The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Knut Drescher - One of the best experts on this subject based on the ideXlab platform.
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bacstalk a comprehensive and interactive image analysis software tool for bacterial Cell biology
Molecular Microbiology, 2020Co-Authors: Raimo Hartmann, Muriel C F Van Teeseling, Martin Thanbichler, Knut DrescherAbstract:Prokaryotic Cells display a striking subCellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, Cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional Cellular outlines, to accurately represent their subCellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon Cell shapes. BacStalk, therefore, contributes to the advancement of Prokaryotic Cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.
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bacstalk a comprehensive and interactive image analysis software tool for bacterial Cell biology
bioRxiv, 2018Co-Authors: Raimo Hartmann, Muriel C F Van Teeseling, Martin Thanbichler, Knut DrescherAbstract:Prokaryotes display a remarkable spatiotemporal organization of processes within individual Cells. Investigations of the underlying mechanisms rely extensively on the analysis of microscopy images. Advanced image analysis software has revolutionized the Cell-biological studies of established model organisms with largely symmetric rod-like Cell shapes. However, algorithms suitable for analyzing features of morphologically more complex model species are lacking, although such unusually shaped organisms have emerged as treasure-troves of new molecular mechanisms and diversity in Prokaryotic Cell biology. To address this problem, we developed BacStalk, a simple, interactive, and easy-to-use MatLab-based soft-ware tool for quantitatively analyzing images of commonly and uncommonly shaped bacteria, including stalked (budding) bacteria. BacStalk automatically detects the separate parts of the Cells (Cell body, stalk, bud, or appendage) as well as their connections, thereby allowing in-depth analyses of the organization of morphologically complex bacteria over time. BacStalk features the generation and visualization of concatenated fluorescence profiles along Cells, stalks, appendages, and buds to trace the spatiotemporal dynamics of fluorescent markers. Cells are interactively linked to demographs, kymographs, Cell lineage analyses, and scatterplots, which enables intuitive and fast data exploration and, thus, significantly speeds up the image analysis process. Furthermore, BacStalk introduces a 2D representation of demo- and kymographs, enabling data representations in which the two spatial dimensions of the Cell are preserved. The software was developed to handle large data sets and to generate publication-grade figures that can be easily edited. BacStalk therefore provides an advanced image analysis platform that extends the spectrum of model organisms for Prokaryotic Cell biology to bacteria with multiple morphologies and life cycles.
Martin Thanbichler - One of the best experts on this subject based on the ideXlab platform.
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bacstalk a comprehensive and interactive image analysis software tool for bacterial Cell biology
Molecular Microbiology, 2020Co-Authors: Raimo Hartmann, Muriel C F Van Teeseling, Martin Thanbichler, Knut DrescherAbstract:Prokaryotic Cells display a striking subCellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, Cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional Cellular outlines, to accurately represent their subCellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon Cell shapes. BacStalk, therefore, contributes to the advancement of Prokaryotic Cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.
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bacstalk a comprehensive and interactive image analysis software tool for bacterial Cell biology
bioRxiv, 2018Co-Authors: Raimo Hartmann, Muriel C F Van Teeseling, Martin Thanbichler, Knut DrescherAbstract:Prokaryotes display a remarkable spatiotemporal organization of processes within individual Cells. Investigations of the underlying mechanisms rely extensively on the analysis of microscopy images. Advanced image analysis software has revolutionized the Cell-biological studies of established model organisms with largely symmetric rod-like Cell shapes. However, algorithms suitable for analyzing features of morphologically more complex model species are lacking, although such unusually shaped organisms have emerged as treasure-troves of new molecular mechanisms and diversity in Prokaryotic Cell biology. To address this problem, we developed BacStalk, a simple, interactive, and easy-to-use MatLab-based soft-ware tool for quantitatively analyzing images of commonly and uncommonly shaped bacteria, including stalked (budding) bacteria. BacStalk automatically detects the separate parts of the Cells (Cell body, stalk, bud, or appendage) as well as their connections, thereby allowing in-depth analyses of the organization of morphologically complex bacteria over time. BacStalk features the generation and visualization of concatenated fluorescence profiles along Cells, stalks, appendages, and buds to trace the spatiotemporal dynamics of fluorescent markers. Cells are interactively linked to demographs, kymographs, Cell lineage analyses, and scatterplots, which enables intuitive and fast data exploration and, thus, significantly speeds up the image analysis process. Furthermore, BacStalk introduces a 2D representation of demo- and kymographs, enabling data representations in which the two spatial dimensions of the Cell are preserved. The software was developed to handle large data sets and to generate publication-grade figures that can be easily edited. BacStalk therefore provides an advanced image analysis platform that extends the spectrum of model organisms for Prokaryotic Cell biology to bacteria with multiple morphologies and life cycles.
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a comprehensive set of plasmids for vanillate and xylose inducible gene expression in caulobacter crescentus
Nucleic Acids Research, 2007Co-Authors: Martin Thanbichler, Antonio A IniestaAbstract:Caulobacter crescentus is widely used as a powerful model system for the study of Prokaryotic Cell biology and development. Analysis of this organism is complicated by a limited selection of tools for genetic manipulation and inducible gene expression. This study reports the identification and functional characterization of a vanillate-regulated promoter (Pvan) which meets all requirements for application as a multi-purpose expression system in Caulobacter, thus complementing the established xylose-inducible system (Pxyl). Furthermore, we introduce a newly constructed set of integrating and replicating shuttle vectors that considerably facilitate Cell biological and physiological studies in Caulobacter. Based on different narrow and broad-host range replicons, they offer a wide choice of promoters, resistance genes, and fusion partners for the construction of fluorescently or affinity-tagged proteins. Since many of these constructs are also suitable for use in other bacteria, this work provides a comprehensive collection of tools that will enrich many areas of microbiological research.
Wei Long - One of the best experts on this subject based on the ideXlab platform.
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enzymatic characterization and crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa pao1
Biochemical and Biophysical Research Communications, 2018Co-Authors: Hui Dong, Jiansong Ju, Shujing Xu, Shanshan Wang, Xin He, Chao Yuan, Wei Long, Sheng LiAbstract:Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of L-alanine to D-alanine. D-alanine is an essential constituent in many Prokaryotic Cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate D-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to D-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr. (C) 2018 Elsevier Inc. All rights reserved.
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enzymatic characterization and crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa pao1
Biochemical and Biophysical Research Communications, 2018Co-Authors: Hui Dong, Shanshan Wang, Chao Yuan, Qingqing Han, Yu Guo, Wei LongAbstract:Abstract Alanine racemase is a pyridoxal-5′-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l -alanine to d -alanine. d -alanine is an essential constituent in many Prokaryotic Cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d -lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d -lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
William Margolin - One of the best experts on this subject based on the ideXlab platform.
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two dictyostelium orthologs of the Prokaryotic Cell division protein ftsz localize to mitochondria and are required for the maintenance of normal mitochondrial morphology
Eukaryotic Cell, 2003Co-Authors: Paul R Gilson, William Margolin, Dale Hereld, Christian Barth, Amelia Savage, Ben R Kiefel, Sui Lay, Paul R Fisher, Peter L BeechAbstract:In bacteria, the protein FtsZ is the principal component of a ring that constricts the Cell at division. Though all mitochondria probably arose through a single, ancient bacterial endosymbiosis, the mitochondria of only certain protists appear to have retained FtsZ, and the protein is absent from the mitochondria of fungi, animals, and higher plants. We have investigated the role that FtsZ plays in mitochondrial division in the genetically tractable protist Dictyostelium discoideum, which has two nuclearly encoded FtsZs, FszA and FszB, that are targeted to the inside of mitochondria. In most wild-type amoebae, the mitochondria are spherical or rod-shaped, but in fsz-null mutants they become elongated into tubules, indicating that a decrease in mitochondrial division has occurred. In support of this role in organelle division, antibodies to FszA and FszA-green fluorescent protein (GFP) show belts and puncta at multiple places along the mitochondria, which may define future or recent sites of division. FszB-GFP, in contrast, locates to an electron-dense, submitochondrial body usually located at one end of the organelle, but how it functions during division is unclear. This is the first demonstration of two differentially localized FtsZs within the one organelle, and it points to a divergence in the roles of these two proteins.
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Themes and variations in Prokaryotic Cell division
FEMS microbiology reviews, 2000Co-Authors: William MargolinAbstract:Perhaps the biggest single task facing a bacterial Cell is to divide into daughter Cells that contain the normal complement of chromosomes. Recent technical and conceptual breakthroughs in bacterial Cell biology, combined with the flood of genome sequence information and the exCellent genetic tools in several model systems, have shed new light on the mechanism of Prokaryotic Cell division. There is good evidence that in most species, a molecular machine, organized by the tubulin-like FtsZ protein, assembles at the site of division and orchestrates the splitting of the Cell. The determinants that target the machine to the right place at the right time are beginning to be understood in the model systems, but it is still a mystery how the machine actually generates the constrictive force necessary for cytokinesis. Moreover, although some Cell division determinants such as FtsZ are present in a broad spectrum of Prokaryotic species, the lack of FtsZ in some species and different profiles of Cell division proteins in different families suggests that there are diverse mechanisms for regulating Cell division.
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inhibition of assembly of bacterial Cell division protein ftsz by the hydrophobic dye 5 5 bis 8 anilino 1 naphthalenesulfonate
Journal of Biological Chemistry, 1998Co-Authors: William MargolinAbstract:To gain further insight into the structural relatedness of tubulin and FtsZ, the tubulin-like Prokaryotic Cell division protein, we tested the effect of tubulin assembly inhibitors on FtsZ assembly. Common tubulin inhibitors, such as colchicine, colcemid, benomyl, and vinblastine, had no effect on Ca2+-promoted GTP-dependent assembly of FtsZ into polymers. However, the hydrophobic probe 5, 5'-bis-(8-anilino-1-naphthalenesulfonate) (bis-ANS) inhibited FtsZ assembly. The potential mechanisms for inhibition are discussed. Titrations of FtsZ with bis-ANS indicated that FtsZ has one high affinity binding site and multiple low affinity binding sites. ANS (8-anilino-1-naphthalenesulfonate), a hydrophobic probe similar to bis-ANS, had no inhibitory effect on FtsZ assembly. Because tubulin assembly has also been shown to be inhibited by bis-ANS but not by ANS, it supports the idea that FtsZ and tubulin share similar conformational properties. Ca2+, which promotes GTP-dependent FtsZ assembly, stimulated binding of bis-ANS or ANS to FtsZ, suggesting that Ca2+ binding induces changes in the hydrophobic conformation of the protein. Interestingly, depletion of bound Ca2+ with EGTA further enhanced bis-ANS fluorescence. These findings suggest that both binding and dissociation of Ca2+ are capable of inducing FtsZ conformational changes, and these changes could promote the GTP-dependent assembly of FtsZ.
Chao Yuan - One of the best experts on this subject based on the ideXlab platform.
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enzymatic characterization and crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa pao1
Biochemical and Biophysical Research Communications, 2018Co-Authors: Hui Dong, Jiansong Ju, Shujing Xu, Shanshan Wang, Xin He, Chao Yuan, Wei Long, Sheng LiAbstract:Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of L-alanine to D-alanine. D-alanine is an essential constituent in many Prokaryotic Cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate D-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to D-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr. (C) 2018 Elsevier Inc. All rights reserved.
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enzymatic characterization and crystal structure of biosynthetic alanine racemase from pseudomonas aeruginosa pao1
Biochemical and Biophysical Research Communications, 2018Co-Authors: Hui Dong, Shanshan Wang, Chao Yuan, Qingqing Han, Yu Guo, Wei LongAbstract:Abstract Alanine racemase is a pyridoxal-5′-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l -alanine to d -alanine. d -alanine is an essential constituent in many Prokaryotic Cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d -lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d -lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
