of the fluorescence resonance energy transfer systems were successfully combined with the properties of classical ring-opening charge transfer systems, which may be beneficially for monitoring pH variations in complex samples.

  5. Acquisition of a Quantitative, Stoichiometrically Conserved Ratiometric Marker of Maturation Status in Stem Cell-Derived Cardiac Myocytes

    Directory of Open Access Journals (Sweden)

    Fikru B. Bedada


    Full Text Available There is no consensus in the stem cell field as to what constitutes the mature cardiac myocyte. Thus, helping formalize a molecular signature for cardiac myocyte maturation would advance the field. In the mammalian heart, inactivation of the “fetal” TNNI gene, TNNI1 (ssTnI, together in temporal concert with its stoichiometric replacement by the adult TNNI gene product, TNNI3 (cTnI, represents a quantifiable ratiometric maturation signature. We examined the TNNI isoform transition in human induced pluripotent stem cell (iPSC cardiac myocytes (hiPSC-CMs and found the fetal TNNI signature, even during long-term culture. Rodent stem cell-derived and primary myocytes, however, transitioned to the adult TnI profile. Acute genetic engineering of hiPSC-CMs enabled a rapid conversion toward the mature TnI profile. While there is no single marker to denote the mature cardiac myocyte, we propose that tracking the cTnI:ssTnI protein isoform ratio provides a valuable maturation signature to quantify myocyte maturation status across laboratories.

  6. Carbon-Dot and Quantum-Dot-Coated Dual-Emission Core-Satellite Silica Nanoparticles for Ratiometric Intracellular Cu(2+) Imaging. (United States)

    Zou, Chenchen; Foda, Mohamed Frahat; Tan, Xuecai; Shao, Kang; Wu, Long; Lu, Zhicheng; Bahlol, Hagar Shendy; Han, Heyou


    Copper (Cu(2+)) is physiologically essential, but excessive Cu(2+) may cause potential risk to plants and animals due to the bioaccumulative properties. Hence, sensitive recognition is crucial to avoid overintake of Cu(2+), and visual recognition is more favored for practical application. In this work, a dual-emission ratiometric fluorescent nanoprobe was developed possessing the required intensity ratio, which can facilitate the sensitive identification of Cu(2+) by the naked eye. The probe hybridizes two fluorescence nanodots (quantum dots (QDs) and carbon dots (CDs)). Although both of them can be viable fluorescence probes for metal ion detection, rarely research has coupled this two different kinds of fluorescence material in one nanosensor to fabricate a selectively ratiometric fluorescence probe for intracellular imaging. The red emitting CdTe/CdS QDs were capped around the silica microsphere to serve as the response signal label, and the blue-emitting CDs, which is insensitive to the analyte, were covalently attached to the QDs surface to act as the reference signal. This core-satellite hybrid sphere not only improves the stability and brightness of QDs significantly but also decreases the cytotoxicity toward HeLa cells tremendously. Moreover, the Cu(2+) could quench the QDs emission effectively but have no ability for reduction of the CDs emission. Accordingly, a simple, efficient, and precise method for tracing Cu(2+) was proposed. The increase of Cu(2+) concentration in the series of 0-3 × 10(-6) M was in accordance with linearly decrease of the F650/F425 ratio. As for practical application, this nanosensor was utilized to the ratiometric fluorescence imaging of copper ions in HeLa cells.

  7. An ion-insensitive cAMP biosensor for long term quantitative ratiometric fluorescence resonance energy transfer (FRET) measurements under variable physiological conditions. (United States)

    Salonikidis, Petrus S; Niebert, Marcus; Ullrich, Tim; Bao, Guobin; Zeug, Andre; Richter, Diethelm W


    Ratiometric measurements with FRET-based biosensors in living cells using a single fluorescence excitation wavelength are often affected by a significant ion sensitivity and the aggregation behavior of the FRET pair. This is an important problem for quantitative approaches. Here we report on the influence of physiological ion concentration changes on quantitative ratiometric measurements by comparing different FRET pairs for a cAMP-detecting biosensor. We exchanged the enhanced CFP/enhanced YFP FRET pair of an established Epac1-based biosensor by the fluorophores mCerulean/mCitrine. In the case of enhanced CFP/enhanced YFP, we showed that changes in proton, and (to a lesser extent) chloride ion concentrations result in incorrect ratiometric FRET signals, which may exceed the dynamic range of the biosensor. Calcium ions have no direct, but an indirect pH-driven effect by mobilizing protons. These ion dependences were greatly eliminated when mCerulean/mCitrine fluorophores were used. For such advanced FRET pairs the biosensor is less sensitive to changes in ion concentration and allows consistent cAMP concentration measurements under different physiological conditions, as occur in metabolically active cells. In addition, we verified that the described FRET pair exchange increased the dynamic range of the FRET efficiency response. The time window for stable experimental conditions was also prolonged by a faster biosensor expression rate in transfected cells and a greatly reduced tendency to aggregate, which reduces cytotoxicity. These properties were verified in functional tests in single cells co-expressing the biosensor and the 5-HT(1A) receptor.

  8. A rhodamine-benzothiazole conjugated sensor for colorimetric, ratiometric and sequential recognition of copper(II) and sulfide in aqueous media (United States)

    Tang, Lijun; Dai, Xin; Wen, Xin; Wu, Di; Zhang, Qiang


    A new rhodamine-benzothiazole conjugated colorimetric sensor 1 that exhibits sequential recognition to Cu2+ and S2- in CH3CN/HEPES buffer (v/v = 1:1, HEPES 10 mM, pH = 7.0) solution has been developed. Sensor 1 displays highly selective and sensitive recognition to Cu2+ with a ratiometric behavior, and the resultant 1-Cu2+ complex can act as a highly selective S2- sensor via Cu2+ displacement approach. The Cu2+ and S2- recognition processes are rapid and reversible, and the Cu2+ and S2- inputs can result in an INHIBIT logic gate.

  9. Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

    Energy Technology Data Exchange (ETDEWEB)

    Noor, M. Omair; Hrovat, David [Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Moazami-Goudarzi, Maryam [Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Espie, George S. [Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Krull, Ulrich J., E-mail: [Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada)


    Highlights: • Solid-phase QD-FRET transduction of isothermal tHDA amplicons on paper substrates. • Ratiometric QD-FRET transduction improves assay precision and lowers the detection limit. • Zeptomole detection limit by an iPad camera after isothermal amplification. • Tunable assay sensitivity by immobilizing different amounts of QD–probe bioconjugates. - Abstract: Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric

  10. Ratiometric two-photon excited photoluminescence of quantum dots triggered by near-infrared-light for real-time detection of nitric oxide release in situ

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Hui [Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory, Qingdao University, Shandong 266071 (China); Gui, Rijun, E-mail: [Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textile, The Growing Base for State Key Laboratory, Qingdao University, Shandong 266071 (China); Sun, Jie; Wang, Yanfeng [Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan 250062 (China)


    Probe-donor integrated nanocomposites were developed from conjugating silica-coated Mn{sup 2+}:ZnS quantum dots (QDs) with MoS{sub 2} QDs and photosensitive nitric oxide (NO) donors (Fe{sub 4}S{sub 3}(NO){sub 7}{sup −}, RBS). Under excitation with near-infrared (NIR) light at 808 nm, the Mn{sup 2+}:ZnS@SiO{sub 2}/MoS{sub 2}-RBS nanocomposites showed the dual-emissive two-photon excited photoluminescence (TPEPL) that induced RBS photolysis to release NO in situ. NO caused TPEPL quenching of Mn{sup 2+}:ZnS QDs, but it produced almost no impact on the TPEPL of MoS{sub 2} QDs. Hence, the nanocomposites were developed as a novel QDs-based ratiometric TPEPL probe for real-time detection of NO release in situ. The ratiometric TPEPL intensity is nearly linear (R{sup 2} = 0.9901) with NO concentration in the range of 0.01∼0.8 μM, which corresponds to the range of NO release time (0∼15 min). The detection limit was calculated to be approximately 4 nM of NO. Experimental results confirmed that this novel ratiometric TPEPL probe possessed high selectivity and sensitivity for the detection of NO against potential competitors, and especially showed high detection performance for NIR-light triggered NO release in tumor intracellular microenvironments. These results would promote the development of versatile probe-donor integrated systems, also providing a facile and efficient strategy to real-time detect the highly controllable drug release in situ, especially in physiological microenvironments. - Highlights: • Mn{sup 2+}:ZnS@SiO{sub 2}/MoS{sub 2}-RBS nanocomposites were developed as a novel ratiometric two-photon excited fluorescence probe. • This probe could conduct real-time detection of nitric oxide release in situ. • High feasibility of this probe was confirmed in tumor intracellular microenvironments.

  11. Preparation of graphene quantum dots based core-satellite hybrid spheres and their use as the ratiometric fluorescence probe for visual determination of mercury(II) ions

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Mengjuan [Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Wang, Chengquan [School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013 (China); Qian, Jing, E-mail: [Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Wang, Kan; Yang, Zhenting; Liu, Qian; Mao, Hanping [Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Wang, Kun, E-mail: [Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China)


    We herein proposed a simple and effective strategy for preparing graphene quantum dots (GQDs)-based core-satellite hybrid spheres and further explored the feasibility of using such spheres as the ratiometric fluorescence probe for the visual determination of Hg{sup 2+}. The red-emitting CdTe QDs were firstly entrapped in the silica nanosphere to reduce their toxicity and improve their photo and chemical stabilities, thus providing a built-in correction for environmental effects, while the GQDs possessing good biocompatibility and low toxicity were electrostatic self-assembly on the silica surface acting as reaction sites. Upon exposure to the increasing contents of Hg{sup 2+}, the blue fluorescence of GQDs can be gradually quenched presumably due to facilitating nonradiative electron/hole recombination annihilation. With the embedded CdTe QDs as the internal standard, the variations of the tested solution display continuous fluorescence color changes from blue to red, which can be easily observed by the naked eye without any sophisticated instrumentations and specially equipped laboratories. This sensor exhibits high sensitivity and selectivity toward Hg{sup 2+} in a broad linear range of 10 nM–22 μM with a low detection limit of 3.3 nM (S/N = 3), much lower than the allowable Hg{sup 2+} contents in drinking water set by U.S. Environmental Protection Agency. This prototype ratiometric probe is of good simplicity, low toxicity, excellent stabilities, and thus potentially attractive for Hg{sup 2+} quantification related biological systems. - Highlights: • A facile strategy for preparing GQDs based core-satellite hybrid spheres was reported. • Such spheres can be used as the ratiometric fluorescence probe for Hg{sup 2+} detection. • The Hg{sup 2+} content can be easily distinguished by the naked eye. • The sensor shows high sensitivity and selectivity toward Hg{sup 2+} detection. • The ratiometric probe is of good simplicity, low toxicity, and

  12. Novel Pyrene-armed Calix[4]arenes through Triazole Connec-tion: Ratiometric Fluorescent Chemosensor for Zn2+ and Promising Structure for Integrated Logic Gates

    Institute of Scientific and Technical Information of China (English)

    ZHU Lin-Na; GONG Shao-Long; GONG Shu-Ling; YANG Chu-Luo; QIN Jin-Gui


    Two novel pyrene-armed calix[4]arenes by triazole connection were synthesized using "click" chemistry. Com-pound 1 with two pyrene subunits appended to the lower rims of the calix[4]arene shows ratiometric fluorescence response toward Zn2+, and selective fluorescence quenching toward heavy metal ions such as Cu2+, Hg2+ and pb2+; while compound 2 with one pyrene subunit exhibits significant fluorescence quenching toward Cu2+ and moderate quenching behaviour toward Hg2+. By utilizing the different fluorescence behavior of 1 toward Zn2+and Cu2+, inhi-bition (INH) and not or (NOR) logic gates were established.

  13. rFRET: A comprehensive, Matlab-based program for analyzing intensity-based ratiometric microscopic FRET experiments. (United States)

    Nagy, Peter; Szabó, Ágnes; Váradi, Tímea; Kovács, Tamás; Batta, Gyula; Szöllősi, János


    Fluorescence or Förster resonance energy transfer (FRET) remains one of the most widely used methods for assessing protein clustering and conformation. Although it is a method with solid physical foundations, many applications of FRET fall short of providing quantitative results due to inappropriate calibration and controls. This shortcoming is especially valid for microscopy where currently available tools have limited or no capability at all to display parameter distributions or to perform gating. Since users of multiparameter flow cytometry usually apply these tools, the absence of these features in applications developed for microscopic FRET analysis is a significant limitation. Therefore, we developed a graphical user interface-controlled Matlab application for the evaluation of ratiometric, intensity-based microscopic FRET measurements. The program can calculate all the necessary overspill and spectroscopic correction factors and the FRET efficiency and it displays the results on histograms and dot plots. Gating on plots and mask images can be used to limit the calculation to certain parts of the image. It is an important feature of the program that the calculated parameters can be determined by regression methods, maximum likelihood estimation (MLE) and from summed intensities in addition to pixel-by-pixel evaluation. The confidence interval of calculated parameters can be estimated using parameter simulations if the approximate average number of detected photons is known. The program is not only user-friendly, but it provides rich output, it gives the user freedom to choose from different calculation modes and it gives insight into the reliability and distribution of the calculated parameters. © 2016 International Society for Advancement of Cytometry.

  14. Quantum dot-DNA aptamer conjugates coupled with capillary electrophoresis: A universal strategy for ratiometric detection of organophosphorus pesticides. (United States)

    Tang, Tingting; Deng, Jingjing; Zhang, Min; Shi, Guoyue; Zhou, Tianshu


    Based on the highly sensitivity and stable-fluorescence of water-soluble CdTe/CdS core-shell quantum dots (QDs) with broad-specificity DNA aptamers, a novel ratiometric detection strategy was proposed for the sensitive detection of organophosphorus pesticides by capillary electrophoresis with laser-induced fluorescence (CE-LIF). The as-prepared QDs were first conjugated with the amino-modified oligonucleotide (AMO) by amidation reaction, which is partial complementary to the DNA aptamer of organophosphorus pesticides. Then QD-labeled AMO (QD-AMO) was incubated with the DNA aptamer to form QD-AMO-aptamer duplex. When the target organophosphorus pesticides were added, they could specifically bind the DNA aptamer, leading to the cleavage of QD-AMO-aptamer duplex, accompany with the release of QD-AMO. As a result, the ratio of peak height between QD-AMO and QD-AMO-aptamer duplex changed in the detection process of CE-LIF. This strategy was subsequently applied for the detection of phorate, profenofos, isocarbophos, and omethoate with the detection limits of 0.20, 0.10, 0.17, and 0.23μM, respectively. This is the first report about using QDs as the signal indicators for organophosphorus pesticides detection based on broad-specificity DNA aptamers by CE-LIF, thus contributing to extend the scope of application of QDs in different fields. The proposed method has great potential to be a universal strategy for rapid detection of aptamer-specific small molecule targets by simply changing the types of aptamer sequences.

  15. Synthesis and spectroscopic–electrochemical properties of novel ratiometric Hg (II) chemosensor containing Bodipy and the N-phenylaza-15-crown-5 moiety

    Energy Technology Data Exchange (ETDEWEB)

    Kursunlu, Ahmed Nuri, E-mail: [Department of Chemistry, University of Selcuk, Campus, 42075 Konya (Turkey); Deveci, Pervin; Guler, Ersin [Department of Chemistry, University of Selcuk, Campus, 42075 Konya (Turkey)


    The aryl-amine containing azacrown ether ring and alkyl-chloro boradiazaindacene (Bodipy) were synthesized by the Schiff base condensation. The absorption and emission of a novel Schiff base derivative (based on azacrown–Bodipy) were performed in presence of different cations such as Zn{sup 2+}, Ga{sup 3+}, Pb{sup 2+}, Hg{sup 2+}, NH{sub 4}{sup +} Ca{sup 2+}, Cu{sup 2+}, Na{sup +}, Ni{sup 2+}, Cd{sup 2+} and Cr{sup 3+}. The complexation property of the Schiff base was studied in dimethylformamide (DMF) by interacting azacrown-ether group and transition metal nitrates–ammonium chloride. The electrochemical behavior of the Schiff base has also been investigated by cyclic voltammetry. All experimental results indicated that the new compound acts as a selective ratiometric chemosensor for Hg{sup 2+}. -- Highlights: ► The Schiff base prepared by several techniques shows a ratiometric fluorescent behavior toward Hg (II) cation such as classical reaction of complexation. ► To the best of our knowledge, this is an important fixation Crown–Bodipy based reactive sensor for Hg (II) cation.

  16. Label-free and ratiometric detection of nuclei acids based on graphene quantum dots utilizing cascade amplification by nicking endonuclease and catalytic G-quadruplex DNAzyme. (United States)

    Wang, Guang-Li; Fang, Xin; Wu, Xiu-Ming; Hu, Xue-Lian; Li, Zai-Jun


    Herein, we report a ratiometric fluorescence assay based on graphene quantum dots (GQDs) for the ultrasensitive DNA detection by coupling the nicking endonuclease assisted target recycling and the G-quadruplex/hemin DNAzyme biocatalysis for cascade signal amplifications. With o-phenylenediamine acted as the substrate of G-quadruplex/hemin DNAzyme, whose oxidization product (that is, 2,3-diaminophenazine, DAP) quenched the fluorescence intensity of GQDs (at 460nm) obviously, accompanied with the emergence of a new emission of DAP (at 564nm). The ratiometric signal variations at the emission wavelengths of 564 and 460nm (I564/I460) were utilized for label-free, sensitive, and selective detection of target DNA. Utilizing the nicking endonuclease assisted target recycling and the G-quadruplex/hemin DNAzyme biocatalysis for amplified cascade generation of DAP, the proposed bioassay exhibited high sensitivity toward target DNA with a detection limit of 30fM. The method also had additional advantages such as facile preparation and easy operation.

  17. Exploring 1,4-dihydroxyanthraquinone as long-range emissive ratiometric fluorescent probe for signaling Zn(2+)/PO4(3-): Ensemble utilization for live cell imaging. (United States)

    Sinha, Sougata; Gaur, Pankaj; Mukherjee, Trinetra; Mukhopadhyay, Subhrakanti; Ghosh, Subrata


    Fluorescent 1,4-dihydroxyanthraquinone 1 was found to demonstrate its ratiometric signaling property upon interaction with divalent zinc (Zn(2+)). While the probe itself exhibited fluorescence emission in the yellow region (λem=544 nm and 567 nm), binding with Zn(2+) induced strong emission in the orange region (λem=600 nm) which was mainly due to a combination of CHEF and ICT mechanism. The probe was found to be highly sensitive toward the detection of zinc and the limit of detection (LOD) was calculated to be 9×10(-7) M. The possibility of using this probe for real-time analysis was strongly supported by the striking stability of fluorescence signal for more than five days with similar fluorescence intensity as observed during instant signaling. The present probe works within physiological pH range and is devoid of any interference caused by the same group elements such as Cd(2+)/Hg(2+). The probe possesses excellent excitation/emission wavelength profile and can penetrate cell membrane to image low concentration of zing inside living system. The in situ formed zinc-probe ensemble was further explored as ratiometric sensing platform for detecting another bio-relevant analyte phosphate anion through a zinc-displacement approach.

  18. Combined surface-enhanced Raman spectroscopy biotags and microfluidic platform for quantitative ratiometric discrimination between noncancerous and cancerous cells in flow (United States)

    Pallaoro, Alessia; Hoonejani, Mehran R.; Braun, Gary B.; Meinhart, Carl; Moskovits, Martin


    Surface-enhanced Raman spectroscopy (SERS) biotags (SBTs) that carry peptides as cell recognition moieties were made from polymer-encapsulated silver nanoparticle dimers, infused with unique Raman reporter molecules. We previously demonstrated their potential use for identification of malignant cells, a central goal in cancer research, through a multiplexed, ratiometric method that can confidently distinguish between cancerous and noncancerous epithelial prostate cells in vitro based on receptor overexpression. Progress has been made toward the application of this quantitative methodology for the identification of cancer cells in a microfluidic flow-focusing device. Beads are used as cell mimics to evaluate the devices. Cells (and beads) are simultaneously incubated with two sets of SBTs while in suspension, then injected into the device for laser interrogation under flow. Each cell event is characterized by a composite Raman spectrum, deconvoluted into its single components to ultimately determine their relative contribution. We have found that using SBTs ratiometrically can provide cell identification in flow, insensitive to normal causes of uncertainty in optical measurements such as variations in focal plane, cell concentration, autofluorescence, and turbidity.

  19. Monitoring of the proton electrochemical gradient in reconstituted vesicles: quantitative measurements of both transmembrane potential and intravesicular pH by ratiometric fluorescent probes. (United States)

    Holoubek, Ales; Vecer, Jaroslav; Sigler, Karel


    Proteoliposomes carrying reconstituted yeast plasma membrane H(+)-ATPase in their lipid membrane or plasma membrane vesicles are model systems convenient for studying basic electrochemical processes involved in formation of the proton electrochemical gradient (Deltamicro(H) (+)) across the microbial or plant cell membrane. Deltapsi- and pH-sensitive fluorescent probes were used to monitor the gradients formed between inner and outer volume of the reconstituted vesicles. The Deltapsi-sensitive fluorescent ratiometric probe oxonol VI is suitable for quantitative measurements of inside-positive Deltapsi generated by the reconstituted H(+)-ATPase. Its Deltapsi response can be calibrated by the K(+)/valinomycin method and ratiometric mode of fluorescence measurements reduces undesirable artefacts. In situ pH-sensitive fluorescent probe pyranine was used for quantitative measurements of pH inside the proteoliposomes. Calibration of pH-sensitive fluorescence response of pyranine entrapped inside proteoliposomes was performed with several ionophores combined in order to deplete the gradients passively formed across the membrane. Presented model system offers a suitable tool for simultaneous monitoring of both components of the proton electrochemical gradient, Deltapsi and DeltapH. This approach should help in further understanding how their formation is interconnected on biomembranes and even how transport of other ions is combined to it.

  20. A regenerative ratiometric electrochemical biosensor for selective detecting Hg²⁺ based on Y-shaped/hairpin DNA transformation. (United States)

    Jia, Jing; Chen, Hong Guo; Feng, Ji; Lei, Jing Lei; Luo, Hong Qun; Li, Nian Bing


    Inspired by dual-signaling ratiometric mechanism which could reduce the influence of the environmental change, a novel, convenient, and reliable method for the detection of mercury ions (Hg(2+)) based on Y-shaped DNA (Y-DNA) was developed. Firstly, the Y-DNA was formed via the simple annealing way of using two different redox probes simultaneously, omitting the multiple operation steps on the electrode. The Y-DNA was immobilized on the gold electrode surface and then an obvious ferrocene (Fc) signal and a weak methylene blue (MB) signal were observed. Upon addition of Hg(2+), the Y-DNA structure was transformed to hairpin structure based on the formation of T-Hg(2+)-T complex. During the transformation, the redox MB gets close to and the redox Fc gets far away from the electrode surface, respectively. This special design allows a reliable Hg(2+) detection with a detection range from 1 nM to 5 μM and a low detection limit down to 0.094 nM. Furthermore, this biosensor exhibits good selectivity and repeatability, and can be easily regenerated by using L-cysteine. This study offers a simple and effective method for designing ratiometric biosensors for detecting other ions and biomolecules.

  1. Efficient On-Off Ratiometric Fluorescence Probe for Cyanide Ion Based on Perturbation of the Interaction between Gold Nanoclusters and a Copper(II)-Phthalocyanine Complex. (United States)

    Shojaeifard, Zahra; Hemmateenejad, Bahram; Shamsipur, Mojtaba


    A new ratiometric fluorescent sensor was developed for the sensitive and selective detection of cyanide ion (CN(-)) in aqueous media. The ratiometric sensing system is based on CN(-) modulated recovery of copper(II) phthalocyanine (Cu(PcTs)) fluorescence signal at the expense of diminished fluorescence intensity of gold nanoclusters (AuNCs). Preliminary experiments revealed that the AuNCs and Cu(PcTs) possess a turn-off effect on each other, the interaction of which being verified through studying their interactions by principle component analysis (PCA) and multivariate cure resolution-alternating least-squares (MCR-ALS) methods. In the presence of CN(-) anion, the AuNCs and Cu(PcTs) interaction was perturbed, so that the fluorescence of Cu (PcTs), already quenched by AuNCs, was found to be efficiently recovered, while the fluorescence intensity of AuNCs was quenched via the formation of a stable [Au(CN)2](-) species. The ratiometric variation of AuNCs and Cu(PcTs) fluorescence intensities leads to designing a highly sensitive probe for CN(-) ion detection. Under the optimal conditions, CN(-) anion was detected without needing any etching time, over the concentration range of 100 nM-220 μM, with a detection limit of 75 nM, which is much lower than the allowable level of CN(-) in water permitted by the World Health Organization (WHO). Moreover, the detection of CN(-) was developed based on the CN(-) effects on the blue and red florescent colors of Cu(PcTs) and AuNCs, respectively. The designed probe displays a continuous color change from red to blue by addition of CN(-), which can be clearly observed by the naked eye in the range of 7-350 μM, under UV lamp. The prepared AuNCs/Cu(PcTs) probe was successfully utilized for the selective and sensitive determination of CN(-) anion in two different types of natural water (Rodbal dam and rainwater) and also in blood serum as a biological sample.

  2. Camera-based ratiometric fluorescence transduction of nucleic acid hybridization with reagentless signal amplification on a paper-based platform using immobilized quantum dots as donors. (United States)

    Noor, M Omair; Krull, Ulrich J


    Paper-based diagnostic assays are gaining increasing popularity for their potential application in resource-limited settings and for point-of-care screening. Achievement of high sensitivity with precision and accuracy can be challenging when using paper substrates. Herein, we implement the red-green-blue color palette of a digital camera for quantitative ratiometric transduction of nucleic acid hybridization on a paper-based platform using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). A nonenzymatic and reagentless means of signal enhancement for QD-FRET assays on paper substrates is based on the use of dry paper substrates for data acquisition. This approach offered at least a 10-fold higher assay sensitivity and at least a 10-fold lower limit of detection (LOD) as compared to hydrated paper substrates. The surface of paper was modified with imidazole groups to assemble a transduction interface that consisted of immobilized QD-probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as an acceptor. A hybridization event that brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs was responsible for a FRET-sensitized emission from the acceptor dye, which served as an analytical signal. A hand-held UV lamp was used as an excitation source and ratiometric analysis using an iPad camera was possible by a relative intensity analysis of the red (Cy3 photoluminescence (PL)) and green (gQD PL) color channels of the digital camera. For digital imaging using an iPad camera, the LOD of the assay in a sandwich format was 450 fmol with a dynamic range spanning 2 orders of magnitude, while an epifluorescence microscope detection platform offered a LOD of 30 fmol and a dynamic range spanning 3 orders of magnitude. The selectivity of the hybridization assay was demonstrated by detection of a single nucleotide polymorphism at a contrast ratio of 60:1. This work provides an

  3. A pyrene-benzthiazolium conjugate portraying aggregation induced emission, a ratiometric detection and live cell visualization of HSO{sub 3}{sup −}

    Energy Technology Data Exchange (ETDEWEB)

    Diwan, Uzra; Kumar, Virendra [Department of Chemistry (Centre of Advanced Study), Faculty of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 (India); Mishra, Rakesh K. [Photosciences and Photonics, Chemical Sciences and Technology Division, CSIR–National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019 (India); Rana, Nishant Kumar; Koch, Biplob; Singh, Manish Kumar [Department of Zoology (Centre of Advanced Study), Faculty of Science, Banaras Hindu University, Varanasi 221005 (India); Upadhyay, K.K., E-mail: [Department of Chemistry (Centre of Advanced Study), Faculty of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 (India)


    The present study deals with the photophysical property of a pyrene-benzthiazolium conjugate R1, as a strong intramolecular charge transfer (ICT) probe exhibiting long wavelength emission in the red region. Unlike traditional planar polyaromatic hydrocarbons whose aggregation generally quenches the light emission, the pyrene based R1 was found to display aggregation-induced emission (AIE) property along with simultaneous increase in its quantum yield upon increasing the water content of the medium. The R1 exhibits high specificity towards HSO{sub 3}{sup −}/SO{sub 3}{sup 2−} by interrupting its own ICT producing there upon a large ratiometric blue shift of ∼220 nm in its emission spectrum. The lowest detection limit for the above measurement was found to be 8.90 × 10{sup −8} M. The fluorescent detection of HSO{sub 3}{sup −} was also demonstrated excellently by test paper strip and silica coated TLC plate incorporating R1. The live cell imaging of HSO{sub 3}{sup −} through R1 in HeLa cells was studied using fluorescence microscopic studies. The particle size and morphological features of R1 and R1-HSO{sub 3}{sup −} aggregates in aqueous solution were characterized by DLS along with SEM analysis.- Highlights: • A pyrene-benzthiazolium conjugate probe (R1) itself showed interesting phenomenon of an aggregation-induced emission (AIE). • R1 emits in the red channel and effectively utilized as a colorimetric and ratiometric fluorescent sensor for HSO{sub 3}{sup −}. • The nano-dimensional spherical particles of R1 got enlarged upon its interaction with the HSO{sub 3}{sup −}. • R1 can efficiently stain HSO{sub 3}{sup −} in live cells and can be used for the on-spot detection of the same.

  4. Ratiometric sensing of metabolites using dual-emitting ZnS:Mn(2+) quantum dots as sole luminophore via surface chemistry design. (United States)

    Gu, Wenliang; Gong, Suqin; Zhou, Yunlong; Xia, Yunsheng


    We herein present an effective and versatile platform for ratiometric sensing of metabolites using intrinsically dual-emitting ZnS:Mn(2+) quantum dots (QDs) as sole reporter. To avoid notoriously non-specific interactions, a special triple-layer "filter screen" around the inorganic QD core is rationally constructed, which is made of oleic acid, cetyltrimethyl ammonium bromide and bio-enzymes. In the presence of the analytes, the in-situ enzymatic H2O2 molecules diffuse and pass through the "filter screen" along the molecule interspace, which then reacts with the inorganic core and leads to more dramatically quenching of the Mn(2+) emission. The ratiometric signal readout is so distinct that can be observed by naked eyes (from orange to violet). In contrast, various coexisting bio-molecules, due to larger size, are well prevented from penetrating the filter screen by steric hindrance effect. So, various potential interfering substances do not disturb the assay. Under optimal conditions, five kinds of the corresponding substrates, namely glucose, cholesterol, lactate, xanthine and uric acid are well quantified by the emission intensity ratio of I470/I615, and the linear ranges are 0.1-200µM, 0.1-200µM, 1-200µM, 1-200µM and 1-200µM, respectively. The detection limits can even reach quasi-picomole levels. Because of favorable analytical performances (excellent selectivity, appropriate sensitivity and broad linear range), the proposed system can direct assay the analytes in blood without any sample pre-treatment.

  5. Förster Resonance Energy Transfer Switchable Self-Assembled Micellar Nanoprobe: Ratiometric Fluorescent Trapping of Endogenous H2S Generation via Fluvastatin-Stimulated Upregulation. (United States)

    Zhao, Chunchang; Zhang, Xiuli; Li, Kaibin; Zhu, Shaojia; Guo, Zhiqian; Zhang, Lili; Wang, Feiyi; Fei, Qiang; Luo, Sihang; Shi, Ping; Tian, He; Zhu, Wei-Hong


    H2S produced in small amounts by mammalian cells has been identified in mediating biological signaling functions. However, the in situ trapping of endogenous H2S generation is still handicapped by a lack of straightforward methods with high selectivity and fast response. Here, we encapsulate a semi-cyanine-BODIPY hybrid dye (BODInD-Cl) and its complementary energy donor (BODIPY1) into the hydrophobic interior of an amphiphilic copolymer (mPEG-DSPE), especially for building up a ratiometric fluorescent H2S nanoprobe with extraordinarily fast response. A remarkable red-shift in the absorption band with a gap of 200 nm in the H2S response can efficiently switch off the Förster resonance energy transfer (FRET) from BODIPY1 to BODInD-Cl, subsequently recovering the donor fluorescence. Impressively, both the interior hydrophobicity of supramolecular micelles and electron-withdrawing nature of indolium unit in BODInD-Cl can sharply increase aromatic nucleophilic substitution with H2S. The ratiometric strategy based on the unique self-assembled micellar aggregate NanoBODIPY achieves an extremely fast response, enabling in situ imaging of endogenous H2S production and mapping its physiological and pathological consequences. Moreover, the amphiphilic copolymer renders the micellar assembly biocompatible and soluble in aqueous solution. The established FRET-switchable macromolecular envelope around BODInD-Cl and BODIPY1 enables cellular uptake, and makes a breakthrough in the trapping of endogenous H2S generation within raw264.7 macrophages upon stimulation with fluvastatin. This study manifests that cystathione γ-lyase (CSE) upregulation contributes to endogenous H2S generation in fluvastatin-stimulated macrophages, along with a correlation between CSE/H2S and activating Akt signaling pathway.

  6. A genetically encoded fluorescent probe in mammalian cells. (United States)

    Chatterjee, Abhishek; Guo, Jiantao; Lee, Hyun Soo; Schultz, Peter G


    Fluorescent reporters are useful in vitro and in vivo probes of protein structure, function, and localization. Here we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), can be site-specifically incorporated into proteins in mammalian cells in response to the TAG codon with high efficiency using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase (aaRS) pair. We further demonstrate that Anap can be used to image the subcellular localization of proteins in live mammalian cells. The small size of Anap, its environment-sensitive fluorescence, and the ability to introduce Anap at specific sites in the proteome by simple mutagenesis make it a unique and valuable tool in eukaryotic cell biology.

  7. A mTurquoise-based cAMP sensor for both FLIM and ratiometric read-out has improved dynamic range.

    Directory of Open Access Journals (Sweden)

    Jeffrey B Klarenbeek

    Full Text Available FRET-based sensors for cyclic Adenosine Mono Phosphate (cAMP have revolutionized the way in which this important intracellular messenger is studied. The currently prevailing sensors consist of the cAMP-binding protein Epac1, sandwiched between suitable donor- and acceptor fluorescent proteins (FPs. Through a conformational change in Epac1, alterations in cellular cAMP levels lead to a change in FRET that is most commonly detected by either Fluorescence Lifetime Imaging (FLIM or by Sensitized Emission (SE, e.g., by simple ratio-imaging. We recently reported a range of different Epac-based cAMP sensors with high dynamic range and signal-to-noise ratio. We showed that constructs with cyan FP as donor are optimal for readout by SE, whereas other constructs with green FP donors appeared much more suited for FLIM detection. In this study, we present a new cAMP sensor, termed (TEpac(VV, which employs mTurquoise as donor. Spectrally very similar to CFP, mTurquoise has about doubled quantum efficiency and unlike CFP, its fluorescence decay is strictly single-exponential. We show that (TEpac(VV appears optimal for detection both by FLIM and SE, that it has outstanding FRET span and signal-to-noise ratio, and improved photostability. Hence, (TEpac(VV should become the cAMP sensor of choice for new experiments, both for FLIM and ratiometric detection.

  8. Near-infrared dual-emission quantum dots-gold nanoclusters nanohybrid via co-template synthesis for ratiometric fluorescent detection and bioimaging of ascorbic acid in vitro and in vivo. (United States)

    Zhao, Peng; He, Kaiyu; Han, Yitao; Zhang, Zhen; Yu, Mengze; Wang, Honghui; Huang, Yan; Nie, Zhou; Yao, Shouzhuo


    Near-infrared (NIR) quantum dots (QDs) have emerged as an attractive bioimaging toolkit for exploring biological events because they can provide deep imaging penetration and low fluorescence background. However, the quantitation process of such NIR QDs generally relies on single-emission intensity change, which is susceptible to a variety of environmental factors. Herein, for the first time, we proposed a protein-directed co-template strategy to synthesize a NIR-based, dual-emission fluorescent nanohybrid (DEFN) constructed from far-red gold nanoclusters and NIR PbS QDs (AuNCs-PbS-QDs). The convenient protein-directed co-template synthesis avoids the tedious chemical coupling and modification required in conventional preparation approaches of DEFNs. Additionally, the dual-emission signals of AuNCs-PbS-QDs exhibit two well-resolved emission peaks (640 and 813 nm) separated by 173 nm, which can eliminate environmental interferences by the built-in correction of ratiometric signal, resulting in a more favorable system for bioimaging and biosensing. Next, the target-responsive capability of this NIR-based DEFN to ascorbic acid (AA) was discovered, enabling the proposed DEFN to ratiometrically detect AA with a linear range of 3-40 μM and a detection limit of 1.5 μM. This DEFN sensor possesses high selectivity, rapid response, and excellent photostability. Moreover, the feasibility of this NIR nanosensor has been fully proved by the ratiometric detection of AA for fruit internal quality assessment, in vitro cellular imaging, and in vivo imaging in nude mice.

  9. 9-Aryl-1,2-dihydropyrrolo[3,4-b]indolizin-3-one (Seoul-Fluor) as a smart platform for colorful ratiometric fluorescent pH sensors. (United States)

    Kim, Eunha; Lee, Sanghee; Park, Seung Bum


    In this communication, we report that 9-aryl-1,2-dihydropyrrolo[3,4-b]indolizin-3-one (Seoul-Fluor) can serve as a potential platform for colorful ratiometric fluorescent pH sensors by simple incorporation of pH responsive elements on Seoul-Fluor. Seoul-Fluor-based fluorescent pH sensors allow the emission- and pH-tuning ability upon protonation by varying their pK(a) values and electronic characteristics of substituents by a rational design.

  10. Design of NIR Chromenylium-Cyanine Fluorophore Library for "Switch-ON" and Ratiometric Detection of Bio-Active Species In Vivo. (United States)

    Wei, Yanfen; Cheng, Dan; Ren, Tianbing; Li, Yinhui; Zeng, Zebing; Yuan, Lin


    The real-time monitoring of key biospecies in the living systems has received thrusting attention during the past decades. Specifically, fluorescent detection based on near-infrared (NIR) fluorescent probes is highly favorable for live cells, live tissues, and even animal imaging, owing to the substantial merits of the NIR window, such as minimal phototoxicity, deep penetration into tissues, and low autofluorescence background. Nevertheless, developing potent NIR fluorescent probes still poses serious challenges to the chemists because traditional NIR fluorophores are less tunable than visible-wavelength fluorophores. To address this issue, here we report a set of novel NIR hybrid fluorophores, namely, the hybrid chromenylium-cyanine fluorophore (CC-Fluor), in which both the fluorescence intensity and the emission wavelength can be easily adjusted by the conformational changes and substitution groups. Compared to known NIR fluorophores, the new CC-Fluors are substantially advantageous for NIR probe development: (1) CC-Fluors display tunable and moderate Stokes shifts and quantum yields; (2) the fluorophores are stable at physiological conditions after long-term incubation; (3) the absorption maxima of CC-Fluors coincide with the common laser spectral lines in mainstream in vivo imaging systems; (4) most importantly, CC-Fluors can be easily modified to prepare NIR probes targeting various biospecies. To fully demonstrate the practical utility of CC-Fluors, we report two innovative NIR probes, a ratiometric pH probe and a turn-on Hg(2+) probe, both are successfully employed in live animal imaging. Hence, the detailed studies allow us to confirm that CC-Fluors can work as an excellent platform for developing NIR probes for the detection of species in living systems.

  11. Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography-tandem mass spectrometry targeted metabolomics. (United States)

    Sampsonidis, Ioannis; Witting, Michael; Koch, Wendelin; Virgiliou, Christina; Gika, Helen G; Schmitt-Kopplin, Philippe; Theodoridis, Georgios A


    In the present work two different approaches, a semi-quantitative and a Derringer function approach, were developed to assist column selection for method development in targeted metabolomics. These approaches were applied in the performance assessment of three HILIC columns with different chemistries (an amide, a diol and a zwitterionic phase). This was the first step for the development of a HILIC UPLC-MS/MS method that should be capable to analyze a large number of polar metabolites. Two gradient elution profiles and two mobile phase pH values were tested for the analysis of multi-analyte mixtures. Acquired chromatographic data were firstly treated by a ratiometric, "semi-quantitative" approach which quantifies various overall analysis parameters (e.g. the percent of detected compounds, retentivity and resolved critical pairs). These parameters were used to assess chromatographic performance in a rather conventional/traditional and cumbersome/labor-intensive way. Secondly, a comprehensive and automated comparison of the three columns was performed by monitoring several well-known chromatographic parameters (peak width, resolution, tailing factor, etc.) using a lab-built programming script which calculates overall desirability utilizing Derringer functions. Derringer functions exhibit the advantage that column performance is ultimately expressed in an objective single and quantitative value which can be easily interpreted. In summary, results show that each column exhibits unique strengths in metabolic profiling of polar compounds. The applied methodology proved useful for the selection of the most effective chromatographic system during method development for LC-MS/MS targeted metabolomics, while it could further assist in the selection of chromatographic conditions for the development of multi-analyte methods.

  12. A molecular imprinting-based turn-on Ratiometric fluorescence sensor for highly selective and sensitive detection of 2,4-dichlorophenoxyacetic acid (2,4-D). (United States)

    Wang, Xiaoyan; Yu, Jialuo; Wu, Xiaqing; Fu, Junqing; Kang, Qi; Shen, Dazhong; Li, Jinhua; Chen, Lingxin


    A novel molecular imprinting-based turn-on ratiometric fluorescence sensor was constructed via a facile sol-gel polymerization for detection of 2,4-dichlorophenoxyacetic acid (2,4-D) on the basis of photoinduced electron transfer (PET) by using nitrobenzoxadiazole (NBD) as detection signal source and quantum dots (QDs) as reference signal source. With the presence and increase of 2,4-D, the amine groups on the surface of QDs@SiO2 could bind with 2,4-D and thereby the NBD fluorescence intensities could be significantly enhanced since the PET process was inhibited, while the QDs maintained constant intensities. Accordingly, the ratio of the dual-emission intensities of green NBD and red QDs could be utilized for turn-on fluorescent detection of 2,4-D, along with continuous color changes from orange-red to green readily observed by the naked eye. The as-prepared fluorescence sensor obtained high sensitivity with a low detection limit of 0.14μM within 5min, and distinguished recognition selectivity for 2,4-D over its analogs. Moreover, the sensor was successfully applied to determine 2,4-D in real water samples, and high recoveries at three spiking levels of 2,4-D ranged from 95.0% to 110.1% with precisions below 4.5%. The simple, rapid and reliable visual sensing strategy would not only provide potential applications for high selective ultratrace analysis of complicated matrices, but also greatly enrich the research connotations of molecularly imprinted sensors.

  13. Micro Electrochemical pH Sensor Applicable for Real-Time Ratiometric Monitoring of pH Values in Rat Brains. (United States)

    Zhou, Jie; Zhang, Limin; Tian, Yang


    To develop in vivo monitoring meter for pH measurements is still the bottleneck for understanding the role of pH plays in the brain diseases. In this work, a selective and sensitive electrochemical pH meter was developed for real-time ratiometric monitoring of pH in different regions of rat brains upon ischemia. First, 1,2-naphthoquinone (1,2-NQ) was employed and optimized as a selective pH recognition element to establish a 2H(+)/2e(-) approach over a wide range of pH from 5.8 to 8.0. The pH meter demonstrated remarkable selectivity toward pH detection against metal ions, amino acids, reactive oxygen species, and other biological species in the brain. Meanwhile, an inner reference, 6-(ferrocenyl)hexanethiol (FcHT), was selected as a built-in correction to avoid the environmental effect through coimmobilization with 1,2-NQ. In addition, three-dimensional gold nanoleaves were electrodeposited onto the electrode surface to amplify the signal by ∼4.0-fold and the measurement was achieved down to 0.07 pH. Finally, combined with the microelectrode technique, the microelectrochemical pH meter was directly implanted into brain regions including the striatum, hippocampus, and cortex and successfully applied in real-time monitoring of pH values in these regions of brain followed by global cerebral ischemia. The results demonstrated that pH values were estimated to 7.21 ± 0.05, 7.13 ± 0.09, and 7.27 ± 0.06 in the striatum, hippocampus, and cortex in the rat brains, respectively, in normal conditions. However, pH decreased to 6.75 ± 0.07 and 6.52 ± 0.03 in the striatum and hippocampus, upon global cerebral ischemia, while a negligible pH change was obtained in the cortex.

  14. Ratiometric analysis in hyperpolarized NMR (I): test of the two-site exchange model and the quantification of reaction rate constants. (United States)

    Li, Lin Z; Kadlececk, Stephen; Xu, He N; Daye, Dania; Pullinger, Benjamin; Profka, Harrilla; Chodosh, Lewis; Rizi, Rahim


    Conventional methods for the analysis of in vivo hyperpolarized (13) C NMR data from the lactate dehydrogenase (LDH) reaction usually make assumptions on the stability of rate constants and/or the validity of the two-site exchange model. In this study, we developed a framework to test the validity of the assumption of stable reaction rate constants and the two-site exchange model in vivo via ratiometric fitting of the time courses of the signal ratio L(t)/P(t). Our analysis provided evidence that the LDH enzymatic kinetics observed by hyperpolarized NMR are in near-equilibrium and satisfy the two-site exchange model for only a specific time window. In addition, we quantified both the forward and reverse exchange rate constants of the LDH reaction for the transgenic and mouse xenograft models of breast cancer using the ratio fitting method developed, which includes only two modeling parameters and is less sensitive to the influence of instrument settings/protocols, such as flip angles, degree of polarization and tracer dosage. We further compared the ratio fitting method with a conventional two-site exchange modeling method, i.e. the differential equation fitting method, using both the experimental and simulated hyperpolarized NMR data. The ratio fitting method appeared to fit better than the differential equation fitting method for the reverse rate constant on the mouse tumor data, with less relative errors on average, whereas the differential equation fitting method also resulted in a negative reverse rate constant for one tumor. The simulation results indicated that the accuracy of both methods depends on the width of the transport function, noise level and rate constant ratio; one method may be more accurate than the other based on the experimental/biological conditions aforementioned. We were able to categorize our tumor models into specific conditions of the computer simulation and to estimate the errors of rate quantification. We also discussed possible

  15. Ultrasmall, water dispersible, TWEEN80 modified Yb:Er:NaGd(WOsub>4sub>)sub>2sub> nanoparticles with record upconversion ratiometric thermal sensitivity and their internalization by mesenchymal stem cells. (United States)

    Cascales, Concepcion; Paino, Carlos; Bazán, Eulalia; Zaldo, Carlos


    This work presents the synthesis by coprecipitation of diamond shaped Yb:Er:NaGd(WOsub>4sub>)sub>2sub> crystalline nanoparticles (NPs) with diagonal dimensions in the 5-7 nm × 10-12 nm range which have been modified with TWEEN80 for their dispersion in water, and their interaction with mesenchymal stem cells (MSCs) proposed as cellular NP vehicles. These NPs belong to a large family of tetragonal Yb:Er:NaT(XOsub>4sub>)sub>2sub> (T=Y, La, Gd, Lu; X= Mo, W) compounds with green (2Hsub>11/2sub>+4Ssub>3/2sub>→4Isub>15/2sub>) Er-related upconversion (UC) efficiency comparable to that of Yb:Er:β-NaYFsub>4sub> reference compound, but with a ratiometric thermal sensitivity (S) 2.5-3.5 times larger than that of the fluoride. At the temperature range of interest for biomedical applications (~293-317 K / 20-44 ºC) S= 108-118 × 10-4 K-1 for 20at%Yb:5at%Er:NaGd(WOsub>4sub>)sub>2sub> NPs, being the largest values so far reported using the 2Hsub>11/2sub>/4Ssub>3/2sub> Er intensity ratiometric method. Cultured MSCs, incubated with these water NP emulsions, internalize and accumulate the NPs enclosed in endosomes/lysosomes. Incubations with up to 10 μg of NPs per ml of culture medium maintain cellular metabolism at 72 h. A thermal assisted excitation path is discussed as responsible for the UC behavior of Yb:Er:NaT(XOsub>4sub>)sub>2sub> compounds.

  16. Simplified quantification of labile proton concentration-weighted chemical exchange rate (k(ws) ) with RF saturation time dependent ratiometric analysis (QUESTRA): normalization of relaxation and RF irradiation spillover effects for improved quantitative chemical exchange saturation transfer (CEST) MRI. (United States)

    Sun, Phillip Zhe


    Chemical exchange saturation transfer MRI is an emerging imaging technique capable of detecting dilute proteins/peptides and microenvironmental properties, with promising in vivo applications. However, chemical exchange saturation transfer MRI contrast is complex, varying not only with the labile proton concentration and exchange rate, but also with experimental conditions such as field strength and radiofrequency (RF) irradiation scheme. Furthermore, the optimal RF irradiation power depends on the exchange rate, which must be estimated in order to optimize the chemical exchange saturation transfer MRI experiments. Although methods including numerical fitting with modified Bloch-McConnell equations, quantification of exchange rate with RF saturation time and power (QUEST and QUESP), have been proposed to address this relationship, they require multiple-parameter non-linear fitting and accurate relaxation measurement. Our work extended the QUEST algorithm with ratiometric analysis (QUESTRA) that normalizes the magnetization transfer ratio at labile and reference frequencies, which effectively eliminates the confounding relaxation and RF spillover effects. Specifically, the QUESTRA contrast approaches its steady state mono-exponentially at a rate determined by the reverse exchange rate (k(ws) ), with little dependence on bulk water T(1) , T(2) , RF power and chemical shift. The proposed algorithm was confirmed numerically, and validated experimentally using a tissue-like phantom of serially titrated pH compartments.

  17. Ratiometric pH fluorescent probe based on indole hemi-cyanine derivative%基于吲哚半花菁结构的比值式pH荧光探针

    Institute of Scientific and Technical Information of China (English)

    曾科; 周彬彬; 龙一国


    A new hemi-cyanine based ratiometric fluorescent pH probe was synthesized. The probe re-sponds to pH with high selectivity and sensitivity. A red-shift of UV-Vis absorption occurred from 422 nm to 525 nm with the increase of pH from 5 to 9 . The fluorescence intensity ratio( R=I513 nm/I553 nm )exhib-its a good linearity with pH within the range of 5. 4~7. 2 at λex =430 nm. MTT assay revealed that the probe has low cytotoxicity.%设计合成了一种基于半花菁类结构的比值式pH荧光探针,能快速响应pH值的变化,对常见金属离子具有较好的抗干扰能力。在pH 5.4~7.2范围内,随着pH值升高,探针紫外可见吸收光谱最大吸收波长由422 nm红移至525 nm。激发波长为430 nm时,荧光发射峰峰高之比( I513 nm/I553 nm )与pH值的变化有良好的线性关系,可用于检测生物体内pH的变化。HeLa细胞毒性试验表明,该探针具有较低的细胞毒性。

  18. Synthesis and application of double quantum dots nanocomposite ratiometric fluorescent sensor for NO%双量子点纳米复合物NO比率荧光探针的合成与应用

    Institute of Scientific and Technical Information of China (English)

    李娜; 孙捷; 王晓静; 孙敬勇; 王兵


    A double quantum dots nanocomposite of CdSe@ SiO2‐CdTe was synthesized based on the electrostatic adsorption .A Cd‐NO complex was formed by the combination of nitric ox‐ide (NO) with Cd ions on the surface of CdTe quantum dots ,which led to CdTe quantum dots fluorescence quenching , without affecting the fluorescence of CdSe quantum dots .Further‐more ,its utility was carried out to detect NO quantitatively according to the linear relationship between the concentrations of NO (0 1.~2 2. μmol/L) and the relevant I603/I532 values of the ratiometric fluorescent sensor .%通过静电吸附作用,合成了CdSe@ SiO2‐CdTe双量子点的纳米复合物.一氧化氮(NO)与CdTe量子点表面Cd离子结合形成Cd‐NO复合物,引起CdTe量子点荧光猝灭,而不影响CdSe量子点的荧光.当NO浓度在01.~22.μmol/L之间变化时,该探针荧光强度比值 I603/I532符合线性关系(R=-09.954),从而实现对NO的定量检测.

  19. Phototoxic effects of lysosome-associated genetically encoded photosensitizer KillerRed (United States)

    Serebrovskaya, Ekaterina O.; Ryumina, Alina P.; Boulina, Maria E.; Shirmanova, Marina V.; Zagaynova, Elena V.; Bogdanova, Ekaterina A.; Lukyanov, Sergey A.; Lukyanov, Konstantin A.


    KillerRed is a unique phototoxic red fluorescent protein that can be used to induce local oxidative stress by green-orange light illumination. Here we studied phototoxicity of KillerRed targeted to cytoplasmic surface of lysosomes via fusion with Rab7, a small GTPase that is known to be attached to membranes of late endosomes and lysosomes. It was found that lysosome-associated KillerRed ensures efficient light-induced cell death similar to previously reported mitochondria- and plasma membrane-localized KillerRed. Inhibitory analysis demonstrated that lysosomal cathepsins play an important role in the manifestation of KillerRed-Rab7 phototoxicity. Time-lapse monitoring of cell morphology, membrane integrity, and nuclei shape allowed us to conclude that KillerRed-Rab7-mediated cell death occurs via necrosis at high light intensity or via apoptosis at lower light intensity. Potentially, KillerRed-Rab7 can be used as an optogenetic tool to direct target cell populations to either apoptosis or necrosis.

  20. Abscisic acid dynamics in roots detected with genetically encoded FRET sensors. (United States)

    Jones, Alexander M; Danielson, Jonas Ah; Manojkumar, Shruti N; Lanquar, Viviane; Grossmann, Guido; Frommer, Wolf B


    Cytosolic hormone levels must be tightly controlled at the level of influx, efflux, synthesis, degradation and compartmentation. To determine ABA dynamics at the single cell level, FRET sensors (ABACUS) covering a range ∼0.2-800 µM were engineered using structure-guided design and a high-throughput screening platform. When expressed in yeast, ABACUS1 detected concentrative ABA uptake mediated by the AIT1/NRT1.2 transporter. Arabidopsis roots expressing ABACUS1-2µ (Kd∼2 µM) and ABACUS1-80µ (Kd∼80 µM) respond to perfusion with ABA in a concentration-dependent manner. The properties of the observed ABA accumulation in roots appear incompatible with the activity of known ABA transporters (AIT1, ABCG40). ABACUS reveals effects of external ABA on homeostasis, that is, ABA-triggered induction of ABA degradation, modification, or compartmentation. ABACUS can be used to study ABA responses in mutants and quantitatively monitor ABA translocation and regulation, and identify missing components. The sensor screening platform promises to enable rapid fine-tuning of the ABA sensors and engineering of plant and animal hormone sensors to advance our understanding of hormone signaling. DOI:

  1. Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors. (United States)

    Brutesco, Catherine; Prévéral, Sandra; Escoffier, Camille; Descamps, Elodie C T; Prudent, Elsa; Cayron, Julien; Dumas, Louis; Ricquebourg, Manon; Adryanczyk-Perrier, Géraldine; de Groot, Arjan; Garcia, Daniel; Rodrigue, Agnès; Pignol, David; Ginet, Nicolas


    Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible Pars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.

  2. Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors (United States)

    Meyer, Andreas; Pellaux, René; Potot, Sébastien; Becker, Katja; Hohmann, Hans-Peter; Panke, Sven; Held, Martin


    Microcompartmentalization offers a high-throughput method for screening large numbers of biocatalysts generated from genetic libraries. Here we present a microcompartmentalization protocol for benchmarking the performance of whole-cell biocatalysts. Gel capsules served as nanolitre reactors (nLRs) for the cultivation and analysis of a library of Bacillus subtilis biocatalysts. The B. subtilis cells, which were co-confined with E. coli sensor cells inside the nLRs, converted the starting material cellobiose into the industrial product vitamin B2. Product formation triggered a sequence of reactions in the sensor cells: (1) conversion of B2 into flavin mononucleotide (FMN), (2) binding of FMN by a RNA riboswitch and (3) self-cleavage of RNA, which resulted in (4) the synthesis of a green fluorescent protein (GFP). The intensity of GFP fluorescence was then used to isolate B. subtilis variants that convert cellobiose into vitamin B2 with elevated efficiency. The underlying design principles of the assay are general and enable the development of similar protocols, which ultimately will speed up the optimization of whole-cell biocatalysts.

  3. Assessing T lymphocyte function and differentiation by genetically encoded reporter systems. (United States)

    Hoekstra, Mirjam E; Dijkgraaf, Feline E; Schumacher, Ton N; Rohr, Jan C


    Upon infection, antigen-specific T lymphocytes become activated, proliferate, differentiate, and acquire various effector functions. Much of our understanding of the molecular mechanisms underlying these processes derives from studies leveraging gene deletion, RNAi, and overexpression approaches. However, these perturbations do not inform on the regulation of gene activity under physiological conditions. Genetic reporter systems that couple biological events to detectable output signals are capable of providing this information. Here, we review the reporter approaches being currently used to investigate various aspects of T cell behavior, and discuss advantages and disadvantages inherent to different designs. We outline emerging applications based on recent advances in other fields, and highlight the potential of synthetic biology and genome engineering to address open questions in the field.

  4. Herpesvirus-Mediated Delivery of a Genetically Encoded Fluorescent Ca2+ Sensor to Canine Cardiomyocytes

    Directory of Open Access Journals (Sweden)

    János Prorok


    Full Text Available We report the development and application of a pseudorabies virus-based system for delivery of troponeon, a fluorescent Ca2+ sensor to adult canine cardiomyocytes. The efficacy of transduction was assessed by calculating the ratio of fluorescently labelled and nonlabelled cells in cell culture. Interaction of the virus vector with electrophysiological properties of cardiomyocytes was evaluated by the analysis of transient outward current (Ito, kinetics of the intracellular Ca2+ transients, and cell shortening. Functionality of transferred troponeon was verified by FRET analysis. We demonstrated that the transfer efficiency of troponeon to cultured adult cardiac myocytes was virtually 100%. We showed that even after four days neither the amplitude nor the kinetics of the Ito current was significantly changed and no major shifts occurred in parameters of [Ca2+]i transients. Furthermore, we demonstrated that infection of cardiomyocytes with the virus did not affect the morphology, viability, and physiological attributes of cells.

  5. Generation of a genetically encoded marker of rod photoreceptor outer segment growth and renewal

    Directory of Open Access Journals (Sweden)

    John J. Willoughby


    Vertebrate photoreceptors are specialized light sensing neurons. The photoreceptor outer segment is a highly modified cilium where photons of light are transduced into a chemical and electrical signal. The outer segment has the typical cilary axoneme but, in addition, it has a large number of densely packed, stacked, intramembranous discs. The molecular and cellular mechanisms that contribute to vertebrate photoreceptor outer segment morphogenesis are still largely unknown. Unlike typical cilia, the outer segment is continuously regenerated or renewed throughout the life of the animal through the combined process of distal outer segment shedding and proximal outer segment growth. The process of outer segment renewal was discovered over forty years ago, but we still lack an understanding of how photoreceptors renew their outer segments and few, if any, molecular mechanisms that regulate outer segment growth or shedding have been described. Our lack of progress in understanding how photoreceptors renew their outer segments has been hampered by the difficulty in measuring rates of renewal. We have created a new method that uses heat-shock induction of a fluorescent protein that can be used to rapidly measure outer segment growth rates. We describe this method, the stable transgenic line we created, and the growth rates observed in larval and adult rod photoreceptors using this new method. This new method will allow us to begin to define the genetic and molecular mechanisms that regulate rod outer segment renewal, a crucial aspect of photoreceptor function and, possibly, viability.

  6. Using genetically encoded fluorescent reporters to image lipid signalling in living plants

    NARCIS (Netherlands)

    J.E.M. Vermeer; T. Munnik


    The discovery of the green fluorescent protein has revolutionized cell biology as it allowed researchers to visualize dynamic processes in living cells. The fusion of fluorescent protein variants with lipid binding domains that bind to specific phospholipids have been very instrumental in investigat

  7. Statistical sulcal shape comparisons: application to the detection of genetic encoding of the central sulcus shape

    DEFF Research Database (Denmark)

    Le Goualher, G; Argenti, A.M.; Duyme, M;


    encoding. When applied to real data, this study highlighted genetic constraints on the shape of the central sulcus. We found from 10 pairs of monozygotic twins that the intrapair modal distance of the central sulcus was significantly smaller than the interpair modal distance, for both the left central...... sulcus (Z = -2.66; P sulcus (Z = -2.26; P sulcus shape were confirmed by applying the same experiment to 10 pairs of normal young individuals (Z = -1.39; Z = -0.63, i.e., values not significant at the P

  8. Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics. (United States)

    Li, Xinran; Wang, Xiang; Zhang, Xiaoli; Zhao, Mingkun; Tsang, Wai Lok; Zhang, Yanling; Yau, Richard Gar Wai; Weisman, Lois S; Xu, Haoxing


    Phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] is a low-abundance phosphoinositide presumed to be localized to endosomes and lysosomes, where it recruits cytoplasmic peripheral proteins and regulates endolysosome-localized membrane channel activity. Cells lacking PI(3,5)P2 exhibit lysosomal trafficking defects, and human mutations in the PI(3,5)P2-metabolizing enzymes cause lysosome-related diseases. The spatial and temporal dynamics of PI(3,5)P2, however, remain unclear due to the lack of a reliable detection method. Of the seven known phosphoinositides, only PI(3,5)P2 binds, in the low nanomolar range, to a cytoplasmic phosphoinositide-interacting domain (ML1N) to activate late endosome and lysosome (LEL)-localized transient receptor potential Mucolipin 1 (TRPML1) channels. Here, we report the generation and characterization of a PI(3,5)P2-specific probe, generated by the fusion of fluorescence tags to the tandem repeats of ML1N. The probe was mainly localized to the membranes of Lamp1-positive compartments, and the localization pattern was dynamically altered by either mutations in the probe, or by genetically or pharmacologically manipulating the cellular levels of PI(3,5)P2. Through the use of time-lapse live-cell imaging, we found that the localization of the PI(3,5)P2 probe was regulated by serum withdrawal/addition, undergoing rapid changes immediately before membrane fusion of two LELs. Our development of a PI(3,5)P2-specific probe may facilitate studies of both intracellular signal transduction and membrane trafficking in the endosomes and lysosomes.

  9. The Use of Ratiometric Fluorescence Measurements of the Voltage Sensitive Dye Di-4-ANEPPS to Examine Action Potential Characteristics and Drug Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (United States)

    Hortigon-Vinagre, M. P.; Zamora, V.; Burton, F. L.; Green, J.; Gintant, G. A.; Smith, G. L.


    Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) and higher throughput platforms have emerged as potential tools to advance cardiac drug safety screening. This study evaluated the use of high bandwidth photometry applied to voltage-sensitive fluorescent dyes (VSDs) to assess drug-induced changes in action potential characteristics of spontaneously active hiPSC-CM. Human iPSC-CM from 2 commercial sources (Cor.4U and iCell Cardiomyocytes) were stained with the VSD di-4-ANEPPS and placed in a specialized photometry system that simultaneously monitors 2 wavebands of emitted fluorescence, allowing ratiometric measurement of membrane voltage. Signals were acquired at 10 kHz and analyzed using custom software. Action potential duration (APD) values were normally distributed in cardiomyocytes (CMC) from both sources though the mean and variance differed significantly (APD90: 229 ± 15 ms vs 427 ± 49 ms [mean ± SD, P < 0.01]; average spontaneous cycle length: 0.99 ± 0.02 s vs 1.47 ± 0.35 s [mean ± SD, P < 0.01], Cor.4U vs iCell CMC, respectively). The 10–90% rise time of the AP (Trise) was ∼6 ms and was normally distributed when expressed as 1/Trise2 in both cell preparations. Both cell types showed a rate dependence analogous to that of adult human cardiac cells. Furthermore, nifedipine, ranolazine, and E4031 had similar effects on cardiomyocyte electrophysiology in both cell types. However, ranolazine and E4031 induced early after depolarization-like events and high intrinsic firing rates at lower concentrations in iCell CMC. These data show that VSDs provide a minimally invasive, quantitative, and accurate method to assess hiPSC-CM electrophysiology and detect subtle drug-induced effects for drug safety screening while highlighting a need to standardize experimental protocols across preparations. PMID:27621282

  10. Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy

    NARCIS (Netherlands)

    Gaietta, Guido M; Giepmans, Ben N G; Deerinck, Thomas J; Smith, W Bryan; Ngan, Lucy; Llopis, Juan; Adams, Stephen R; Tsien, Roger Y; Ellisman, Mark H


    Combinations of molecular tags visible in light and electron microscopes become particularly advantageous in the analysis of dynamic cellular components like the Golgi apparatus. This organelle disassembles at the onset of mitosis and, after a sequence of poorly understood events, reassembles after

  11. Fluorescence-based characterization of genetically encoded peptides that fold in live cells: progress toward a generic hairpin scaffold (United States)

    Cheng, Zihao; Campbell, Robert E.


    Binding proteins suitable for expression and high affinity molecular recognition in the cytoplasm or nucleus of live cells have numerous applications in the biological sciences. In an effort to add a new minimal motif to the growing repertoire of validated non-immunoglobulin binding proteins, we have undertaken the development of a generic protein scaffold based on a single β-hairpin that can fold efficiently in the cytoplasm. We have developed a method, based on the measurement of fluorescence resonance energy transfer (FRET) between a genetically fused cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), that allows the structural stability of recombinant β-hairpin peptides to be rapidly assessed both in vitro and in vivo. We have previously reported the validation of this method when applied to a 16mer tryptophan zipper β-hairpin. We now describe the use of this method to evaluate the potential of a designed 20mer β-hairpin peptide with a 3rd Trp/Trp cross-strand pair to function as a generic protein scaffold. Quantitative analysis of the FRET efficiency, resistance to proteolysis (assayed by loss of FRET), and circular dichroism spectra revealed that the 20mer peptide is significantly more tolerant of destabilizing mutations than the 16mer peptide. Furthermore, we experimentally demonstrate that the in vitro determined β-hairpin stabilities are well correlated with in vivo β-hairpin stabilities as determined by FRET measurements of colonies of live bacteria expressing the recombinant peptides flanked by CFP and YFP. Finally, we report on our progress to develop highly folded 24mer and 28mer β-hairpin peptides through the use of fluorescence-based library screening.

  12. Genetically encoded photocrosslinkers locate the high-affinity binding site of antidepressant drugs in the human serotonin transporter

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Andersen, Jacob; Hall, Lena Sørensen;


    Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode photocrosslin......Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode...

  13. Ratiometric fluorescence imaging of free Zn2+ in brain (United States)

    Thompson, Richard B.; Suh, Sang W.; Frederickson, Christopher J.


    Recently, the function of zinc in the axonal boutons of hippocampal neurons has come under increased scrutiny as evidence has emerged of a putative role for this metal ion in neural damage following insults such as ischemia, blunt force trauma, and seizure. Indeed, the nonpathological role of free zinc in the brain remains cryptic after more than 40 years. We have used a biosensing approach to determine free zinc ion concentrations by fluorescence lifetime, intensity, intensity ratio, or anisotropy changes caused by binding of zinc to variants of a protein, apocarbonic anhydrase II (apo-CA). This approach permits real time measurement of zinc down to picomolar levels, with no perceptible interference from other divalent metal ions abundant in serum and tissue, such as calcium and magnesium. Recently, we used apo-CA together with a fluorescent ligand whose binding is metal-dependent to obtain the first fluorescence micrographs of zinc release from a rat hippocampus model in response to electrical stimulus. In our view, elucidation of the zinc fluxes in neural tissue ultimately requires quantitation, as in the case of calcium. Recent results will be shown.

  14. Ratiometric Imaging of Extracellular pH in Dental Biofilms

    DEFF Research Database (Denmark)

    Schlafer, Sebastian; Dige, Irene


    The pH in bacterial biofilms on teeth is of central importance for dental caries, a disease with a high worldwide prevalence. Nutrients and metabolites are not distributed evenly in dental biofilms. A complex interplay of sorption to and reaction with organic matter in the biofilm reduces...... the diffusion paths of solutes and creates steep gradients of reactive molecules, including organic acids, across the biofilm. Quantitative fluorescent microscopic methods, such as fluorescence life time imaging or pH ratiometry, can be employed to visualize pH in different microenvironments of dental biofilms....... pH ratiometry exploits a pH-dependent shift in the fluorescent emission of pH-sensitive dyes. Calculation of the emission ratio at two different wavelengths allows determining local pH in microscopic images, irrespective of the concentration of the dye. Contrary to microelectrodes the technique...

  15. Two-photon scanning microscopy of in vivo sensory responses of cortical neurons genetically encoded with a fluorescent voltage sensor in rat

    Directory of Open Access Journals (Sweden)

    Kurt F Ahrens


    Full Text Available A fluorescent voltage sensor protein Flare was created from a Kv1.4 potassium channel with YFP situated to report voltage-induced conformational changes in vivo. The RNA virus Sindbis introduced Flare into neurons in the binocular visual crescent in rat. Injection sites were selected based on intrinsic optical imaging. Expression of Flare occurred in the cell bodies and dendritic processes. Neurons imaged in vivo using two-photon scanning microscopy typically revealed the soma best, discernable against the background labeling of the neuropil. Somatic fluorescence changes were correlated with flashed visual stimuli; however, averaging was essential to observe these changes. This study demonstrates that the genetic modification of single neurons to express a fluorescent voltage sensor can be used to assess neuronal activity in vivo.

  16. Two-photon scanning microscopy of in vivo sensory responses of cortical neurons genetically encoded with a fluorescent voltage sensor in rat (United States)

    Ahrens, Kurt F.; Heider, Barbara; Lee, Hanson; Isacoff, Ehud Y.; Siegel, Ralph M.


    A fluorescent voltage sensor protein “Flare” was created from a Kv1.4 potassium channel with YFP situated to report voltage-induced conformational changes in vivo. The RNA virus Sindbis introduced Flare into neurons in the binocular region of visual cortex in rat. Injection sites were selected based on intrinsic optical imaging. Expression of Flare occurred in the cell bodies and dendritic processes. Neurons imaged in vivo using two-photon scanning microscopy typically revealed the soma best, discernable against the background labeling of the neuropil. Somatic fluorescence changes were correlated with flashed visual stimuli; however, averaging was essential to observe these changes. This study demonstrates that the genetic modification of single neurons to express a fluorescent voltage sensor can be used to assess neuronal activity in vivo. PMID:22461770

  17. A comparison of donor-acceptor pairs for genetically encoded FRET sensors: application to the Epac cAMP sensor as an example.

    Directory of Open Access Journals (Sweden)

    Gerard N M van der Krogt

    Full Text Available We recently reported on CFP-Epac-YFP, an Epac-based single polypeptide FRET reporter to resolve cAMP levels in living cells. In this study, we compared and optimized the fluorescent protein donor/acceptor pairs for use in biosensors such as CFP-Epac-YFP. Our strategy was to prepare a wide range of constructs consisting of different donor and acceptor fluorescent proteins separated by a short linker. Constructs were expressed in HEK293 cells and tested for FRET and other relevant properties. The most promising pairs were subsequently used in an attempt to improve the FRET span of the Epac-based cAMP sensor. The results show significant albeit not perfect correlation between performance in the spacer construct and in the Epac sensor. Finally, this strategy enabled us to identify improved sensors both for detection by sensitized emission and by fluorescent lifetime imaging. The present overview should be helpful in guiding development of future FRET sensors.

  18. Heat transfer analysis of unsteady graphene oxide nanofluid flow using a fuzzy identifier evolved by genetically encoded mutable smart bee algorithm

    Directory of Open Access Journals (Sweden)

    Mohammadreza Azimi


    Full Text Available In the current research, the unsteady two dimensional Graphene Oxide water based nanofluid heat transfer between two moving parallel plates is analyzed using an intelligent black-box identifier. The developed intelligent tool is known as evolvable evolutionary fuzzy inference system (EE-FIS which is based on the integration of low-level fuzzy programming and hyper-level evolutionary computing concepts. Here, the authors propose the use of a modified evolutionary algorithm (EA which is called hybrid genetic mutable smart bee algorithm (HGMSBA. The proposed HGMSBA is used to evolve both antecedent and consequent parts of fuzzy rule base. Besides, it tries to prune the rule base of fuzzy inference system (FIS to decrease its computational complexity and increase its interpretability. By considering the prediction error of the fuzzy identifier as the objective function of HGMSBA, an automatic soft interpolation machine is developed which can intuitively increase the robustness and accuracy of the final model. Here, HGMSBA-FIS is used to provide a nonlinear map between inputs, i.e. nanoparticles solid volume fraction (ϕ, Eckert number (Ec and a moving parameter which describes the movements of plates (S, and output, i.e. Nusselt number (Nu. Prior to proceeding with the modeling process, a comprehensive numerical comparative study is performed to investigate the potentials of the proposed model for nonlinear system identification. After demonstrating the efficacy of HGMSBA for training the FIS, the system is applied to the considered problem. Based on the obtained results, it can be inferred that the developed HGMSBA-FIS black-box identifier can be used as a very authentic tool with respect to accuracy and robustness. Besides, as the proposed black-box is not a physics-based identifier, it frees experts from the cumbersome mathematical formulations, and can be used for advanced real-time applications such as model-based control. The simulations indicate that the gradient of Nu has a direct nonlinear relation with the values of ϕ and Ec. It is also observed that an increase in the value of S decreases the value of Nu.

  19. Genetically encoded synthesis of protein-based polymers with precisely specified molecular weight and sequence by recursive directional ligation: examples from the elastin-like polypeptide system. (United States)

    Meyer, Dan E; Chilkoti, Ashutosh


    We report a new strategy for the synthesis of genes encoding repetitive, protein-based polymers of specified sequence, chain length, and architecture. In this stepwise approach, which we term "recursive directional ligation" (RDL), short gene segments are seamlessly combined in tandem using recombinant DNA techniques. The resulting larger genes can then be recursively combined until a gene of a desired length is obtained. This approach is modular and can be used to combine genes encoding different polypeptide sequences. We used this method to synthesize three different libraries of elastin-like polypeptides (ELPs); each library encodes a unique ELP sequence with systematically varied molecular weights. We also combined two of these sequences to produce a block copolymer. Because the thermal properties of ELPs depend on their sequence and chain length, the synthesis of these polypeptides provides an example of the importance of precise control over these parameters that is afforded by RDL.

  20. Mapping the subcellular distribution of α-synuclein in neurons using genetically encoded probes for correlated light and electron microscopy: implications for Parkinson's disease pathogenesis. (United States)

    Boassa, Daniela; Berlanga, Monica L; Yang, Mary Ann; Terada, Masako; Hu, Junru; Bushong, Eric A; Hwang, Minju; Masliah, Eliezer; George, Julia M; Ellisman, Mark H


    Modifications to the gene encoding human α-synuclein have been linked to the development of Parkinson's disease. The highly conserved structure of α-synuclein suggests a functional interaction with membranes, and several lines of evidence point to a role in vesicle-related processes within nerve terminals. Using recombinant fusions of human α-synuclein, including new genetic tags developed for correlated light microscopy and electron microscopy (the tetracysteine-biarsenical labeling system or the new fluorescent protein for electron microscopy, MiniSOG), we determined the distribution of α-synuclein when overexpressed in primary neurons at supramolecular and cellular scales in three dimensions (3D). We observed specific association of α-synuclein with a large and otherwise poorly characterized membranous organelle system of the presynaptic terminal, as well as with smaller vesicular structures within these boutons. Furthermore, α-synuclein was localized to multiple elements of the protein degradation pathway, including multivesicular bodies in the axons and lysosomes within neuronal cell bodies. Examination of synapses in brains of transgenic mice overexpressing human α-synuclein revealed alterations of the presynaptic endomembrane systems similar to our findings in cell culture. Three-dimensional electron tomographic analysis of enlarged presynaptic terminals in several brain areas revealed that these terminals were filled with membrane-bounded organelles, including tubulovesicular structures similar to what we observed in vitro. We propose that α-synuclein overexpression is associated with hypertrophy of membrane systems of the presynaptic terminal previously shown to have a role in vesicle recycling. Our data support the conclusion that α-synuclein is involved in processes associated with the sorting, channeling, packaging, and transport of synaptic material destined for degradation.

  1. Mapping the subcellular distribution of alpha-synuclein in neurons using genetically encoded probes for correlated light and electron microscopy: Implications for Parkinson’s disease pathogenesis (United States)

    Boassa, D.; Berlanga, M.L.; Yang, M.-L.; Terada, M.; Hu, J.; Bushong, E.A.; Hwang, M.; Masliah, E.; George, J.M.; Ellisman, M.H.


    Modifications to the gene encoding human alpha-synuclein have been linked to development of Parkinson’s disease. The highly conserved structure of alpha-synuclein suggests a functional interaction with membranes, and several lines of evidence point to a role in vesicle-related processes within nerve terminals. Using recombinant fusions of human alpha-synuclein including new genetic tags developed for correlated LM and EM (the tetracysteine-biarsenical labeling system or the new fluorescent protein for EM, MiniSOG), we determined the distribution of alpha-synuclein when over-expressed in primary neurons at supramolecular and cellular scales, in three dimensions (3D). We observed specific association of alpha-synuclein with a large and otherwise poorly characterized membranous organelle system of the presynaptic terminal, as well as with smaller vesicular structures within these boutons. Furthermore, alpha-synuclein was localized to multiple elements of the protein degradation pathway, including multivesicular bodies in the axons and lysosomes within neuronal cell bodies. Examination of synapses in brains of transgenic mice over-expressing human alpha-synuclein revealed alterations of the presynaptic endomembrane systems similar to our findings in cell culture. 3D electron tomographic analysis of enlarged presynaptic terminals in several brain areas revealed that these terminals were filled with membrane-bounded organelles, including tubulo-vesicular structures similar to what observed in vitro. We propose that alpha-synuclein over-expression is associated with hypertrophy of membrane systems of the presynaptic terminal previously shown to have a role in vesicle recycling. Our data support the conclusion that alpha- synuclein is involved in processes associated with the sorting, channeling, packaging and transport of synaptic material destined for degradation. PMID:23392688

  2. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy.

    Directory of Open Access Journals (Sweden)

    Alex Costa

    Full Text Available Selective Plane Illumination Microscopy (SPIM is an imaging technique particularly suited for long term in-vivo analysis of transparent specimens, able to visualize small organs or entire organisms, at cellular and eventually even subcellular resolution. Here we report the application of SPIM in Calcium imaging based on Förster Resonance Energy Transfer (FRET. Transgenic Arabidopsis plants expressing the genetically encoded-FRET-based Ca(2+ probe Cameleon, in the cytosol or nucleus, were used to demonstrate that SPIM enables ratiometric fluorescence imaging at high spatial and temporal resolution, both at tissue and single cell level. The SPIM-FRET technique enabled us to follow nuclear and cytosolic Ca(2+ dynamics in Arabidopsis root tip cells, deep inside the organ, in response to different stimuli. A relevant physiological phenomenon, namely Ca(2+ signal percolation, predicted in previous studies, has been directly visualized.

  3. H2O2 dynamics in the malaria parasite Plasmodium falciparum (United States)

    Rahbari, Mahsa; Bogeski, Ivan


    Hydrogen peroxide is an important antimicrobial agent but is also crucially involved in redox signaling and pathogen-host cell interactions. As a basis for systematically investigating intracellular H2O2 dynamics and regulation in living malaria parasites, we established the genetically encoded fluorescent H2O2 sensors roGFP2-Orp1 and HyPer-3 in Plasmodium falciparum. Both ratiometric redox probes as well as the pH control SypHer were expressed in the cytosol of blood-stage parasites. Both redox sensors showed reproducible sensitivity towards H2O2 in the lower micromolar range in vitro and in the parasites. Due to the pH sensitivity of HyPer-3, we used parasites expressing roGFP2-Orp1 for evaluation of short-, medium-, and long-term effects of antimalarial drugs on H2O2 levels and detoxification in Plasmodium. None of the quinolines or artemisinins tested had detectable direct effects on the H2O2 homeostasis at pharmacologically relevant concentrations. However, pre-treatment of the cells with antimalarial drugs or heat shock led to a higher tolerance towards exogenous H2O2. The systematic evaluation and comparison of the two genetically encoded cytosolic H2O2 probes in malaria parasites provides a basis for studying parasite-host cell interactions or drug effects with spatio-temporal resolution while preserving cell integrity. PMID:28369083

  4. Fluorogenic ratiometric dipodal optode containing imine-amide linkages: exploiting subtle thorium (IV) ion sensing. (United States)

    Tayade, Kundan; Kaur, Amanpreet; Tetgure, Sandesh; Chaitanya, G Krishana; Singh, Narinder; Kuwar, Anil


    The (13E,19E)-N1',N3'-bis[4-(diethylamino)-2-hydroxybenzylidene]malonohydrazide (L) has been developed for the detection of Th(4+) ions using dual channel signalling system. The UV-vis absorbance and fluorescence spectroscopic data revealed the formation of L-Th(4+) complex in 1:1 equilibrium. The density functional theory (DFT) also confirms the optimum binding cavity for the recognition of metal ion. The binding constant computed from different mathematical models for an assembly of L-Th(4+). The detection limit of L for Th(4+) recognition is to a concentration down to 0.1 μM (0.023 μg g(-1)). The present sensing system is also successfully applied for the detection of Th(4+) ion present in soil near nuclear atomic plants.

  5. Fluorescence lifetime imaging of membrane lipid order with a ratiometric fluorescent probe. (United States)

    Kilin, Vasyl; Glushonkov, Oleksandr; Herdly, Lucas; Klymchenko, Andrey; Richert, Ludovic; Mely, Yves


    To monitor the lateral segregation of lipids into liquid-ordered (Lo) and -disordered (Ld) phases in lipid membranes, environment-sensitive dyes that partition in both phases but stain them differently have been developed. Of particular interest is the dual-color F2N12S probe, which can discriminate the two phases through the ratio of its two emission bands. These bands are associated with the normal (N(∗)) and tautomer (T(∗)) excited-state species that result from an excited-state intramolecular proton transfer. In this work, we investigated the potency of the time-resolved fluorescence parameters of F2N12S to discriminate lipid phases in model and cell membranes. Both the long and mean lifetime values of the T(∗) form of F2N12S were found to differ by twofold between Ld and Lo phases as a result of the restriction in the relative motions of the two aromatic moieties of F2N12S imposed by the highly packed Lo phase. This differed from the changes in the ratio of the two emission bands between the two phases, which mainly resulted from the decreased hydration of the N(∗) form in the Lo phase. Importantly, the strong difference in lifetimes between the two phases was preserved when cholesterol was added to the Ld phase. The two phases could be imaged with high contrast by fluorescence lifetime imaging microscopy (FLIM) on giant unilamellar vesicles. FLIM images of F2N12S-labeled live HeLa cells confirmed that the plasma membrane was mainly in the Lo-like phase. Furthermore, the two phases were found to be homogeneously distributed all over the plasma membrane, indicating that they are highly mixed at the spatiotemporal resolution of the FLIM setup. Finally, FLIM could also be used to sensitively monitor the change in lipid phase upon cholesterol depletion and apoptosis.

  6. Manipulating the Surface Chemistry of Quantum Dots for Sensitive Ratiometric Fluorescence Detection of Sulfur Dioxide. (United States)

    Li, Huihui; Zhu, Houjuan; Sun, Mingtai; Yan, Yehan; Zhang, Kui; Huang, Dejian; Wang, Suhua


    Herein, we report a novel approach to the rapid visual detection of gaseous sulfur dioxide (SO2) by manipulating the surface chemistry of 3-aminopropyltriethoxysilane (APTS)-modified quantum dots (QDs) using fluorescent coumarin-3-carboxylic acid (CCA) for specific reaction with SO2. The CCA molecules are attached to the surface amino groups of the QDs through electrostatic attraction, thus the fluorescence of CCA is greatly suppressed because of the formation of an ion-pair complex between the ATPS-modified QDs and CCA. Such an interaction is vulnerable to SO2 because SO2 can readily react with surface amino groups to form strong charge-transfer complexes and subsequently release the strongly fluorescent CCA molecules. The mechanism has been carefully verified through a series of control experiments. Upon exposure to different amounts of SO2, the fluorescent color of the nanoparticle-based sensor displays continuously changes from red to blue. Most importantly, the approach owns high selectivity for SO2 and a tolerance of interference, which enables the sensor to detect SO2 in a practical application. Using this fluorescence-based sensing method, we have achieved a visual detection limit of 6 ppb for gaseous SO2.

  7. Ratiometric imaging of calcium during ischemia-reperfusion injury in isolated mouse hearts using Fura-2

    Directory of Open Access Journals (Sweden)

    Venkataraman Raghav


    Full Text Available Abstract Background We present an easily implementable method for measuring Fura-2 fluorescence from isolated mouse hearts using a commercially available switching light source and CCD camera. After calibration, it provides a good estimate of intracellular [Ca2+] with both high spatial and temporal resolutions, permitting study of changes in dispersion of diastolic [Ca2+], Ca2+ transient dynamics, and conduction velocities in mouse hearts. In a proof-of-principle study, we imaged isolated Langendorff-perfused mouse hearts with reversible regional myocardial infarctions. Methods Isolated mouse hearts were perfused in the Landendorff-mode and loaded with Fura-2. Hearts were then paced rapidly and subjected to 15 minutes of regional ischemia by ligation of the left anterior descending coronary artery, following which the ligation was removed to allow reperfusion for 15 minutes. Fura-2 fluorescence was recorded at regular intervals using a high-speed CCD camera. The two wavelengths of excitation light were interleaved at a rate of 1 KHz with a computer controlled switching light source to illuminate the heart. Results Fura-2 produced consistent Ca2+ transients from different hearts. Ligating the coronary artery rapidly generated a well defined region with a dramatic rise in diastolic Ca2+ without a significant change in transient amplitude; Ca2+ handling normalized during reperfusion. Conduction velocity was reduced by around 50% during ischemia, and did not recover significantly when monitored for 15 minutes following reperfusion. Conclusions Our method of imaging Fura-2 from isolated whole hearts is capable of detecting pathological changes in intracellular Ca2+ levels in cardiac tissue. The persistent change in the conduction velocities indicates that changes to tissue connectivity rather than altered intracellular Ca2+ handling may be underlying the electrical instabilities commonly seen in patients following a myocardial infarction.

  8. Ratiometric near infrared luminescent thermometer based on lanthanide metal-organic frameworks (United States)

    Yue, Dan; Zhang, Jun; Zhao, Dian; Lian, Xiusheng; Cui, Yuanjing; Yang, Yu; Qian, Guodong


    A near infrared luminescent MOFs thermometer (Nd0.676Yb0.324BTC) was prepared via a simple solvothermal method using Ln3+ (Ln=Nd, Yb) ions and 1, 3, 5-benznenetricarboxylic acid (H3BTC), and characterized by PXRD, TGA, ICP, and photoluminescence (PL) spectrum. These results indicate that the Nd0.676Yb0.324BTC displays high relative sensitivity and excellent repeatability in the physiological temperature range (288-323 K), and the maximum relative sensitivity is determined to be 1.187% K-1 at 323 K. These NIR luminescent MOFs may have potential applications in physiological temperature sensing.

  9. Label-free discrimination of normal and pulmonary cancer tissues using multiphoton fluorescence ratiometric microscopy (United States)

    Wang, Chun-Chin; Wu, Ruei-Jr; Lin, Sung-Jan; Chen, Yang-Fang; Dong, Chen-Yuan


    We performed multiphoton excited autofluorescence and second harmonic generation microscopy for the distinction of normal, lung adenocarcinoma (LAC), and squamous cell carcinoma (SCC) specimens. In addition to morphological distinction, we derived quantitative metrics of cellular redox ratios for cancer discrimination. Specifically, the redox ratios of paired normal/SCC and normal/LAC specimens were found to be 0.53±0.05/0.41±0.06 and 0.56±0.02/0.35±0.06, respectively. The lower redox ratios in cancer specimens, indicating an increase in metabolic activity. These results show that the combination of morphological multiphoton imaging along with redox ratio indices can be used for the discrimination of normal and pulmonary cancer tissues.

  10. Identification of intensity ratio break points from photon arrival trajectories in ratiometric single molecule spectroscopy. (United States)

    Bingemann, Dieter; Allen, Rachel M


    We describe a statistical method to analyze dual-channel photon arrival trajectories from single molecule spectroscopy model-free to identify break points in the intensity ratio. Photons are binned with a short bin size to calculate the logarithm of the intensity ratio for each bin. Stochastic photon counting noise leads to a near-normal distribution of this logarithm and the standard student t-test is used to find statistically significant changes in this quantity. In stochastic simulations we determine the significance threshold for the t-test's p-value at a given level of confidence. We test the method's sensitivity and accuracy indicating that the analysis reliably locates break points with significant changes in the intensity ratio with little or no error in realistic trajectories with large numbers of small change points, while still identifying a large fraction of the frequent break points with small intensity changes. Based on these results we present an approach to estimate confidence intervals for the identified break point locations and recommend a bin size to choose for the analysis. The method proves powerful and reliable in the analysis of simulated and actual data of single molecule reorientation in a glassy matrix.

  11. Synthesis and characterization of ratiometric nanosensors for pH quantification: a mixed micelle approach

    DEFF Research Database (Denmark)

    Ek, Pramod Kumar; Almdal, Kristoffer; Andresen, Thomas Lars


    and is prone to batch-to-batch variations, which is undesirable for succeeding sensor calibrations and cellular measurements. Here we provide a new synthetic approach for preparing nanoparticle pH sensors based on self-organization principles, which in comparison to earlier strategies offers a much higher...

  12. Genetically-Encoded Photocrosslinkers Determine the Biological Binding Site of Exendin-4 in the N-Terminal Domain of the Intact Human Glucagon-Like Peptide-1 Receptor (GLP-1R). (United States)

    Koole, Cassandra; Reynolds, Christopher A; Mobarec, Juan C; Hick, Caroline; Sexton, Patrick M; Sakmar, Thomas P


    The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, functional receptor-ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-L-phenylalanine (azF) into N-terminal residues of a full-length, functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocrosslinking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Crosslinking data were compared directly to the crystal structure of the isolated N-terminal extracellular domain (ECD) of the GLP-1R in complex with exendin(9-39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocrosslinking constraints highlights the potential influence of environmental conditions on the conformation of the receptor-peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide-receptor interactions, and should be combined with additional experimental constraints to reveal peptide-receptor interactions occurring in the dynamic, native, full-length receptor state.

  13. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)


    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  14. Dual Readout BRET/FRET Sensors for Measuring Intracellular Zinc (United States)


    Genetically encoded FRET-based sensor proteins have significantly contributed to our current understanding of the intracellular functions of Zn2+. However, the external excitation required for these fluorescent sensors can give rise to photobleaching and phototoxicity during long-term imaging, limits applications that suffer from autofluorescence and light scattering, and is not compatible with light-sensitive cells. For these applications, sensor proteins based on Bioluminescence Resonance Energy Transfer (BRET) would provide an attractive alternative. In this work, we used the bright and stable luciferase NanoLuc to create the first genetically encoded BRET sensors for measuring intracellular Zn2+. Using a new sensor approach, the NanoLuc domain was fused to the Cerulean donor domain of two previously developed FRET sensors, eCALWY and eZinCh-2. In addition to preserving the excellent Zn2+ affinity and specificity of their predecessors, these newly developed sensors enable both BRET- and FRET-based detection. While the dynamic range of the BRET signal for the eCALWY-based BLCALWY-1 sensor was limited by the presence of two competing BRET pathways, BRET/FRET sensors based on the eZinCh-2 scaffold (BLZinCh-1 and -2) yielded robust 25–30% changes in BRET ratio. In addition, introduction of a chromophore-silencing mutation resulted in a BRET-only sensor (BLZinCh-3) with increased BRET response (50%) and an unexpected 10-fold increase in Zn2+ affinity. The combination of robust ratiometric response, physiologically relevant Zn2+ affinities, and stable and bright luminescence signal offered by the BLZinCh sensors allowed monitoring of intracellular Zn2+ in plate-based assays as well as intracellular BRET-based imaging in single living cells in real time. PMID:27547982

  15. Characterization of the ER-Targeted Low Affinity Ca2+ Probe D4ER

    Directory of Open Access Journals (Sweden)

    Elisa Greotti


    Full Text Available Calcium ion (Ca2+ is a ubiquitous intracellular messenger and changes in its concentration impact on nearly every aspect of cell life. Endoplasmic reticulum (ER represents the major intracellular Ca2+ store and the free Ca2+ concentration ([Ca2+] within its lumen ([Ca2+]ER can reach levels higher than 1 mM. Several genetically-encoded ER-targeted Ca2+ sensors have been developed over the last years. However, most of them are non-ratiometric and, thus, their signal is difficult to calibrate in live cells and is affected by shifts in the focal plane and artifactual movements of the sample. On the other hand, existing ratiometric Ca2+ probes are plagued by different drawbacks, such as a double dissociation constant (Kd for Ca2+, low dynamic range, and an affinity for the cation that is too high for the levels of [Ca2+] in the ER lumen. Here, we report the characterization of a recently generated ER-targeted, Förster resonance energy transfer (FRET-based, Cameleon probe, named D4ER, characterized by suitable Ca2+ affinity and dynamic range for monitoring [Ca2+] variations within the ER. As an example, resting [Ca2+]ER have been evaluated in a known paradigm of altered ER Ca2+ homeostasis, i.e., in cells expressing a mutated form of the familial Alzheimer’s Disease-linked protein Presenilin 2 (PS2. The lower Ca2+ affinity of the D4ER probe, compared to that of the previously generated D1ER, allowed the detection of a conspicuous, more clear-cut, reduction in ER Ca2+ content in cells expressing mutated PS2, compared to controls.

  16. Ratiometric dosing of anticancer drug combinations: controlling drug ratios after systemic administration regulates therapeutic activity in tumor-bearing mice. (United States)

    Mayer, Lawrence D; Harasym, Troy O; Tardi, Paul G; Harasym, Natashia L; Shew, Clifford R; Johnstone, Sharon A; Ramsay, Euan C; Bally, Marcel B; Janoff, Andrew S


    Anticancer drug combinations can act synergistically or antagonistically against tumor cells in vitro depending on the ratios of the individual agents comprising the combination. The importance of drug ratios in vivo, however, has heretofore not been investigated, and combination chemotherapy treatment regimens continue to be developed based on the maximum tolerated dose of the individual agents. We systematically examined three different drug combinations representing a range of anticancer drug classes with distinct molecular mechanisms (irinotecan/floxuridine, cytarabine/daunorubicin, and cisplatin/daunorubicin) for drug ratio-dependent synergy. In each case, synergistic interactions were observed in vitro at certain drug/drug molar ratio ranges (1:1, 5:1, and 10:1, respectively), whereas other ratios were additive or antagonistic. We were able to maintain fixed drug ratios in plasma of mice for 24 hours after i.v. injection for all three combinations by controlling and overcoming the inherent dissimilar pharmacokinetics of individual drugs through encapsulation in liposomal carrier systems. The liposomes not only maintained drug ratios in the plasma after injection, but also delivered the formulated drug ratio directly to tumor tissue. In vivo maintenance of drug ratios shown to be synergistic in vitro provided increased efficacy in preclinical tumor models, whereas attenuated antitumor activity was observed when antagonistic drug ratios were maintained. Fixing synergistic drug ratios in pharmaceutical carriers provides an avenue by which anticancer drug combinations can be optimized prospectively for maximum therapeutic activity during preclinical development and differs from current practice in which dosing regimens are developed empirically in late-stage clinical trials based on tolerability.

  17. Smart protein biogate as a mediator to regulate competitive host-guest interaction for sensitive ratiometric electrochemical assay of prion (United States)

    Yu, Peng; Zhang, Xiaohua; Zhou, Jiawan; Xiong, Erhu; Li, Xiaoyu; Chen, Jinhua


    A novel competitive host-guest strategy regulated by protein biogate was developed for sensitive and selective analysis of prion protein. The methylene blue (MB)-tagged prion aptamer (MB-Apt) was introduced to the multiwalled carbon nanotubes-β-cyclodextrins (MWCNTs-β-CD) composites-modified glassy carbon (GC) electrode through the host-guest interaction between β-CD and MB. In the absence of prion, MB-Apt could be displaced by ferrocenecarboxylic acid (FCA) due to its stronger binding affinity to β-CD, resulting in a large oxidation peak of FCA. However, in the presence of prion, the specific prion-aptamer interaction drove the formation of protein biogate to seal the cavity of β-CD, which hindered the guest displacement of MB by FCA and resulted in the oxidation peak current of MB (IMB) increased and that of FCA (IFCA) decreased. The developed aptasensor showed good response towards the target (prion protein) with a low detection limit of 160 fM. By changing the specific aptamers, this strategy could be easily extended to detect other proteins, showing promising potential for extensive applications in bioanalysis.

  18. Synthesis and Application of Ratiometric and "Turn-On" Fluorescent pH Sensors: An Advanced Organic Undergraduate Laboratory (United States)

    Hutt, Johnathon T.; Aron, Zachary D.


    An upper-division organic chemistry laboratory experiment exploring fluorescent sensing over two laboratory periods and part of a third is described. Two functionally distinct pH-responsive sensors are prepared through a dehydrative three-component coupling reaction. During the abbreviated (<1 h) first laboratory period, students set up…

  19. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas


    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  20. A fluorescent coumarin-thiophene hybrid as a ratiometric chemosensor for anions: Synthesis, photophysics, anion sensing and orbital interactions (United States)

    Yanar, Ufuk; Babür, Banu; Pekyılmaz, Damla; Yahaya, Issah; Aydıner, Burcu; Dede, Yavuz; Seferoğlu, Zeynel


    A colorimetric and fluorimetric fluorescent chemosensor (CT-2), having a coumarin ring as a signaling unit and an acetamido thiophene ring as an H-donor receptor, has been synthesized from amino derivative (CT-1) of CT-2 for the purpose of recognition of anions in DMSO. The absorption and emission maxima were both determined for the fluorescent dye in different solvents. Both hypsochromic shift at the absorption maximum, and quenching of fluorescence after interactions between the anions and the receptoric part, were observed. This phenomenon was explained using orbital interactions based on quantum chemical calculations. The selectivity and sensitivity of CT-2 for F-, Cl-, Br-, I-, AcO-, CN-, H2PO4-, HSO4- and ClO4- anions were determined with spectrophotometric, fluorimetric and 1H NMR titration techniques and it was found that CT-2 be utilized for the detection of CN-, F- and AcO- in the presence of other ions as competitors. Color and fluorescence changes visible to the naked eye and under UV (365 nm) were observed upon addition of CN-, F- and AcO- to the solution of chemosensor (CT-2) in DMSO. The sensor showed no colorimetric and fluorimetric response for the anions such as Cl-, Br-, I-, H2PO4-, HSO4-, and ClO4-. However, 1H NMR titration shows that the chemosensor was more sensitive to CN-, than F- and AcO- at the stochiometric ratio of 1:2.5 respectively. Additionally, the compounds CT-1 and CT-2 showed good thermal stability for practical applications.

  1. Image processing for non-ratiometric measurement of membrane voltage using fluorescent reporters and pulsed laser illumination. (United States)

    Silve, Aude; Rocke, Sarah; Frey, Wolfgang


    The measurement of transmembrane voltages induced by pulsed electric field exposure can be achieved by using fluorescent dyes like ANNINE-6. Such approach requires a quantitative determination of the fluorescence intensity along the cell's membrane by image processing. When high temporal resolution is required, the illumination source is frequently a dye-laser which causes high fluctuations in the intensity of illumination which in turn affects the fluorescence intensity and thus the quality of the results. We propose an image processing technique that allows to overcome the fluctuations and to produce quantitative data. It uses the optical background noise as a correcting factor. Standard deviation in the fluctuations is thus efficiently reduced by at least a factor of 2.5. Additionally we draw attention to the fact that the parasitic component of the laser radiation (ASE) can also suppress fluctuations although it deteriorates wavelength precision.

  2. Ratiometric, filter-free optical sensor based on a complementary metal oxide semiconductor buried double junction photodiode. (United States)

    Yung, Ka Yi; Zhan, Zhiyong; Titus, Albert H; Baker, Gary A; Bright, Frank V


    We report a complementary metal oxide semiconductor integrated circuit (CMOS IC) with a buried double junction (BDJ) photodiode that (i) provides a real-time output signal that is related to the intensity ratio at two emission wavelengths and (ii) simultaneously eliminates the need for an optical filter to block Rayleigh scatter. We demonstrate the BDJ platform performance for gaseous NH3 and aqueous pH detection. We also compare the BDJ performance to parallel results obtained by using a slew scanned fluorimeter (SSF). The BDJ results are functionally equivalent to the SSF results without the need for any wavelength filtering or monochromators and the BDJ platform is not prone to errors associated with source intensity fluctuations or sensor signal drift.

  3. A simple and inexpensive high resolution color ratiometric planar optode imaging approach: application to oxygen and pH sensing

    DEFF Research Database (Denmark)

    Larsen, M.; Borisov, S. M.; Grunwald, B.


    A simple, high resolution colormetric planar optode imaging approach is presented. The approach is simple and inexpensive yet versatile, and can be used to study the two-dimensional distribution and dynamics of a range of analytes. The imaging approach utilizes the inbuilt color filter of standar...

  4. In vivo readout of CFTR function: ratiometric measurement of CFTR-dependent secretion by individual, identifiable human sweat glands.

    Directory of Open Access Journals (Sweden)

    Jeffrey J Wine

    Full Text Available To assess CFTR function in vivo, we developed a bioassay that monitors and compares CFTR-dependent and CFTR-independent sweat secretion in parallel for multiple (~50 individual, identified glands in each subject. Sweating was stimulated by intradermally injected agonists and quantified by optically measuring spherical sweat bubbles in an oil-layer that contained dispersed, water soluble dye particles that partitioned into the sweat bubbles, making them highly visible. CFTR-independent secretion (M-sweat was stimulated with methacholine, which binds to muscarinic receptors and elevates cytosolic calcium. CFTR-dependent secretion (C-sweat was stimulated with a β-adrenergic cocktail that elevates cytosolic cAMP while blocking muscarinic receptors. A C-sweat/M-sweat ratio was determined on a gland-by-gland basis to compensate for differences unrelated to CFTR function, such as gland size. The average ratio provides an approximately linear readout of CFTR function: the heterozygote ratio is ~0.5 the control ratio and for CF subjects the ratio is zero. During assay development, we measured C/M ratios in 6 healthy controls, 4 CF heterozygotes, 18 CF subjects and 4 subjects with 'CFTR-related' conditions. The assay discriminated all groups clearly. It also revealed consistent differences in the C/M ratio among subjects within groups. We hypothesize that these differences reflect, at least in part, levels of CFTR expression, which are known to vary widely. When C-sweat rates become very low the C/M ratio also tended to decrease; we hypothesize that this nonlinearity reflects ductal fluid absorption. We also discovered that M-sweating potentiates the subsequent C-sweat response. We then used potentiation as a surrogate for drugs that can increase CFTR-dependent secretion. This bioassay provides an additional method for assessing CFTR function in vivo, and is well suited for within-subject tests of systemic, CFTR-directed therapeutics.

  5. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I. (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas


    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  6. Expression of multiple transgenes from a single construct using viral 2A peptides in Drosophila.

    Directory of Open Access Journals (Sweden)

    Richard W Daniels

    Full Text Available Expression of multiple reporter or effector transgenes in the same cell from a single construct is increasingly necessary in various experimental paradigms. The discovery of short, virus-derived peptide sequences that mediate a ribosome-skipping event enables generation of multiple separate peptide products from one mRNA. Here we describe methods and vectors to facilitate easy production of polycistronic-like sequences utilizing these 2A peptides tailored for expression in Drosophila both in vitro and in vivo. We tested the separation efficiency of different viral 2A peptides in cultured Drosophila cells and in vivo and found that the 2A peptides from porcine teschovirus-1 (P2A and Thosea asigna virus (T2A worked best. To demonstrate the utility of this approach, we used the P2A peptide to co-express the red fluorescent protein tdTomato and the genetically-encoded calcium indicator GCaMP5G in larval motorneurons. This technique enabled ratiometric calcium imaging with motion correction allowing us to record synaptic activity at the neuromuscular junction in an intact larval preparation through the cuticle. The tools presented here should greatly facilitate the generation of 2A peptide-mediated expression of multiple transgenes in Drosophila.

  7. Sodium channels as gateable non-photonic sensors for membrane-delimited reactive species. (United States)

    Ojha, Navin K; Nematian-Ardestani, Ehsan; Neugebauer, Sophie; Borowski, Benjamin; El-Hussein, Ahmed; Hoshi, Toshinori; Leipold, Enrico; Heinemann, Stefan H


    Reactive oxygen species (ROS) and reactive oxygen intermediates (ROI) play crucial roles in physiological processes. While excessive ROS damages cells, small fluctuations in ROS levels represent physiological signals important for vital functions. Despite the physiological importance of ROS, many fundamental questions remain unanswered, such as which types of ROS occur in cells, how they distribute inside cells, and how long they remain in an active form. The current study presents a ratiometric sensor of intracellular ROS levels based on genetically engineered voltage-gated sodium channels (roNaV). roNaV can be used for detecting oxidative modification that occurs near the plasma membrane with a sensitivity similar to existing fluorescence-based ROS sensors. Moreover, roNaV has several advantages over traditional sensors because it does not need excitation light for sensing, and thus, can be used to detect phototoxic cellular modifications. In addition, the ROS dynamic range of roNaV is easily manipulated in real time by means of the endogenous channel inactivation mechanism. Measurements on ROS liberated from intracellular Lucifer Yellow and genetically encoded KillerRed have revealed an assessment of ROS lifetime in individual mammalian cells. Flashlight-induced ROS concentration decayed with two major time constants of about 10 and 1000 ms.

  8. In vivo intracellular pH measurements in tobacco and Arabidopsis reveal an unexpected pH gradient in the endomembrane system. (United States)

    Martinière, Alexandre; Bassil, Elias; Jublanc, Elodie; Alcon, Carine; Reguera, Maria; Sentenac, Hervé; Blumwald, Eduardo; Paris, Nadine


    The pH homeostasis of endomembranes is essential for cellular functions. In order to provide direct pH measurements in the endomembrane system lumen, we targeted genetically encoded ratiometric pH sensors to the cytosol, the endoplasmic reticulum, and the trans-Golgi, or the compartments labeled by the vacuolar sorting receptor (VSR), which includes the trans-Golgi network and prevacuoles. Using noninvasive live-cell imaging to measure pH, we show that a gradual acidification from the endoplasmic reticulum to the lytic vacuole exists, in both tobacco (Nicotiana tabacum) epidermal (ΔpH -1.5) and Arabidopsis thaliana root cells (ΔpH -2.1). The average pH in VSR compartments was intermediate between that of the trans-Golgi and the vacuole. Combining pH measurements with in vivo colocalization experiments, we found that the trans-Golgi network had an acidic pH of 6.1, while the prevacuole and late prevacuole were both more alkaline, with pH of 6.6 and 7.1, respectively. We also showed that endosomal pH, and subsequently vacuolar trafficking of soluble proteins, requires both vacuolar-type H(+) ATPase-dependent acidification as well as proton efflux mediated at least by the activity of endosomal sodium/proton NHX-type antiporters.

  9. Ratiometric measurements of adiponectin by mass spectrometry in bottlenose dolphins (Tursiops truncatus with iron overload reveal an association with insulin resistance and glucagon

    Directory of Open Access Journals (Sweden)

    Benjamin A Neely


    Full Text Available High molecular weight (HMW adiponectin levels are reduced in humans with type 2 diabetes and insulin resistance. Similar to humans with insulin resistance, managed bottlenose dolphins (Tursiops truncatus diagnosed with hemochromatosis (iron overload have higher levels of 2 h post-prandial plasma insulin than healthy controls. A parallel reaction monitoring assay for dolphin serum adiponectin was developed based on tryptic peptides identified by mass spectrometry. Using identified post-translational modifications, a differential measurement was constructed. Total and unmodified adiponectin levels were measured in sera from dolphins with (n=4 and without (n=5 iron overload. This measurement yielded total adiponectin levels as well as site specific percent unmodified adiponectin that may inversely correlate with HMW adiponectin. Differences in insulin levels between iron overload cases and controls were observed 2 h post-prandial, but not during the fasting state. Thus, post-prandial as well as fasting serum adiponectin levels were measured to determine whether adiponectin and insulin would follow similar patterns. There was no difference in total adiponectin or percent unmodified adiponectin from case or control fasting animals. There was no difference in post-prandial total adiponectin levels between case and control dolphins (mean ± S.D. at 763 ± 298 and 727 ± 291 pmol/ml, respectively (p = 0.91; however, percent unmodified adiponectin was significantly higher in post-prandial cases compared controls (30.0 ± 6.3 versus 17.0 ± 6.6%, respectively; p = 0.016. Interestingly, both total and percent unmodified adiponectin were correlated with glucagon levels in controls (r = 0.999, p < 0.001, but not in cases, which is possibly a reflection of insulin resistance. Although total adiponectin levels were not significantly different, the elevated percent unmodified adiponectin follows a trend similar to HMW adiponectin reported for humans with metabolic disorders.

  10. Programmable illumination and high-speed, multi-wavelength, confocal microscopy using a digital micromirror.

    Directory of Open Access Journals (Sweden)

    Franck P Martial

    Full Text Available Confocal microscopy is routinely used for high-resolution fluorescence imaging of biological specimens. Most standard confocal systems scan a laser across a specimen and collect emitted light passing through a single pinhole to produce an optical section of the sample. Sequential scanning on a point-by-point basis limits the speed of image acquisition and even the fastest commercial instruments struggle to resolve the temporal dynamics of rapid cellular events such as calcium signals. Various approaches have been introduced that increase the speed of confocal imaging. Nipkov disk microscopes, for example, use arrays of pinholes or slits on a spinning disk to achieve parallel scanning which significantly increases the speed of acquisition. Here we report the development of a microscope module that utilises a digital micromirror device as a spatial light modulator to provide programmable confocal optical sectioning with a single camera, at high spatial and axial resolution at speeds limited by the frame rate of the camera. The digital micromirror acts as a solid state Nipkov disk but with the added ability to change the pinholes size and separation and to control the light intensity on a mirror-by-mirror basis. The use of an arrangement of concave and convex mirrors in the emission pathway instead of lenses overcomes the astigmatism inherent with DMD devices, increases light collection efficiency and ensures image collection is achromatic so that images are perfectly aligned at different wavelengths. Combined with non-laser light sources, this allows low cost, high-speed, multi-wavelength image acquisition without the need for complex wavelength-dependent image alignment. The micromirror can also be used for programmable illumination allowing spatially defined photoactivation of fluorescent proteins. We demonstrate the use of this system for high-speed calcium imaging using both a single wavelength calcium indicator and a genetically encoded

  11. A single and rapid calcium wave at egg activation in Drosophila

    Directory of Open Access Journals (Sweden)

    Anna H. York-Andersen


    Full Text Available Activation is an essential process that accompanies fertilisation in all animals and heralds major cellular changes, most notably, resumption of the cell cycle. While activation involves wave-like oscillations in intracellular Ca2+ concentration in mammals, ascidians and polychaete worms and a single Ca2+ peak in fish and frogs, in insects, such as Drosophila, to date, it has not been shown what changes in intracellular Ca2+ levels occur. Here, we utilise ratiometric imaging of Ca2+ indicator dyes and genetically encoded Ca2+ indicator proteins to identify and characterise a single, rapid, transient wave of Ca2+ in the Drosophila egg at activation. Using genetic tools, physical manipulation and pharmacological treatments we demonstrate that the propagation of the Ca2+ wave requires an intact actin cytoskeleton and an increase in intracellular Ca2+ can be uncoupled from egg swelling, but not from progression of the cell cycle. We further show that mechanical pressure alone is not sufficient to initiate a Ca2+ wave. We also find that processing bodies, sites of mRNA decay and translational regulation, become dispersed following the Ca2+ transient. Based on this data we propose the following model for egg activation in Drosophila: exposure to lateral oviduct fluid initiates an increase in intracellular Ca2+ at the egg posterior via osmotic swelling, possibly through mechano-sensitive Ca2+ channels; a single Ca2+ wave then propagates in an actin dependent manner; this Ca2+ wave co-ordinates key developmental events including resumption of the cell cycle and initiation of translation of mRNAs such as bicoid.

  12. Improved method for efficient imaging of intracellular Cl(-) with Cl-Sensor using conventional fluorescence setup. (United States)

    Friedel, Perrine; Bregestovski, Piotr; Medina, Igor


    Chloride (Cl(-)) homeostasis is known to be fundamental for central nervous system functioning. Alterations in intracellular Cl(-) concentration ([Cl(-)]i) and changes in the efficacy of Cl(-) extrusion are involved in numerous neurological disorders. Therefore, there is a strong need for studies of the dynamics of [Cl(-)]i in different cell types under physiological conditions and during pathology. Several previous works reported having successfully achieved recording of [Cl(-)]i using genetically encoded Cl-Sensor that is composed of the cyan fluorescent protein (CFP) and Cl(-)-sensitive mutant of the yellow fluorescent protein (YFPCl). However, all reported works were performed using specially designed setups with ultra-sensitive CCD cameras. Our multiple attempts to monitor Cl(-)-dependent fluorescence of Cl-Sensor using conventional epifluorescence microscopes did not yield successful results. In the present work, we have analysed the reason of our failures and found that they were caused by a strong inactivation of the YFPCl component of Cl-Sensor during excitation of the CFP with 430 nm light. Based on the obtained results, we reduced 20-fold the intensity of the 430 nm excitation and modified the recording protocol that allows now stable long-lasting ratiometric measurements of Cl-Sensor fluorescence in different cell types including cultured hippocampal neurons and their tiny dendrites and spines. Simultaneous imaging and patch clamp recording revealed that in mature neurons, the novel protocol allows detection of as little as 2 mM changes of [Cl(-)]i from the resting level of 5-10 mM. We demonstrate also a usefulness of the developed [Cl(-)]i measurement procedure for large scale screening of the activity of exogenously expressed potassium-chloride co-transporter KCC2, a major neuronal Cl(-) extruder that is implicated in numerous neurological disorders and is a target for novel therapeutical treatments.

  13. Improved method for efficient imaging of intracellular Cl- with Cl-Sensor using conventional fluorescence setup

    Directory of Open Access Journals (Sweden)

    Perrine eFriedel


    Full Text Available Chloride (Cl- homeostasis is known to be fundamental for central nervous system functioning. Alterations in intracellular Cl- concentration ([Cl-]i and changes in the efficacy of Cl- extrusion are involved in numerous neurological disorders. Therefore there is a strong need for studies of the dynamics of [Cl-]i in different cell types under physiological conditions and during pathology. Several previous works reported having successfully achieved recording of [Cl-]i using genetically encoded Cl-Sensor that is composed of the cyan fluorescent protein (CFP and Cl--sensitive mutant of the yellow fluorescent protein (YFPCl. However all reported works were performed using specially designed setups with ultra-sensitive CCD cameras. Our multiple attempts to monitor Cl--dependent fluorescence of Cl-Sensor using conventional epifluorescence microscopes did not yield successful results. In the present work, we have analysed the reason of our failures and found that they were caused by a strong inactivation of the YFPCl component of Cl-Sensor during excitation of the CFP with 430 nm light. Based on the obtained results, we reduced 20-fold the intensity of the 430 nm excitation and modified the recording protocol that allows now stable long-lasting ratiometric measurements of Cl-Sensor fluorescence in different cell types including cultured hippocampal neurons and their tiny dendrites and spines. Simultaneous imaging and patch clamp recording revealed that in mature neurons, the novel protocol allows detection of as little as 2 mM changes of [Cl-]i from the resting level of 5-10 mM. We demonstrate also a usefulness of the developed [Cl-]i measurement procedure for large scale screening of the activity of exogenously expressed potassium-chloride co-transporter KCC2, a major neuronal Cl- extruder, that is implicated in numerous neurological disorders and is a target for novel therapeutical treatments.

  14. Transient increase in neuronal chloride concentration by neuroactive amino acids released from glioma cells

    Directory of Open Access Journals (Sweden)

    Cristina eBertollini


    Full Text Available Neuronal chloride concentration ([Cl-]i is known to be dynamically modulated and alterations in Cl- homeostasis may occur in the brain at physiological and pathological conditions, being also likely involved in glioma-related seizures. However, the mechanism leading to changes in neuronal [Cl-]i during glioma invasion are still unclear. To characterize the potential effect of glioma released soluble factors on neuronal [Cl-]i, we used genetically encoded CFP/YFP-based ratiometric Cl-Sensor transiently expressed in cultured hippocampal neurons. Exposition of neurons to glioma conditioned medium (GCM caused rapid and transient elevation of [Cl-]i, resulting in the increase of fluorescence ratio, which was strongly reduced by blockers of ionotropic glutamate receptors APV and NBQX. Furthermore, in HEK cells expressing GluR1-AMPA receptors, GCM activated ionic current with efficacy similar to those caused by glutamate, supporting the notion that GCM contains glutamate or glutamatergic agonists, which cause neuronal depolarization, activation of NMDA and AMPA/KA receptors leading to elevation of [Cl-]i. Chromatographic analysis of the GCM showed that it contained several aminoacids, including glutamate, whose release from glioma cells did not occur via the most common glial mechanisms of transport, or in response to hypoosmotic stress. GCM also contained glycine, whose action contrasted the glutamate effect. Indeed, strychnine application significantly increased GCM-induced depolarization and [Cl-]i rise. GCM-evoked [Cl-]i elevation was not inhibited by antagonists of Cl- transporters and significantly reduced in the presence of anion channels blocker NPPB, suggesting that Cl-selective channels are a major route for GCM-induced Cl- influx. Altogether, these data show that glioma released aminoacids may dynamically alter Cl- equilibrium in surrounding neurons, deeply interfering with their inhibitory balance, likely leading to physiological and

  15. Towards Behavior Control for Evolutionary Robot Based on RL with ENN

    Directory of Open Access Journals (Sweden)

    Jingan Yang


    In comparison with the conventional behavior network and the adaptive behavior method, our algorithm simplified the genetic encoding complexity, improved the convergence rate  and the network performance.

  16. Design of selective 8-methylquinolinol based ratiometric Fe{sup 2+} and Fe{sup 3+}/H{sub 2}PO{sub 4}{sup −} fluorescent chemosensor mimicking NOR and IMPLICATION logic gates

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Gurjaspreet, E-mail:; Singh, Jandeep; Singh, Jasbhinder; Mangat, Satinderpal Singh


    This report describes an on–off module of a fluorescent probe for selectively sensing of Fe(II) and Fe(III) ions by a single chemosensor with unique output optical response and is being reported for the first time. The probe 8-methylquinolinyl-1,2,3-triazolyl silatrane (QTS) was efficiently developed using click silylation route, followed by transetherification of silane. Moreover, the color change in probe QTS by response of this colorimetric sensor can be visualized by naked eye. The anti-quenching response for quenched QTS–Fe{sup 3+} fluorescence spectra by addition of H{sub 2}PO{sub 4}{sup −} ions in the MeOH/H{sub 2}O solvent system results into reversion of fluorescence maximum. These fluctuations in spectral response, under electronic behavior, can be viewed to mimic as NOR and IMPLICATION logic gate. - Highlights: • The probe 8-methylquinolinyl-1,2,3-triazolyl silatrane (QTS) was efficiently developed by using click silylation route. • The fluorescence emission response of sensor QTS towards Fe{sup 3+} ions show 'turn-on' mode, with red shift of 79 nm. • UV–vis spectra illustrate increase in absorption maxima on sensing of both ionic species.

  17. Ratiometric Fluorescent Probe for the Detection of Glutathione in Living Cells%用于检测细胞内谷胱甘肽的比率型荧光探针

    Institute of Scientific and Technical Information of China (English)

    杨润洁; 唐尧; 朱维平


    A fluorescent probe(4) for the detection of biothiols was designed and synthesized and its proper-ties for labeling glutathione was investigated. After reaction with glutathione in 2-[ 4-( 2-hydroxyethyl )-1-piperazinyl] ethanesulfonic acid ( HEPES ) buffer, the color of solution changed from light yellow to pink, which could be detected by naked eyes. Meanwhile, the fluorescence was enhanced at 608 nm. Probe 4 was useful for measuring glutathione at concentrations ranging from 1. 6 × 10-5 to 2 × 10-4 mol/L with a detection limit of 8. 9 ×10-7 mol/L. Besides, probe 4 was sensitive to glutathione in MCF-7 cells, which emitted red fluorescence when it was incubated with MCF-7 cells.%设计合成了1种用于检测生物巯基的比率型荧光探针(4),并考察了其对谷胱甘肽的识别作用.在4-羟乙基哌嗪乙磺酸(HEPES)缓冲液中,探针4可与谷胱甘肽快速反应,溶液颜色由淡黄色变为粉红色,从而实现"裸眼"检测,且在608 nm处的荧光信号增强.在1.6×10-5~2×10-4 mol/L范围内,探针4能够定量检测谷胱甘肽,检出限为8.9×10-7 mol/L.此外,探针4还可用于MCF-7细胞中谷胱甘肽的成像.

  18. Determination of metal ions by fluorescence anisotropy exhibits a broad dynamic range (United States)

    Thompson, Richard B.; Maliwal, Badri P.; Fierke, Carol A.


    Recently, we have shown that metal ions free in solution may be determined at low levels by fluorescence anisotropy (polarization) measurements. Anisotropy measurements enjoy the advantages of wavelength ratiometric techniques for determining metal ions such as calcium, because anisotropy measurements are ratiometric as well. Furthermore, fluorescence anisotropy may be imaged in the microscope. An advantage of anisotropy not demonstrated for wavelength ratiometric approaches using indicators such as Fura-2 and Indo-1 is that under favorable circumstances anisotropy-based determinations exhibit a much broader dynamic range in metal ion concentration. Determinations of free Zn(II) in the picomolar range are demonstrated.

  19. Measuring Phagosomal pH by Fluorescence Microscopy. (United States)

    Canton, Johnathan; Grinstein, Sergio


    Dual wavelength ratiometric imaging has become a powerful tool for the study of pH in intracellular compartments. It allows for the dynamic imaging of live cells while accounting for changes in the focal plane, differential loading of the fluorescent probe, and photobleaching caused by repeated image acquisitions. Ratiometric microscopic imaging has the added advantage over whole population methods of being able to resolve individual cells and even individual organelles. In this chapter we provide a detailed discussion of the basic principles of ratiometric imaging and its application to the measurement of phagosomal pH, including probe selection, the necessary instrumentation, and calibration methods.

  20. Fast kinetics of calcium signaling and sensor design. (United States)

    Tang, Shen; Reddish, Florence; Zhuo, You; Yang, Jenny J


    Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change.

  1. Achieving sustainable cultivation of potatoes (United States)

    Every phase of the production cycle impacts the sustainability of potato. Potato physiology determines how genetically encoded developmental attributes interact with local environmental conditions as modified through agricultural practice to produce a perishable crop. In this chapter we highlight ho...

  2. Sensing Cardiac Electrical Activity With a Cardiac Myocyte--Targeted Optogenetic Voltage Indicator

    NARCIS (Netherlands)

    Chang Liao, Mei-Ling; de Boer, Teun P; Mutoh, Hiroki; Raad, Nour; Richter, Claudia; Wagner, Eva; Downie, Bryan R; Unsöld, Bernhard; Arooj, Iqra; Streckfuss-Bömeke, Katrin; Döker, Stephan; Luther, Stefan; Guan, Kaomei; Wagner, Stefan; Lehnart, Stephan E; Maier, Lars S; Stühmer, Walter; Wettwer, Erich; van Veen, Toon; Morlock, Michael M; Knöpfel, Thomas; Zimmermann, Wolfram-Hubertus


    RATIONALE: Monitoring and controlling cardiac myocyte activity with optogenetic tools offer exciting possibilities for fundamental and translational cardiovascular research. Genetically encoded voltage indicators may be particularly attractive for minimal invasive and repeated assessments of cardiac

  3. INTRSECT: single-component targeting of cells using multiple-feature Boolean logic (United States)

    Fenno, Lief E.; Mattis, Joanna; Ramakrishnan, Charu; Hyun, Minsuk; Lee, Soo Yeun; He, Miao; Tucciarone, Jason; Selimbeyoglu, Aslihan; Berndt, Andre; Grosenick, Logan; Zalocusky, Kelly A.; Bernstein, Hannah; Swanson, Haley; Perry, Chelsey; Diester, Ilka; Boyce, Frederick M.; Bass, Caroline E.; Neve, Rachael; Huang, Z. Josh; Deisseroth, Karl


    Precisely defining the roles of specific cell types is an intriguing and challenging frontier in the study of intact biological systems, and has stimulated the rapid development of genetically-encoded observation and control tools. However, targeting these tools with adequate specificity remains challenging: most cell types are best defined by the intersection of two or more features such as active promoter elements, location, and connectivity. Here we have combined recombinase tools with engineered introns to achieve expression of genetically-encoded payloads conditional upon multiple cell-type features, using Boolean logical operations all governed by a single versatile vector. We use this approach to target intersectionally-specified populations of inhibitory interneurons in mammalian hippocampus and neurons of the ventral tegmental area defined by both genetic and wiring properties. This flexible and modular approach may expand the application of genetically-encoded interventional and observational tools for intact-systems biology. PMID:24908100

  4. Normalized polarization ratios for the analysis of cell polarity.

    Directory of Open Access Journals (Sweden)

    Raz Shimoni

    Full Text Available The quantification and analysis of molecular localization in living cells is increasingly important for elucidating biological pathways, and new methods are rapidly emerging. The quantification of cell polarity has generated much interest recently, and ratiometric analysis of fluorescence microscopy images provides one means to quantify cell polarity. However, detection of fluorescence, and the ratiometric measurement, is likely to be sensitive to acquisition settings and image processing parameters. Using imaging of EGFP-expressing cells and computer simulations of variations in fluorescence ratios, we characterized the dependence of ratiometric measurements on processing parameters. This analysis showed that image settings alter polarization measurements; and that clustered localization is more susceptible to artifacts than homogeneous localization. To correct for such inconsistencies, we developed and validated a method for choosing the most appropriate analysis settings, and for incorporating internal controls to ensure fidelity of polarity measurements. This approach is applicable to testing polarity in all cells where the axis of polarity is known.

  5. A Guide to Fluorescent Protein FRET Pairs (United States)

    Bajar, Bryce T.; Wang, Emily S.; Zhang, Shu; Lin, Michael Z.; Chu, Jun


    Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies. PMID:27649177

  6. Elastin-like polypeptides: biomedical applications of tunable biopolymers. (United States)

    MacEwan, Sarah R; Chilkoti, Ashutosh


    Artificial repetitive polypeptides have grown in popularity as a bioinspired alternative to synthetic polymers. The genetically encoded synthesis, monodispersity, potential lack of toxicity, and biocompatibility are attractive features of these biopolymers for biological applications. Elastin-like polypeptides (ELPs) are one such class of biopolymers that are of particular interest because of their "smart"-stimuli responsive-properties. Herein, we discuss the genetically encoded design and recombinant synthesis of ELPs that enable precise control of their physicochemical properties and which have led to a wide range of biomedical applications of these biopolymers in the last decade.

  7. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein

    NARCIS (Netherlands)

    Shaner, Nathan C; Campbell, Robert E; Steinbach, Paul A; Giepmans, Ben N G; Palmer, Amy E; Tsien, Roger Y


    Fluorescent proteins are genetically encoded, easily imaged reporters crucial in biology and biotechnology. When a protein is tagged by fusion to a fluorescent protein, interactions between fluorescent proteins can undesirably disturb targeting or function. Unfortunately, all wild-type yellow-to-red

  8. Expanding the eukaryotic genetic code (United States)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.


    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  9. Unnatural reactive amino acid genetic code additions (United States)

    Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G


    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  10. Unnatural reactive amino acid genetic code additions (United States)

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.


    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  11. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.


    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  12. Mammalian cell-based optimization of the biarsenical-binding tetracysteine motif for improved fluorescence and affinity

    NARCIS (Netherlands)

    Martin, Brent R; Giepmans, Ben N G; Adams, Stephen R; Tsien, Roger Y


    Membrane-permeant biarsenical dyes such as FlAsH and ReAsH fluoresce upon binding to genetically encoded tetracysteine motifs expressed in living cells, yet spontaneous nonspecific background staining can prevent detection of weakly expressed or dilute proteins. If the affinity of the tetracysteine

  13. Neural Stem Cell Delivery of Therapeutic Antibodies to Treat Breast Cancer Brain Metastases (United States)


    and Engineering Neural Stem Cells for Delivery of Genetically Encoded 259 References 1. Snyder, EY., Deichter, DL., Walsh, C., Arnold- Aldea , S...acquired with a Zeiss Axio Imager M1m microscope equipped with a digital camera, using 10x or 20x air objectives. Digital images were analyzed using

  14. A novel analytical method for in vivo phosphate tracking (Corrigendum in FEBS Letters, 2007, 581 p. 579)

    DEFF Research Database (Denmark)

    Gu, H.; Lalonde, S.; Okumoto, S.;


    Genetically-encoded fluorescence resonance energy transfer (FRET) sensors for phosphate (Pi) (FLIPPi) were engineered by fusing a predicted Synechococcus phosphate-binding protein (PiBP) to eCFP and Venus. Purified fluorescent indicator protein for inorganic phosphate (FLIPPi), in which the fluor...

  15. Diverse organo-peptide macrocycles via a fast and catalyst-free oxime/intein-mediated dual ligation. (United States)

    Satyanarayana, Maragani; Vitali, Francesca; Frost, John R; Fasan, Rudi


    Macrocyclic Organo-Peptide Hybrids (MOrPHs) can be prepared from genetically encoded polypeptides via a chemoselective and catalyst-free reaction between a trifunctional oxyamino/amino-thiol synthetic precursor and an intein-fusion protein incorporating a bioorthogonal keto group.

  16. Visualization of Plasticity in Fear-Evoked Calcium Signals in Midbrain Dopamine Neurons (United States)

    Gore, Bryan B.; Soden, Marta E.; Zweifel, Larry S.


    Dopamine is broadly implicated in fear-related processes, yet we know very little about signaling dynamics in these neurons during active fear conditioning. We describe the direct imaging of calcium signals of dopamine neurons during Pavlovian fear conditioning using fiber-optic confocal microscopy coupled with the genetically encoded calcium…

  17. Recording intracellular molecular events from the outside: glycosylphosphatidylinositol-anchored avidin as a reporter protein for in vivo imaging.

    NARCIS (Netherlands)

    Lehmann, S.A.; Garayoa, E.G.; Blanc, A.; Keist, R.; Schibli, R.; Rudin, M.


    With the emergence of multimodal imaging strategies, genetically encoded reporters that can be flexibly combined with any imaging modality become highly attractive. Here we describe the use of glycosylphosphatidylinositol (GPI)-anchored avidin, an avidin moiety targeted to the extracellular side of

  18. A single-stranded architecture for cotranscriptional folding of RNA nanostructures

    DEFF Research Database (Denmark)

    Geary, Cody; Rothemund, Paul; Andersen, Ebbe Sloth


    Artificial DNA and RNA structures have been used as scaffolds for a variety of nanoscale devices. In comparison to DNA structures, RNA structures have been limited in size, but they also have advantages: RNA can fold during transcription and thus can be genetically encoded and expressed in cells...

  19. Direct imaging of glycans in Arabidopsis roots via click labeling of metabolically incorporated azido-monosaccharides

    NARCIS (Netherlands)

    Hoogenboom, Jorin; Berghuis, Nathalja; Cramer, Dario; Geurts, Rene; Zuilhof, Han; Wennekes, Tom


    Background: Carbohydrates, also called glycans, play a crucial but not fully understood role in plant health and development. The non-template driven formation of glycans makes it impossible to image them in vivo with genetically encoded fluorescent tags and related molecular biology approaches. A s

  20. Bacterial protein toxins : tools to study mammalian molecular cell biology

    NARCIS (Netherlands)

    Wüthrich, I.W.


    Bacterial protein toxins are genetically encoded proteinaceous macromolecules that upon exposure causes perturbation of cellular metabolism in a susceptible host. A bacterial toxin can work at a distance from the site of infection, and has direct and quantifiable actions. Bacterial protein toxins ca

  1. Imaging real-time HIV-1 virion fusion with FRET-based biosensors (United States)

    Jones, Daniel M.; Padilla-Parra, Sergi


    We have produced a novel, simple and rapid method utilising genetically encodable FRET-based biosensors to permit the detection of HIV-1 virion fusion in living cells. These biosensors show high sensitivity both spatially and temporally, and allow the real-time recovery of HIV-1 fusion kinetics in both single cells and cell populations simultaneously. PMID:26300212

  2. Correlating Whole Brain Neural Activity with Behavior in Head-Fixed Larval Zebrafish. (United States)

    Orger, Michael B; Portugues, Ruben


    We present a protocol to combine behavioral recording and imaging using 2-photon laser-scanning microscopy in head-fixed larval zebrafish that express a genetically encoded calcium indicator. The steps involve restraining the larva in agarose, setting up optics that allow projection of a visual stimulus and infrared illumination to monitor behavior, and analysis of the neuronal and behavioral data.

  3. A Pyrenyl-Appended Triazole-Based Calix arene as a Fluorescent Sensor for Iodide Ion

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Seung; Park, Sun Young; Kim, Sang Hoon [Korea University, Seoul (Korea, Republic of); Thuery, Pierre [CEA, IRAMIS, SCM, LCCEf, Yvette (France); Matthews, Susan E. [University of East Anglia, Norwich (United Kingdom); Souane, Rachid; Vicens, Jacques [IPHC-UdS-ECPM-CNRS, Cedex (France)


    The synthesis and evaluation of a novel calix arene-based fluorescent chemosensor 1 for the detection of I. is described. The fluorescent changes observed upon addition of various anions show that 1 is selective for I. over other anions. Addition of I. results in ratiometric measurements with 1 : 1 complex ratio.

  4. Monitoring of extracellular pH in young dental biofilms grown in vivo in the presence and absence of sucrose

    DEFF Research Database (Denmark)

    Dige, Irene; Baelum, Vibeke; Nyvad, Bente


    BACKGROUND AND OBJECTIVE: pH in dental biofilms is of central importance for the development of caries. We used the ratiometric pH-sensitive dye C-SNARF-4 in combination with digital image analysis to monitor extracellular pH in dental biofilms grown in situ with and without sucrose supply. DESIG...

  5. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya;


    We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific...

  6. Expanding the dynamic measurement range for polymeric nanoparticle pH sensors

    DEFF Research Database (Denmark)

    Sun, Honghao; Almdal, Kristoffer; Andresen, Thomas Lars


    Conventional optical nanoparticle pH sensors that are designed for ratiometric measurements in cells have been based on utilizing one sensor fluorophore and one reference fluorophore in each nanoparticle, which results in a relatively narrow dynamic measurement range. This results in substantial...

  7. Investigations of Antiangiogenic Mechanisms Using Novel Imaging Techniques (United States)


    for ratiometric oxy- gen sensing comprising a cyanine dye standard and an O2-sensitive Pt porphyrin phosphor in a sol–gel matrix and demonstrated its...Previously, ratiometry had been achieved with ternary mixtures of a cyanine dye standard and an O2- sensitive Pt porphyrin phosphor in a sol gel

  8. Poly(L-Lysine)-pyranine-3 coacervate mediated nanoparticle-assembly: fabrication of dynamic pH-responsive containers. (United States)

    Amali, Arlin Jose; Singh, Shashi; Rangaraj, Nandini; Patra, Digambara; Rana, Rohit Kumar


    Counter-ion condensation of Poly(L-Lysine) in the presence of pyranine-3 generates spherical coacervates, which then template the assembly of silica nanoparticles to form microcapsule structures that dynamically control the optical ratiometric sensing of both the change in pH and release of the probe molecule.

  9. The Role of L- and T-Type Calcium Channels in Local and Remote Calcium Responses in Rat Mesenteric Terminal Arterioles

    DEFF Research Database (Denmark)

    Braunstein, Thomas Hartig; Inoue, Ryuji; Cribbs, Leanne;


    Background/Aims: The roles of intercellular communication and T-type versus L-type voltage-dependent Ca(2+) channels (VDCCs) in conducted vasoconstriction to local KCl-induced depolarization were investigated in mesenteric arterioles. Methods: Ratiometric Ca(2+) imaging (R) using Fura-PE3...

  10. ATP-Evoked Intracellular Ca(2+) Signaling of Different Supporting Cells in the Hearing Mouse Hemicochlea

    NARCIS (Netherlands)

    Horváth, T; Polony, G; Fekete, Á; Aller, M; Halmos, G; Lendvai, B; Heinrich, Ansgard; Sperlágh, B; Vizi, E S; Zelles, T


    Hearing and its protection is regulated by ATP-evoked Ca(2+) signaling in the supporting cells of the organ of Corti, however, the unique anatomy of the cochlea hampers observing these mechanisms. For the first time, we have performed functional ratiometric Ca(2+) imaging (fura-2) in three different

  11. Purinergic receptors have different effects in rat exocrine pancreas. Calcium signals monitored by fura-2 using confocal microscopy

    DEFF Research Database (Denmark)

    Novak, Ivana; Nitschke, Roland; Amstrup, Jan


    Pancreatic ducts have several types of purinergic P2 receptors, however, nothing is known about P2 receptors in acini. The aim was to establish whether acini express functional P2 receptors coupled to intracellular Ca2+ signals and to measure the signals ratiometrically in a confocal laser scanni...

  12. In silico Evolutionary Developmental Neurobiology and the Origin of Natural Language (United States)

    Szathmáry, Eörs; Szathmáry, Zoltán; Ittzés, Péter; Orbaán, Geroő; Zachár, István; Huszár, Ferenc; Fedor, Anna; Varga, Máté; Számadó, Szabolcs

    It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related skills. At the heart of this project is the Evolutionary Neurogenetic Algorithm (ENGA) that is deliberately biomimetic. The design of the system was inspired by important biological phenomena such as brain ontogenesis, neuron morphologies, and indirect genetic encoding. Neuronal networks were selected and were allowed to reproduce as a function of their performance in the given task. The selected neuronal networks in all scenarios were able to solve the communication problem they had to face. The most striking feature of the model is that it works with highly indirect genetic encoding--just as brains do.

  13. Imaging the nanomolar range of nitric oxide with an amplifier-coupled fluorescent indicator in living cells (United States)

    Sato, Moritoshi; Hida, Naoki; Umezawa, Yoshio


    Nitric oxide (NO) is a small uncharged free radical that is involved in diverse physiological and pathophysiological mechanisms. NO is generated by three isoforms of NO synthase, endothelial, neuronal, and inducible ones. When generated in vascular endothelial cells, NO plays a key role in vascular tone regulation, in particular. Here, we describe an amplifier-coupled fluorescent indicator for NO to visualize physiological nanomolar dynamics of NO in living cells (detection limit of 0.1 nM). This genetically encoded high-sensitive indicator revealed that 1 nM of NO, which is enough to relax blood vessels, is generated in vascular endothelial cells even in the absence of shear stress. The nanomolar range of basal endothelial NO thus revealed appears to be fundamental to vascular homeostasis. fluorescence resonance energy transfer | genetic encoding

  14. Measuring intracellular redox conditions using GFP-based sensors

    DEFF Research Database (Denmark)

    Björnberg, Olof; Ostergaard, Henrik; Winther, Jakob R


    Recent years have seen the development of methods for analyzing the redox conditions in specific compartments in living cells. These methods are based on genetically encoded sensors comprising variants of Green Fluorescent Protein in which vicinal cysteine residues have been introduced at solvent......-exposed positions. Several mutant forms have been identified in which formation of a disulfide bond between these cysteine residues results in changes of their fluorescence properties. The redox sensors have been characterized biochemically and found to behave differently, both spectroscopically and in terms...... of redox properties. As genetically encoded sensors they can be expressed in living cells and used for analysis of intracellular redox conditions; however, which parameters are measured depends on how the sensors interact with various cellular redox components. Results of both biochemical and cell...

  15. SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents. (United States)

    Zhao, Yuzheng; Hu, Qingxun; Cheng, Feixiong; Su, Ni; Wang, Aoxue; Zou, Yejun; Hu, Hanyang; Chen, Xianjun; Zhou, Hai-Meng; Huang, Xinzhi; Yang, Kai; Zhu, Qian; Wang, Xue; Yi, Jing; Zhu, Linyong; Qian, Xuhong; Chen, Lixin; Tang, Yun; Loscalzo, Joseph; Yang, Yi


    The altered metabolism of tumor cells confers a selective advantage for survival and proliferation, and studies have shown that targeting such metabolic shifts may be a useful therapeutic strategy. We developed an intensely fluorescent, rapidly responsive, pH-resistant, genetically encoded sensor of wide dynamic range, denoted SoNar, for tracking cytosolic NAD(+) and NADH redox states in living cells and in vivo. SoNar responds to subtle perturbations of various pathways of energy metabolism in real time, and allowed high-throughput screening for new agents targeting tumor metabolism. Among > 5,500 unique compounds, we identified KP372-1 as a potent NQO1-mediated redox cycling agent that produced extreme oxidative stress, selectively induced cancer cell apoptosis, and effectively decreased tumor growth in vivo. This study demonstrates that genetically encoded sensor-based metabolic screening could serve as a valuable approach for drug discovery.

  16. Optogenetics: a new enlightenment age for zebrafish neurobiology. (United States)

    Del Bene, Filippo; Wyart, Claire


    Zebrafish became a model of choice for neurobiology because of the transparency of its brain and because of its amenability to genetic manipulation. In particular, at early stages of development the intact larva is an ideal system to apply optical techniques for deep imaging in the nervous system, as well as genetically encoded tools for targeting subsets of neurons and monitoring and manipulating their activity. For these applications,new genetically encoded optical tools, fluorescent sensors, and light-gated channels have been generated,creating the field of "optogenetics." It is now possible to monitor and control neuronal activity with minimal perturbation and unprecedented spatio-temporal resolution.We describe here the main achievements that have occurred in the last decade in imaging and manipulating neuronal activity in intact zebrafish larvae. We provide also examples of functional dissection of neuronal circuits achieved with the applications of these techniques in the visual and locomotor systems.

  17. Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe (United States)

    Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao


    Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions.

  18. Fluorescent Ensemble Based on Bispyrene Fluorophore and Surfactant Assemblies: Sensing and Discriminating Proteins in Aqueous Solution. (United States)

    Fan, Junmei; Ding, Liping; Bo, Yu; Fang, Yu


    A particular bispyrene fluorophore (1) with two pyrene moieties covalently linked via a hydrophilic spacer was synthesized. Fluorescence measurements reveal that the fluorescence emission of 1 could be well modulated by a cationic surfactant, dodecyltrimethylammonium bromide (DTAB). Protein sensing studies illustrate that the selected ensemble based on 1/DTAB assemblies exhibits ratiometric responses to nonmetalloproteins and turn-off responses to metalloproteins, which can be used to differentiate the two types of proteins. Moreover, negatively charged nonmetalloproteins can be discriminated from the positively charged ones according to the difference in ratiometric responses. Fluorescence sensing studies with control bispyrenes indicate that the polarity of the spacer connecting two pyrene moieties plays an important role in locating bispyrene fluorophore in DTAB assemblies, which further influences its sensing behaviors to noncovalent interacting proteins. This study sheds light on the influence of the probe structure on the sensing performance of a fluorescent ensemble based on probe and surfactant assemblies.

  19. Cross-linked self-assembled micelle based nanosensor for intracellular pH measurements

    DEFF Research Database (Denmark)

    Ek, Pramod Kumar; Søndergaard, Rikke Vicki; Windschiegl, Barbara


    A micelle based nanosensor was synthesized and investigated as a ratiometric pH sensor for use in measurements in living cells by fluorescent microscopy. The nanosensor synthesis was based on self-assembly of an amphiphilic triblock copolymer, which was chemically cross-linked after micelle......-linked by an amidation reaction using 3,6,9-trioxaundecandioic acid cross-linker. The cross-linked micelle was functionalized with two pH sensitive fluorophores and one reference fluorophore, which resulted in a highly uniform ratiometric pH nanosensor with a diameter of 29 nm. The use of two sensor fluorophores...... provided a sensor with a very broad measurement range that seems to be influenced by the chemical design of the sensor. Cell experiments show that the sensor is capable of monitoring the pH distributions in HeLa cells....

  20. Heteroaromatic donors in donor-acceptor-donor based fluorophores facilitate zinc ion sensing and cell imaging. (United States)

    Sreejith, Sivaramapanicker; Divya, Kizhumuri P; Jayamurthy, Purushothaman; Mathew, Jomon; Anupama, V N; Philips, Divya Susan; Anees, Palappuravan; Ajayaghosh, Ayyappanpillai


    The excited state intra molecular charge transfer (ICT) property of fluorophores has been extensively used for the design of fluorescent chemosensors. Herein, we report the synthesis and properties of three donor–π-acceptor–π-donor (D–π-A–π-D) based molecular probes BP, BT and BA. Two heteroaromatic rings, pyrrole (BP), and thiophene (BT) and a non-heteroaromatic ring N-alkoxy aniline (BA) were selected as donor moieties which were linked to a bipyridine binding site through a vinylic linkage. The heteroaromatic systems BP and BT perform selective and ratiometric emission signalling for zinc ions whereas the non-heteroaromatic probe BA does not. The advantages of the D–π-A–π-D design strategy in the design of ICT based probes for the selective fluorescent ratiometric signalling of zinc ions in biological media is discussed. Further, the use of BP, BT and BA for imaging Zn(2+) ions from MCF-7 cell lines is demonstrated.

  1. Optical highlighter molecules in neurobiology. (United States)

    Datta, Sandeep Robert; Patterson, George H


    The development of advanced optical methods has played a key role in propelling progress in neurobiology. Genetically-encoded fluorescent molecules found in nature have enabled labeling of individual neurons to study their physiology and anatomy. Here we discuss the recent use of both native and synthetic optical highlighter proteins to address key problems in neurobiology, including questions relevant to synaptic function, neuroanatomy, and the organization of neural circuits.

  2. Culture Prefigures Cognition in Pan/Homo Bonobos

    Directory of Open Access Journals (Sweden)



    Full Text Available This article questions traditional approaches to the study of primate cognition. Because of a widespread assumption that cognition in non-human primates is genetically encoded, these approaches neglect how profoundly apes’ cultural rearing experiences affect test results. We describe how three advanced cognitive abilities – imitation, theory of mind and language – emerged in bonobos maturing in a Pan/Homo culture.

  3. Struktur und Reaktionsmechanismus der Pyrrolysinsynthase (PylD)

    KAUST Repository

    Quitterer, Felix


    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product.

  4. Chemoenzymatic Fc Glycosylation via Engineered Aldehyde Tags



    Glycoproteins with chemically defined glycosylation sites and structures are important biopharmaceutical targets and critical tools for glycobiology. One approach toward constructing such molecules involves chemical glycosylation of aldehyde-tagged proteins. Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. We replaced the natural Fc N-glycosylation sequon with a five amino-acid sequence that ...

  5. A new genetic representation for quadratic assignment problem

    Directory of Open Access Journals (Sweden)

    Kratica Jozef


    Full Text Available In this paper, we propose a new genetic encoding for well known Quadratic Assignment Problem (QAP. The new encoding schemes are implemented with appropriate objective function and modified genetic operators. The numerical experiments were carried out on the standard QAPLIB data sets known from the literature. The presented results show that in all cases proposed genetic algorithm reached known optimal solutions in reasonable time.

  6. Social Defeat: Impact on Fear Extinction and Amygdala-Prefrontal Cortical Theta Synchrony in 5-HTT Deficient Mice


    Venu Narayanan; Heiming, Rebecca S.; Friederike Jansen; Jörg Lesting; Norbert Sachser; Hans-Christian Pape; Thomas Seidenbecher


    Emotions, such as fear and anxiety, can be modulated by both environmental and genetic factors. One genetic factor is for example the genetically encoded variation of the serotonin transporter (5-HTT) expression. In this context, the 5-HTT plays a key role in the regulation of central 5-HT neurotransmission, which is critically involved in the physiological regulation of emotions including fear and anxiety. However, a systematic study which examines the combined influence of environmental and...

  7. Phage as a Genetically Modifiable Supramacromolecule in Chemistry, Materials and Medicine


    Cao, Binrui; Yang, Mingying; Mao, Chuanbin


    Filamentous bacteriophage (phage) is a genetically modifiable supramacromolecule. It can be pictured as a semiflexible nanofiber (~900 nm long and ~8 nm wide) made of a DNA core and a protein shell with the former genetically encoding the latter. Although phage bioengineering and phage display techniques were developed before the 1990s, these techniques have not been widely used for chemistry, materials, and biomedical research from the perspective of supramolecular chemistry until recently. ...

  8. Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes


    Chow, Brian Y.; Chuong, Amy S; Klapoetke, Nathan C.; Edward S Boyden


    The life and operation of cells involve many physiological processes that take place over fast timescales of milliseconds to minutes. Genetically-encoded technologies for driving or suppressing specific fast physiological processes in intact cells, perhaps embedded within intact tissues in living organisms, are critical for the ability to understand how these physiological processes contribute to emergent cellular and organismal functions and behaviors. Such “synthetic physiology” tools are o...

  9. A novel fluorescent sensor for measurement of CFTR function by flow cytometry. (United States)

    Vijftigschild, Lodewijk A W; van der Ent, Cornelis K; Beekman, Jeffrey M


    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis. CFTR-dependent iodide transport measured by fluorescent quenching of ectopically expressed halide-sensitive yellow fluorescent protein (YFP) is widely being used to study CFTR function by microscopy or plate readers. Since YFP fluorescence in these systems is dependent on YFP expression levels and iodide concentration, differences in sensor expression level between experimental units are normalized at the start of each experiment. To allow accurate measurement of CFTR function by flow cytometry, we reasoned that co-expression of an iodide insensitive fluorescent protein would allow for normalization of sensor expression levels and more accurate quantification of CFTR function. Our data indicated that dsRed and mKate fluorescence are iodide insensitive, and we determined an optimal format for co-expression of these fluorescent proteins with halide-sensitive YFP. We showed using microscopy that ratiometric measurement (YFP/mKate) corrects for differences in sensor expression levels. Ratiometric measurements were essential to accurately measure CFTR function by flow cytometry that we here describe for the first time. Mixing of wild type or mutant CFTR expressing cells indicated that addition of approximately 10% of wild type CFTR expressing cells could be distinguished by ratiometric YFP quenching. Flow cytometric ratiometric YFP quenching also allowed us to study CFTR mutants associated with differential residual function upon ectopic expression. Compared with conventional plate-bound CFTR function assays, the flow cytometric approach described here can be used to study CFTR function in suspension cells. It may be further adapted to study CFTR function in heterologous cell populations using cell surface markers and selection of cells that display high CFTR function by cell sorting.

  10. Nanosensors for biotechnological and medical research; Nanosensoren fuer die biotechnologische und medizinische Forschung

    Energy Technology Data Exchange (ETDEWEB)

    Mohr, Gerhard J.; Trupp, Sabine [Fraunhofer-Institut fuer Zuverlaessigkeit und Mikrointegration (IZM-M), Regensburg (Germany). Arbeitsgruppe Sensormaterialien; Schulz, Anja [Dublin City University (Ireland). National Center for Sensor Research, Optical Sensors Laboratory; Doussineau, Tristan [Friedrich-Schiller-Universitaet Jena (Germany). Institut fuer Physikalische Chemie


    Nanosensors are introduced that enable a reliable and continuous monitoring of pH. The pH-nanosensors are obtained by covalent immobilisation of indicator dyes to different types of polymer particles. Additional reference dyes allow for a ratiometric and quantitative detection of signal changes. Possible applications are in biological and medical analytics, e.g. monitoring the cellular pH of cancer cells to evaluate drug effects, and also in micro-reactors and sensor-arrays. (orig.)

  11. All-optical thermal microscopy of laser-excited waveguides


    He, R.; De Aldana, J.R.V.; Pedrola, G.L.; Chen, F.; JAQUE, D.


    We report on a unique combination of high-resolution confocal microscopy and ratiometric luminescence thermometry to obtain thermal images of 800 nm pumped ultrafast laser-inscribed waveguides in a Nd:YAG crystal. Thermal images evidence a strong localization of thermal load in the waveguide active volume. Comparison between experimental data and numerical simulations reveals that ultrafast laser-inscribed damage tracks in Nd:YAG crystals behave both as low-index and low-thermal conductivity ...

  12. Photoacoustic Imaging: Semiconducting Oligomer Nanoparticles as an Activatable Photoacoustic Probe with Amplified Brightness for In Vivo Imaging of pH (Adv. Mater. 19/2016). (United States)

    Miao, Qingqing; Lyu, Yan; Ding, Dan; Pu, Kanyi


    Despite the great potential of photoacoustic imaging in the life sciences, the development of smart activatable photoacoustic probes remains elusive. On page 3662, K. Pu and co-workers report a facile nanoengineering approach based on semiconducting oligomer nano-particles to develop ratiometric photoacoustic probes with amplified brightness and enhanced sensing capability for accurate photoacoustic mapping of pH in the tumors of living mice.

  13. Fluorescent probes sensitive to changes in the cholesterol-to-phospholipids molar ratio in human platelet membranes during atherosclerosis (United States)

    Posokhov, Yevgen


    Environment-sensitive fluorescent probes were used for the spectroscopic visualization of pathological changes in human platelet membranes during cerebral atherosclerosis. It has been estimated that the ratiometric probes 2-(2‧-hydroxyphenyl)-5-phenyl-1,3,4-oxadiazole and 2-phenyl-phenanthr[9,10]oxazole can detect changes in the cholesterol-to-phospholipids molar ratio in human platelet membranes during the disease.

  14. Multiplexed modular genetic targeting of quantum dots. (United States)

    Saurabh, Saumya; Beck, Lauren E; Maji, Suvrajit; Baty, Catherine J; Wang, Yi; Yan, Qi; Watkins, Simon C; Bruchez, Marcel P


    While DNA-directed nanotechnology is now a well-established platform for bioinspired nanoscale assembly in vitro, the direct targeting of various nanomaterials in living biological systems remains a significant challenge. Hybrid biological systems with integrated and targeted nanomaterials may have interesting and exploitable properties, so methods for targeting various nanomaterials to precise biological locations are required. Fluorescence imaging has benefited from the use of nanoparticles with superior optical properties compared to fluorescent organic dyes or fluorescent proteins. While single-particle tracking (SPT) in living cells with genetically encoded proteins is limited to very short trajectories, the high photon output of genetically targeted and multiplexed quantum dots (QDs) would enable long-trajectory analysis of multiple proteins. However, challenges with genetic targeting of QDs limit their application in these experiments. In this report, we establish a modular method for targeting QD nanoparticles selectively to multiple genetically encoded tags by precomplexing QD-streptavidin conjugates with cognate biotinylated hapten molecules. This approach enables labeling and SPT of multiple genetically encoded proteins on living cells at high speed and can label expressed proteins in the cytosol upon microinjection into living cells. While we demonstrate labeling with three distinct QD conjugates, the approach can be extended to other specific hapten-affinity molecule interactions and alternative nanoparticles, enabling precise directed targeting of nanoparticles in living biological systems.

  15. Self-labelling enzymes as universal tags for fluorescence microscopy, super-resolution microscopy and electron microscopy. (United States)

    Liss, Viktoria; Barlag, Britta; Nietschke, Monika; Hensel, Michael


    Research in cell biology demands advanced microscopy techniques such as confocal fluorescence microscopy (FM), super-resolution microscopy (SRM) and transmission electron microscopy (TEM). Correlative light and electron microscopy (CLEM) is an approach to combine data on the dynamics of proteins or protein complexes in living cells with the ultrastructural details in the low nanometre scale. To correlate both data sets, markers functional in FM, SRM and TEM are required. Genetically encoded markers such as fluorescent proteins or self-labelling enzyme tags allow observations in living cells. Various genetically encoded tags are available for FM and SRM, but only few tags are suitable for CLEM. Here, we describe the red fluorescent dye tetramethylrhodamine (TMR) as a multimodal marker for CLEM. TMR is used as fluorochrome coupled to ligands of genetically encoded self-labelling enzyme tags HaloTag, SNAP-tag and CLIP-tag in FM and SRM. We demonstrate that TMR can additionally photooxidize diaminobenzidine (DAB) to an osmiophilic polymer visible on TEM sections, thus being a marker suitable for FM, SRM and TEM. We evaluated various organelle markers with enzymatic tags in mammalian cells labelled with TMR-coupled ligands and demonstrate the use as efficient and versatile DAB photooxidizer for CLEM approaches.

  16. Calcium imaging of cortical neurons using Fura-2 AM. (United States)

    Barreto-Chang, Odmara L; Dolmetsch, Ricardo E


    Calcium imaging is a common technique that is useful for measuring calcium signals in cultured cells. Calcium imaging techniques take advantage of calcium indicator dyes, which are BAPTA-based organic molecules that change their spectral properties in response to the binding of Ca2+ ions. Calcium indicator dyes fall into two categories, ratio-metric dyes like Fura-2 and Indo-1 and single-wavelength dyes like Fluo-4. Ratio-metric dyes change either their excitation or their emission spectra in response to calcium, allowing the concentration of intracellular calcium to be determined from the ratio of fluorescence emission or excitation at distinct wavelengths. The main advantage of using ratio-metric dyes over single wavelength probes is that the ratio signal is independent of the dye concentration, illumination intensity, and optical path length allowing the concentration of intracellular calcium to be determined independently of these artifacts. One of the most common calcium indicators is Fura-2, which has an emission peak at 505 nM and changes its excitation peak from 340 nm to 380 nm in response to calcium binding. Here we describe the use of Fura-2 to measure intracellular calcium elevations in neurons and other excitable cells.

  17. Laser-induced fluorescence reader with a turbidimetric system for sandwich-type immunoassay using nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Y.H.; Lim, H.B., E-mail:


    Graphical abstract: Laser-induced fluorescence reader with ratiometric correction for sandwich-type immunoassay using nanoparticles. - Highlights: • Laser-induced fluorescence system with ratiometric correction was developed. • The system reduced experimental error caused by particle loss and aggregation. • The detection limit of about 39 pg mL{sup −1} for salinomycin was obtained. • Calibration linearity and sensitivity were also significantly improved. • The system has the potential for bioanalysis using various nanoparticles. - Abstract: A unique laser-induced fluorescence (LIF) reader equipped with a turbidimetric system was developed for a sandwich-type immunoassay using nanoparticles. The system was specifically designed to reduce experimental error caused by particle loss, aggregation and sinking, and to improve analytical performance through ratiometric measurement of the fluorescence with respect to the turbidimetric absorbance. For application to determine the concentration of salinomycin, magnetic nanoparticles (MNPs) and FITC-doped silica nanoparticles (colored balls) immobilized with antibody were synthesized for magnetic extraction and for tagging as a fluorescence probe, respectively. The detection limit of about 39 pg mL{sup −1} was obtained, which was an improvement of about 2-fold compared to that obtained without employment of the turbidimetric system. Calibration linearity and sensitivity were also improved, with increase from 0.8601 to 0.9905 in the R{sup 2}-coefficient and by 1.92-fold for the curve slope, respectively. The developed LIF reader has the potential to be used for fluorescence measurements using various nanomaterials, such as quantum dots.

  18. Development of biosensors and their application in metabolic engineering

    DEFF Research Database (Denmark)

    Zhang, Jie; Jensen, Michael Krogh; Keasling, Jay


    for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule binding...... and ease of implementation with high-throughput analysis. Here we describe recent progress in biosensor development and their applications in a metabolic engineering context. We also highlight examples of how biosensors can be integrated with synthetic circuits to exert feedback regulation...

  19. Fluorogen-based reporters for fluorescence imaging: a review (United States)

    Jullien, Ludovic; Gautier, Arnaud


    Fluorescence bioimaging has recently jumped into a new area of spatiotemporal resolution and sensitivity thanks to synergistic advances in both optical physics and probe/biosensor design. This review focuses on the recent development of genetically encodable fluorescent reporters that bind endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activate their fluorescence. We highlight the innovative engineering and design that gave rise to these new natural and synthetic fluorescent reporters, and describe some of the emerging applications in imaging and biosensing.

  20. Stimulus responsive elastin biopolymers: applications in medicine and biotechnology (United States)

    Chilkoti, Ashutosh; Christensen, Trine; MacKay, J Andrew


    Elastin-like polypeptides (ELPs) are artificial polypeptides, derived from Val-Pro-Gly-Xaa-Gly (VPGXG) pentapeptide repeats found in human tropoelastin, that reversibly coacervate above a critical temperature. Genetically encodable ELPs are monodisperse, stimuli responsive, and biocompatible, properties that make them attractive for drug delivery and tissue engineering. The potential of ELPs to self-assemble into nanostructures in response to environmental triggers is another interesting feature of these polypeptides that promises to lead to a host of new applications. PMID:17055770

  1. Peptide-based Biopolymers in Biomedicine and Biotechnology (United States)

    Chow, Dominic; Nunalee, Michelle L.; Lim, Dong Woo; Simnick, Andrew J.; Chilkoti, Ashutosh


    Peptides are emerging as a new class of biomaterials due to their unique chemical, physical, and biological properties. The development of peptide-based biomaterials is driven by the convergence of protein engineering and macromolecular self-assembly. This review covers the basic principles, applications, and prospects of peptide-based biomaterials. We focus on both chemically synthesized and genetically encoded peptides, including poly-amino acids, elastin-like polypeptides, silk-like polymers and other biopolymers based on repetitive peptide motifs. Applications of these engineered biomolecules in protein purification, controlled drug delivery, tissue engineering, and biosurface engineering are discussed. PMID:19122836

  2. The evolution of secondary organization in immune system gene libraries

    Energy Technology Data Exchange (ETDEWEB)

    Hightower, R.; Forrest, S. [New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science; Perelson, A.S. [Los Alamos National Lab., NM (United States)


    A binary model of the immune system is used to study the effects of evolution on the genetic encoding for antibody molecules. We report experiments which show that the evolution of immune system genes, simulated by the genetic algorithm, can induce a high degree of genetic organization even though that organization is not explicitly required by the fitness function. This secondary organization is related to the true fitness of an individual, in contrast to the sampled fitness which is the explicit fitness measure used to drive the process of evolution.

  3. Chromate Binding and Removal by the Molybdate-Binding Protein ModA. (United States)

    Karpus, Jason; Bosscher, Michael; Ajiboye, Ifedayo; Zhang, Liang; He, Chuan


    Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards.

  4. Arduino Due based tool to facilitate in vivo two-photon excitation microscopy. (United States)

    Artoni, Pietro; Landi, Silvia; Sato, Sebastian Sulis; Luin, Stefano; Ratto, Gian Michele


    Two-photon excitation spectroscopy is a powerful technique for the characterization of the optical properties of genetically encoded and synthetic fluorescent molecules. Excitation spectroscopy requires tuning the wavelength of the Ti:sapphire laser while carefully monitoring the delivered power. To assist laser tuning and the control of delivered power, we developed an Arduino Due based tool for the automatic acquisition of high quality spectra. This tool is portable, fast, affordable and precise. It allowed studying the impact of scattering and of blood absorption on two-photon excitation light. In this way, we determined the wavelength-dependent deformation of excitation spectra occurring in deep tissues in vivo.

  5. The D3cpv Cameleon reports Ca²⁺ dynamics in plant mitochondria with similar kinetics of the YC3.6 Cameleon, but with a lower sensitivity. (United States)

    Loro, G; Ruberti, C; Zottini, M; Costa, A


    Mitochondria are key organelles involved in many aspects of plant physiology and, their ability to generate specific Ca²⁺ signatures in response to abiotic and biotic stimuli has been reported as one of their roles. The recent identification of the mammalian mitochondrial Ca²⁺ uniporter opens a new research area in plant biology. To study the mitochondrial Ca²⁺ handling, it is essential to have a reliable probe. Here we have reported the generation of an Arabidopsis transgenic line expressing the genetically encoded probe Cameleon D3cpv targeted to mitochondria, and compared its properties with the already known Cameleon YC3.6.

  6. Lipid Storage Disorders Block Lysosomal Trafficking By Inhibiting TRP Channel and Calcium Release



    Lysosomal lipid accumulation, defects in membrane trafficking, and altered Ca2+ homeostasis are common features in many lysosomal storage diseases. Mucolipin TRP channel 1 (TRPML1) is the principle Ca2+ channel in the lysosome. Here we show that TRPML1-mediated lysosomal Ca2+ release, measured using a genetically-encoded Ca2+ indicator (GCaMP3) attached directly to TRPML1 and elicited by a potent membrane-permeable synthetic agonist, is dramatically reduced in Niemann-Pick (NP) disease cells....

  7. RNA fluorescence with light-up aptamers (United States)

    Ouellet, Jonathan


    Seeing is not only believing; it also includes understanding. Cellular imaging with GFP in live cells has been transformative in many research fields. Modulation of cellular regulation is tightly regulated and innovative imaging technologies contribute to further understand cellular signaling and physiology. New types of genetically encoded biosensors have been developed over the last decade. They are RNA aptamers that bind with their cognate fluorogen ligands and activate their fluorescence. The emergence and the evolution of these RNA aptamers as well as their conversion into a wide spectrum of applications are examined in a global way.

  8. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD)

    KAUST Repository

    Quitterer, Felix


    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. SLAP: Small Labeling Pair for Single-Molecule Super-Resolution Imaging. (United States)

    Wieneke, Ralph; Raulf, Anika; Kollmannsperger, Alina; Heilemann, Mike; Tampé, Robert


    Protein labeling with synthetic fluorescent probes is a key technology in chemical biology and biomedical research. A sensitive and efficient modular labeling approach (SLAP) was developed on the basis of a synthetic small-molecule recognition unit (Ni-trisNTA) and the genetically encoded minimal protein His6-10 -tag. High-density protein tracing by SLAP was demonstrated. This technique allows super-resolution fluorescence imaging and fulfills the necessary sampling criteria for single-molecule localization-based imaging techniques. It avoids masking by large probes, for example, antibodies, and supplies sensitive, precise, and robust size analysis of protein clusters (nanodomains).

  10. Optogenetics for gene expression in mammalian cells. (United States)

    Müller, Konrad; Naumann, Sebastian; Weber, Wilfried; Zurbriggen, Matias D


    Molecular switches that are controlled by chemicals have evolved as central research instruments in mammalian cell biology. However, these tools are limited in terms of their spatiotemporal resolution due to freely diffusing inducers. These limitations have recently been addressed by the development of optogenetic, genetically encoded, and light-responsive tools that can be controlled with the unprecedented spatiotemporal precision of light. In this article, we first provide a brief overview of currently available optogenetic tools that have been designed to control diverse cellular processes. Then, we focus on recent developments in light-controlled gene expression technologies and provide the reader with a guideline for choosing the most suitable gene expression system.

  11. Optogenetic control of transcription in zebrafish.

    Directory of Open Access Journals (Sweden)

    Hongtao Liu

    Full Text Available Light inducible protein-protein interactions are powerful tools to manipulate biological processes. Genetically encoded light-gated proteins for controlling precise cellular behavior are a new and promising technology, called optogenetics. Here we exploited the blue light-induced transcription system in yeast and zebrafish, based on the blue light dependent interaction between two plant proteins, blue light photoreceptor Cryptochrome 2 (CRY2 and the bHLH transcription factor CIB1 (CRY-interacting bHLH 1. We demonstrate the utility of this system by inducing rapid transcription suppression and activation in zebrafish.

  12. Functionalization of carbon nanotubes with a pH-responsive molecule to produce a pH sensor

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Liping; Nakayama, Tomonobu; Tomimoto, Hiroyuki; Shingaya, Yoshitaka [Nano Functionality Integration Group, National Institute for Materials Science, Tsukuba 305-0044 (Japan); Huang Qing, E-mail: zhao.liping@nims.go.j, E-mail: NAKAYAMA.Tomonobu@nims.go.j [Nanoscale Materials Center, National Institute for Materials Science, Tsukuba 305-0044 (Japan)


    Carbon nanotubes were functionalized with the ratiometric pH-responsive dye molecule 6,8-dihydroxy-1,3-pyrenedisulfonic acid disodium salt, which enabled them to indicate pH values over the range of pH 5.6-8.3. The nanotubes were coated with a layer of electron-donating ZnPc, which strengthened the CNT-dye interaction. The range of pH response is relevant for biological systems, which makes the nanotubes suitable for a wide range of applications within nanobiotechnology.

  13. A simple optode based imaging technique to measure O2 distribution and dynamics in tap water biofilms

    DEFF Research Database (Denmark)

    Staal, Marc Jaap; Prest, E.; Vrouwenvelder, H.;


    A ratiometric luminescence intensity imaging approach is presented, which enables spatial O2 measurements in biofilm reactors with transparent planar O2 optodes. Optodes consist of an O2 sensitive luminescent dye immobilized in a 1–10 µm thick polymeric layer on a transparent carrier, e.g. a glass...... window. The method is based on sequential imaging of the O2 dependent luminescence intensity, which are subsequently normalized with luminescent intensity images recorded under anoxic conditions. We present 2-dimensional O2 distribution images at the base of a tap water biofilm measured with the new...

  14. A novel fluorescent turn-on probe for bisulfite based on NBD chromophore

    Indian Academy of Sciences (India)

    Puhui Xie; Guangqin Gao; Wenjie Zhang; Guoyu Yang; Qiu Jin


    A novel fluorescent turn-on probe (compound 1) for bisulfite based on 7-nitrobenz-2-oxa-1,3-diazole (NBD) chromophore has been developed. Its sensing behavior toward various anions was investigated by absorption and fluorescence techniques. This probe shows a selective, turn-on fluorescent response and ratiometric colorimetric response toward bisulfite in aqueous acetonitrile solutions. The possible recognition mechanism of probe 1 toward bisulfite was illustrated by MS spectra analysis and DFT calculations Probe 1 was used to determine bisulfite in real-life samples with good recoveries.

  15. Characterization of corneal damage from Pseudomonas aeruginosa infection by the use of multiphoton microscopy (United States)

    Chang, Yu-Lin; Chen, Wei-Liang; Lo, Wen; Chen, Shean-Jen; Tan, Hsin-Yuan; Dong, Chen-Yuan


    Using multiphoton autofluorescence (MAF) and second harmonic generation (SHG) microscopy, we investigate the morphology and the structure of the corneal epithelium and stroma collagen of bovine cornea following injection of Pseudomonas aeruginosa. We found that corneal epithelial cells are damaged and stromal collagen becoming increasingly autofluorescent with time. We also characterized infected cornea cultured for 0, 6, 12, and 24 h by quantitative ratiometric MAF to SHG index (MAFSI) analysis. MAFSI results show that the destruction of the stromal collagen corresponds to a decrease in SHG intensity and increase of MAF signal with time.

  16. Intravital FRET: Probing Cellular and Tissue Function in Vivo

    Directory of Open Access Journals (Sweden)

    Helena Radbruch


    Full Text Available The development of intravital Förster Resonance Energy Transfer (FRET is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo—ratiometrically and time-resolved by fluorescence lifetime imaging—and show their concrete application in the context of neuroinflammation in adult mice.

  17. Fluorescence Resonance Energy Transfer (FRET) sensor

    CERN Document Server

    Hussain, Syed Arshad; Chakraborty, Sekhar; Saha, Jaba; Roy, Arpan Datta; Chakraborty, Santanu; Debnath, Pintu; Bhattacharjee, D


    The applications of Fluorescence resonance energy transfer (FRET) have expanded tremendously in the last 25 years, and the technique has become a staple technique in many biological and biophysical fields. FRET can be used as spectroscopic ruler in various areas such as structural elucidation of biological molecules and their interactions, in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting, and metallic nanomaterials etc. Based on the mechanism of FRET a variety of novel chemical sensors and Biosensors have been developed. This review highlights the recent applications of sensitive and selective ratiometric FRET based sensors.

  18. A Eu/Tb-mixed MOF for luminescent high-temperature sensing (United States)

    Wang, Huizhen; Zhao, Dian; Cui, Yuangjing; Yang, Yu; Qian, Guodong


    Temperature measurements and thermal mapping using luminescent MOF operating in the high-temperature range are of great interest in the micro-electronic diagnosis. In this paper, we report a thermostable Eu/Tb-mixed MOF Eu0.37Tb0.63-BTC-a exhibiting strong luminescence at elevated temperature, which can serve as a ratiometric luminescent thermometer for high-temperature range. The high-temperature operating range (313-473 K), high relative sensitivity and accurate temperature resolution, make such a Eu/Tb-mixed MOF useful for micro-electronic diagnosis.

  19. Long-gauge FBGs interrogated by DTR3 for dynamic distributed strain measurement of helicopter blade model (United States)

    Nishiyama, M.; Igawa, H.; Kasai, T.; Watanabe, N.


    In this paper, we describe characteristics of distributed strain sensing based on a Delayed Transmission/Reflection Ratiometric Reflectometry (DTR3) scheme with a long-gauge Fiber Bragg Grating (FBG), which is attractive to dynamic structural deformation monitoring such as a helicopter blade and an airplane wing. The DTR3 interrogator using the longgauge FBG has capability of detecting distributed strain with 50 cm spatial resolution in 100 Hz sampling rate. We evaluated distributed strain sensing characteristics of the long-gauge FBG attached on a 5.5 m helicopter blade model in static tests and free vibration dynamic tests.

  20. Fluorescence lifetime-based biosensing of zinc: Origin of the broad dynamic range. (United States)

    Thompson, R B; Patchan, M W


    Fluorescence lifetime-based chemical sensors have recently been described for applications in medicine, environmental monitoring, and bioprocess control. These sensors transduce the level of the analyte as a change in the apparent fluorescence lifetime of an indicator phase. We have previously developed a wavelength-ratiometric fluorescence biosensor for zinc based on binding of zinc and dansylamide to apo-carbonic anhydrase which exhibited high sensitivity and selectivity. We demonstrate that the apo-carbonic anhydrase/dansylamide indicator system is very well suited for lifetime-based sensing, with a subnanomolar detection limit and greater than 1000-fold dynamic range. The theoretical basis for the wide dynamic range is discussed.

  1. Intracellular calcium dynamics in cortical microglia responding to focal laser injury in the PC::G5-tdT reporter mouse

    Directory of Open Access Journals (Sweden)

    Amir ePozner


    Full Text Available Microglia, the resident immune cells of the brain parenchyma, are highly responsive to tissue injury. Following cell damage, microglial processes redirect their motility from randomly scouting the extracellular space to specifically reaching toward the compromised tissue. While the cell morphology aspects of this defense mechanism have been characterized, the intracellular events underlying these responses remain largely unknown. Specifically, the role of intracellular Ca2+ dynamics has not been systematically investigated in acutely activated microglia due to technical difficulty. Here we used live two-photon imaging of the mouse cortex ubiquitously expressing the genetically encoded Ca2+ indicator GCaMP5G and fluorescent marker tdTomato in central nervous system microglia. We found that spontaneous Ca2+ transients in microglial somas and processes were generally low (only 4% of all microglia showing transients within 20 min, but baseline activity increased about 8-fold when the animals were treated with LPS 12 h before imaging. When challenged with focal laser injury, an additional surge in Ca2+ activity was observed in the somas and protruding processes. Notably, coherent and simultaneous Ca2+ rises in multiple microglial cells were occasionally detected in LPS-treated animals. We show that Ca2+ transients were predominantly mediated via purinergic receptors. This work demonstrates the usefulness of genetically encoded Ca2+ indicators for investigation of microglial physiology.

  2. Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents

    Directory of Open Access Journals (Sweden)

    Jennifer H Hou


    Full Text Available The cardiac action potential (AP and the consequent cytosolic Ca2+ transient are key indicators of cardiac function. Natural developmental processes, as well as many drugs and pathologies change the waveform, propagation, or variability (between cells or over time of these parameters. Here we apply a genetically encoded dual-function calcium and voltage reporter (CaViar to study the development of the zebrafish heart in vivo between 1.5 and 4 days post fertilization (dpf. We developed a high-sensitivity spinning disk confocal microscope and associated software for simultaneous three-dimensional optical mapping of voltage and calcium. We produced a transgenic zebrafish line expressing CaViar under control of the heart-specific cmlc2 promoter, and applied ion channel blockers at a series of developmental stages to map the maturation of the action potential in vivo. Early in development, the AP initiated via a calcium current through L-type calcium channels. Between 90 – 102 hours post fertilization (hpf, the ventricular AP switched to a sodium-driven upswing, while the atrial AP remained calcium driven. In the adult zebrafish heart, a sodium current drives the AP in both the atrium and ventricle. Simultaneous voltage and calcium imaging with genetically encoded reporters provides a new approach for monitoring cardiac development, and the effects of drugs on cardiac function.

  3. Very long-term memories may be stored in the pattern of holes in the perineuronal net. (United States)

    Tsien, Roger Y


    A hypothesis and the experiments to test it propose that very long-term memories, such as fear conditioning, are stored as the pattern of holes in the perineuronal net (PNN), a specialized ECM that envelops mature neurons and restricts synapse formation. The 3D intertwining of PNN and synapses would be imaged by serial-section EM. Lifetimes of PNN vs. intrasynaptic components would be compared with pulse-chase (15)N labeling in mice and (14)C content in human cadaver brains. Genetically encoded indicators and antineoepitope antibodies should improve spatial and temporal resolution of the in vivo activity of proteases that locally erode PNN. Further techniques suggested include genetic KOs, better pharmacological inhibitors, and a genetically encoded snapshot reporter, which will capture the pattern of activity throughout a large ensemble of neurons at a time precisely defined by the triggering illumination, drive expression of effector genes to mark those cells, and allow selective excitation, inhibition, or ablation to test their functional importance. The snapshot reporter should enable more precise inhibition or potentiation of PNN erosion to compare with behavioral consequences. Finally, biosynthesis of PNN components and proteases would be imaged.

  4. Development of a Cell-Based Fluorescence Resonance Energy Transfer Reporter for Bacillus anthracis Lethal Factor Protease

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, R H; Steenblock, E R; Camarero, J A


    We report the construction of a cell-based fluorescent reporter for anthrax lethal factor (LF) protease activity using the principle of fluorescence resonance energy transfer (FRET). This was accomplished by engineering an Escherichia coli cell line to express a genetically encoded FRET reporter and LF protease. Both proteins were encoded in two different expression plasmids under the control of different tightly controlled inducible promoters. The FRET-based reporter was designed to contain a LF recognition sequence flanked by the FRET pair formed by CyPet and YPet fluorescent proteins. The length of the linker between both fluorescent proteins was optimized using a flexible peptide linker containing several Gly-Gly-Ser repeats. Our results indicate that this FRET-based LF reporter was readily expressed in E. coli cells showing high levels of FRET in vivo in the absence of LF. The FRET signal, however, decreased 5 times after inducing LF expression in the same cell. These results suggest that this cell-based LF FRET reporter may be used to screen genetically encoded libraries in vivo against LF.

  5. Intelligent Design of Nano-Scale Molecular Imaging Agents

    Directory of Open Access Journals (Sweden)

    Takeaki Ozawa


    Full Text Available Visual representation and quantification of biological processes at the cellular and subcellular levels within living subjects are gaining great interest in life science to address frontier issues in pathology and physiology. As intact living subjects do not emit any optical signature, visual representation usually exploits nano-scale imaging agents as the source of image contrast. Many imaging agents have been developed for this purpose, some of which exert nonspecific, passive, and physical interaction with a target. Current research interest in molecular imaging has mainly shifted to fabrication of smartly integrated, specific, and versatile agents that emit fluorescence or luminescence as an optical readout. These agents include luminescent quantum dots (QDs, biofunctional antibodies, and multifunctional nanoparticles. Furthermore, genetically encoded nano-imaging agents embedding fluorescent proteins or luciferases are now gaining popularity. These agents are generated by integrative design of the components, such as luciferase, flexible linker, and receptor to exert a specific on–off switching in the complex context of living subjects. In the present review, we provide an overview of the basic concepts, smart design, and practical contribution of recent nano-scale imaging agents, especially with respect to genetically encoded imaging agents.

  6. Apoptosis induction-related cytosolic calcium responses revealed by the dual FRET imaging of calcium signals and caspase-3 activation in a single cell. (United States)

    Miyamoto, Akitoshi; Miyauchi, Hiroshi; Kogure, Takako; Miyawaki, Atsushi; Michikawa, Takayuki; Mikoshiba, Katsuhiko


    Stimulus-induced changes in the intracellular Ca(2+) concentration control cell fate decision, including apoptosis. However, the precise patterns of the cytosolic Ca(2+) signals that are associated with apoptotic induction remain unknown. We have developed a novel genetically encoded sensor of activated caspase-3 that can be applied in combination with a genetically encoded sensor of the Ca(2+) concentration and have established a dual imaging system that enables the imaging of both cytosolic Ca(2+) signals and caspase-3 activation, which is an indicator of apoptosis, in the same cell. Using this system, we identified differences in the cytosolic Ca(2+) signals of apoptotic and surviving DT40 B lymphocytes after B cell receptor (BCR) stimulation. In surviving cells, BCR stimulation evoked larger initial Ca(2+) spikes followed by a larger sustained elevation of the Ca(2+) concentration than those in apoptotic cells; BCR stimulation also resulted in repetitive transient Ca(2+) spikes, which were mediated by the influx of Ca(2+) from the extracellular space. Our results indicate that the observation of both Ca(2+) signals and cells fate in same cell is crucial to gain an accurate understanding of the function of intracellular Ca(2+) signals in apoptotic induction.

  7. The spatio-temporal dynamics of PKA activity profile during mitosis and its correlation to chromosome segregation. (United States)

    Vandame, Pauline; Spriet, Corentin; Trinel, Dave; Gelaude, Armance; Caillau, Katia; Bompard, Coralie; Biondi, Emanuele; Bodart, Jean-François


    The cyclic adenosine monophosphate dependent kinase protein (PKA) controls a variety of cellular processes including cell cycle regulation. Here, we took advantages of genetically encoded FRET-based biosensors, using an AKAR-derived biosensor to characterize PKA activity during mitosis in living HeLa cells using a single-cell approach. We measured PKA activity changes during mitosis. HeLa cells exhibit a substantial increase during mitosis, which ends with telophase. An AKAREV T>A inactive form of the biosensor and H89 inhibitor were used to ascertain for the specificity of the PKA activity measured. On a spatial point of view, high levels of activity near to chromosomal plate during metaphase and anaphase were detected. By using the PKA inhibitor H89, we assessed the role of PKA in the maintenance of a proper division phenotype. While this treatment in our hands did not impaired cell cycle progression in a drastic manner, inhibition of PKA leads to a dramatic increase in chromososme misalignement on the spindle during metaphase that could result in aneuploidies. Our study emphasizes the insights that can be gained with genetically encoded FRET-based biosensors, which enable to overcome the shortcomings of classical methologies and unveil in vivo PKA spatiotemporal profiles in HeLa cells.

  8. Studying the mechanism of neurostimulation by infrared laser light using GCaMP6s and Rhodamine B imaging (United States)

    Moreau, David; Lefort, Claire; Bardet, Sylvia M.; O'Connor, Rodney P.


    Infrared laser light radiation can be used to depolarize neurons and to stimulate neural activity. The absorption of infrared radiation and heating of biological tissue is thought to be the underlying mechanism of this phenomenon whereby local temperature increases in the plasma membrane of cells either directly influence membrane properties or act via temperature sensitive ion channels. Action potentials are typically measured electrically in neurons with microelectrodes, but they can also be observed using fluorescence microscopy techniques that use synthetic or genetically encoded calcium indicators. In this work, we studied the impact of infrared laser light on neuronal calcium signals to address the mechanism of these thermal effects. Cultured primary mouse hippocampal neurons expressing the genetically encoded calcium indicator GCaMP6s were used in combination with the temperature sensitive fluorophore Rhodamine B to measure calcium signals and temperature changes at the cellular level. Here we present our all-optical strategy for studying the influence of infrared laser light on neuronal activity.

  9. An Engineered Split Intein for Photoactivated Protein Trans-Splicing.

    Directory of Open Access Journals (Sweden)

    Stanley Wong

    Full Text Available Protein splicing is mediated by inteins that auto-catalytically join two separated protein fragments with a peptide bond. Here we engineered a genetically encoded synthetic photoactivatable intein (named LOVInC, by using the light-sensitive LOV2 domain from Avena sativa as a switch to modulate the splicing activity of the split DnaE intein from Nostoc punctiforme. Periodic blue light illumination of LOVInC induced protein splicing activity in mammalian cells. To demonstrate the broad applicability of LOVInC, synthetic protein systems were engineered for the light-induced reassembly of several target proteins such as fluorescent protein markers, a dominant positive mutant of RhoA, caspase-7, and the genetically encoded Ca2+ indicator GCaMP2. Spatial precision of LOVInC was demonstrated by targeting activity to specific mammalian cells. Thus, LOVInC can serve as a general platform for engineering light-based control for modulating the activity of many different proteins.

  10. Colorful protein-based fluorescent probes for collagen imaging.

    Directory of Open Access Journals (Sweden)

    Stijn J A Aper

    Full Text Available Real-time visualization of collagen is important in studies on tissue formation and remodeling in the research fields of developmental biology and tissue engineering. Our group has previously reported on a fluorescent probe for the specific imaging of collagen in live tissue in situ, consisting of the native collagen binding protein CNA35 labeled with fluorescent dye Oregon Green 488 (CNA35-OG488. The CNA35-OG488 probe has become widely used for collagen imaging. To allow for the use of CNA35-based probes in a broader range of applications, we here present a toolbox of six genetically-encoded collagen probes which are fusions of CNA35 to fluorescent proteins that span the visible spectrum: mTurquoise2, EGFP, mAmetrine, LSSmOrange, tdTomato and mCherry. While CNA35-OG488 requires a chemical conjugation step for labeling with the fluorescent dye, these protein-based probes can be easily produced in high yields by expression in E. coli and purified in one step using Ni2+-affinity chromatography. The probes all bind specifically to collagen, both in vitro and in porcine pericardial tissue. Some first applications of the probes are shown in multicolor imaging of engineered tissue and two-photon imaging of collagen in human skin. The fully-genetic encoding of the new probes makes them easily accessible to all scientists interested in collagen formation and remodeling.

  11. Optogenetic control of ROS production

    Directory of Open Access Journals (Sweden)

    Andrew P. Wojtovich


    Full Text Available Reactive Oxygen Species (ROS are known to cause oxidative damage to DNA, proteins and lipids. In addition, recent evidence suggests that ROS can also initiate signaling cascades that respond to stress and modify specific redox-sensitive moieties as a regulatory mechanism. This suggests that ROS are physiologically-relevant signaling molecules. However, these sensor/effector molecules are not uniformly distributed throughout the cell. Moreover, localized ROS damage may elicit site-specific compensatory measures. Thus, the impact of ROS can be likened to that of calcium, a ubiquitous second messenger, leading to the prediction that their effects are exquisitely dependent upon their location, quantity and even the timing of generation. Despite this prediction, ROS signaling is most commonly intuited through the global administration of chemicals that produce ROS or by ROS quenching through global application of antioxidants. Optogenetics, which uses light to control the activity of genetically-encoded effector proteins, provides a means of circumventing this limitation. Photo-inducible genetically-encoded ROS-generating proteins (RGPs were originally employed for their phototoxic effects and cell ablation. However, reducing irradiance and/or fluence can achieve sub-lethal levels of ROS that may mediate subtle signaling effects. Hence, transgenic expression of RGPs as fusions to native proteins gives researchers a new tool to exert spatial and temporal control over ROS production. This review will focus on the new frontier defined by the experimental use of RGPs to study ROS signaling.

  12. ICT based molecular recognition of 2,5-dinitrophenol in methanol

    Energy Technology Data Exchange (ETDEWEB)

    Chattopadhyay, Soumi [Department of Chemistry, The University of Burdwan, Golapbag, Burdwan 713104 (India); Chaudhuri, Tandrima, E-mail: [Department of Chemistry, Dr. Bhupendranath Dutta Smriti Mahavidyalaya, Burdwan 713407, West Bengal (India); Banerjee, Manas [Department of Chemistry, The University of Burdwan, Golapbag, Burdwan 713104 (India)


    The first report of wavelength ratiometric sensing of electron deficient nitroaromatic explosive, 2,5-dinitrophenol (N4) with photoluminescent electron rich Schiff base H{sub 2}salen (A1) derived from 1,2-ethanediamine and salicyldehyde and related complexes [Zn(salen)]·H{sub 2}O (A2) and [Ni(salen)]·H{sub 2}O (A3) in methanol is presented. DFT based optimization reveals that NACs (N1–N5) induce the formation of 1:2 donor–acceptor complexes with the salen based compounds. - Highlights: • Ratiometric sensing of nitroaromatics, especially 2,5-dinitrophenol (N4), is demonstrated. • H{sub 2}salen (A1) exhibit equilibrium with nitroaromatics except 2,5-dinitrophenol in excited state. • [Ni(salen)]·H{sub 2}O (A3) exhibits both ground and excited state equilibrium with only 2,5-dinitrophenol among five NACs. • Nitroaromatics form 1:2 donor–acceptor complexes with salen type compounds.

  13. Polypeptide micelles with dual pH activatable dyes for sensing cells and cancer imaging. (United States)

    Gong, Ping; Yang, Yueting; Yi, Huqiang; Fang, Shengtao; Zhang, Pengfei; Sheng, Zonghai; Gao, Guanhui; Gao, Duyang; Cai, Lintao


    pH is an important control parameter for maintenance of cell viability and tissue functions. pH monitoring provides valuable information on cell metabolic processes and the living environment. In this study, we prepared dual pH-sensitive, fluorescent dye-loaded polypeptide nanoparticles (DPNs) for ratiometric sensing of pH changes in living cells. DPNs contain two types of dyes: N-(rhodamine B) lactam cystamine (RBLC), an acid activatable fluorescent dye with increased fluorescence in an acidic environment, and fluorescein isothiocyanate (FITC), a base activatable fluorescent dye with enhanced fluorescence in an alkaline environment. Hence, DPNs exhibited a dual response signal with strong red fluorescence and weak green fluorescence under acidic conditions; in contrast, they showed strong green fluorescence and almost no red fluorescence under alkaline and neutral conditions. The favorable inverse pH responses of the two fluorescent dyes resulted in ratiometric pH determination for DPNs with an optimized pH-sensitive range of pH 4.5-7.5. Quantitative analysis of the intracellular pH of intact MCF-7 cells has been successfully demonstrated with our nanosensor. Moreover, single acid activatable fluorescent dye doped polypeptide nanoparticles that only contained RBLC can distinguish tumor tissue from normal tissue by monitoring the acidic extracellular environment.

  14. Multi-parametric imaging of tumor spheroids with ultra-bright and tunable nanoparticle O2 probes (United States)

    Dmitriev, Ruslan I.; Borisov, Sergey M.; Jenkins, James; Papkovsky, Dmitri B.


    Multi-modal probes allow for flexible choice of imaging equipment when performing quenched-phosphorescence O2 measurements: one- or two-photon, PLIM or intensity-based ratiometric read-outs. Spectral and temporal (e.g. FLIMPLIM) discrimination can be used to image O2 together with pH, Ca2+, mitochondrial membrane potential, cell death markers or cell/organelle specific markers. However, the main challenge of existing nanoparticle probes is their limited diffusion across thick (> 20-50 μm) 3D cell models such as tumor spheroids. Here, we present new class of polymeric nanoparticle probes having tunable size, charge, cell-penetrating ability, and reporter dyes. Being spectrally similar to the recently described MM2, PA2 and other O2 probes, they are 5-10 times brighter, demonstrate improved ratiometric response and their surface chemistry can be easily modified. With cultures of 2D and 3D cell models (fibroblasts, PC12 aggregates, HCT116 human colon cancer spheroids) we found cell-specific staining by these probes. However, the efficient staining of model of interest can be tuned by changing number of positive and negative surface groups at nanoparticle, to allow most efficient loading. We also demonstrate how real-time monitoring of oxygenation can be used to select optimal spheroid production with low variability in size and high cell viability.

  15. Fluorescent biosensors illuminate calcium levels within defined beta-cell endosome subpopulations. (United States)

    Albrecht, Tobias; Zhao, Yongxin; Nguyen, Trang Hai; Campbell, Robert E; Johnson, James D


    Live cell imaging has revealed that calcium ions (Ca(2+)) pass in and out of many cellular organelles. However, technical hurdles have limited measurements of Ca(2+) in acidic organelles, such as endosomes. Although evidence hints that endosomes play a role in Ca(2+) signaling, direct measurements within endosomal lumina represent one of the final frontiers in organelle imaging. To measure Ca(2+) in a TiVAMP-positive endosome sub-population, the pH-resistant ratiometric Ca(2+) biosensor GEM-GECO1 and the ratiometric pH biosensor mKeima were used. A positive correlation between acidic endosomal pH and higher Ca(2+) was observed within these Rab5a- and Rab7-positive compartments. Ca(2+) concentration in most endosomes was estimated to be below 2μM, lower than Ca(2+) levels in several other intracellular stores, indicating that endosomes may take up Ca(2+) during physiological stimulation. Indeed, endosomes accumulated Ca(2+) during glucose-stimulation, a condition where endosomal pH did not change. Our biosensors permitted the first measurements revealing a role for endosomes in cellular Ca(2+) homeostasis during physiological stimulation.

  16. In vivo determination of organellar pH using a universal wavelength-based confocal microscopy approach. (United States)

    Pineda Rodó, Albert; Váchová, Libuše; Palková, Zdena


    Many essential cellular processes are affected by transmembrane H(+) gradients and intracellular pH (pHi). The research of such metabolic events calls for a non-invasive method to monitor pHi within individual subcellular compartments. We present a novel confocal microscopy approach for the determination of organellar pHi in living cells expressing pH-dependent ratiometric fluorescent proteins. Unlike conventional intensity-based fluorometry, our method relies on emission wavelength scans at single-organelle resolution to produce wavelength-based pH estimates both accurate and robust to low-signal artifacts. Analyses of Ato1p-pHluorin and Ato1p-mCherry yeast cells revealed previously unreported wavelength shifts in pHluorin emission which, together with ratiometric mCherry, allowed for high-precision quantification of actual physiological pH values and evidenced dynamic pHi changes throughout the different stages of yeast colony development. Additionally, comparative pH quantification of Ato1p-pHluorin and Met17p-pHluorin cells implied the existence of a significant pHi gradient between peripheral and internal cytoplasm of cells from colonies occurring in the ammonia-producing alkali developmental phase. Results represent a step forward in the study of pHi regulation and subcellular metabolic functions beyond the scope of this study.

  17. Digital balanced detection for fast optical computerized tomography (United States)

    Hafiz, Rehan; Ozanyan, Krikor B.


    Analogue Balanced Photo-detection has found extensive usage in high- sensitivity small signal applications e.g. coherent heterodyne detection. It is particularly effective for laser intensity noise removal. Nevertheless, the high cost of the commercially available analogue systems makes them unsuitable for multi-channel applications, such as fast tomography. In this paper a flexible, scalable, inexpensive and compact solution for multi channel digital balanced detection is presented. The proposed system has two components: an analogue front-end, comprising a differential photodiode amplifier for minimizing the external interference noise, and a digital balanced noise remover. The latter component initially calculates a balancing factor (BF) from the average power ratio of the signal and reference photocurrents, measured with the object removed from the signal path. Three digital balancing algorithms (DBAx) are considered for subsequent processing. In DBA1, BF is directly used in real-time ratiometric calculations. In DBA2, the BF is adjusted in real time by monitoring the window-averaged power of the received photocurrents. In DBA3, first the baseline is removed using differentiation and then ratiometric detection is performed. Using the digital alternative only one measurement of the reference beam is necessary for single-source, multi-channel detection systems. The data from multiple channels are processed in parallel by pipelined hardware, configured as a state machine. The proposed system leads to a fast optical computerized tomography system using digital balanced detection.

  18. Albumin-NIR dye self-assembled nanoparticles for photoacoustic pH imaging and pH-responsive photothermal therapy effective for large tumors. (United States)

    Chen, Qian; Liu, Xiaodong; Zeng, Jianfeng; Cheng, Zhenping; Liu, Zhuang


    Real-time in vivo pH imaging in the tumor, as well as designing therapies responsive to the acidic tumor microenvironment to achieve optimized therapeutic outcomes have been of great interests in the field of nanomedicine. Herein, a pH-responsive near-infrared (NIR) croconine (Croc) dye is able to induce the self-assembly of human serum albumin (HSA) to form HSA-Croc nanoparticles useful not only for real-time ratiometric photoacoustic pH imaging of the tumor, but also for pH responsive photothermal therapy with unexpected great performance against tumors with relatively large sizes. Such HSA-Croc nanoparticles upon intravenous injection exhibit efficient tumor homing. As the decrease of pH, the absorption of Croc at 810 nm would increase while that at 680 nm would decrease, allowing real-time pH sensing in the tumor by double-wavelength ratiometric photoacoustic imaging, which reveals the largely decreased pH inside the cores of large tumors. Moreover, utilizing HSA-Croc as a pH-responsive photothermal agent, effective photothermal ablation of large tumors is realized, likely owing to the more evenly distributed intratumoral heating compared to that achieved by conventional pH-insensitive photothermal agents, which are effective mostly for tumors with small sizes.

  19. Research of the relationship of intracellular acidification and apoptosis in Hela cells based on pH nanosensors

    Institute of Scientific and Technical Information of China (English)

    HE XiaoXiao; WANG Yan; WANG KeMin; PENG JiaoFeng; LIU Fang; TAN WeiHong


    In this paper, the relationship of intracellular acidification and apoptosis in Hela cells induced by vincristine sulfate has been studied by use of the ratiometric pH nanosensors that have been developed by our group, employing fluorescein isothiocyanate (FITC) doped as the pH-sensitive dye and Tris(2,2'-bipyidyl) dichlororuthenium(Ⅱ) hexahydrate (RuBpy) doped as reference dye. The pH change of the Hela cells induced by vincristine sulfate has been monitored in vivo, in situ and real time by use of the ratiometric pH nanosensors. The experimental results show that the pH of the apoptotic Hela cells induced by vincristine sulfate has been acidified from 7.11 to 6.51, and the percentage of intracellular acidification is correlated with the induced concentration and incubation time of the vincristine sulfate. The further study of the percentage of intracellular acidification and the percentage of apoptosis of Hela cells at the same time reveals that apoptosis of Hela cells induced by vincristine sulfate is preceded by intracellular acidification. These results would provide theoretical foundation for the therapy of cancer through interfering the pH of cells by use of vincristine sulfate or other anti-cancer drugs.

  20. Iopamidol as a responsive MRI-chemical exchange saturation transfer contrast agent for pH mapping of kidneys: In vivo studies in mice at 7 T. (United States)

    Longo, Dario Livio; Dastrù, Walter; Digilio, Giuseppe; Keupp, Jochen; Langereis, Sander; Lanzardo, Stefania; Prestigio, Simone; Steinbach, Oliver; Terreno, Enzo; Uggeri, Fulvio; Aime, Silvio


    Iopamidol (Isovue®-Bracco Diagnostic Inc.) is a clinically approved X-Ray contrast agent used in the last 30 years for a wide variety of diagnostic applications with a very good clinical acceptance. Iopamidol contains two types of amide functionalities that can be exploited for the generation of chemical exchange saturation transfer effect. The exchange rate of the two amide proton pools is markedly pH-dependent. Thus, a ratiometric method for pH assessment has been set-up based on the comparison of the saturation transfer effects induced by selective irradiation of the two resonances. This ratiometric approach allows to rule out the concentration effect of the contrast agent and provides accurate pH measurements in the 5.5-7.4 range. Upon injection of Iopamidol into healthy mice, it has been possible to acquire pH maps of kidney regions. Furthermore, it has been also shown that the proposed method is able to report about pH-changes induced in control mice fed with acidified or basified water for a period of a week before image acquisition.

  1. In vivo determination of organellar pH using a universal wavelength-based confocal microscopy approach.

    Directory of Open Access Journals (Sweden)

    Albert Pineda Rodó

    Full Text Available Many essential cellular processes are affected by transmembrane H(+ gradients and intracellular pH (pHi. The research of such metabolic events calls for a non-invasive method to monitor pHi within individual subcellular compartments. We present a novel confocal microscopy approach for the determination of organellar pHi in living cells expressing pH-dependent ratiometric fluorescent proteins. Unlike conventional intensity-based fluorometry, our method relies on emission wavelength scans at single-organelle resolution to produce wavelength-based pH estimates both accurate and robust to low-signal artifacts. Analyses of Ato1p-pHluorin and Ato1p-mCherry yeast cells revealed previously unreported wavelength shifts in pHluorin emission which, together with ratiometric mCherry, allowed for high-precision quantification of actual physiological pH values and evidenced dynamic pHi changes throughout the different stages of yeast colony development. Additionally, comparative pH quantification of Ato1p-pHluorin and Met17p-pHluorin cells implied the existence of a significant pHi gradient between peripheral and internal cytoplasm of cells from colonies occurring in the ammonia-producing alkali developmental phase. Results represent a step forward in the study of pHi regulation and subcellular metabolic functions beyond the scope of this study.

  2. Research of the relationship of intracellular acidification and apoptosis in Hela cells based on pH nanosensors

    Institute of Scientific and Technical Information of China (English)


    In this paper,the relationship of intracellular acidification and apoptosis in Hela cells induced by vin-cristine sulfate has been studied by use of the ratiometric pH nanosensors that have been developed by our group,employing fluorescein isothiocyanate(FITC) doped as the pH-sensitive dye and Tris(2,2’-bipyidyl) dichlororuthenium(II) hexahydrate(RuBpy) doped as reference dye. The pH change of the Hela cells induced by vincristine sulfate has been monitored in vivo,in situ and real time by use of the ratiometric pH nanosensors. The experimental results show that the pH of the apoptotic Hela cells induced by vincristine sulfate has been acidified from 7.11 to 6.51,and the percentage of intra-cellular acidification is correlated with the induced concentration and incubation time of the vincristine sulfate. The further study of the percentage of intracellular acidification and the percentage of apop-tosis of Hela cells at the same time reveals that apoptosis of Hela cells induced by vincristine sulfate is preceded by intracellular acidification. These results would provide theoretical foundation for the therapy of cancer through interfering the pH of cells by use of vincristine sulfate or other anti-cancer drugs.

  3. Monitoring of extracellular pH in young dental biofilms grown in situ in the presence and absence of sucrose

    DEFF Research Database (Denmark)

    Dige, Irene; Bælum, Vibeke; Schlafer, Sebastian;

    biofilms. Fluorescence emissions of C-SNARF-4 in deep layers of each biofilm were recorded ex-vivo with confocal microscopy for 15 min (3 sites) or for 1 h (6 sites) after exposure to a 100 µl salivary solution with 0.4% glucose in custom-made wells. The ratiometric pH data were analyzed using a mixed......pH in dental biofilms is of central importance for the development of caries. We used the ratiometric pH-sensitive dye C-SNARF-4 in combination with digital image analysis to monitor extracellular pH in dental biofilms grown in situ with and without sucrose supply. 48-h dental biofilms from 10......-effects linear regression procedure. Extracellular pH dropped rapidly in most examined sites after addition of glucose. Distinct pH microenvironments were observed within single biofilms. Variance components analyses showed similar variation between sites within the same biofilm (var=0.02-0.04 (se=0...

  4. Fluorescence measurements of serotonin-induced V-ATPase-dependent pH changes at the luminal surface in salivary glands of the blowfly Calliphora vicina. (United States)

    Rein, Julia; Zimmermann, Bernhard; Hille, Carsten; Lang, Ingo; Walz, Bernd; Baumann, Otto


    Secretion in blowfly salivary glands is induced by the neurohormone serotonin and powered by a vacuolar-type H(+)-ATPase (V-ATPase) located in the apical membrane of the secretory cells. We have established a microfluorometric method for analysing pH changes at the luminal surface of the secretory epithelial cells by using the fluorescent dye 5-N-hexadecanoyl-aminofluorescein (HAF). After injection of HAF into the lumen of the tubular salivary gland, the fatty acyl chain of the dye molecule partitions into the outer leaflet of the plasma membrane and its pH-sensitive fluorescent moiety is exposed at the cell surface. Confocal imaging has confirmed that HAF distributes over the entire apical membrane of the secretory cells and remains restricted to this membrane domain. Ratiometric analysis of HAF fluorescence demonstrates that serotonin leads to a reversible dose-dependent acidification at the luminal surface. Inhibition by concanamycin A confirms that the serotonin-induced acidification at the luminal surface is due to H(+) transport across the apical membrane via V-ATPase. Measurements with pH-sensitive microelectrodes corroborate a serotonin-induced luminal acidification and demonstrate that luminal pH decreases by about 0.4 pH units at saturating serotonin concentrations. We conclude that ratiometric measurements of HAF fluorescence provide an elegant method for monitoring V-ATPase-dependent H(+) transport in the blowfly salivary gland in vivo and for analysing the spatiotemporal pattern of pH changes at the luminal surface.

  5. Bright and photostable push-pull pyrene dye visualizes lipid order variation between plasma and intracellular membranes (United States)

    Niko, Yosuke; Didier, Pascal; Mely, Yves; Konishi, Gen-Ichi; Klymchenko, Andrey S.


    Imaging lipid organization in cell membranes requires advanced fluorescent probes. Here, we show that a recently synthesized push-pull pyrene (PA), similarly to popular probe Laurdan, changes the emission maximum as a function of lipid order, but outperforms it by spectroscopic properties. In addition to red-shifted absorption compatible with common 405 nm diode laser, PA shows higher brightness and much higher photostability than Laurdan in apolar membrane environments. Moreover, PA is compatible with two-photon excitation at wavelengths >800 nm, which was successfully used for ratiometric imaging of coexisting liquid ordered and disordered phases in giant unilamellar vesicles. Fluorescence confocal microscopy in Hela cells revealed that PA efficiently stains the plasma membrane and the intracellular membranes at >20-fold lower concentrations, as compared to Laurdan. Finally, ratiometric imaging using PA reveals variation of lipid order within different cellular compartments: plasma membranes are close to liquid ordered phase of model membranes composed of sphingomyelin and cholesterol, while intracellular membranes are much less ordered, matching well membranes composed of unsaturated phospholipids without cholesterol. These differences in the lipid order were confirmed by fluorescence lifetime imaging (FLIM) at the blue edge of PA emission band. PA probe constitutes thus a new powerful tool for biomembrane research.

  6. Live-cell imaging of mammalian RNAs with Spinach2 (United States)

    Strack, Rita L.; Jaffrey, Samie R.


    The ability to monitor RNAs of interest in living cells is crucial to understanding the function, dynamics, and regulation of this important class of molecules. In recent years, numerous strategies have been developed with the goal of imaging individual RNAs of interest in living cells, each with their own advantages and limitations. This chapter provides an overview of current methods of live-cell RNA imaging, including a detailed discussion of genetically encoded strategies for labeling RNAs in mammalian cells. This chapter then focuses on the development and use of “RNA mimics of GFP” or Spinach technology for tagging mammalian RNAs, and includes a detailed protocol for imaging 5S and CGG60 RNA with the recently described Spinach2 tag. PMID:25605384

  7. VAMP4 Is an Essential Cargo Molecule for Activity-Dependent Bulk Endocytosis. (United States)

    Nicholson-Fish, Jessica C; Kokotos, Alexandros C; Gillingwater, Thomas H; Smillie, Karen J; Cousin, Michael A


    The accurate formation of synaptic vesicles (SVs) and incorporation of their protein cargo during endocytosis is critical for the maintenance of neurotransmission. During intense neuronal activity, a transient and acute accumulation of SV cargo occurs at the plasma membrane. Activity-dependent bulk endocytosis (ADBE) is the dominant SV endocytosis mode under these conditions; however, it is currently unknown how ADBE mediates cargo retrieval. We examined the retrieval of different SV cargo molecules during intense stimulation using a series of genetically encoded pH-sensitive reporters in neuronal cultures. The retrieval of only one reporter, VAMP4-pHluorin, was perturbed by inhibiting ADBE. This selective recovery was confirmed by the enrichment of endogenous VAMP4 in purified bulk endosomes formed by ADBE. VAMP4 was also essential for ADBE, with a cytoplasmic di-leucine motif being critical for this role. Therefore, VAMP4 is the first identified ADBE cargo and is essential for this endocytosis mode to proceed.

  8. Recent progress in design of protein-based fluorescent biosensors and their cellular applications. (United States)

    Tamura, Tomonori; Hamachi, Itaru


    Protein-based fluorescent biosensors have emerged as key bioanalytical tools to visualize and quantify a wide range of biological substances and events in vitro, in cells, and even in vivo. On the basis of the construction method, the protein-based fluorescent biosensors can be principally classified into two classes: (1) genetically encoded fluorescent biosensors harnessing fluorescent proteins (FPs) and (2) semisynthetic biosensors comprised of protein scaffolds and synthetic fluorophores. Recent advances in protein engineering and chemical biology not only allowed the further optimization of conventional biosensors but also facilitated the creation of novel biosensors based on unique strategies. In this review, we survey the recent studies in the development and improvement of protein-based fluorescent biosensors and highlight the successful applications to live cell and in vivo imaging. Furthermore, we provide perspectives on possible future directions of the technique.

  9. Geometrical assembly of ultrastable protein templates for nanomaterials (United States)

    Glover, Dominic J.; Giger, Lars; Kim, Steve S.; Naik, Rajesh R.; Clark, Douglas S.


    The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein-protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.

  10. The RootChip: an integrated microfluidic chip for plant science. (United States)

    Grossmann, Guido; Guo, Woei-Jiun; Ehrhardt, David W; Frommer, Wolf B; Sit, Rene V; Quake, Stephen R; Meier, Matthias


    Studying development and physiology of growing roots is challenging due to limitations regarding cellular and subcellular analysis under controlled environmental conditions. We describe a microfluidic chip platform, called RootChip, that integrates live-cell imaging of growth and metabolism of Arabidopsis thaliana roots with rapid modulation of environmental conditions. The RootChip has separate chambers for individual regulation of the microenvironment of multiple roots from multiple seedlings in parallel. We demonstrate the utility of The RootChip by monitoring time-resolved growth and cytosolic sugar levels at subcellular resolution in plants by a genetically encoded fluorescence sensor for glucose and galactose. The RootChip can be modified for use with roots from other plant species by adapting the chamber geometry and facilitates the systematic analysis of root growth and metabolism from multiple seedlings, paving the way for large-scale phenotyping of root metabolism and signaling.

  11. The RootChip: An Integrated Microfluidic Chip for Plant Science[W][OA (United States)

    Grossmann, Guido; Guo, Woei-Jiun; Ehrhardt, David W.; Frommer, Wolf B.; Sit, Rene V.; Quake, Stephen R.; Meier, Matthias


    Studying development and physiology of growing roots is challenging due to limitations regarding cellular and subcellular analysis under controlled environmental conditions. We describe a microfluidic chip platform, called RootChip, that integrates live-cell imaging of growth and metabolism of Arabidopsis thaliana roots with rapid modulation of environmental conditions. The RootChip has separate chambers for individual regulation of the microenvironment of multiple roots from multiple seedlings in parallel. We demonstrate the utility of The RootChip by monitoring time-resolved growth and cytosolic sugar levels at subcellular resolution in plants by a genetically encoded fluorescence sensor for glucose and galactose. The RootChip can be modified for use with roots from other plant species by adapting the chamber geometry and facilitates the systematic analysis of root growth and metabolism from multiple seedlings, paving the way for large-scale phenotyping of root metabolism and signaling. PMID:22186371

  12. Remote control of myosin and kinesin motors using light-activated gearshifting. (United States)

    Nakamura, Muneaki; Chen, Lu; Howes, Stuart C; Schindler, Tony D; Nogales, Eva; Bryant, Zev


    Cytoskeletal motors perform critical force generation and transport functions in eukaryotic cells. Engineered modifications of motor function provide direct tests of protein structure-function relationships and potential tools for controlling cellular processes or for harnessing molecular transport in artificial systems. Here, we report the design and characterization of a panel of cytoskeletal motors that reversibly change gears--speed up, slow down or switch directions--when exposed to blue light. Our genetically encoded structural designs incorporate a photoactive protein domain to enable light-dependent conformational changes in an engineered lever arm. Using in vitro motility assays, we demonstrate robust spatiotemporal control over motor function and characterize the kinetics of the optical gearshifting mechanism. We have used a modular approach to create optical gearshifting motors for both actin-based and microtubule-based transport.

  13. Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics. (United States)

    Smits, Arne H; Borrmann, Annika; Roosjen, Mark; van Hest, Jan C M; Vermeulen, Michiel


    Epitope-tagging is an effective tool to facilitate protein enrichment from crude cell extracts. Traditionally, N- or C-terminal fused tags are employed, which, however, can perturb protein function. Unnatural amino acids (UAAs) harboring small reactive handles can be site-specifically incorporated into proteins, thus serving as a potential alternative for conventional protein tags. Here, we introduce Click-MS, which combines the power of site-specific UAA incorporation, bioorthogonal chemistry, and quantitative mass spectrometry-based proteomics to specifically enrich a single protein of interest from crude mammalian cell extracts. By genetic encoding of p-azido-l-phenylalanine, the protein of interest can be selectively captured using copper-free click chemistry. We use Click-MS to enrich proteins that function in different cellular compartments, and we identify protein-protein interactions, showing the great potential of Click-MS for interaction proteomics workflows.

  14. Functional fluorescent Ca2+ indicator proteins in transgenic mice under TET control.

    Directory of Open Access Journals (Sweden)

    Mazahir T Hasan


    Full Text Available Genetically encoded fluorescent calcium indicator proteins (FCIPs are promising tools to study calcium dynamics in many activity-dependent molecular and cellular processes. Great hopes-for the measurement of population activity, in particular-have therefore been placed on calcium indicators derived from the green fluorescent protein and their expression in (selected neuronal populations. Calcium transients can rise within milliseconds, making them suitable as reporters of fast neuronal activity. We here report the production of stable transgenic mouse lines with two different functional calcium indicators, inverse pericam and camgaroo-2, under the control of the tetracycline-inducible promoter. Using a variety of in vitro and in vivo assays, we find that stimuli known to increase intracellular calcium concentration (somatically triggered action potentials (APs and synaptic and sensory stimulation can cause substantial and rapid changes in FCIP fluorescence of inverse pericam and camgaroo-2.

  15. Simultaneous imaging of GFP, CFP and collagen in tumors in vivo using multiphoton microscopy

    Directory of Open Access Journals (Sweden)

    Segall Jeffrey E


    Full Text Available Abstract Background The development of multiphoton laser scanning microscopy has greatly facilitated the imaging of living tissues. However, the use of genetically encoded fluorescent proteins to distinguish different cell types in living animals has not been described at single cell resolution using multiphoton microscopy. Results Here we describe a method for the simultaneous imaging, by multiphoton microscopy, of Green Fluorescent Protein, Cyan Fluorescent Protein and collagen in vivo in living tumors. This novel method enables: 1 the simultaneous visualization of overall cell shape and sub-cellular structures such as the plasma membrane or proteins of interest in cells inside living animals, 2 direct comparison of the behavior of single cells from different cell lines in the same microenvironment in vivo. Conclusion Using this multi-fluor, multiphoton technique, we demonstrate that motility and metastatic differences between carcinoma cells of differing metastatic potential can be imaged in the same animal simultaneously at sub-cellular resolution.

  16. Scanless functional imaging of hippocampal networks using patterned two-photon illumination through GRIN lenses

    KAUST Repository

    Moretti, Claudio


    Patterned illumination through the phase modulation of light is increasingly recognized as a powerful tool to investigate biological tissues in combination with two-photon excitation and light-sensitive molecules. However, to date two-photon patterned illumination has only been coupled to traditional microscope objectives, thus limiting the applicability of these methods to superficial biological structures. Here, we show that phase modulation can be used to efficiently project complex two-photon light patterns, including arrays of points and large shapes, in the focal plane of graded index (GRIN) lenses. Moreover, using this approach in combination with the genetically encoded calcium indicator GCaMP6, we validate our system performing scanless functional imaging in rodent hippocampal networks in vivo ~1.2 mm below the brain surface. Our results open the way to the application of patterned illumination approaches to deep regions of highly scattering biological tissues, such as the mammalian brain.

  17. Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis. (United States)

    Palioura, Sotiria; Herkel, Johannes; Simonović, Miljan; Lohse, Ansgar W; Söll, Dieter


    Selenocysteine, the 21st genetically encoded amino acid, is the major form of the antioxidant trace element selenium in the human body. In eukaryotes and archaea its synthesis proceeds through a phosphorylated intermediate in a tRNA-dependent fashion. The final step of selenocysteine formation is catalyzed by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) that converts phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec). The human SepSecS protein is also known as soluble liver antigen/liver pancreas (SLA/LP), which represents one of the antigens of autoimmune hepatitis. Here we review the discovery of human SepSecS and the current understanding of the immunogenicity of SLA/LP in autoimmune hepatitis.

  18. Chronic calcium imaging of neurons in the mouse visual cortex using a troponin C-based indicator. (United States)

    Santos, Alexandre Ferrão; Hübener, Mark


    This protocol describes the use of the genetically encoded troponin C-based calcium indicator TN-XXL to chronically monitor the functional properties of single neocortical neurons in the mouse visual cortex. A cranial window is implanted over the brain of a mouse expressing TN-XXL in pyramidal neurons of the cerebral cortex. Several days later, the visual cortex is mapped and photographed to facilitate repeated imaging of the same region using two-photon microscopy. Initial two-photon imaging may be done ∼2 wk after the window is implanted. We show the application of this technique for long-term in vivo imaging of stimulus response properties. Beyond providing functional information, long-term imaging of TN-XXL-labeled neurons also enables the simultaneous monitoring of structural properties down to the level of single dendritic spines.

  19. Imaging of calcium dynamics in pollen tube cytoplasm. (United States)

    Barberini, María Laura; Muschietti, Jorge


    Cytoplasmic calcium [(Ca(2+))cyt] is a central component of cellular signal transduction pathways. In plants, many external and internal stimuli transiently elevate (Ca(2+))cyt, initiating downstream responses that control different features of plant development. In pollen tubes the establishment of an oscillatory gradient of calcium at the tip is essential for polarized growth. Disruption of the cytosolic Ca(2+) gradient by chelators or channel blockers inhibits pollen tube growth. To quantify the physiological role of (Ca(2+))cyt in cellular systems, genetically encoded Ca(2+) indicators such as Yellow Cameleons (YCs) have been developed. The Cameleons are based on a fluorescence resonance energy transfer (FRET) process. Here, we describe a method for imaging cytoplasmic Ca(2+) dynamics in growing pollen tubes that express the fluorescent calcium indicator Yellow Cameleon 3.6 (YC 3.6), using laser-scanning confocal microscopy.

  20. Imaging calcium in neurons. (United States)

    Grienberger, Christine; Konnerth, Arthur


    Calcium ions generate versatile intracellular signals that control key functions in all types of neurons. Imaging calcium in neurons is particularly important because calcium signals exert their highly specific functions in well-defined cellular subcompartments. In this Primer, we briefly review the general mechanisms of neuronal calcium signaling. We then introduce the calcium imaging devices, including confocal and two-photon microscopy as well as miniaturized devices that are used in freely moving animals. We provide an overview of the classical chemical fluorescent calcium indicators and of the protein-based genetically encoded calcium indicators. Using application examples, we introduce new developments in the field, such as calcium imaging in awake, behaving animals and the use of calcium imaging for mapping single spine sensory inputs in cortical neurons in vivo. We conclude by providing an outlook on the prospects of calcium imaging for the analysis of neuronal signaling and plasticity in various animal models.

  1. Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo. (United States)

    Yang, Helen H; St-Pierre, François; Sun, Xulu; Ding, Xiaozhe; Lin, Michael Z; Clandinin, Thomas R


    A mechanistic understanding of neural computation requires determining how information is processed as it passes through neurons and across synapses. However, it has been challenging to measure membrane potential changes in axons and dendrites in vivo. We use in vivo, two-photon imaging of novel genetically encoded voltage indicators, as well as calcium imaging, to measure sensory stimulus-evoked signals in the Drosophila visual system with subcellular resolution. Across synapses, we find major transformations in the kinetics, amplitude, and sign of voltage responses to light. We also describe distinct relationships between voltage and calcium signals in different neuronal compartments, a substrate for local computation. Finally, we demonstrate that ON and OFF selectivity, a key feature of visual processing across species, emerges through the transformation of membrane potential into intracellular calcium concentration. By imaging voltage and calcium signals to map information flow with subcellular resolution, we illuminate where and how critical computations arise.

  2. Analog Module Placement Design Using Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)


    This paper presents a novel genetic algorithm for analog module placement based on ageneralization of the two-dimensional bin packing problem. The genetic encoding and operators assure that allproblem constraints are always satisfied. Thus the potential problems of adding penalty terms to the costfunction are eliminated so that the search configuration space is drastically decreased. The dedicated costfunction is based on the special requirements of analog integrated circuits. A fractional factorial experimentwas conducted using an orthogonal array to study the algorithm parameters. A meta GA was applied todetermine the optimal parameter values. The algorithm was tested with several local benchmark circuits. Theexperimental results show that the algorithm has better performance than the simulated annealing approachwith satisfactory results comparable to manual placement. This study demonstrates the effectiveness of thegenetic algorithm in the analog module placement problem. The algorithm has been successfully used in alayout synthesis tool.

  3. Imaging neuronal populations in behaving rodents: paradigms for studying neural circuits underlying behavior in the mammalian cortex. (United States)

    Chen, Jerry L; Andermann, Mark L; Keck, Tara; Xu, Ning-Long; Ziv, Yaniv


    Understanding the neural correlates of behavior in the mammalian cortex requires measurements of activity in awake, behaving animals. Rodents have emerged as a powerful model for dissecting the cortical circuits underlying behavior attributable to the convergence of several methods. Genetically encoded calcium indicators combined with viral-mediated or transgenic tools enable chronic monitoring of calcium signals in neuronal populations and subcellular structures of identified cell types. Stable one- and two-photon imaging of neuronal activity in awake, behaving animals is now possible using new behavioral paradigms in head-fixed animals, or using novel miniature head-mounted microscopes in freely moving animals. This mini-symposium will highlight recent applications of these methods for studying sensorimotor integration, decision making, learning, and memory in cortical and subcortical brain areas. We will outline future prospects and challenges for identifying the neural underpinnings of task-dependent behavior using cellular imaging in rodents.

  4. Engineering an NADPH/NADP+ Redox Biosensor in Yeast

    DEFF Research Database (Denmark)

    Zhang, Jie; Sonnenschein, Nikolaus; Pihl, Thomas Peter Boye


    Genetically encoded biosensors have emerged as powerful tools for timely and precise in vivo evaluation of cellular metabolism. In particular, biosensors that can couple intercellular cues with downstream signaling responses are currently attracting major attention within health science...... and biotechnology. Still, there is a need for bioprospecting and engineering of more biosensors to enable real-time monitoring of specific cellular states and controlling downstream actuation. In this study, we report the engineering and application of a transcription factor-based NADPH/NADP+ redox biosensor...... in the budding yeast Saccharomyces cerevisiae. Using the biosensor, we are able to monitor the cause of oxidative stress by chemical induction, and changes in NADPH/NADP+ ratios caused by genetic manipulations. Because of the regulatory potential of the biosensor, we also show that the biosensor can actuate upon...

  5. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

    Directory of Open Access Journals (Sweden)

    Juan A. González-Vera


    Full Text Available Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.

  6. A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time. (United States)

    Seo, Daeha; Southard, Kaden M; Kim, Ji-Wook; Lee, Hyun Jung; Farlow, Justin; Lee, Jung-Uk; Litt, David B; Haas, Thomas; Alivisatos, A Paul; Cheon, Jinwoo; Gartner, Zev J; Jun, Young-Wook


    Tools capable of imaging and perturbing mechanical signaling pathways with fine spatiotemporal resolution have been elusive, despite their importance in diverse cellular processes. The challenge in developing a mechanogenetic toolkit (i.e., selective and quantitative activation of genetically encoded mechanoreceptors) stems from the fact that many mechanically activated processes are localized in space and time yet additionally require mechanical loading to become activated. To address this challenge, we synthesized magnetoplasmonic nanoparticles that can image, localize, and mechanically load targeted proteins with high spatiotemporal resolution. We demonstrate their utility by investigating the cell-surface activation of two mechanoreceptors: Notch and E-cadherin. By measuring cellular responses to a spectrum of spatial, chemical, temporal, and mechanical inputs at the single-molecule and single-cell levels, we reveal how spatial segregation and mechanical force cooperate to direct receptor activation dynamics. This generalizable technique can be used to control and understand diverse mechanosensitive processes in cell signaling. VIDEO ABSTRACT.

  7. Hydrophilic trans-Cyclooctenylated Noncanonical Amino Acids for Fast Intracellular Protein Labeling. (United States)

    Kozma, Eszter; Nikić, Ivana; Varga, Balázs R; Aramburu, Iker Valle; Kang, Jun Hee; Fackler, Oliver T; Lemke, Edward A; Kele, Péter


    Introduction of bioorthogonal functionalities (e.g., trans-cyclooctene-TCO) into a protein of interest by site-specific genetic encoding of non-canonical amino acids (ncAAs) creates uniquely targetable platforms for fluorescent labeling schemes in combination with tetrazine-functionalized dyes. However, fluorescent labeling of an intracellular protein is usually compromised by high background, arising from the hydrophobicity of ncAAs; this is typically compensated for by hours-long washout to remove excess ncAAs from the cellular interior. To overcome these problems, we designed, synthesized, and tested new, hydrophilic TCO-ncAAs. One derivative, DOTCO-lysine was genetically incorporated into proteins with good yield. The increased hydrophilicity shortened the excess ncAA washout time from hours to minutes, thus permitting rapid labeling and subsequent fluorescence microscopy.

  8. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. (United States)

    Johnston, Chad W; Skinnider, Michael A; Wyatt, Morgan A; Li, Xiang; Ranieri, Michael R M; Yang, Lian; Zechel, David L; Ma, Bin; Magarvey, Nathan A


    Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC-MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products.

  9. Automated identification of depsipeptide natural products by an informatic search algorithm. (United States)

    Skinnider, Michael A; Johnston, Chad W; Zvanych, Rostyslav; Magarvey, Nathan A


    Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts. We validated this technology by identifying several depsipeptides from novel producers, and located a large number of novel depsipeptide gene clusters for future study. This approach highlights the value of chemoinformatic search methods for the discovery of genetically encoded metabolites by targeting specific areas of chemical space.

  10. Density-dependent adaptive resistance allows swimming bacteria to colonize an antibiotic gradient. (United States)

    Hol, Felix J H; Hubert, Bert; Dekker, Cees; Keymer, Juan E


    During antibiotic treatment, antibiotic concentration gradients develop. Little is know regarding the effects of antibiotic gradients on populations of nonresistant bacteria. Using a microfluidic device, we show that high-density motile Escherichia coli populations composed of nonresistant bacteria can, unexpectedly, colonize environments where a lethal concentration of the antibiotic kanamycin is present. Colonizing bacteria establish an adaptively resistant population, which remains viable for over 24 h while exposed to the antibiotic. Quantitative analysis of multiple colonization events shows that collectively swimming bacteria need to exceed a critical population density in order to successfully colonize the antibiotic landscape. After colonization, bacteria are not dormant but show both growth and swimming motility under antibiotic stress. Our results highlight the importance of motility and population density in facilitating adaptive resistance, and indicate that adaptive resistance may be a first step to the emergence of genetically encoded resistance in landscapes of antibiotic gradients.

  11. Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties. (United States)

    Kofler, Stefan; Ackaert, Chloé; Samonig, Martin; Asam, Claudia; Briza, Peter; Horejs-Hoeck, Jutta; Cabrele, Chiara; Ferreira, Fatima; Duschl, Albert; Huber, Christian; Brandstetter, Hans


    Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.

  12. Understanding Synaptogenesis and Functional Connectome in C. elegans by Imaging Technology (United States)

    Hong, Jung-Hwa; Park, Mikyoung


    Formation of functional synapses is a fundamental process for establishing neural circuits and ultimately for expressing complex behavior. Extensive research has interrogated how such functional synapses are formed and how synapse formation contributes to the generation of neural circuitry and behavior. The nervous system of Caenorhabditis elegans, due to its relatively simple structure, the transparent body, and tractable genetic system, has been adapted as an excellent model to investigate synapses and the functional connectome. Advances in imaging technology together with the improvement of genetically encoded molecular tools enabled us to visualize synapses and neural circuits of the animal model, which provide insights into our understanding of molecules and their signaling pathways that mediate synapse formation and neuronal network modulation. Here, we review synaptogenesis in active zones and the mapping of local connectome in C. elegans nervous system whose understandings have been extended by the advances in imaging technology along with the genetic molecular tools. PMID:27445787

  13. Fast gene transfer into the adult zebrafish brain by herpes simplex virus 1 (HSV-1 and electroporation: methods and optogenetic applications

    Directory of Open Access Journals (Sweden)

    Ming eZou


    Full Text Available The zebrafish has various advantages as a model organism to analyze the structure and function of neural circuits but efficient viruses or other tools for fast gene transfer are lacking. We show that transgenes can be introduced directly into the adult zebrafish brain by herpes simplex type I viruses (HSV-1 or electroporation. We developed a new procedure to target electroporation to defined brain areas and identified promoters that produced strong long-term expression. The fast workflow of electroporation was exploited to express multiple channelrhodopsin-2 variants and genetically encoded calcium indicators in telencephalic neurons for measurements of neuronal activity and synaptic connectivity. The results demonstrate that HSV-1 and targeted electroporation are efficient tools for gene delivery into the zebrafish brain, similar to adeno-associated viruses and lentiviruses in other species. These methods fill an important gap in the spectrum of molecular tools for zebrafish and are likely to have a wide range of applications.

  14. Phanta: a non-fluorescent photochromic acceptor for pcFRET.

    Directory of Open Access Journals (Sweden)

    Craig Don Paul

    Full Text Available We have developed an orange non-fluorescent photochromic protein (quantum yield, 0.003 we call Phanta that is useful as an acceptor in pcFRET applications. Phanta can be repeatedly inter-converted between the two absorbing states by alternate exposure to cyan and violet light. The absorption spectra of Phanta in one absorbing state shows excellent overlap with the emission spectra of a number of donor green fluorescent proteins including the commonly used EGFP. We show that the Phanta-EGFP FRET pair is suitable for monitoring the activation of caspase 3 in live cells using readily available instrumentation and a simple protocol that requires the acquisition of two donor emission images corresponding to Phanta in each of its photoswitched states. This the first report of a genetically encoded non-fluorescent acceptor for pcFRET.

  15. Photoclick chemistry: a fluorogenic light-triggered in vivo ligation reaction. (United States)

    Ramil, Carlo P; Lin, Qing


    The ability to use chemical reactivity to monitor and control biomolecular processes with a spatial and temporal precision motivated the development of light-triggered in vivo chemistries. To this end, the photoinduced tetrazole-alkene cycloaddition, also termed 'photoclick chemistry' offers a very rapid chemical ligation platform for the manipulation of biomolecules and matrices in vivo. Here we outline the recent developments in the optimization of this chemistry, ranging from the search for substrates that offer two-photon photoactivatability, superior reaction kinetics, and/or genetic encodability, to the study of the reaction mechanism. The applications of the photoclick chemistry in protein labeling in vitro and in vivo as well as in preparing 'smart' hydrogels for 3D cell culture are highlighted.

  16. Initial Photophysical Characterization of the Proteorhodopsin Optical Proton Sensor (PROPS

    Directory of Open Access Journals (Sweden)

    Jay eNadeau


    Full Text Available Fluorescence is not frequently used as a tool for investigating the photocycles of rhodopsins, largely because of the low quantum yield of the retinal chromophore. However, a new class of genetically encoded voltage sensors is based upon rhodopsins and their fluorescence. The first such sensor reported in the literature was the proteorhodopsin optical proton sensor (PROPS, which is capable of indicating membrane voltage changes in bacteria by means of changes in fluorescence. However, the properties of this fluorescence, such as its lifetime decay components and its origin in the protein photocycle, remain unknown. This paper reports steady-state and nanoscale time-resolved emission of this protein expressed in two strains of Escherichia coli, before and after membrane depolarization. The voltage-dependence of a particularly long lifetime component is established. Additional work to improve quantum yields and improve the general utility of PROPS is suggested.

  17. The old 3-oxoadipate pathway revisited: new insights in the catabolism of aromatics in the saprophytic fungus Aspergillus nidulans. (United States)

    Martins, Tiago M; Hartmann, Diego O; Planchon, Sébastien; Martins, Isabel; Renaut, Jenny; Silva Pereira, Cristina


    Aspergilli play major roles in the natural turnover of elements, especially through the decomposition of plant litter, but the end catabolism of lignin aromatic hydrocarbons remains largely unresolved. The 3-oxoadipate pathway of their degradation combines the catechol and the protocatechuate branches, each using a set of specific genes. However, annotation for most of these genes is lacking or attributed to poorly- or un-characterised families. Aspergillus nidulans can utilise as sole carbon/energy source either benzoate or salicylate (upstream aromatic metabolites of the protocatechuate and the catechol branches, respectively). Using this cultivation strategy and combined analyses of comparative proteomics, gene mining, gene expression and characterisation of particular gene-replacement mutants, we precisely assigned most of the steps of the 3-oxoadipate pathway to specific genes in this fungus. Our findings disclose the genetically encoded potential of saprophytic Ascomycota fungi to utilise this pathway and provide means to untie associated regulatory networks, which are vital to heightening their ecological significance.

  18. The nature of chemical innovation: new enzymes by evolution. (United States)

    Arnold, Frances H


    I describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N-H insertion, C-H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists' favorite transformations with the exquisite selectivity and tunability of enzymes.

  19. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells. (United States)

    Niopek, Dominik; Benzinger, Dirk; Roensch, Julia; Draebing, Thomas; Wehler, Pierre; Eils, Roland; Di Ventura, Barbara


    The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light.

  20. Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

    DEFF Research Database (Denmark)

    Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas;


    Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that t...... possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format....... that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce...

  1. Molecular neuroanatomy: a generation of progress. (United States)

    Pollock, Jonathan D; Wu, Da-Yu; Satterlee, John S


    The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.

  2. Small-molecule control of protein function through Staudinger reduction (United States)

    Luo, Ji; Liu, Qingyang; Morihiro, Kunihiko; Deiters, Alexander


    Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small-molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl transfer RNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small-molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (enhanced green fluorescent protein), protein translocation (nuclear localization sequence), DNA recombination (Cre) and gene editing (Cas9).

  3. Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α-Synuclein-Induced Cytotoxicity in Baker's Yeast. (United States)

    Jagadish, Krishnappa; Gould, Andrew; Borra, Radhika; Majumder, Subhabrata; Mushtaq, Zahid; Shekhtman, Alexander; Camarero, Julio A


    We report for the first time the recombinant expression of fully folded bioactive cyclotides inside live yeast cells by using intracellular protein trans-splicing in combination with a highly efficient split-intein. This approach was successfully used to produce the naturally occurring cyclotide MCoTI-I and the engineered bioactive cyclotide MCoCP4. Cyclotide MCoCP4 was shown to reduce the toxicity of human α-synuclein in live yeast cells. Cyclotide MCoCP4 was selected by phenotypic screening from cells transformed with a mixture of plasmids encoding MCoCP4 and inactive cyclotide MCoTI-I in a ratio of 1:5×10(4). This demonstrates the potential for using yeast to perform phenotypic screening of genetically encoded cyclotide-based libraries in eukaryotic cells.

  4. Brain-wide neuronal dynamics during motor adaptation in zebrafish. (United States)

    Ahrens, Misha B; Li, Jennifer M; Orger, Michael B; Robson, Drew N; Schier, Alexander F; Engert, Florian; Portugues, Ruben


    A fundamental question in neuroscience is how entire neural circuits generate behaviour and adapt it to changes in sensory feedback. Here we use two-photon calcium imaging to record the activity of large populations of neurons at the cellular level, throughout the brain of larval zebrafish expressing a genetically encoded calcium sensor, while the paralysed animals interact fictively with a virtual environment and rapidly adapt their motor output to changes in visual feedback. We decompose the network dynamics involved in adaptive locomotion into four types of neuronal response properties, and provide anatomical maps of the corresponding sites. A subset of these signals occurred during behavioural adjustments and are candidates for the functional elements that drive motor learning. Lesions to the inferior olive indicate a specific functional role for olivocerebellar circuitry in adaptive locomotion. This study enables the analysis of brain-wide dynamics at single-cell resolution during behaviour.

  5. Biophysical Properties of Optogenetic Tools and Their Application for Vision Restoration Approaches (United States)

    Klapper, Simon D.; Swiersy, Anka; Bamberg, Ernst; Busskamp, Volker


    Optogenetics is the use of genetically encoded light-activated proteins to manipulate cells in a minimally invasive way using light. The most prominent example is channelrhodopsin-2 (ChR2), which allows the activation of electrically excitable cells via light-dependent depolarization. The combination of ChR2 with hyperpolarizing-light-driven ion pumps such as the Cl− pump halorhodopsin (NpHR) enables multimodal remote control of neuronal cells in culture, tissue, and living animals. Very soon, it became obvious that this method offers a chance of gene therapy for many diseases affecting vision. Here, we will give a brief introduction to retinal function and retinal diseases; optogenetic vision restoration strategies will be highlighted. We will discuss the functional and structural properties of rhodopsin-based optogenetic tools and analyze the potential for the application of vision restoration. PMID:27642278

  6. Cotransport of H+, lactate, and H2O in porcine retinal pigment epithelial cells

    DEFF Research Database (Denmark)

    Hamann, Steffen; Kiilgaard, Jens Folke; la Cour, Morten;


    and placed in a perfusion chamber in which the solution facing the retinal membrane could be changed rapidly. Two types of experiments were performed: Changes in cell water volume were measured by self-quenching of the fluorescent dye Calcein, and changes in intracellular pH were measured ratiometrically......) for the H(+) and lactate fluxes. The data suggest that H(2)O is cotransported along with H(+) and lactate ions in MCT1 localized to the retinal membrane. The study emphasizes the importance of this cotransporter in the maintenance of water homeostasis and pH in the subretinal space of a mammalian tissue...... and supports our previous study performed by an invasive technique in an amphibian tissue....

  7. A benzothiazole-based fluorescent probe for distinguishing and bioimaging of Hg(2+) and Cu(2). (United States)

    Gu, Biao; Huang, Liyan; Su, Wei; Duan, Xiaoli; Li, Haitao; Yao, Shouzhuo


    A new benzothiazole-based fluorescent probe 2-(benzo[d]thiazol-2-yl)-4-(1,3- dithian-2-yl)phenol (BT) with two different reaction sites, a thioacetal group (site 1 for Hg(2+)), and O and N atoms of the benzothiazole dye (site 2 for Cu(2+)), was designed and synthesized. The probe BT showed ratiometric fluorescent response to Hg(2+) and fluorescence quenching behavior to Cu(2+), which induces naked-eye fluorescent color changes from green to blue and colorless, respectively. Moreover, it displayed highly sensitivity and selectivity toward Hg(2+) and Cu(2+) without interference from other metal ions. The sensing mechanisms were also confirmed by (1)H NMR titration, mass spectrum and Job's plot analyses. Finally, probe BT was successfully used for fluorescent imaging of Hg(2+) and Cu(2+) in living cells, demonstrating its potential applications in biological science.

  8. Application of magnetic and core-shell nanoparticles to determine enrofloxacin and its metabolite using laser induced fluorescence microscope. (United States)

    Kim, Suji; Ko, Junga; Lim, H B


    A unique analytical method using nanoparticles and laser-induced fluorescence microscopy (LIFM) was developed to determine enrofloxacin in this work. For sample pretreatment, two different kinds of particles, i.e., synthesized dye-doped core-shell silica nanoparticles and magnetic micro-particles (MPs), were used for fluorescent tagging and concentrating the enrofloxacin, respectively. The antibody of enrofloxacin was immobilized on the synthesized FITC-doped core-shell nanoparticles, and the enrofloxacin target was extracted by the MPs. At this moment, the average number of antibodies on each core-shell silica nanoparticle was ~0.9, which was determined by the fluorescence ratiometric method. The described method was demonstrated for a meat sample to determine enrofloxacin using LIFM, and the result was compared with enzyme-linked immunosorbent assay (ELISA). The developed technique allowed the simplified analytical procedure, improved the detection limit about 54-fold compared to ELISA.

  9. Synthesis, characterization and ion recognition studies of lower rim 1,3-di{rhodamine} conjugate of calix[4]arene

    Indian Academy of Sciences (India)

    Jugun Prakash Chinta; Jayaraman Dessingou; Chebrolu Pulla Rao


    An amido-linked rhodamine conjugate of calix[4]arene, L has been synthesized and characterized. Metal ion recognition properties of L have been studied by emission and absorption techniques with 14 different metal ions including the transition ones. Results show that, L exhibits ratiometric emission intensity towards Hg2+, Fe2+, Fe3+, Cu2+, Pb2+ and Zn2+. Composition of the complex formed in the solution has been found to be 1:2 (L:M+), based on the Job’s plot. The L can also act as a chemosensor for Hg2+ through naked eye detection. Fluorescence quenching observed at 485 nm follows an order, Hg2+>>Fe3+∼Cu2+>Zn2+>Pb2+>Ca2+, while the enhancement observed at 580 nm follows, Hg2+>>Fe2+∼Pb2+>Zn2+. Mode of interaction of M+ with L is by the ring opening of spirolactam moiety.

  10. Intracellular ion monitoring using a gold-core polymer-shell nanosensor architecture. (United States)

    Stanca, S E; Nietzsche, S; Fritzsche, W; Cranfield, C G; Biskup, C


    In this study, we describe the design of new ratiometric fluorescent nanosensors, whose architecture is based on a gold core surrounded by a poly(vinyl alcohol)-polyacetal shell. To the gold core, indicator dyes and reference dyes are attached via a cysteine linker. This nanosensor architecture is flexible with regards to the number and types of fluorophore linkages possible. The robust poly(vinyl alcohol)-polyacetal shell protects the fluorophores linked to the core from non-specific interactions with intracellular proteins. The nanosensors developed in this way are biocompatible and can be easily incorporated into mammalian cells without the use of transfection agents. Here, we show the application of these nanosensors for intracellular pH and sodium ion measurements.

  11. Intracellular ion monitoring using a gold-core polymer-shell nanosensor architecture

    Energy Technology Data Exchange (ETDEWEB)

    Stanca, S E; Cranfield, C G; Biskup, C [Biomolecular Photonics Group, University Hospital Jena, Teichgraben 8, 07743 Jena (Germany); Nietzsche, S [Centre for Electron Microscopy, University Hospital Jena, Ziegel-muehlenweg 1, 07743 Jena (Germany); Fritzsche, W, E-mail:, E-mail:, E-mail: [Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena (Germany)


    In this study, we describe the design of new ratiometric fluorescent nanosensors, whose architecture is based on a gold core surrounded by a poly(vinyl alcohol)-polyacetal shell. To the gold core, indicator dyes and reference dyes are attached via a cysteine linker. This nanosensor architecture is flexible with regards to the number and types of fluorophore linkages possible. The robust poly(vinyl alcohol)-polyacetal shell protects the fluorophores linked to the core from non-specific interactions with intracellular proteins. The nanosensors developed in this way are biocompatible and can be easily incorporated into mammalian cells without the use of transfection agents. Here, we show the application of these nanosensors for intracellular pH and sodium ion measurements.

  12. Intravital multiphoton photoconversion with a cell membrane dye. (United States)

    Turcotte, Raphaël; Wu, Juwell W; Lin, Charles P


    Photoconversion, an irreversible shift in a fluorophore emission spectrum after light exposure, is a powerful tool for marking cellular and subcellular compartments and tracking their dynamics in vivo. This paper reports on the photoconversion properties of Di-8-ANEPPS, a commercially available membrane dye. When illuminated with near-infrared femtosecond laser pulses, Di-8-ANEPPS undergoes multiphoton photoconversion as indicated by the supralinear dependence of the conversion rate ρpc on the incident power (ρpc∝Iexc2.27), and by the ability to photoconvert a thin optical section in a three-dimensional matrix. The characteristic emission spectrum changed from red to blue, and ratiometric analysis on single cells in vitro revealed a 65-fold increase in the blue to red wavelength ratio after photoconversion. The spectral shift is preserved in vivo for hours, making Di-8-ANEPPS a useful dye for intravital cell marking and tracking applications.

  13. Recruitment of the intracellular Ca2+ by ultrashort electric stimuli: the impact of pulse duration. (United States)

    Semenov, Iurii; Xiao, Shu; Pakhomova, Olga N; Pakhomov, Andrei G


    Nanosecond-duration electric stimuli are distinguished by the ability to permeabilize intracellular membranes and recruit Ca2+ from intracellular stores. We quantified this effect in non-excitable cells (CHO) using ratiometric Ca2+ imaging with Fura-2. In a Ca(2+)-free medium, 10-, 60-, and 300-ns stimuli evoked Ca2+ transients by mobilization of Ca2+ from the endoplasmic reticulum. With 2 mM external Ca2+, the transients included both extra- and intracellular components. The recruitment of intracellular Ca2+ increased as the stimulus duration decreased. At the threshold of 200-300 nM, the transients were amplified by calcium-induced calcium release. We conclude that nanosecond stimuli mimic Ca2+ signaling while bypassing the usual receptor- and channels-mediated cascades. The recruitment of the intracellular Ca2+ can be controlled by the duration of the stimulus.

  14. Absolute photoacoustic thermometry in deep tissue. (United States)

    Yao, Junjie; Ke, Haixin; Tai, Stephen; Zhou, Yong; Wang, Lihong V


    Photoacoustic thermography is a promising tool for temperature measurement in deep tissue. Here we propose an absolute temperature measurement method based on the dual temperature dependences of the Grüneisen parameter and the speed of sound in tissue. By taking ratiometric measurements at two adjacent temperatures, we can eliminate the factors that are temperature irrelevant but difficult to correct for in deep tissue. To validate our method, absolute temperatures of blood-filled tubes embedded ~9 mm deep in chicken tissue were measured in a biologically relevant range from 28°C to 46°C. The temperature measurement accuracy was ~0.6°C. The results suggest that our method can be potentially used for absolute temperature monitoring in deep tissue during thermotherapy.

  15. QD-Based FRET Probes at a Glance

    Directory of Open Access Journals (Sweden)

    Armen Shamirian


    Full Text Available The unique optoelectronic properties of quantum dots (QDs give them significant advantages over traditional organic dyes, not only as fluorescent labels for bioimaging, but also as emissive sensing probes. QD sensors that function via manipulation of fluorescent resonance energy transfer (FRET are of special interest due to the multiple response mechanisms that may be utilized, which in turn imparts enhanced flexibility in their design. They may also function as ratiometric, or “color-changing” probes. In this review, we describe the fundamentals of FRET and provide examples of QD-FRET sensors as grouped by their response mechanisms such as link cleavage and structural rearrangement. An overview of early works, recent advances, and various models of QD-FRET sensors for the measurement of pH and oxygen, as well as the presence of metal ions and proteins such as enzymes, are also provided.

  16. Study on the effects of cefotaxime on intracellular Ca2+ in human peripheral lymphocytes by fluoremetry

    Institute of Scientific and Technical Information of China (English)

    Dan Dan Wang; Hai Yan Wang; Ye Hong Zhou; Chun Gui Zhao; Chuan Dong; Shao Min Shuang


    Characteristic of Fura-2-Ca2+ interaction was studied based on the fluorescence technique. The apparent dissociation constants(Kd) of the Fura-2-Ca2+ complex were determined at different temperature. The effect of cefotaxime (CEFA) on intracellular Ca2+concentration ([Ca2+]i) was discussed by using a ratiometric fluorescence dye Fura-2 as a probe. The basal [Ca2+]i in resting human peripheral lymphocytes was 100 ± 7 nmol/L but after treatment with cefotaxime, the changes of [Ca2+]i were observed in different conditions. In the concentration range of 1-30 μmol/L of cefotaxime [Ca2+]i increased, as a result of releasing intracellular Ca2+ stores. Higher concentration of cefotaxime (50-500 μmol/L) stimulated to decrease of [Ca2+]i.

  17. Synthesis of Cross-Linked Polymeric Micelle pH Nanosensors

    DEFF Research Database (Denmark)

    Ek, Pramod Kumar; Jølck, Rasmus Irming; Andresen, Thomas Lars


    The design flexibility that polymeric micelles offer in the fabrication of optical nanosensors for ratiometric pH measurements is investigated. pH nanosensors based on polymeric micelles are synthesized either by a mixed-micellization approach or by a postmicelle modification strategy. In the mixed......-micellization approach, self-assembly of functionalized unimers followed by shell cross-linking by copper-catalyzed azide-alkyne cycloaddition (CuAAC) results in stabilized cRGD-functionalized micelle pH nanosensors. In the postmicelle modification strategy, simultaneous cross-linking and fluorophore conjugation...... at the micelle shell using CuAAC results in a stabilized micelle pH nanosensor. Compared to the postmicelle modification strategy, the mixed-micellization approach increases the control of the overall composition of the nanosensors.Both approaches provide stable nanosensors with similar pKa profiles and thereby...

  18. Gradient ascent pulse engineering for rapid exchange saturation transfer (United States)

    Rancan, G.; Nguyen, T. T.; Glaser, S. J.


    Efforts in the clinical translation of the paraCEST contrast agent Yb-HPDO3A have prompted an investigation into saturation pulse optimality under energy constraints. The GRAPE algorithm has been adapted and implemented for saturation pulse optimization with chemical exchange. The flexibility of the methodology, both in extracting the microscopical parameter ensemble for the algorithm as well as in determining the characteristics of this new class of rising amplitude waveforms allows rapid testing and implementation. Optimal pulses achieve higher saturation efficiencies than the continuous wave gold standard for rapid and especially for variable exchange rates, as brought about by pH-catalysis. Gains of at least 5-15% without any tradeoff have been confirmed both on a spectrometer and on a clinical imager. Pool specific solutions, with pulses optimized for a specific exchange rate value, additionally increase the flexibility of the CEST ratiometric analysis. A simple experimental approach to determine close to optimal triangular pulses is presented.

  19. Reciprocal cholinergic and GABAergic modulation of the small ventrolateral pacemaker neurons of Drosophila's circadian clock neuron network. (United States)

    Lelito, Katherine R; Shafer, Orie T


    The relatively simple clock neuron network of Drosophila is a valuable model system for the neuronal basis of circadian timekeeping. Unfortunately, many key neuronal classes of this network are inaccessible to electrophysiological analysis. We have therefore adopted the use of genetically encoded sensors to address the physiology of the fly's circadian clock network. Using genetically encoded Ca(2+) and cAMP sensors, we have investigated the physiological responses of two specific classes of clock neuron, the large and small ventrolateral neurons (l- and s-LN(v)s), to two neurotransmitters implicated in their modulation: acetylcholine (ACh) and γ-aminobutyric acid (GABA). Live imaging of l-LN(v) cAMP and Ca(2+) dynamics in response to cholinergic agonist and GABA application were well aligned with published electrophysiological data, indicating that our sensors were capable of faithfully reporting acute physiological responses to these transmitters within single adult clock neuron soma. We extended these live imaging methods to s-LN(v)s, critical neuronal pacemakers whose physiological properties in the adult brain are largely unknown. Our s-LN(v) experiments revealed the predicted excitatory responses to bath-applied cholinergic agonists and the predicted inhibitory effects of GABA and established that the antagonism of ACh and GABA extends to their effects on cAMP signaling. These data support recently published but physiologically untested models of s-LN(v) modulation and lead to the prediction that cholinergic and GABAergic inputs to s-LN(v)s will have opposing effects on the phase and/or period of the molecular clock within these critical pacemaker neurons.

  20. Species specificity in major urinary proteins by parallel evolution.

    Directory of Open Access Journals (Sweden)

    Darren W Logan

    Full Text Available Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1 diversity, to enable the signaling of multiple behaviors, 2 dynamic regulation, to indicate age and dominance, and 3 species-specificity. Recently, the major urinary proteins (Mups have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues.Our results show that the mouse Mup gene cluster is composed of two subgroups: an older, more divergent class of genes and pseudogenes, and a second class with high sequence identity formed by recent sequential duplications of a single gene/pseudogene pair. Previous work suggests that truncated Mup pseudogenes may encode a family of functional hexapeptides with the potential for pheromone activity. Sequence comparison, however, reveals that they have limited coding potential. Similar analyses of nine other completed genomes find Mup gene expansions in divergent lineages, including those of rat, horse and grey mouse lemur, occurring independently from a single ancestral Mup present in other placental mammals. Our findings illustrate that increasing genomic complexity of the Mup gene family is not evolutionarily isolated, but is instead a recurring mechanism of generating coding diversity consistent with a species

  1. Genetic dissection of GABAergic neural circuits in mouse neocortex

    Directory of Open Access Journals (Sweden)

    Hiroki eTaniguchi


    Full Text Available Diverse and flexible cortical functions rely on the ability of neural circuits to perform multiple types of neuronal computations. GABAergic inhibitory interneurons significantly contribute to this task by regulating the balance of activity, synaptic integration, spiking, synchrony, and oscillation in a neural ensemble. GABAergic interneruons display a high degree of cellular diversity in morphology, physiology, connectivity, and gene expression. A considerable number of subtypes of GABAergic interneurons diversify modes of cortical inhibition, enabling various types of information processing in the cortex. Thus, comprehensively understanding fate specification, circuit assembly and physiological function of GABAergic interneurons is a key to elucidate the principles of cortical wiring and function. Recent advances in genetically encoded molecular tools have made a breakthrough to systematically study cortical circuitry at the molecular, cellular, circuit, and whole animal levels. However, the biggest obstacle to fully applying the power of these to analysis of GABAergic circuits was that there were no efficient and reliable methods to express them in subtypes of GABAergic interneurons. Here, I first summarize cortical interneuron diversity and current understanding of mechanisms, by which distinct classes of GABAergic interneurons are generated. I then review recent development in genetically encoded molecular tools for neural circuit research, and genetic targeting of GABAergic interneuron subtypes, particulary focusing on our recent effort to develop and characterize Cre/CreER knockin lines. Finally, I highlight recent success in genetic targeting of chandelier cells (ChCs, the most unique and distinct GABAergic interneuron subtype, and discuss what kind of questions need to be addressed to understand development and function of cortical inhibitory circuits.

  2. Design of lanthanide fingers: compact lanthanide-binding metalloproteins. (United States)

    am Ende, Christopher W; Meng, Hai Yun; Ye, Mao; Pandey, Anil K; Zondlo, Neal J


    Lanthanides have interesting chemical properties; these include luminescent, magnetic, and catalytic functions. Toward the development of proteins incorporating novel functions, we have designed a new lanthanide-binding motif, lanthanide fingers. These were designed based on the Zif268 zinc finger, which exhibits a beta beta alpha structural motif. Lanthanide fingers utilize an Asp(2)Glu(2) metal-coordination environment to bind lanthanides through a tetracarboxylate peptide ligand. The iterative design of a general lanthanide-binding peptide incorporated the following key elements: 1) residues with high alpha-helix and beta-sheet propensities in the respective secondary structures; 2) an optimized big box alpha-helix N-cap; 3) a Schellman alpha-helix C-cap motif; and 4) an optional D-Pro-Ser type II' beta-turn in the beta-hairpin. The peptides were characterized for lanthanide binding by circular dichroism (CD), NMR, and fluorescence spectroscopy. In all instances, stabilization of the peptide secondary structures resulted in an increase in metal affinity. The optimized protein design was a 25-residue peptide that was a general lanthanide-binding motif; this binds all lanthanides examined in a competitive aqueous environment, with a dissociation constant of 9.3 microM for binding Er(3+). CD spectra of the peptide-lanthanide complexes are similar to those of zinc fingers and other beta beta alpha proteins. Metal binding involves residues from the N-terminal beta-hairpin and the C terminal alpha-helical segments of the peptide. NMR data indicated that metal binding induced a global change in the peptide structure. The D-Pro-Ser type II' beta-turn motif could be replaced by Thr-Ile to generate genetically encodable lanthanide fingers. Replacement of the central Phe with Trp generated genetically encodable lanthanide fingers that exhibited terbium luminescence greater than that of an EF-hand peptide.

  3. Vipericidins: a novel family of cathelicidin-related peptides from the venom gland of South American pit vipers. (United States)

    Falcao, C B; de La Torre, B G; Pérez-Peinado, C; Barron, A E; Andreu, D; Rádis-Baptista, G


    Cathelicidins are phylogenetically ancient, pleiotropic host defense peptides-also called antimicrobial peptides (AMPs)-expressed in numerous life forms for innate immunity. Since even the jawless hagfish expresses cathelicidins, these genetically encoded host defense peptides are at least 400 million years old. More recently, cathelicidins with varying antipathogenic activities and cytotoxicities were discovered in the venoms of poisonous snakes; for these creatures, cathelicidins may also serve as weapons against prey and predators, as well as for innate immunity. We report herein the expression of orthologous cathelicidin genes in the venoms of four different South American pit vipers (Bothrops atrox, Bothrops lutzi, Crotalus durissus terrificus, and Lachesis muta rhombeata)-distant relatives of Asian cobras and kraits, previously shown to express cathelicidins-and an elapid, Pseudonaja textilis. We identified six novel, genetically encoded peptides: four from pit vipers, collectively named vipericidins, and two from the elapid. These new venom-derived cathelicidins exhibited potent killing activity against a number of bacterial strains (S. pyogenes, A. baumannii, E. faecalis, S. aureus, E. coli, K. pneumoniae, and P. aeruginosa), mostly with relatively less potent hemolysis, indicating their possible usefulness as lead structures for the development of new anti-infective agents. It is worth noting that these South American snake venom peptides are comparable in cytotoxicity (e.g., hemolysis) to human cathelicidin LL-37, and much lower than other membrane-active peptides such as mastoparan 7 and melittin from bee venom. Overall, the excellent bactericidal profile of vipericidins suggests they are a promising template for the development of broad-spectrum peptide antibiotics.

  4. An approach to estimate spatial distribution of analyte within cells using spectrally-resolved fluorescence microscopy (United States)

    Sharma, Dharmendar Kumar; Irfanullah, Mir; Basu, Santanu Kumar; Madhu, Sheri; De, Suman; Jadhav, Sameer; Ravikanth, Mangalampalli; Chowdhury, Arindam


    While fluorescence microscopy has become an essential tool amongst chemists and biologists for the detection of various analyte within cellular environments, non-uniform spatial distribution of sensors within cells often restricts extraction of reliable information on relative abundance of analytes in different subcellular regions. As an alternative to existing sensing methodologies such as ratiometric or FRET imaging, where relative proportion of analyte with respect to the sensor can be obtained within cells, we propose a methodology using spectrally-resolved fluorescence microscopy, via which both the relative abundance of sensor as well as their relative proportion with respect to the analyte can be simultaneously extracted for local subcellular regions. This method is exemplified using a BODIPY sensor, capable of detecting mercury ions within cellular environments, characterized by spectral blue-shift and concurrent enhancement of emission intensity. Spectral emission envelopes collected from sub-microscopic regions allowed us to compare the shift in transition energies as well as integrated emission intensities within various intracellular regions. Construction of a 2D scatter plot using spectral shifts and emission intensities, which depend on the relative amount of analyte with respect to sensor and the approximate local amounts of the probe, respectively, enabled qualitative extraction of relative abundance of analyte in various local regions within a single cell as well as amongst different cells. Although the comparisons remain semi-quantitative, this approach involving analysis of multiple spectral parameters opens up an alternative way to extract spatial distribution of analyte in heterogeneous systems. The proposed method would be especially relevant for fluorescent probes that undergo relatively nominal shift in transition energies compared to their emission bandwidths, which often restricts their usage for quantitative ratiometric imaging in

  5. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones. (United States)

    Rodriguez-Manzano, Jesus; Karymov, Mikhail A; Begolo, Stefano; Selck, David A; Zhukov, Dmitriy V; Jue, Erik; Ismagilov, Rustem F


    Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests.

  6. Modulation of vacuolar pH is required for replication of Edwardsiella ictaluri in channel catfish macrophages. (United States)

    Baumgartner, Wes A; Dubytska, Lidiya; Rogge, Matthew L; Mottram, Peter J; Thune, Ronald L


    Previous in vitro work demonstrated that Edwardsiella ictaluri produces an acid-activated urease that can modulate environmental pH through the production of ammonia from urea. Additional work revealed that expression of the E. ictaluri type III secretion system (T3SS) is upregulated by acidic pH. Both the urease and the T3SS were previously shown to be essential to intracellular replication. In this work, fluorescence microscopy with LysoTracker Red DND-99 (LTR) indicated that E. ictaluri-containing vacuoles (ECV) became acidified following ingestion by head kidney-derived macrophages (HKDM). In vivo ratiometric imaging demonstrated a lowered ECV pH, which fell to as low as pH 4 but subsequently increased to pH 6 or greater. Inhibition of vacuolar H(+)-ATPases by use of the specific inhibitor bafilomycin A1 abrogated both ECV acidification and intracellular replication in HKDM. Failure of an E. ictaluri urease knockout mutant to increase the ECV pH in the in vivo ratiometric assay suggests that ammonia produced by the urease reaction mediates the pH increase. Additionally, when the specific arginase inhibitor l-norvaline was used to treat E. ictaluri-infected HKDM, the ECV failed to neutralize and E. ictaluri was unable to replicate. This indicates that the HKDM-encoded arginase enzyme produces the urea used by the E. ictaluri urease enzyme. Failure of the ECV to acidify would prevent both upregulation of the T3SS and activation of the urease enzyme, either of which would prevent E. ictaluri from replicating in HKDM. Failure of the ECV to neutralize would result in a vacuolar pH too low to support E. ictaluri replication.

  7. A Novel Nicotinamide Adenine Dinucleotide Correction Method for Mitochondrial Ca(2+) Measurement with FURA-2-FF in Single Permeabilized Ventricular Myocytes of Rat. (United States)

    Lee, Jeong Hoon; Ha, Jeong Mi; Leem, Chae Hun


    Fura-2 analogs are ratiometric fluoroprobes that are widely used for the quantitative measurement of [Ca(2+)]. However, the dye usage is intrinsically limited, as the dyes require ultraviolet (UV) excitation, which can also generate great interference, mainly from nicotinamide adenine dinucleotide (NADH) autofluorescence. Specifically, this limitation causes serious problems for the quantitative measurement of mitochondrial [Ca(2+)], as no available ratiometric dyes are excited in the visible range. Thus, NADH interference cannot be avoided during quantitative measurement of [Ca(2+)] because the majority of NADH is located in the mitochondria. The emission intensity ratio of two different excitation wavelengths must be constant when the fluorescent dye concentration is the same. In accordance with this principle, we developed a novel online method that corrected NADH and Fura-2-FF interference. We simultaneously measured multiple parameters, including NADH, [Ca(2+)], and pH/mitochondrial membrane potential; Fura-2-FF for mitochondrial [Ca(2+)] and TMRE for Ψm or carboxy-SNARF-1 for pH were used. With this novel method, we found that the resting mitochondrial [Ca(2+)] concentration was 1.03 µM. This 1 µM cytosolic Ca(2+) could theoretically increase to more than 100 mM in mitochondria. However, the mitochondrial [Ca(2+)] increase was limited to ~30 µM in the presence of 1 µM cytosolic Ca(2+). Our method solved the problem of NADH signal contamination during the use of Fura-2 analogs, and therefore the method may be useful when NADH interference is expected.

  8. Simultaneous spectroscopic measurements of the interior temperature and induced cargo release from pore-restricted mesoporous silica nanoparticles (United States)

    Dong, Juyao; Zink, Jeffrey I.


    Temperature changes initiated within nano structures are being increasingly used to externally activate responsive delivery vehicles. Yet, the precise measurement of the nano environment temperature increase and its correlation with the induced macroscopic cargo release are difficult to achieve. In this study, we focus on a photothermally activated drug delivery system based on mesoporous silica nanoparticles, and use an optical nanothermometer - NaYF4:Yb3+,Er3+ crystals - for a ratiometric temperature measurement. Using fluorescent dyes as the payload molecule, both the nanoparticle interior temperature change and the macroscopic cargo release amount are monitored simultaneously by fluorescent spectroscopy. We found that the cargo release lags the temperature increase by about 5 min, revealing the threshold temperature that the particles have to reach before a substantial release could happen. Using this spectroscopic method, we are able to directly compare and correlate a nano environment event with its stimulated macroscopic results.Temperature changes initiated within nano structures are being increasingly used to externally activate responsive delivery vehicles. Yet, the precise measurement of the nano environment temperature increase and its correlation with the induced macroscopic cargo release are difficult to achieve. In this study, we focus on a photothermally activated drug delivery system based on mesoporous silica nanoparticles, and use an optical nanothermometer - NaYF4:Yb3+,Er3+ crystals - for a ratiometric temperature measurement. Using fluorescent dyes as the payload molecule, both the nanoparticle interior temperature change and the macroscopic cargo release amount are monitored simultaneously by fluorescent spectroscopy. We found that the cargo release lags the temperature increase by about 5 min, revealing the threshold temperature that the particles have to reach before a substantial release could happen. Using this spectroscopic method, we are

  9. Carbon dots with strong excitation-dependent fluorescence changes towards pH. Application as nanosensors for a broad range of pH

    Energy Technology Data Exchange (ETDEWEB)

    Barati, Ali [Faculty of Chemistry, Institute for Advanced Studies in Basic Sciences, Zanjan (Iran, Islamic Republic of); Department of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of); Shamsipur, Mojtaba, E-mail: [Department of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of); Abdollahi, Hamid, E-mail: [Faculty of Chemistry, Institute for Advanced Studies in Basic Sciences, Zanjan (Iran, Islamic Republic of)


    In this study, preparation of novel pH-sensitive N-doped carbon dots (NCDs) using glucose and urea is reported. The prepared NCDs present strong excitation-dependent fluorescence changes towards the pH that is a new behavior from these nanomaterials. By taking advantage of this unique behavior, two separated ratiometric pH sensors using emission spectra of the NCDs for both acidic (pH 2.0 to 8.0) and basic (pH 7.0 to 14.0) ranges of pH are constructed. Additionally, by considering the entire Excitation–Emission Matrix (EEM) of NCDs as analytical signal and using a suitable multivariate calibration method, a broad range of pH from 2.0 to 14.0 was well calibrated. The multivariate calibration method was independent from the concentration of NCDs and resulted in a very low average prediction error of 0.067 pH units. No changes in the predicted pH under UV irradiation (for 3 h) and at high ionic strength (up to 2 M NaCl) indicated the high stability of this pH nanosensor. The practicality of this pH nanosensor for pH determination in real water samples was validated with good accuracy and repeatability. - Highlights: • Novel pH-sensitive carbon dots with strong FL changes towards pH are reported. • Ratiometric FL pH-sensors for both acidic and basic ranges of pH are constructed. • Multivariate calibration methods were used to calibrate a broad range of pH. • Using EEM of carbon dots and ANN, pH from 2.0 to 14.0 was well calibrated. • The pH prediction is stable even at high ionic strength up to 2 M NaCl.

  10. Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy. (United States)

    Ou, Horng D; Deerinck, Thomas J; Bushong, Eric; Ellisman, Mark H; O'Shea, Clodagh C


    Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host's cellular environment, their natural in situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940's and subsequent application to cells in the 1950's. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and

  11. pH landscapes in a novel five-species model of early dental biofilm.

    Directory of Open Access Journals (Sweden)

    Sebastian Schlafer

    Full Text Available BACKGROUND: Despite continued preventive efforts, dental caries remains the most common disease of man. Organic acids produced by microorganisms in dental plaque play a crucial role for the development of carious lesions. During early stages of the pathogenetic process, repeated pH drops induce changes in microbial composition and favour the establishment of an increasingly acidogenic and aciduric microflora. The complex structure of dental biofilms, allowing for a multitude of different ecological environments in close proximity, remains largely unexplored. In this study, we designed a laboratory biofilm model that mimics the bacterial community present during early acidogenic stages of the caries process. We then performed a time-resolved microscopic analysis of the extracellular pH landscape at the interface between bacterial biofilm and underlying substrate. METHODOLOGY/PRINCIPAL FINDINGS: Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus mitis, Streptococcus downei and Actinomyces naeslundii were employed in the model. Biofilms were grown in flow channels that allowed for direct microscopic analysis of the biofilms in situ. The architecture and composition of the biofilms were analysed using fluorescence in situ hybridization and confocal laser scanning microscopy. Both biofilm structure and composition were highly reproducible and showed similarity to in-vivo-grown dental plaque. We employed the pH-sensitive ratiometric probe C-SNARF-4 to perform real-time microscopic analyses of the biofilm pH in response to salivary solutions containing glucose. Anaerobic glycolysis in the model biofilms created a mildly acidic environment. Decrease in pH in different areas of the biofilms varied, and distinct extracellular pH-microenvironments were conserved over several hours. CONCLUSIONS/SIGNIFICANCE: The designed biofilm model represents a promising tool to determine the effect of potential therapeutic agents on biofilm growth

  12. Thiazole derivative-modified upconversion nanoparticles for Hg2+ detection in living cells (United States)

    Gu, Bin; Zhou, Yi; Zhang, Xiao; Liu, Xiaowang; Zhang, Yuhai; Marks, Robert; Zhang, Hua; Liu, Xiaogang; Zhang, Qichun


    Mercury ion (Hg2+) is an extremely toxic ion, which will accumulate in human bodies and cause severe nervous system damage. Therefore, the sensitive and efficient monitoring of Hg2+ in human bodies is of great importance. Upconversion nanoparticle (UCNPs) based nano probes exhibit no autofluorescence, deep penetration depth and chemical stability in biological samples, as well as a large anti-stokes shift. In this study, we have developed thiazole-derivative-functionalized UCNPs, and employed an upconversion emission intensity ratio of 540 nm to 803 nm (I540/I803) as a ratiometric signal to detect Hg2+ in living cells showing excellent photo stability and high selectivity. Our nano probe was characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). The low cytotoxicity of our probe was confirmed by an MTT assay and the UCL test in HeLa cells was carried out by confocal microscopy. Our results demonstrated that organic-dye-functionalized UCNPs should be a good strategy for detecting toxic metal ions when studying cellular biosystems.Mercury ion (Hg2+) is an extremely toxic ion, which will accumulate in human bodies and cause severe nervous system damage. Therefore, the sensitive and efficient monitoring of Hg2+ in human bodies is of great importance. Upconversion nanoparticle (UCNPs) based nano probes exhibit no autofluorescence, deep penetration depth and chemical stability in biological samples, as well as a large anti-stokes shift. In this study, we have developed thiazole-derivative-functionalized UCNPs, and employed an upconversion emission intensity ratio of 540 nm to 803 nm (I540/I803) as a ratiometric signal to detect Hg2+ in living cells showing excellent photo stability and high selectivity. Our nano probe was characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). The low cytotoxicity of our probe was confirmed by an MTT assay and the UCL test in HeLa cells was carried out by

  13. Characterization of excited-state reactions with instant spectra of fluorescence kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Tomin, Vladimir I., E-mail:; Ushakou, Dzmitryi V.


    Comprehensible knowledge of the excited-state proton transfer processes in organic compounds is overwhelmingly important not only for physics, but also chemistry and Life Sciences, since they play a key role in main processes of photosynthesis and functioning of biological organisms. Moreover compounds with Excited-State Intramolecular Proton Transfer (ESIPT) are in the focus of the interest of scientists throughout the world, because dual fluorescence spectra of such objects corresponding to two forms of molecular structure (normal and photoproduct) are very sensitive to characteristics of molecular microenvironment. This property allows to use such substances as fluorescent probes for diverse applications in chemistry and Life Sciences. But at the same time studying of proton transfer processes is not simple, because this process is characterized by extremely fast times (on picoseconds time scale and less order) and very often contribution of reverse reactions is essentially complicates an interpretation of observed properties of dual fluorescence. Hence, understanding of a role of reversible reactions is crucial for a comprehensive description of all processes accompanying excited state reactions. We discuss new approach for treatment ESIPT reaction on the basis of experimentally measured instant spectra of dual fluorescence and temporal behavior of ratiometric signal of normal to tautomer form intensities. Simple analytical expressions show in transparent way how to distinguish a degree of reverse reaction contribution to ratiometric signal. A validation of the approach under consideration is fulfilled with two different flavonols – 3-hydroxyflavone and 4′-(Dimethylamino)-3-hydroxyflavone – representing two extreme cases in affecting reversible reaction on dual emission. A comparing of new approach and traditional method when we analyze kinetics of separate the N* and T* fluorescence bands decays, has been carried out. - Highlights: • The excited

  14. Towards Behavior Control for Evolutionary Robot Based on RL with ENN

    Directory of Open Access Journals (Sweden)

    Jingan Yang


    Full Text Available This paper proposes a behavior-switching control strategy of anevolutionary robotics based on Artificial NeuralNetwork (ANN and Genetic Algorithms (GA. This method is able not only to construct thereinforcement learning models for autonomous robots and evolutionary robot modules thatcontrol behaviors and reinforcement learning environments, and but also to perform thebehavior-switching control and obstacle avoidance of an evolutionary robotics (ER intime-varying environments with static and moving obstacles by combining ANN and GA.The experimental results on thebasic behaviors and behavior-switching control have demonstrated that ourmethod can perform the decision-making strategy and parameters set opimization ofFNN and GA by learning and can escape successfully from the trap of a localminima and avoid \\emph{"motion deadlock" status} of humanoid soccer robotics agents,and reduce the oscillation of the planned trajectory betweenthe multiple obstacles by crossover and mutation. Some results of the proposed algorithmhave been successfully applied to our simulation humanoid robotics soccer team CIT3Dwhich won \\emph{the 1st prize} of RoboCup Championship and ChinaOpen2010 (July 2010 and \\emph{the $2^{nd}$ place}of the official RoboCup World Championship on 5-11 July, 2011 in Istanbul, Turkey.As compared with the conventional behavior network and the adaptive behavior method,the genetic encoding complexity of our algorithm is simplified, and the networkperformance and the {\\em convergence rate $\\rho$} have been greatlyimproved.

  15. Mitochondrial Calcium Uptake Modulates Synaptic Vesicle Endocytosis in Central Nerve Terminals. (United States)

    Marland, Jamie Roslin Keynes; Hasel, Philip; Bonnycastle, Katherine; Cousin, Michael Alan


    Presynaptic calcium influx triggers synaptic vesicle (SV) exocytosis and modulates subsequent SV endocytosis. A number of calcium clearance mechanisms are present in central nerve terminals that regulate intracellular free calcium levels both during and after stimulation. During action potential stimulation, mitochondria rapidly accumulate presynaptic calcium via the mitochondrial calcium uniporter (MCU). The role of mitochondrial calcium uptake in modulating SV recycling has been debated extensively, but a definitive conclusion has not been achieved. To directly address this question, we manipulated the expression of the MCU channel subunit in primary cultures of neurons expressing a genetically encoded reporter of SV turnover. Knockdown of MCU resulted in ablation of activity-dependent mitochondrial calcium uptake but had no effect on the rate or extent of SV exocytosis. In contrast, the rate of SV endocytosis was increased in the absence of mitochondrial calcium uptake and slowed when MCU was overexpressed. MCU knockdown did not perturb activity-dependent increases in presynaptic free calcium, suggesting that SV endocytosis may be controlled by calcium accumulation and efflux from mitochondria in their immediate vicinity.

  16. [World"--an unlikely scenario of the life origin and early ecolution on Earth]. (United States)

    Bregestowski, P D


    The most widely accepted modern scenario of prebiotic evolution that led to the emergence of the first cells on our planet is the "RNA World"--a hypothetical period of the early Earth's biosphere, when the information transfer and all the processes necessary for the functioning of the primary systems were provided by replicating RNA molecules. The essence of the "RNA World" hypothesis is based on two postulates: 1) at the initial stages of the origin of life, RNA molecules performed all functions necessary for reproduction and replication of biological molecules: informational, catalytic and structural; 2) at a certain stage of evolution arose separation of RNA and DNA, appeared genetically encoded proteins and occurred a transition to the modern world of living systems functioning. However, the analysis shows that the hypothesis of "RNA World" has a number of unsurmountable problems of chemical and informational nature. The biggest of them are: a) the unreliability of the initial components synthesis; b) a catastrophic rise of polynucleotide chains instability with their elongation; c) catastrophically low probability of formation of sequences possessing meaningful information; d) lack of a mechanism determining the regularities division of the membrane vesicles permeable to nitrogen bases and other RNA components; e) lack of driving forces for the transition from the RNA world to the much more complex world based on DNA and RNA. Therefore, the "RNA World" scenario seems unlikely.

  17. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. (United States)

    Kellenberger, Colleen A; Wilson, Stephen C; Hickey, Scott F; Gonzalez, Tania L; Su, Yichi; Hallberg, Zachary F; Brewer, Thomas F; Iavarone, Anthony T; Carlson, Hans K; Hsieh, Yu-Fang; Hammond, Ming C


    Cyclic dinucleotides are an expanding class of signaling molecules that control many aspects of bacterial physiology. A synthase for cyclic AMP-GMP (cAG, also referenced as 3'-5', 3'-5' cGAMP) called DncV is associated with hyperinfectivity of Vibrio cholerae but has not been found in many bacteria, raising questions about the prevalence and function of cAG signaling. We have discovered that the environmental bacterium Geobacter sulfurreducens produces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membranes, and Motility) as specific receptors for cAG. GEMM-Ib riboswitches regulate genes associated with extracellular electron transfer; thus cAG signaling may control aspects of bacterial electrophysiology. These findings expand the role of cAG beyond organisms that harbor DncV and beyond pathogenesis to microbial geochemistry, which is important to environmental remediation and microbial fuel cell development. Finally, we have developed an RNA-based fluorescent biosensor for live-cell imaging of cAG. This selective, genetically encodable biosensor will be useful to probe the biochemistry and cell biology of cAG signaling in diverse bacteria.

  18. Neural Circuits on a Chip

    Directory of Open Access Journals (Sweden)

    Md. Fayad Hasan


    Full Text Available Neural circuits are responsible for the brain’s ability to process and store information. Reductionist approaches to understanding the brain include isolation of individual neurons for detailed characterization. When maintained in vitro for several days or weeks, dissociated neurons self-assemble into randomly connected networks that produce synchronized activity and are capable of learning. This review focuses on efforts to control neuronal connectivity in vitro and construct living neural circuits of increasing complexity and precision. Microfabrication-based methods have been developed to guide network self-assembly, accomplishing control over in vitro circuit size and connectivity. The ability to control neural connectivity and synchronized activity led to the implementation of logic functions using living neurons. Techniques to construct and control three-dimensional circuits have also been established. Advances in multiple electrode arrays as well as genetically encoded, optical activity sensors and transducers enabled highly specific interfaces to circuits composed of thousands of neurons. Further advances in on-chip neural circuits may lead to better understanding of the brain.

  19. Synchronous circadian voltage rhythms with asynchronous calcium rhythms in the suprachiasmatic nucleus. (United States)

    Enoki, Ryosuke; Oda, Yoshiaki; Mieda, Michihiro; Ono, Daisuke; Honma, Sato; Honma, Ken-Ichi


    The suprachiasmatic nucleus (SCN), the master circadian clock, contains a network composed of multiple types of neurons which are thought to form a hierarchical and multioscillator system. The molecular clock machinery in SCN neurons drives membrane excitability and sends time cue signals to various brain regions and peripheral organs. However, how and at what time of the day these neurons transmit output signals remain largely unknown. Here, we successfully visualized circadian voltage rhythms optically for many days using a genetically encoded voltage sensor, ArcLightD. Unexpectedly, the voltage rhythms are synchronized across the entire SCN network of cultured slices, whereas simultaneously recorded Ca(2+) rhythms are topologically specific to the dorsal and ventral regions. We further found that the temporal order of these two rhythms is cell-type specific: The Ca(2+) rhythms phase-lead the voltage rhythms in AVP neurons but Ca(2+) and voltage rhythms are nearly in phase in VIP neurons. We confirmed that circadian firing rhythms are also synchronous and are coupled with the voltage rhythms. These results indicate that SCN networks with asynchronous Ca(2+) rhythms produce coherent voltage rhythms.

  20. Mapping of voltage sensor positions in resting and inactivated mammalian sodium channels by LRET. (United States)

    Kubota, Tomoya; Durek, Thomas; Dang, Bobo; Finol-Urdaneta, Rocio K; Craik, David J; Kent, Stephen B H; French, Robert J; Bezanilla, Francisco; Correa, Ana M


    Voltage-gated sodium channels (Navs) play crucial roles in excitable cells. Although vertebrate Nav function has been extensively studied, the detailed structural basis for voltage-dependent gating mechanisms remain obscure. We have assessed the structural changes of the Nav voltage sensor domain using lanthanide-based resonance energy transfer (LRET) between the rat skeletal muscle voltage-gated sodium channel (Nav1.4) and fluorescently labeled Nav1.4-targeting toxins. We generated donor constructs with genetically encoded lanthanide-binding tags (LBTs) inserted at the extracellular end of the S4 segment of each domain (with a single LBT per construct). Three different Bodipy-labeled, Nav1.4-targeting toxins were synthesized as acceptors: β-scorpion toxin (Ts1)-Bodipy, KIIIA-Bodipy, and GIIIA-Bodipy analogs. Functional Nav-LBT channels expressed in Xenopus oocytes were voltage-clamped, and distinct LRET signals were obtained in the resting and slow inactivated states. Intramolecular distances computed from the LRET signals define a geometrical map of Nav1.4 with the bound toxins, and reveal voltage-dependent structural changes related to channel gating.

  1. 改进遗传算法在人群行为仿真中的应用%The simulation of improved genetic algorithms of crowd behavior

    Institute of Scientific and Technical Information of China (English)



    For the combinatorial optimization problem of crowd behavior simulation multi-objective and consuained,proposed a improved genetic algorithm in the application of group behavior simulation.By setting the special data structure to simulate the process of a variety of constraint rules,genetic encoding of genetic algorithm,fittness evaluation function implement of crowd behavior simulation.Simulation experiment verified that the method can greatly reduce the search space,and enables optimal results.%针对目前人群行为仿真中多目标,有约束的组合优化问题,提出了一种改进遗传算法在人群行为仿真的应用方案.通过设定特殊的数据结构、仿真过程中的各种约束规则、遗传算法中的基因编码、适应度评价函数实现了人群行为仿真.仿真实验验证了该算法可以大大减少搜索空间,并能使结果达到最优.

  2. Engineered cell-cell communication via DNA messaging

    Directory of Open Access Journals (Sweden)

    Ortiz Monica E


    Full Text Available Abstract Background Evolution has selected for organisms that benefit from genetically encoded cell-cell communication. Engineers have begun to repurpose elements of natural communication systems to realize programmed pattern formation and coordinate other population-level behaviors. However, existing engineered systems rely on system-specific small molecules to send molecular messages among cells. Thus, the information transmission capacity of current engineered biological communication systems is physically limited by specific biomolecules that are capable of sending only a single message, typically “regulate transcription.” Results We have engineered a cell-cell communication platform using bacteriophage M13 gene products to autonomously package and deliver heterologous DNA messages of varying lengths and encoded functions. We demonstrate the decoupling of messages from a common communication channel via the autonomous transmission of various arbitrary genetic messages. Further, we increase the range of engineered DNA messaging across semisolid media by linking message transmission or receipt to active cellular chemotaxis. Conclusions We demonstrate decoupling of a communication channel from message transmission within engineered biological systems via the autonomous targeted transduction of user-specified heterologous DNA messages. We also demonstrate that bacteriophage M13 particle production and message transduction occurs among chemotactic bacteria. We use chemotaxis to improve the range of DNA messaging, increasing both transmission distance and communication bit rates relative to existing small molecule-based communication systems. We postulate that integration of different engineered cell-cell communication platforms will allow for more complex spatial programming of dynamic cellular consortia.

  3. Measuring E(GSH) and H2O2 with roGFP2-based redox probes. (United States)

    Morgan, Bruce; Sobotta, Mirko C; Dick, Tobias P


    Redox biochemistry plays an important role in a wide range of cellular events. However, investigation of cellular redox processes is complicated by the large number of cellular redox couples, which are often not in equilibrium with one another and can vary significantly between subcellular compartments and cell types. Further, it is becoming increasingly clear that different redox systems convey different biological information; thus it makes little sense to talk of an overall "cellular redox state". To gain a more differentiated understanding of cellular redox biology, quantitative, redox couple-specific, in vivo measurements are necessary. Unfortunately our ability to investigate specific redox couples or redox-reactive molecules with the necessary degree of spatiotemporal resolution is very limited. The development of genetically encoded redox biosensors offers a promising new way to investigate redox biology. Recently developed redox-sensitive green fluorescent proteins (roGFPs), genetically fused to redox-active proteins, allow rapid equilibration of the roGFP moiety with a specific redox couple. Two probes based on this principle are now available: Grx1-roGFP2 for the measurement of glutathione redox potential (E(GSH)) and roGFP2-Orp1 for measuring changes in H(2)O(2) concentration. Here we provide a detailed protocol for the use of these probes in both yeast and mammalian systems using either plate-reader- or microscopy-based measurements.

  4. CD44 expression in endothelial colony-forming cells regulates neurovascular trophic effect (United States)

    Sakimoto, Susumu; Marchetti, Valentina; Aguilar, Edith; Lee, Kelsey; Usui, Yoshihiko; Bucher, Felicitas; Trombley, Jennifer K.; Fallon, Regis; Wagey, Ravenska; Peters, Carrie; Scheppke, Elizabeth L.; Westenskow, Peter D.


    Vascular abnormalities are a common component of eye diseases that often lead to vision loss. Vaso-obliteration is associated with inherited retinal degenerations, since photoreceptor atrophy lowers local metabolic demands and vascular support to those regions is no longer required. Given the degree of neurovascular crosstalk in the retina, it may be possible to use one cell type to rescue another cell type in the face of severe stress, such as hypoxia or genetically encoded cell-specific degenerations. Here, we show that intravitreally injected human endothelial colony-forming cells (ECFCs) that can be isolated and differentiated from cord blood in xeno-free media collect in the vitreous cavity and rescue vaso-obliteration and neurodegeneration in animal models of retinal disease. Furthermore, we determined that a subset of the ECFCs was more effective at anatomically and functionally preventing retinopathy; these cells expressed high levels of CD44, the hyaluronic acid receptor, and IGFBPs (insulin-like growth factor–binding proteins). Injection of cultured media from ECFCs or only recombinant human IGFBPs also rescued the ischemia phenotype. These results help us to understand the mechanism of ECFC-based therapies for ischemic insults and retinal neurodegenerative diseases. PMID:28138561

  5. Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

    Energy Technology Data Exchange (ETDEWEB)

    Akerboom, Jasper; Velez Rivera, Jonathan D.; Rodriguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Hernandez, Hector H.; Tian, Lin; Hires, S. Andrew; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.; (MIT); (Puerto Rico); (HHMI)


    The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca{sup 2+}-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

  6. Screening action potentials: The power of light

    Directory of Open Access Journals (Sweden)

    Lars eKaestner


    Full Text Available Action potentials reflect the concerted activity of all electrogenic constituents in the plasma membrane during the excitation of a cell. Therefore, the action potential is an integrated readout and a promising parameter to detect electrophysiological failures or modifications thereof in diagnosis as well as in drug screens. Cellular action potentials can be recorded by optical approaches. To fulfill the pre-requirements to scale up for e.g. pharmacological screens the following preparatory work has to be provided: (i model cells under investigation need to represent target cells in the best possible manner; (ii optical sensors that can be either small molecule dyes or genetically encoded potential probes need to provide a reliable readout with minimal interaction with the naive behavior of the cells and (iii devices need to be capable to stimulate the cells, read out the signals with the appropriate speed as well as provide the capacity for a sufficient throughput. Here we discuss several scenarios for all three categories in the field of cardiac physiology and pharmacology and provide a perspective to use the power of light in screening cardiac action potentials.

  7. The use of quantum molecular calculations to guide a genetic algorithm: a way to search for new chemistry. (United States)

    Durrant, Marcus C


    The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction.

  8. Biosynthetic origin of natural products isolated from marine microorganism-invertebrate assemblages. (United States)

    Simmons, T Luke; Coates, R Cameron; Clark, Benjamin R; Engene, Niclas; Gonzalez, David; Esquenazi, Eduardo; Dorrestein, Pieter C; Gerwick, William H


    In all probability, natural selection began as ancient marine microorganisms were required to compete for limited resources. These pressures resulted in the evolution of diverse genetically encoded small molecules with a variety of ecological and metabolic roles. Remarkably, many of these same biologically active molecules have potential utility in modern medicine and biomedical research. The most promising of these natural products often derive from organisms richly populated by associated microorganisms (e.g., marine sponges and ascidians), and often there is great uncertainty about which organism in these assemblages is making these intriguing metabolites. To use the molecular machinery responsible for the biosynthesis of potential drug-lead natural products, new tools must be applied to delineate their genetic and enzymatic origins. The aim of this perspective is to highlight both traditional and emerging techniques for the localization of metabolic pathways within complex marine environments. Examples are given from the literature as well as recent proof-of-concept experiments from the authors' laboratories.

  9. Helical crystallization on nickel-lipid nanotubes: perfringolysin O as a model protein. (United States)

    Dang, Thanh X; Milligan, Ronald A; Tweten, Rodney K; Wilson-Kubalek, Elizabeth M


    To facilitate purification and subsequent structural studies of recombinant proteins the most widely used genetically encoded tag is the histidine tag (His-tag) which specifically binds to N-nitrilotriacetic-acid-chelated nickel ions. Lipids derivatized with a nickel-chelating head group can be mixed with galactosylceramide glycolipids to prepare lipid nanotubes that bind His-tagged proteins. In this study, we use His-tagged perfringolysin O (PFO), a soluble toxin secreted by the bacterial pathogen Clostridium perfringens, as a model protein to test the utility of nickel-lipid nanotubes as a tool for structural studies of His-tagged proteins. PFO is a member of the cholesterol dependent cytolysin family (CDC) of oligomerizing, pore-forming toxins found in a variety of Gram-positive bacterial pathogens. CDC pores have been difficult to study by X-ray crystallography because they are membrane associated and vary in size. We demonstrate that both a wild-type and a mutant form of PFO form helical arrays on nickel-lipid containing nanotubes. Cryo-electron microscopy and image analysis of the helical arrays were used to reconstruct a 3D density map of wild-type PFO. This study suggests that the use of nickel-lipid nanotubes may offer a general approach for structural studies of recombinant proteins and may provide insights into the molecular interactions of proteins that have a natural affinity for a membrane surface.

  10. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. (United States)

    Mills, Jeremy H; Khare, Sagar D; Bolduc, Jill M; Forouhar, Farhad; Mulligan, Vikram Khipple; Lew, Scott; Seetharaman, Jayaraman; Tong, Liang; Stoddard, Barry L; Baker, David


    Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2'-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ∼40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.

  11. A new way to rapidly create functional, fluorescent fusion proteins: random insertion of GFP with an in vitro transposition reaction

    Directory of Open Access Journals (Sweden)

    Jakobsdottir Klara B


    Full Text Available Abstract Background The jellyfish green fluorescent protein (GFP can be inserted into the middle of another protein to produce a functional, fluorescent fusion protein. Finding permissive sites for insertion, however, can be difficult. Here we describe a transposon-based approach for rapidly creating libraries of GFP fusion proteins. Results We tested our approach on the glutamate receptor subunit, GluR1, and the G protein subunit, αs. All of the in-frame GFP insertions produced a fluorescent protein, consistent with the idea that GFP will fold and form a fluorophore when inserted into virtually any domain of another protein. Some of the proteins retained their signaling function, and the random nature of the transposition process revealed permissive sites for insertion that would not have been predicted on the basis of structural or functional models of how that protein works. Conclusion This technique should greatly speed the discovery of functional fusion proteins, genetically encodable sensors, and optimized fluorescence resonance energy transfer pairs.

  12. Conflict between Intrinsic Leaf Asymmetry and Phyllotaxis in the Resupinate Leaves of Alstroemeria psittacina. (United States)

    Chitwood, Daniel H; Naylor, Daniel T; Thammapichai, Paradee; Weeger, Axelle C S; Headland, Lauren R; Sinha, Neelima R


    Spiral phyllotactic patterning is the result of intricate auxin transport relationships in the shoot apical meristem (SAM) that act to place auxin maxima at the future sites of leaf initiation. Inherent to this process is a bias in auxin distribution in leaf primordia, such that increased auxin is found on the descending side of the leaf (toward the older neighbor) compared to the ascending side (toward the younger neighbor), creating phyllotactically dependent leaf asymmetry. Separate from phyllotactic-dependent asymmetry is handedness in plants - that is, genetically encoded, fixed chirality, such as the twining of certain vines and the torsions induced by microtubule mutations. Here, we perform a morphometric analysis on the resupinate leaves of Alstroemeria psittacina. Interestingly, the twist in leaves always occurs in a single direction, regardless of the phyllotactic direction of the plant. Because of the resupination, leaves in this species possess an inherent handedness. However, this asymmetry is modulated in a phyllotactic-dependent manner, consistent with the known developmental constraints of phyllotaxis upon leaf morphology. This creates the interesting circumstance in A. psittacina that leaves arising from plants with a counter-clockwise phyllotactic direction are (1) more asymmetric, (2) larger, and (3) possess symmetrical shape differences relative to leaves from plants with clockwise phyllotaxis. The mechanism underlying these differences likely involves a developmental delay in clockwise leaves caused by the conflict between the phyllotaxis-dependent asymmetry and asymmetry resulting from resupination. The evolutionary implications of a dimorphic population without a genetic basis for selection to act upon are discussed.

  13. The Suzuki–Miyaura Cross-Coupling as a Versatile Tool for Peptide Diversification and Cyclization

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    Tom Willemse


    Full Text Available The (site-selective derivatization of amino acids and peptides represents an attractive field with potential applications in the establishment of structure–activity relationships and labeling of bioactive compounds. In this respect, bioorthogonal cross-coupling reactions provide valuable means for ready access to peptide analogues with diversified structure and function. Due to the complex and chiral nature of peptides, mild reaction conditions are preferred; hence, a suitable cross-coupling reaction is required for the chemical modification of these challenging substrates. The Suzuki reaction, involving organoboron species, is appropriate given the stability and environmentally benign nature of these reactants and their amenability to be applied in (partial aqueous reaction conditions, an expected requirement upon the derivatization of peptides. Concerning the halogenated reaction partner, residues bearing halogen moieties can either be introduced directly as halogenated amino acids during solid-phase peptide synthesis (SPPS or genetically encoded into larger proteins. A reversed approach building in boron in the peptidic backbone is also possible. Furthermore, based on this complementarity, cyclic peptides can be prepared by halogenation, and borylation of two amino acid side chains present within the same peptidic substrate. Here, the Suzuki–Miyaura reaction is a tool to induce the desired cyclization. In this review, we discuss diverse amino acid and peptide-based applications explored by means of this extremely versatile cross-coupling reaction. With the advent of peptide-based drugs, versatile bioorthogonal conversions on these substrates have become highly valuable.

  14. Noradrenalin and dopamine receptors both control cAMP-PKA signaling throughout the cerebral cortex

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    Shinobu eNomura


    Full Text Available Noradrenergic fibers innervate the entire cerebral cortex, whereas the cortical distribution ofdopaminergic fibers is more restricted. However, the relative functional impact ofnoradrenalin and dopamine receptors in various cortical regions is largely unknown. Using aspecific genetic label, we first confirmed that noradrenergic fibers innervate the entire cortexwhereas dopaminergic fibers were present in all layers of restricted medial and lateral areasbut only in deep layers of other areas. Imaging of a genetically-encoded sensor revealed thatnoradrenalin and dopamine widely activate PKA in cortical pyramidal neurons of frontal,parietal and occipital regions with scarce dopaminergic fibers. Responses to noradrenalin hadhigher amplitude, velocity and occurred at more than 10 fold lower dose than those elicited bydopamine, whose amplitude and velocity increased along the antero-posterior axis. Thepharmacology of these responses was consistent with the involvement of Gs-coupled beta1adrenergic and D1/D5 dopaminergic receptors, but the inhibition of both noradrenalin anddopamine responses by beta adrenergic antagonists was suggestive of the existence of beta1-D1/D5 heteromeric receptors. Responses also involved Gi-coupled alpha2 adrenergic and D2-like dopaminergic receptors that markedly reduced their amplitude and velocity andcontributed to their cell-to-cell heterogeneity. Our results reveal that noradrenalin anddopamine receptors both control cAMP-PKA signaling throughout the cerebral cortex withmoderate regional and laminar differences. These receptors can thus mediate widespreadeffects of both catecholamines, which are reportedly co-released by cortical noradrenergicfibers beyond the territory of dopaminergic fibers.

  15. Simultaneous high-speed imaging and optogenetic inhibition in the intact mouse brain (United States)

    Bovetti, Serena; Moretti, Claudio; Zucca, Stefano; Dal Maschio, Marco; Bonifazi, Paolo; Fellin, Tommaso


    Genetically encoded calcium indicators and optogenetic actuators can report and manipulate the activity of specific neuronal populations. However, applying imaging and optogenetics simultaneously has been difficult to establish in the mammalian brain, even though combining the techniques would provide a powerful approach to reveal the functional organization of neural circuits. Here, we developed a technique based on patterned two-photon illumination to allow fast scanless imaging of GCaMP6 signals in the intact mouse brain at the same time as single-photon optogenetic inhibition with Archaerhodopsin. Using combined imaging and electrophysiological recording, we demonstrate that single and short bursts of action potentials in pyramidal neurons can be detected in the scanless modality at acquisition frequencies up to 1 kHz. Moreover, we demonstrate that our system strongly reduces the artifacts in the fluorescence detection that are induced by single-photon optogenetic illumination. Finally, we validated our technique investigating the role of parvalbumin-positive (PV) interneurons in the control of spontaneous cortical dynamics. Monitoring the activity of cellular populations on a precise spatiotemporal scale while manipulating neuronal activity with optogenetics provides a powerful tool to causally elucidate the cellular mechanisms underlying circuit function in the intact mammalian brain.

  16. Photobleaching and phototoxicity of KillerRed in tumor spheroids induced by continuous wave and pulsed laser illumination. (United States)

    Kuznetsova, Daria S; Shirmanova, Marina V; Dudenkova, Varvara V; Subochev, Pavel V; Turchin, Ilya V; Zagaynova, Elena V; Lukyanov, Sergey A; Shakhov, Boris E; Kamensky, Vladislav A


    The purpose of this study was to evaluate photobleaching of the genetically encoded photosensitizer KillerRed in tumor spheroids upon pulsed and continuous wave (CW) laser irradiation and to analyze the mechanisms of cancer cell death after the treatment. We observed the light-dose dependent mechanism of KillerRed photobleaching over a wide range of fluence rates. Loss of fluorescence was limited to 80% at light doses of 150 J/cm(2) and more. Based on the bleaching curves, six PDT regimes were applied for irradiation using CW and pulsed regimes at a power density of 160 mW/cm(2) and light doses of 140 J/cm(2) , 170 J/cm(2) and 200 J/cm(2). Irradiation of KillerRed-expressing spheroids in the pulsed mode (pulse duration 15 ns, pulse repetition rate 10 Hz) induced predominantly apoptotic cell death, while in the case of CW mode the cancer cells underwent necrosis. In general, these results improve our understanding of photobleaching mechanisms in GFP-like proteins and show the importance of appropriate selection of treatment mode for PDT with KillerRed. Representative fluorescence image of two KillerRed-expressing spheroids before and immediately after CW irradiation.

  17. Lipid droplets, lipophagy, and beyond. (United States)

    Wang, Chao-Wen


    Lipids are essential components for life. Their various structural and physical properties influence diverse cellular processes and, thereby, human health. Lipids are not genetically encoded but are synthesized and modified by complex metabolic pathways, supplying energy, membranes, signaling molecules, and hormones to affect growth, physiology, and response to environmental insults. Lipid homeostasis is crucial, such that excess fatty acids (FAs) can be harmful to cells. To prevent such lipotoxicity, cells convert excess FAs into neutral lipids for storage in organelles called lipid droplets (LDs). These organelles do not simply manage lipid storage and metabolism but also are involved in protein quality management, pathogenesis, immune responses, and, potentially, neurodegeneration. In recent years, a major trend in LD biology has centered around the physiology of lipid mobilization via lipophagy of fat stored within LDs. This review summarizes key findings in LD biology and lipophagy, offering novel insights into this rapidly growing field. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.

  18. A quantitative real-time approach for discriminating apoptosis and necrosis (United States)

    Lekshmi, Asha; Varadarajan, Shankara Narayanan; Lupitha, Santhik Subhasingh; Indira, Deepa; Mathew, Krupa Ann; Chandrasekharan Nair, Aneesh; Nair, Mydhily; Prasad, Tilak; Sekar, Hari; Gopalakrishnan, Anurup Kochucherukkan; Murali, Abitha; Santhoshkumar, Thankayyan Retnabai


    Apoptosis and necrosis are the two major forms of cell death mechanisms. Both forms of cell death are involved in several physiological and pathological conditions and also in the elimination of cancer cells following successful chemotherapy. Large number of cellular and biochemical assays have evolved to determine apoptosis or necrosis for qualitative and quantitative purposes. A closer analysis of the assays and their performance reveal the difficulty in using any of these methods as a confirmatory approach, owing to the secondary induction of necrosis in apoptotic cells. This highlights the essential requirement of an approach with a real-time analysis capability for discriminating the two forms of cell death. This paper describes a sensitive live cell-based method for distinguishing apoptosis and necrosis at single-cell level. The method uses cancer cells stably expressing genetically encoded FRET-based active caspase detection probe and DsRed fluorescent protein targeted to mitochondria. Caspase activation is visualized by loss of FRET upon cleavage of the FRET probe, while retention of mitochondrial fluorescence and loss of FRET probe before its cleavage confirms necrosis. The absence of cleavage as well as the retention of mitochondrial fluorescence indicates live cells. The method described here forms an extremely sensitive tool to visualize and quantify apoptosis and necrosis, which is adaptable for diverse microscopic, flow cytometric techniques and high-throughput imaging platforms with potential application in diverse areas of cell biology and oncology drug screening. PMID:28179996

  19. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET (United States)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda


    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.

  20. A green fluorescent protein with photoswitchable emission from the deep sea.

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    Alexander Vogt

    Full Text Available A colorful variety of fluorescent proteins (FPs from marine invertebrates are utilized as genetically encoded markers for live cell imaging. The increased demand for advanced imaging techniques drives a continuous search for FPs with new and improved properties. Many useful FPs have been isolated from species adapted to sun-flooded habitats such as tropical coral reefs. It has yet remained unknown if species expressing green fluorescent protein (GFP-like proteins also exist in the darkness of the deep sea. Using a submarine-based and -operated fluorescence detection system in the Gulf of Mexico, we discovered ceriantharians emitting bright green fluorescence in depths between 500 and 600 m and identified a GFP, named cerFP505, with bright fluorescence emission peaking at 505 nm. Spectroscopic studies showed that approximately 15% of the protein bulk feature reversible ON/OFF photoswitching that can be induced by alternating irradiation with blue und near-UV light. Despite being derived from an animal adapted to essentially complete darkness and low temperatures, cerFP505 maturation in living mammalian cells at 37 degrees C, its brightness and photostability are comparable to those of EGFP and cmFP512 from shallow water species. Therefore, our findings disclose the deep sea as a potential source of GFP-like molecular marker proteins.

  1. Cre-lox neurogenetics: 20 years of versatile applications in brain research and counting...

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    Joe Z Tsien


    Full Text Available Defining and manipulating specific neurons in the brain have garnered enormous interest in recent years, because such an approach is now recognized as crucial for deepening our understanding of how the brain works. When I started out to explore the Cre-loxP recombination for brain research in early 1990s, it was written off as a dead-end project by a young fool. Yet over the past 20 years, Cre-lox recombination-mediated neurogenetics has emerged as one of the most powerful and versatile technology platforms for cell-specific gene knockouts, transgenic overexpression, Brainbow imaging, neural pathway tracing with retrovirus and CLARITY, chemical genetics, and optogenetics. Its popularity and greater utility in neuroscience research is also largely thanks to the NIH’s bold Blueprint for Neuroscience Research Initiative to launch several Cre-driver resource projects, as well as individual laboratories and private research organizations. With newly-discovered, genetically-encoded molecules that are capable of responding to sonar and magnetic stimulation, for sonogenetics or magnetogenetics, respectively, or detecting rapid voltage changes in neurons, Cre-lox neurogenetics will continue to aid brain research for years to come.

  2. Optogenetic inhibition of synaptic release with chromophore-assisted light inactivation (CALI). (United States)

    Lin, John Y; Sann, Sharon B; Zhou, Keming; Nabavi, Sadegh; Proulx, Christophe D; Malinow, Roberto; Jin, Yishi; Tsien, Roger Y


    Optogenetic techniques provide effective ways of manipulating the functions of selected neurons with light. In the current study, we engineered an optogenetic technique that directly inhibits neurotransmitter release. We used a genetically encoded singlet oxygen generator, miniSOG, to conduct chromophore assisted light inactivation (CALI) of synaptic proteins. Fusions of miniSOG to VAMP2 and synaptophysin enabled disruption of presynaptic vesicular release upon illumination with blue light. In cultured neurons and hippocampal organotypic slices, synaptic release was reduced up to 100%. Such inhibition lasted >1 hr and had minimal effects on membrane electrical properties. When miniSOG-VAMP2 was expressed panneuronally in Caenorhabditis elegans, movement of the worms was reduced after illumination, and paralysis was often observed. The movement of the worms recovered overnight. We name this technique Inhibition of Synapses with CALI (InSynC). InSynC is a powerful way to silence genetically specified synapses with light in a spatially and temporally precise manner.

  3. Using Plasmids as DNA Vaccines for Infectious Diseases. (United States)

    Tregoning, John S; Kinnear, Ekaterina


    DNA plasmids can be used to induce a protective (or therapeutic) immune response by delivering genes encoding vaccine antigens. That naked DNA (without the refinement of coat proteins or host evasion systems) can cross from outside the cell into the nucleus and be expressed is particularly remarkable given the sophistication of the immune system in preventing infection by pathogens. As a result of the ease, low cost, and speed of custom gene synthesis, DNA vaccines dangle a tantalizing prospect of the next wave of vaccine technology, promising individual designer vaccines for cancer or mass vaccines with a rapid response time to emerging pandemics. There is considerable enthusiasm for the use of DNA vaccination as an approach, but this enthusiasm should be tempered by the successive failures in clinical trials to induce a potent immune response. The technology is evolving with the development of improved delivery systems that increase expression levels, particularly electroporation and the incorporation of genetically encoded adjuvants. This review will introduce some key concepts in the use of DNA plasmids as vaccines, including how the DNA enters the cell and is expressed, how it induces an immune response, and a summary of clinical trials with DNA vaccines. The review also explores the advances being made in vector design, delivery, formulation, and adjuvants to try to realize the promise of this technology for new vaccines. If the immunogenicity and expression barriers can be cracked, then DNA vaccines may offer a step change in mass vaccination.


    Kim, Y. S.; Kim, T. H.; Mckemy, D. D.; Bae, Y. C.


    Transient receptor potential melastatin 8 (TRPM8) is activated by innocuous cool and noxious cold and plays a crucial role in cold-induced acute pain and pain hypersensitivity. To help understand the mechanism of TRPM8-mediated cold perception under normal and pathologic conditions, we used light microscopic immunohistochemistry and Western blot analysis in mice expressing a genetically encoded axonal tracer in TRPM8-positive (+) neurons. We investigated the coexpression of TRPM8 and vesicular glutamate transporter 1 (VGLUT1) and VGLUT2 in the trigeminal ganglion (TG) and the dental pulp before and after inducing pulpal inflammation. Many TRPM8+ neurons in the TG and axons in the dental pulp expressed VGLUT2, while none expressed VGLUT1. TRPM8+ axons were dense in the pulp horn and peripheral pulp and also frequently observed in the dentinal tubules. Following pulpal inflammation, the proportion of VGLUT2+ and of VGLUT2+/TRPM8+ neurons increased significantly, whereas that of TRPM8+ neurons remained unchanged. Our findings suggest the existence of VGLUT2 (but not VGLUT1)-mediated glutamate signaling in TRPM8+ neurons possibly underlying the cold-induced acute pain and hypersensitivity to cold following pulpal inflammation. PMID:26166724

  5. Engineering a dirhodium artificial metalloenzyme for selective olefin cyclopropanation. (United States)

    Srivastava, Poonam; Yang, Hao; Ellis-Guardiola, Ken; Lewis, Jared C


    Artificial metalloenzymes (ArMs) formed by incorporating synthetic metal catalysts into protein scaffolds have the potential to impart to chemical reactions selectivity that would be difficult to achieve using metal catalysts alone. In this work, we covalently link an alkyne-substituted dirhodium catalyst to a prolyl oligopeptidase containing a genetically encoded L-4-azidophenylalanine residue to create an ArM that catalyses olefin cyclopropanation. Scaffold mutagenesis is then used to improve the enantioselectivity of this reaction, and cyclopropanation of a range of styrenes and donor-acceptor carbene precursors were accepted. The ArM reduces the formation of byproducts, including those resulting from the reaction of dirhodium-carbene intermediates with water. This shows that an ArM can improve the substrate specificity of a catalyst and, for the first time, the water tolerance of a metal-catalysed reaction. Given the diversity of reactions catalysed by dirhodium complexes, we anticipate that dirhodium ArMs will provide many unique opportunities for selective catalysis.

  6. Single fluorescent protein-based Ca2+ sensors with increased dynamic range

    Directory of Open Access Journals (Sweden)

    Labas Yulii A


    Full Text Available Abstract Background Genetically encoded sensors developed on the basis of green fluorescent protein (GFP-like proteins are becoming more and more popular instruments for monitoring cellular analytes and enzyme activities in living cells and transgenic organisms. In particular, a number of Ca2+ sensors have been developed, either based on FRET (Fluorescence Resonance Energy Transfer changes between two GFP-mutants or on the change in fluorescence intensity of a single circularly permuted fluorescent protein (cpFP. Results Here we report significant progress on the development of the latter type of Ca2+ sensors. Derived from the knowledge of previously reported cpFP-based sensors, we generated a set of cpFP-based indicators with different spectral properties and fluorescent responses to changes in Ca2+ concentration. Two variants, named Case12 and Case16, were characterized by particular high brightness and superior dynamic range, up to 12-fold and 16.5-fold increase in green fluorescence between Ca2+-free and Ca2+-saturated forms. We demonstrated the high potential of these sensors on various examples, including monitoring of Ca2+ response to a prolonged glutamate treatment in cortical neurons. Conclusion We believe that expanded dynamic range, high brightness and relatively high pH-stability should make Case12 and Case16 popular research tools both in scientific studies and high throughput screening assays.

  7. H-independent glutamine transport in plant root tips.

    Directory of Open Access Journals (Sweden)

    Huaiyu Yang

    Full Text Available BACKGROUND: Glutamine is one of the primary amino acids in nitrogen assimilation and often the most abundant amino acid in plant roots. To monitor this important metabolite, a novel genetically encoded fluorescent FRET-reporter was constructed and expressed in Arabidopsis thaliana. As a candidate for the glutamine fluxes, the root tip localized, putative amino acid transporter CAT8 was analyzed and heterologously expressed in yeast and oocytes. PRINCIPAL FINDINGS: Rapid and reversible in vivo fluorescence changes were observed in reporter-expressing root tips upon exposure and removal of glutamine. FRET changes were detected at acid and neutral pH and in the presence of a protonophore, suggesting that part of the glutamine fluxes were independent of the pH. The putative amino acid transporter CAT8 transported glutamine, had a half maximal activity at approximately 100 microM and the transport was independent of external pH. CAT8 localized not only to the plasma membrane, but additionally to the tonoplast, when tagged with GFP. Ultrastructural analysis confirmed this dual localization and additionally identified CAT8 in membranes of autophagosomes. Loss-of function of CAT8 did not affect growth in various conditions, but over-expressor plants had increased sensitivity to a structural substrate analog, the glutamine synthetase inhibitor L-methionine sulfoximine. CONCLUSIONS: The combined data suggest that proton-independent glutamine facilitators exist in root tips.

  8. The 1.6 Å resolution structure of a FRET-optimized Cerulean fluorescent protein (United States)

    Watkins, Jennifer L.; Kim, Hanseong; Markwardt, Michele L.; Chen, Liqing; Fromme, Raimund; Rizzo, Mark A.; Wachter, Rebekka M.


    Genetically encoded cyan fluorescent proteins (CFPs) bearing a tryptophan-derived chromophore are commonly used as energy-donor probes in Förster resonance energy transfer (FRET) experiments useful in live cell-imaging applications. In recent years, significant effort has been expended on eliminating the structural and excited-state heterogeneity of these proteins, which has been linked to undesirable photophysical properties. Recently, mCerulean3, a descendant of enhanced CFP, was introduced as an optimized FRET donor protein with a superior quantum yield of 0.87. Here, the 1.6 Å resolution X-ray structure of mCerulean3 is reported. The chromophore is shown to adopt a planar trans configuration at low pH values, indicating that the acid-induced isomerization of Cerulean has been eliminated. β-Strand 7 appears to be well ordered in a single conformation, indicating a loss of conformational heterogeneity in the vicinity of the chromophore. Although the side chains of Ile146 and Leu167 appear to exist in two rotamer states, they are found to be well packed against the indole group of the chromophore. The Ser65 reversion mutation allows improved side-chain packing of Leu220. A structural comparison with mTurquoise2 is presented and additional engineering strategies are discussed. PMID:23633585

  9. The 1.6 Å resolution structure of a FRET-optimized Cerulean fluorescent protein

    Energy Technology Data Exchange (ETDEWEB)

    Watkins, Jennifer L.; Kim, Hanseong [Arizona State University, Tempe, AZ 85287-1604 (United States); Markwardt, Michele L. [University of Maryland School of Medicine, Baltimore, MD 21201-1559 (United States); Chen, Liqing; Fromme, Raimund [Arizona State University, Tempe, AZ 85287-1604 (United States); Rizzo, Mark A. [University of Maryland School of Medicine, Baltimore, MD 21201-1559 (United States); Wachter, Rebekka M., E-mail: [Arizona State University, Tempe, AZ 85287-1604 (United States)


    The high resolution X-ray structure of the cyan fluorescent protein mCerulean3 demonstrates that different combinations of correlated residue substitutions can provide near optimum quantum yield values for fluorescence. Genetically encoded cyan fluorescent proteins (CFPs) bearing a tryptophan-derived chromophore are commonly used as energy-donor probes in Förster resonance energy transfer (FRET) experiments useful in live cell-imaging applications. In recent years, significant effort has been expended on eliminating the structural and excited-state heterogeneity of these proteins, which has been linked to undesirable photophysical properties. Recently, mCerulean3, a descendant of enhanced CFP, was introduced as an optimized FRET donor protein with a superior quantum yield of 0.87. Here, the 1.6 Å resolution X-ray structure of mCerulean3 is reported. The chromophore is shown to adopt a planar trans configuration at low pH values, indicating that the acid-induced isomerization of Cerulean has been eliminated. β-Strand 7 appears to be well ordered in a single conformation, indicating a loss of conformational heterogeneity in the vicinity of the chromophore. Although the side chains of Ile146 and Leu167 appear to exist in two rotamer states, they are found to be well packed against the indole group of the chromophore. The Ser65 reversion mutation allows improved side-chain packing of Leu220. A structural comparison with mTurquoise2 is presented and additional engineering strategies are discussed.

  10. Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance. (United States)

    Lórenz-Fonfría, Víctor A; Bamann, Christian; Resler, Tom; Schlesinger, Ramona; Bamberg, Ernst; Heberle, Joachim


    The discovery of channelrhodopsins introduced a new class of light-gated ion channels, which when genetically encoded in host cells resulted in the development of optogenetics. Channelrhodopsin-2 from Chlamydomonas reinhardtii, CrChR2, is the most widely used optogenetic tool in neuroscience. To explore the connection between the gating mechanism and the influx and efflux of water molecules in CrChR2, we have integrated light-induced time-resolved infrared spectroscopy and electrophysiology. Cross-correlation analysis revealed that ion conductance tallies with peptide backbone amide I vibrational changes at 1,665(-) and 1,648(+) cm(-1). These two bands report on the hydration of transmembrane α-helices as concluded from vibrational coupling experiments. Lifetime distribution analysis shows that water influx proceeded in two temporally separated steps with time constants of 10 μs (30%) and 200 μs (70%), the latter phase concurrent with the start of ion conductance. Water efflux and the cessation of the ion conductance are synchronized as well, with a time constant of 10 ms. The temporal correlation between ion conductance and hydration of helices holds for fast (E123T) and slow (D156E) variants of CrChR2, strengthening its functional significance.

  11. Synaptic Vesicle Recycling Is Unaffected in the Ts65Dn Mouse Model of Down Syndrome. (United States)

    Marland, Jamie R K; Smillie, Karen J; Cousin, Michael A


    Down syndrome (DS) is the most common genetic cause of intellectual disability, and arises from trisomy of human chromosome 21. Accumulating evidence from studies of both DS patient tissue and mouse models has suggested that synaptic dysfunction is a key factor in the disorder. The presence of several genes within the DS trisomy that are either directly or indirectly linked to synaptic vesicle (SV) endocytosis suggested that presynaptic dysfunction could underlie some of these synaptic defects. Therefore we determined whether SV recycling was altered in neurons from the Ts65Dn mouse, the best characterised model of DS to date. We found that SV exocytosis, the size of the SV recycling pool, clathrin-mediated endocytosis, activity-dependent bulk endocytosis and SV generation from bulk endosomes were all unaffected by the presence of the Ts65Dn trisomy. These results were obtained using battery of complementary assays employing genetically-encoded fluorescent reporters of SV cargo trafficking, and fluorescent and morphological assays of fluid-phase uptake in primary neuronal culture. The absence of presynaptic dysfunction in central nerve terminals of the Ts65Dn mouse suggests that future research should focus on the established alterations in excitatory / inhibitory balance as a potential route for future pharmacotherapy.

  12. Synaptic Vesicle Recycling Is Unaffected in the Ts65Dn Mouse Model of Down Syndrome.

    Directory of Open Access Journals (Sweden)

    Jamie R K Marland

    Full Text Available Down syndrome (DS is the most common genetic cause of intellectual disability, and arises from trisomy of human chromosome 21. Accumulating evidence from studies of both DS patient tissue and mouse models has suggested that synaptic dysfunction is a key factor in the disorder. The presence of several genes within the DS trisomy that are either directly or indirectly linked to synaptic vesicle (SV endocytosis suggested that presynaptic dysfunction could underlie some of these synaptic defects. Therefore we determined whether SV recycling was altered in neurons from the Ts65Dn mouse, the best characterised model of DS to date. We found that SV exocytosis, the size of the SV recycling pool, clathrin-mediated endocytosis, activity-dependent bulk endocytosis and SV generation from bulk endosomes were all unaffected by the presence of the Ts65Dn trisomy. These results were obtained using battery of complementary assays employing genetically-encoded fluorescent reporters of SV cargo trafficking, and fluorescent and morphological assays of fluid-phase uptake in primary neuronal culture. The absence of presynaptic dysfunction in central nerve terminals of the Ts65Dn mouse suggests that future research should focus on the established alterations in excitatory / inhibitory balance as a potential route for future pharmacotherapy.

  13. A FRET Biosensor for ROCK Based on a Consensus Substrate Sequence Identified by KISS Technology. (United States)

    Li, Chunjie; Imanishi, Ayako; Komatsu, Naoki; Terai, Kenta; Amano, Mutsuki; Kaibuchi, Kozo; Matsuda, Michiyuki


    Genetically-encoded biosensors based on Förster/fluorescence resonance energy transfer (FRET) are versatile tools for studying the spatio-temporal regulation of signaling molecules within not only the cells but also tissues. Perhaps the hardest task in the development of a FRET biosensor for protein kinases is to identify the kinase-specific substrate peptide to be used in the FRET biosensor. To solve this problem, we took advantage of kinase-interacting substrate screening (KISS) technology, which deduces a consensus substrate sequence for the protein kinase of interest. Here, we show that a consensus substrate sequence for ROCK identified by KISS yielded a FRET biosensor for ROCK, named Eevee-ROCK, with high sensitivity and specificity. By treating HeLa cells with inhibitors or siRNAs against ROCK, we show that a substantial part of the basal FRET signal of Eevee-ROCK was derived from the activities of ROCK1 and ROCK2. Eevee-ROCK readily detected ROCK activation by epidermal growth factor, lysophosphatidic acid, and serum. When cells stably-expressing Eevee-ROCK were time-lapse imaged for three days, ROCK activity was found to increase after the completion of cytokinesis, concomitant with the spreading of cells. Eevee-ROCK also revealed a gradual increase in ROCK activity during apoptosis. Thus, Eevee-ROCK, which was developed from a substrate sequence predicted by the KISS technology, will pave the way to a better understanding of the function of ROCK in a physiological context.

  14. Using Linear Agarose Channels to Study Drosophila Larval Crawling Behavior. (United States)

    Sun, Xiao; Heckscher, Ellie S


    Drosophila larval crawling is emerging as a powerful model to study neural control of sensorimotor behavior. However, larval crawling behavior on flat open surfaces is complex, including: pausing, turning, and meandering. This complexity in the repertoire of movement hinders detailed analysis of the events occurring during a single crawl stride cycle. To overcome this obstacle, linear agarose channels were made that constrain larval behavior to straight, sustained, rhythmic crawling. In principle, because agarose channels and the Drosophila larval body are both optically clear, the movement of larval structures labeled by genetically-encoded fluorescent probes can be monitored in intact, freely-moving larvae. In the past, larvae were placed in linear channels and crawling at the level of whole organism, segment, and muscle were analyzed(1). In the future, larvae crawling in channels can be used for calcium imaging to monitor neuronal activity. Moreover, these methods can be used with larvae of any genotype and with any researcher-designed channel. Thus the protocol presented below is widely applicable for studies using the Drosophila larva as a model to understand motor control.

  15. SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation. (United States)

    Takemoto, Kiwamu; Matsuda, Tomoki; Sakai, Naoki; Fu, Donald; Noda, Masanori; Uchiyama, Susumu; Kotera, Ippei; Arai, Yoshiyuki; Horiuchi, Masataka; Fukui, Kiichi; Ayabe, Tokiyoshi; Inagaki, Fuyuhiko; Suzuki, Hiroshi; Nagai, Takeharu


    Chromophore-assisted light inactivation (CALI) is a powerful technique for acute perturbation of biomolecules in a spatio-temporally defined manner in living specimen with reactive oxygen species (ROS). Whereas a chemical photosensitizer including fluorescein must be added to specimens exogenously and cannot be restricted to particular cells or sub-cellular compartments, a genetically-encoded photosensitizer, KillerRed, can be controlled in its expression by tissue specific promoters or subcellular localization tags. Despite of this superiority, KillerRed hasn't yet become a versatile tool because its dimerization tendency prevents fusion with proteins of interest. Here, we report the development of monomeric variant of KillerRed (SuperNova) by direct evolution using random mutagenesis. In contrast to KillerRed, SuperNova in fusion with target proteins shows proper localization. Furthermore, unlike KillerRed, SuperNova expression alone doesn't perturb mitotic cell division. Supernova retains the ability to generate ROS, and hence promote CALI-based functional analysis of target proteins overcoming the major drawbacks of KillerRed.

  16. The Human SepSecS-tRNA[superscript Sec] Complex Reveals the Mechanism of Selenocysteine Formation

    Energy Technology Data Exchange (ETDEWEB)

    Palioura, Sotiria; Sherrer, R. Lynn; Steitz, Thomas A.; Söll, Dieter; Simonovic, Miljan; (Yale); (UIC)


    Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNA{sup Sec} in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate-dependent mechanism of Sec-tRNA{sup Sec} formation. Two tRNA{sup Sec} molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13-base pair acceptor-T{Upsilon}C arm (where {Upsilon} indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA{sup Sec}, but not free phosphoserine, to be oriented properly for the reaction to occur.

  17. Sequence-non-specific effects generated by various types of RNA interference triggers. (United States)

    Olejniczak, Marta; Urbanek, Martyna O; Jaworska, Edyta; Witucki, Lukasz; Szczesniak, Michal W; Makalowska, Izabela; Krzyzosiak, Wlodzimierz J


    RNA interference triggers such as short interfering RNA (siRNA) or genetically encoded short hairpin RNA (shRNA) and artificial miRNA (sh-miR) are widely used to silence the expression of specific genes. In addition to silencing selected targets, RNAi reagents may induce various side effects, including immune responses. To determine the molecular markers of immune response activation when using RNAi reagents, we analyzed the results of experiments gathered in the RNAimmuno (v 2.0) and GEO Profiles databases. To better characterize and compare cellular responses to various RNAi reagents in one experimental system, we designed a reagent series in corresponding siRNA, D-siRNA, shRNA and sh-miR forms. To exclude sequence-specific effects the reagents targeted 3 different transcripts (Luc, ATXN3 and HTT). We demonstrate that RNAi reagents induce a broad variety of sequence-non-specific effects, including the deregulation of cellular miRNA levels. Typical siRNAs are weak stimulators of interferon response but may saturate the miRNA biogenesis pathway, leading to the downregulation of highly expressed miRNAs, whereas plasmid-based reagents induce known markers of immune response and may alter miRNA levels and their isomiR composition.

  18. ROZA-XL, an improved FRET based biosensor with an increased dynamic range for visualizing zeta associated protein 70 kD (ZAP-70) tyrosine kinase activity in live T cells. (United States)

    Cadra, Sophie; Gucciardi, Alexia; Valignat, Marie-Pierre; Theodoly, Olivier; Vacaflores, Aldo; Houtman, Jon C D; Lellouch, Annemarie C


    Genetically encoded FRET based biosensors allow one to visualize the spatial and temporal evolution of specific enzyme activities in live cells. We have previously reported the creation of a FRET based biosensor specific for Zeta-Associated Protein -70 kD (ZAP-70) (Randriamampita et al., 2008), a Syk family protein tyrosine kinase. ZAP-70 is essential for early T cell receptor (TCR) signaling events, T lymphocyte development and has also been implicated in integrin mediated T lymphocyte migration. In order to facilitate the study of ZAP-70 kinase activity during dynamic phenomena such as immunological synapse formation or cell migration, we have designed and prepared a second generation of ZAP-70 specific biosensors. Here we describe a novel biosensor named ROZA-XL, that displays a 3-4 times greater dynamic range than its predecessor and possesses a robust baseline FRET value when expressed in the Jurkat human T cell line. We demonstrate that the robust behavior of this biosensor allows for rapid analysis of TCR mediated of ZAP-70 kinase activity at a single cell level, as shown in a simple end point assay in which ROZA-XL expressing cells are allowed to interact with stimulatory anti-CD3epsilon coated coverslips.

  19. Guidelines for the use of protein domains in acidic phospholipid imaging (United States)

    Platre, Matthieu Pierre; Jaillais, Yvon


    Acidic phospholipids are minor membrane lipids but critically important for signaling events. The main acidic phospholipids are phosphatidylinositol phosphates (PIPs also known as phosphoinositides), phosphatidylserine (PS) and phosphatidic acid (PA). Acidic phospholipids are precursors of second messengers of key signaling cascades or are second messengers themselves. They regulate the localization and activation of many proteins, and are involved in virtually all membrane trafficking events. As such, it is crucial to understand the subcellular localization and dynamics of each of these lipids within the cell. Over the years, several techniques have emerged in either fixed or live cells to analyze the subcellular localization and dynamics of acidic phospholipids. In this chapter, we review one of them: the use of genetically encoded biosensors that are based on the expression of specific lipid binding domains (LBDs) fused to fluorescent proteins. We discuss how to design such sensors, including the criteria for selecting the lipid binding domains of interest and to validate them. We also emphasize the care that must be taken during data analysis as well as the main limitations and advantages of this approach. PMID:26552684

  20. Genetic Code Expansion as a Tool to Study Regulatory Processes of Transcription (United States)

    Schmidt, Moritz; Summerer, Daniel


    The expansion of the genetic code with noncanonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.