The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
Bo Xu - One of the best experts on this subject based on the ideXlab platform.
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profiling and annotation of human kidney Glomerulus proteome
Proteome Science, 2013Co-Authors: Yutaka Yoshida, Ying Zhang, Bo Xu, Masaaki Nameta, Hidehiko Fujinaka, Sameh Magdeldin, Tomoo Makiguchi, Toshikazu Ikoma, Eishin YaoitaAbstract:Background The comprehensive analysis of human kidney Glomerulus we previously performed using highly purified glomeruli, provided a dataset of 6,686 unique proteins representing 2,966 distinct genes. This dataset, however, contained considerable redundancy resulting from identification criteria under which all the proteins matched with the same set of peptides and its subset were reported as identified proteins. In this study we reanalyzed the raw data using the Mascot search engine and highly stringent criteria in order to select proteins with the highest scores matching peptides with scores exceeding the “Identity Threshold” and one or more unique peptides. This enabled us to exclude proteins with lower scores which only matched the same set of peptides or its subset. This approach provided a high-confidence, non-redundant dataset of identified proteins for extensive profiling, annotation, and comparison with other proteome datasets that can provide biologically relevant knowledge of Glomerulus proteome.
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Human kidney Glomerulus proteome and biomarker discovery of kidney diseases
Proteomics Clinical Applications, 2008Co-Authors: Yutaka Yoshida, Masahito Miyamoto, Izumi Taguchi, Ying Zhang, Bo Xu, Eishin Yaoita, Hidehiko Fujinaka, Tadashi YamamotoAbstract:The kidney Glomerulus is the site of plasma filtration and production of primary urine in the kidney. The structure not only plays a pivotal role in ultrafiltration of plasma into urine but also is the locus of kidney diseases progressing to chronic renal failure. Patients afflicted with these glomerular diseases frequently progress to irreversible loss of renal function and inevitably require replacement therapies. The diagnosis and treatment of glomerular diseases are now based on clinical manifestations, urinary protein excretion level, and renal pathology of needle biopsy specimens. The molecular mechanisms underlying the progression of glomerular diseases are still obscure despite a great number of clinical and experimental studies. Proteomics is a particularly promising approach for the discovery of proteins relevant to physiological and pathophysiological processes, and has been recently employed in nephrology. Although until now most efforts of proteomic analysis have been conducted with urine, the biological fluid that is easily collected without invasive procedures, proteomic analysis of the Glomerulus, the tissue most proximal to the disease loci, is the most straightforward approach. In this review, we attempt to outline the current status of clinical proteomics of the Glomerulus and provide a perspective of protein biomarker discovery of glomerular diseases.
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in depth proteomic profiling of the normal human kidney Glomerulus using two dimensional protein prefractionation in combination with liquid chromatography tandem mass spectrometry
Journal of Proteome Research, 2007Co-Authors: Masahito Miyamoto, Yutaka Yoshida, Izumi Taguchi, Yoshimi Nagasaka, Masayuki Tasaki, Ying Zhang, Bo Xu, Masaaki Nameta, Hiroshi Sezaki, Lino Munoz CuellarAbstract:The kidney Glomerulus plays a pivotal role in ultrafiltration of plasma into urine and also is the locus of kidney disease progressing to chronic renal failure. We have focused proteomic analysis on the Glomerulus that is most proximal to the disease locus. In the present study, we aimed to provide a confident, in-depth profiling of the Glomerulus proteome. The glomeruli were highly purified from the kidney cortex from a male, 68-year-old patient who underwent nephroureterectomy due to ureter carcinoma. The patient was normal in clinical examinations including serum creatinine and urea levels and liver function, and did not receive any chemotherapy and radiotherapy. The cortical tissue was histologically normal, and no significant deposition of immunoglobulins and complement C3 was observed. We employed a novel strategy of protein separation using 1D (SDS-PAGE) and 2D (solution-phase IEF in combination with SDS-PAGE) prefractionation prior to the shotgun analysis with LC−MS/MS. The protein prefractionatio...
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two dimensional electrophoretic profiling of normal human kidney Glomerulus proteome and construction of an extensible markup language xml based database
Proteomics, 2005Co-Authors: Yutaka Yoshida, Kenji Miyazaki, Junichi Kamiie, Masao Sato, Seiji Okuizumi, Akihisa Kenmochi, Kenichi Kamijo, Takuji Nabetani, Akira Tsugita, Bo XuAbstract:To contribute to physiology and pathophysiology of the Glomerulus of human kidney, we have launched a proteomic study of human Glomerulus, and compiled a profile of proteins expressed in the Glomerulus of normal human kidney by two-dimensional gel electrophoresis (2-DE) and identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking-up under a phase-contrast microscope. The glomerular proteins were separated by 2-DE with 24 cm immobilized pH gradient strips in the 3-10 range in the first dimension and 26 X 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver-stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in-gel digester, and a MALDI-TOF MS and/or a LC-MS/MS. From 2-DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2-DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)-based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/ hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human Glomerulus in health and disease.
Yutaka Yoshida - One of the best experts on this subject based on the ideXlab platform.
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profiling and annotation of human kidney Glomerulus proteome
Proteome Science, 2013Co-Authors: Yutaka Yoshida, Ying Zhang, Bo Xu, Masaaki Nameta, Hidehiko Fujinaka, Sameh Magdeldin, Tomoo Makiguchi, Toshikazu Ikoma, Eishin YaoitaAbstract:Background The comprehensive analysis of human kidney Glomerulus we previously performed using highly purified glomeruli, provided a dataset of 6,686 unique proteins representing 2,966 distinct genes. This dataset, however, contained considerable redundancy resulting from identification criteria under which all the proteins matched with the same set of peptides and its subset were reported as identified proteins. In this study we reanalyzed the raw data using the Mascot search engine and highly stringent criteria in order to select proteins with the highest scores matching peptides with scores exceeding the “Identity Threshold” and one or more unique peptides. This enabled us to exclude proteins with lower scores which only matched the same set of peptides or its subset. This approach provided a high-confidence, non-redundant dataset of identified proteins for extensive profiling, annotation, and comparison with other proteome datasets that can provide biologically relevant knowledge of Glomerulus proteome.
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Human kidney Glomerulus proteome and biomarker discovery of kidney diseases
Proteomics Clinical Applications, 2008Co-Authors: Yutaka Yoshida, Masahito Miyamoto, Izumi Taguchi, Ying Zhang, Bo Xu, Eishin Yaoita, Hidehiko Fujinaka, Tadashi YamamotoAbstract:The kidney Glomerulus is the site of plasma filtration and production of primary urine in the kidney. The structure not only plays a pivotal role in ultrafiltration of plasma into urine but also is the locus of kidney diseases progressing to chronic renal failure. Patients afflicted with these glomerular diseases frequently progress to irreversible loss of renal function and inevitably require replacement therapies. The diagnosis and treatment of glomerular diseases are now based on clinical manifestations, urinary protein excretion level, and renal pathology of needle biopsy specimens. The molecular mechanisms underlying the progression of glomerular diseases are still obscure despite a great number of clinical and experimental studies. Proteomics is a particularly promising approach for the discovery of proteins relevant to physiological and pathophysiological processes, and has been recently employed in nephrology. Although until now most efforts of proteomic analysis have been conducted with urine, the biological fluid that is easily collected without invasive procedures, proteomic analysis of the Glomerulus, the tissue most proximal to the disease loci, is the most straightforward approach. In this review, we attempt to outline the current status of clinical proteomics of the Glomerulus and provide a perspective of protein biomarker discovery of glomerular diseases.
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in depth proteomic profiling of the normal human kidney Glomerulus using two dimensional protein prefractionation in combination with liquid chromatography tandem mass spectrometry
Journal of Proteome Research, 2007Co-Authors: Masahito Miyamoto, Yutaka Yoshida, Izumi Taguchi, Yoshimi Nagasaka, Masayuki Tasaki, Ying Zhang, Bo Xu, Masaaki Nameta, Hiroshi Sezaki, Lino Munoz CuellarAbstract:The kidney Glomerulus plays a pivotal role in ultrafiltration of plasma into urine and also is the locus of kidney disease progressing to chronic renal failure. We have focused proteomic analysis on the Glomerulus that is most proximal to the disease locus. In the present study, we aimed to provide a confident, in-depth profiling of the Glomerulus proteome. The glomeruli were highly purified from the kidney cortex from a male, 68-year-old patient who underwent nephroureterectomy due to ureter carcinoma. The patient was normal in clinical examinations including serum creatinine and urea levels and liver function, and did not receive any chemotherapy and radiotherapy. The cortical tissue was histologically normal, and no significant deposition of immunoglobulins and complement C3 was observed. We employed a novel strategy of protein separation using 1D (SDS-PAGE) and 2D (solution-phase IEF in combination with SDS-PAGE) prefractionation prior to the shotgun analysis with LC−MS/MS. The protein prefractionatio...
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two dimensional electrophoretic profiling of normal human kidney Glomerulus proteome and construction of an extensible markup language xml based database
Proteomics, 2005Co-Authors: Yutaka Yoshida, Kenji Miyazaki, Junichi Kamiie, Masao Sato, Seiji Okuizumi, Akihisa Kenmochi, Kenichi Kamijo, Takuji Nabetani, Akira Tsugita, Bo XuAbstract:To contribute to physiology and pathophysiology of the Glomerulus of human kidney, we have launched a proteomic study of human Glomerulus, and compiled a profile of proteins expressed in the Glomerulus of normal human kidney by two-dimensional gel electrophoresis (2-DE) and identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking-up under a phase-contrast microscope. The glomerular proteins were separated by 2-DE with 24 cm immobilized pH gradient strips in the 3-10 range in the first dimension and 26 X 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver-stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in-gel digester, and a MALDI-TOF MS and/or a LC-MS/MS. From 2-DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2-DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)-based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/ hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human Glomerulus in health and disease.
Ryota Homma - One of the best experts on this subject based on the ideXlab platform.
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narrowly confined and Glomerulus specific onset latencies of odor evoked calcium transients in the juxtaglomerular cells of the mouse main olfactory bulb
eNeuro, 2019Co-Authors: Ryota Homma, Xiaohua Lv, Tokiharu Sato, Fumiaki Imamura, Shaoqun Zeng, Shin NagayamaAbstract:Abstract Odor information is transmitted from olfactory sensory neurons to principal neurons at the glomeruli of the olfactory bulb. The intraglomerular neuronal circuit also includes hundreds of interneurons referred to as juxtaglomerular (JG) cells. Stimulus selectivity is well correlated among many JG cells that are associated with the same Glomerulus, consistent with their highly homogeneous sensory inputs. However, much less is known about the temporal aspects of their activity, including the temporal coordination of their odor-evoked responses. As many JG cells within a glomerular module respond to the same stimulus, the extent to which their activity is temporally aligned will affect the temporal profile of their population inhibitory inputs. Using random-access high-speed two-photon microscopy, we recorded the odor-evoked calcium transients of mouse JG cells and compared the onset latency and rise time among neurons putatively associated with the same and different glomeruli. Whereas the overall onset latencies of odor-evoked transients were distributed across a ∼150 ms time window, those from cells putatively associated with the same Glomerulus were confined to a much narrower window of several tens of milliseconds. This result suggests that onset latency primarily depends on the associated Glomerulus. We also observed glomerular specificity in the rise time. The Glomerulus-specific temporal pattern of odor-evoked activity implies that the temporal patterns of inputs from the intraglomerular circuit are unique to individual Glomerulus–odor pairs, which may contribute to efficient shaping of the temporal pattern of activity in the principal neurons.
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Sparsened neuronal activity in an optogenetically activated olfactory Glomerulus
Scientific Reports, 2018Co-Authors: Oliver Braubach, Tuce Tombaz, Tristan Geiller, Ryota Homma, Thomas Bozza, Lawrence B. Cohen, Yunsook ChoiAbstract:Glomeruli are the functional units of olfactory information processing but little remains known about their individual unit function. This is due to their widespread activation by odor stimuli. We expressed channelrhodopsin-2 in a single olfactory sensory neuron type, and used laser stimulation and simultaneous in vivo calcium imaging to study the responses of a single Glomerulus to optogenetic stimulation. Calcium signals in the neuropil of this Glomerulus were representative of the sensory input and nearly identical if evoked by intensity-matched odor and laser stimuli. However, significantly fewer glomerular layer interneurons and olfactory bulb output neurons (mitral cells) responded to optogenetic versus odor stimuli, resulting in a small and spatially compact optogenetic glomerular unit response. Temporal features of laser stimuli were represented with high fidelity in the neuropil of the Glomerulus and the mitral cells, but not in interneurons. Increases in laser stimulus intensity were encoded by larger signal amplitudes in all compartments of the Glomerulus, and by the recruitment of additional interneurons and mitral cells. No spatial expansion of the glomerular unit response was observed in response to stronger input stimuli. Our data are among the first descriptions of input-output transformations in a selectively activated olfactory Glomerulus.
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narrowly confined and Glomerulus specific onset latencies of odor evoked calcium transients in the periglomerular cells of the mouse main olfactory bulb
bioRxiv, 2018Co-Authors: Ryota Homma, Xiaohua Lv, Tokiharu Sato, Fumiaki Imamura, Shaoqun Zeng, Shin NagayamaAbstract:Odor information is transmitted from olfactory sensory neurons to principal neurons at the glomeruli of the olfactory bulb. The intraglomerular neuronal circuit also includes hundreds of GABAergic interneurons referred to as periglomerular (PG) cells. Stimulus selectivity is well correlated among PG cells that are associated with the same Glomerulus, consistent with their highly homogeneous sensory inputs. However, much less is known about the temporal aspects of their activity, including the temporal coordination of their odor-evoked responses. As many PG cells within a glomerular module respond to the same stimulus, the extent to which their activity is temporally aligned will affect the temporal profile of their population inhibitory inputs. Using random-access high-speed two-photon microscopy, we recorded the odor-evoked calcium transients of mouse PG cells and compared the onset latency and rise time among neurons putatively associated with the same and different glomeruli. Whereas the overall onset latencies of odor-evoked transients were distributed across a ~150 ms time window, those from cells putatively associated with the same Glomerulus were confined to a much narrower window of several tens of milliseconds. This result suggests that onset latency primarily depends on the associated Glomerulus. We also observed glomerular specificity in the rise time. The Glomerulus-specific temporal pattern of odor-evoked activity implies that the temporal patterns of inhibitory inputs are unique to individual Glomerulus-odor pairs, which may contribute to efficient shaping of the temporal pattern of activity in the principal neurons.
E. È Saftenku - One of the best experts on this subject based on the ideXlab platform.
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Modeling of slow glutamate diffusion and AMPA receptor activation in the cerebellar Glomerulus.
Journal of Theoretical Biology, 2005Co-Authors: E. È SaftenkuAbstract:Abstract Synaptic conductances are influenced markedly by the geometry of the space surrounding the synapse since the transient glutamate concentration in the synaptic cleft is determined by this geometry. Our paper is an attempt to understand the reasons for slow glutamate diffusion in the cerebellar Glomerulus, a structure situated around the enlarged mossy fiber terminal in the cerebellum and surrounded by a glial sheath. For this purpose, analytical expressions for glutamate diffusion in the Glomerulus were considered in models with two-, three-, and fractional two-three-dimensional (2D–3D) geometry with an absorbing boundary. The time course of average glutamate concentration in the synaptic cleft of the mossy fiber–granule cell connection was calculated for both direct release of glutamate from the same synaptic unit, and for cumulative spillover of glutamate from neighboring release sites. Several kinetic schemes were examined, and the parameters of the diffusion models were estimated by identifying theoretical activation of AMPA receptors with direct release and spillover components of published experimental AMPA receptor-mediated EPSCs. For model selection, the correspondence of simulated paired-pulse ratio and EPSC increase after prevention of desensitization to experimental values were also taken into consideration. Our results suggest at least a 7- to 10-fold lower apparent diffusion coefficient of glutamate in the porous medium of the Glomerulus than in water. The modeling of glutamate diffusion in the 2D–3D geometry gives the best fit of experimental EPSCs. We show that it could be only partly explained by normal diffusion of glutamate in the complex geometry of the Glomerulus. We assume that anomalous diffusion of glutamate occurs in the Glomerulus. A good match of experimental estimations and theoretical parameters, obtained in the simulations that use an approximation of anomalous diffusion by a solution for fractional Brownian motion, confirms our assumption.
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Modeling of slow glutamate diffusion and AMPA receptor activation in the cerebellar Glomerulus
Journal of Theoretical Biology, 2005Co-Authors: E. È SaftenkuAbstract:Synaptic conductances are influenced markedly by the geometry of the space surrounding the synapse since the transient glutamate concentration in the synaptic cleft is determined by this geometry. Our paper is an attempt to understand the reasons for slow glutamate diffusion in the cerebellar Glomerulus, a structure situated around the enlarged mossy fiber terminal in the cerebellum and surrounded by a glial sheath. For this purpose, analytical expressions for glutamate diffusion in the Glomerulus were considered in models with two-, three-, and fractional two-three-dimensional (2D-3D) geometry with an absorbing boundary. The time course of average glutamate concentration in the synaptic cleft of the mossy fiber-granule cell connection was calculated for both direct release of glutamate from the same synaptic unit, and for cumulative spillover of glutamate from neighboring release sites. Several kinetic schemes were examined, and the parameters of the diffusion models were estimated by identifying theoretical activation of AMPA receptors with direct release and spillover components of published experimental AMPA receptor-mediated EPSCs. For model selection, the correspondence of simulated paired-pulse ratio and EPSC increase after prevention of desensitization to experimental values were also taken into consideration. Our results suggest at least a 7- to 10-fold lower apparent diffusion coefficient of glutamate in the porous medium of the Glomerulus than in water. The modeling of glutamate diffusion in the 2D-3D geometry gives the best fit of experimental EPSCs. We show that it could be only partly explained by normal diffusion of glutamate in the complex geometry of the Glomerulus. We assume that anomalous diffusion of glutamate occurs in the Glomerulus. A good match of experimental estimations and theoretical parameters, obtained in the simulations that use an approximation of anomalous diffusion by a solution for fractional Brownian motion, confirms our assumption. © 2005 Elsevier Ltd. All rights reserved.
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Determinants of slowed diffusion in the complex space of the cerebellar Glomerulus
Neurophysiology, 2004Co-Authors: E. È SaftenkuAbstract:Using analytical solutions for two- and three-dimensional (2D and 3D, respectively) and fractal 2D/3D geometry with an absorbing boundary, we modeled glutamate diffusion in a Glomerulus, the structure situated around the mossy fiber (MF) terminal in the cerebellum and surrounded by a glial sheath. The model with fractal geometry gave the best fit of experimental AMPA and NMDA receptor-mediated evoked postsynaptic currents (EPSC) at the MF-granule cell synapse. A comparison of the numerically integrated glutamate concentration in an idealized model of Glomerulus morphology with analytical solutions reveals that the peculiarities of Glomerulus geometry can explain the better fit by the solution with fractal dimension only of experimental EPSC arising from local release, but not from spillover of glutamate. An asynchronous vesicle release only slightly influences the shape of the spillover waveform. Anomalously slow diffusion of glutamate can be an explanation of the observed discrepancy between experimental results and simulations with the 3D model. A good fit of spillover-induced EPSC obtained in the simulations that use a solution for fractional Brownian motion and a match of experimental estimations and theoretical parameters of the diffusion model confirms this assumption.
Shin Nagayama - One of the best experts on this subject based on the ideXlab platform.
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narrowly confined and Glomerulus specific onset latencies of odor evoked calcium transients in the juxtaglomerular cells of the mouse main olfactory bulb
eNeuro, 2019Co-Authors: Ryota Homma, Xiaohua Lv, Tokiharu Sato, Fumiaki Imamura, Shaoqun Zeng, Shin NagayamaAbstract:Abstract Odor information is transmitted from olfactory sensory neurons to principal neurons at the glomeruli of the olfactory bulb. The intraglomerular neuronal circuit also includes hundreds of interneurons referred to as juxtaglomerular (JG) cells. Stimulus selectivity is well correlated among many JG cells that are associated with the same Glomerulus, consistent with their highly homogeneous sensory inputs. However, much less is known about the temporal aspects of their activity, including the temporal coordination of their odor-evoked responses. As many JG cells within a glomerular module respond to the same stimulus, the extent to which their activity is temporally aligned will affect the temporal profile of their population inhibitory inputs. Using random-access high-speed two-photon microscopy, we recorded the odor-evoked calcium transients of mouse JG cells and compared the onset latency and rise time among neurons putatively associated with the same and different glomeruli. Whereas the overall onset latencies of odor-evoked transients were distributed across a ∼150 ms time window, those from cells putatively associated with the same Glomerulus were confined to a much narrower window of several tens of milliseconds. This result suggests that onset latency primarily depends on the associated Glomerulus. We also observed glomerular specificity in the rise time. The Glomerulus-specific temporal pattern of odor-evoked activity implies that the temporal patterns of inputs from the intraglomerular circuit are unique to individual Glomerulus–odor pairs, which may contribute to efficient shaping of the temporal pattern of activity in the principal neurons.
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narrowly confined and Glomerulus specific onset latencies of odor evoked calcium transients in the periglomerular cells of the mouse main olfactory bulb
bioRxiv, 2018Co-Authors: Ryota Homma, Xiaohua Lv, Tokiharu Sato, Fumiaki Imamura, Shaoqun Zeng, Shin NagayamaAbstract:Odor information is transmitted from olfactory sensory neurons to principal neurons at the glomeruli of the olfactory bulb. The intraglomerular neuronal circuit also includes hundreds of GABAergic interneurons referred to as periglomerular (PG) cells. Stimulus selectivity is well correlated among PG cells that are associated with the same Glomerulus, consistent with their highly homogeneous sensory inputs. However, much less is known about the temporal aspects of their activity, including the temporal coordination of their odor-evoked responses. As many PG cells within a glomerular module respond to the same stimulus, the extent to which their activity is temporally aligned will affect the temporal profile of their population inhibitory inputs. Using random-access high-speed two-photon microscopy, we recorded the odor-evoked calcium transients of mouse PG cells and compared the onset latency and rise time among neurons putatively associated with the same and different glomeruli. Whereas the overall onset latencies of odor-evoked transients were distributed across a ~150 ms time window, those from cells putatively associated with the same Glomerulus were confined to a much narrower window of several tens of milliseconds. This result suggests that onset latency primarily depends on the associated Glomerulus. We also observed glomerular specificity in the rise time. The Glomerulus-specific temporal pattern of odor-evoked activity implies that the temporal patterns of inhibitory inputs are unique to individual Glomerulus-odor pairs, which may contribute to efficient shaping of the temporal pattern of activity in the principal neurons.