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Bernard Henrissat - One of the best experts on this subject based on the ideXlab platform.
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Characterization of the β-glucuronidase Pn3Pase as the founding member of glycoside hydrolase family GH169.
2020Co-Authors: Paeton L. Wantuch, Bernard Henrissat, Satya Jella, Jeremy A. Duke, Jarrod J. Mousa, John Glushka, Fikri Y. AvciAbstract:Paenibacillus sp. 32352 is a soil-dwelling bacterium capable of producing an enzyme, Pn3Pase that degrades the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (Pn3P). Recent reports on Pn3Pase have demonstrated its initial characterization and potential for protection against highly virulent S. pneumoniae serotype 3 infections. Initial experiments revealed this enzyme functions as an exo-β1,4-glucuronidase cleaving the β(1,4) linkage between glucuronic acid and glucose. However, the catalytic mechanism of this enzyme is still unknown. Here, we report the detailed biochemical analysis of Pn3Pase. Pn3Pase shows no significant sequence similarity to known glycoside hydrolase (GH) families, thus this novel enzyme establishes a new carbohydrate-active enzyme (CAZy) GH family. Site-directed mutagenesis studies revealed two catalytic residues along with truncation mutants defining essential domains for function. Pn3Pase and its mutants were screened for activity, substrate binding and kinetics. Additionally, nuclear magnetic resonance spectroscopy analysis revealed that Pn3Pase acts through a retaining mechanism. This study exhibits Pn3Pase activity at the structural and mechanistic level to establish the new CAZy GH family GH169 belonging to the large GH-A clan. This study will also serve toward generating Pn3Pase derivatives with optimal activity and pharmacokinetics aiding in the use of Pn3Pase as a novel therapeutic approach against type 3 S. pneumoniae infections.
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Additional file 5: Table S3. of De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
2018Co-Authors: David Eccles, Bernard Henrissat, Jodie Chandler, Mali Camberis, Sergey Koren, Graham Le Gros, Jonathan EwbankAbstract:CAZy analysis (see Excel file). (XLSX 265 kb
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MOESM1 of Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
2018Co-Authors: Shingo Miyauchi, Elodie Drula, Bernard Henrissat, AnaĂŻs Rancon, Hayat Hage, Delphine Chaduli, Anne Favel, Sacha Grisel, Isabelle HerpoĂŤl-gimbert, Francisco Ruiz-dueĂąasAbstract:Additional file 1: Table S1. List of predicted Auxiliary Activity enzymes from CAZy families AA2 and AA3 encoded in the genome of Polyporus brumalis BRFM 1820. Expert annotations for AA3 sub-families, versatile peroxidases (VP), manganese peroxidases (MnP) and generic peroxidases (GP) are indicated. The Cellobiose Dehydrogenase with the modular structure AA8-AA3_1, ProtID #1364243, is not indicated
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the CAZy database the carbohydrate active enzyme CAZy database principles and usage guidelines
2017Co-Authors: Elodie Drula, Pedro M. Coutinho, Vincent Lombard, Bernard Henrissat, Nicolas TerraponAbstract:Carbohydrate-Active enZymes (CAZymes) assemble, breakdown, and modify glycans and glycoconjugates using their catalytic and binding modules (functional protein domains). The CAZy database offers since 1998 an online and continuously updated classification of CAZyme modules (Lombard et al. 2014). Each module family in the CAZy classification has been created based on experimentally characterized protein modules from the literature, and the families are populated by related module sequences from public protein sequence databases. Since no universal threshold allows the systematic classification of the various CAZyme families, CAZy annotations result from an expert combination of module modeling/calibration and human curation. CAZy annotations are made publicly available for all proteins released by GenBank (Benson et al. 2012), Swiss-Prot (Boutet et al. 2016) and the Protein Data Bank (PDB; http://www.rcsb.org; (Berman et al. 2000)). Further, functional and 3-D structural information, curated from the literature on a regular basis, constitute essential added values to the CAZy annotation. In this spirit, the display of ligand information from crystallographic complexes has been recently developed (Lombard et al. 2014). This chapter will guide the reader through the usage of CAZy to search enzyme annotations. It will also answer frequent questions such as (i) how to obtain CAZy annotations for a specific protein, a genome, or a metagenome, (ii) how to have a newly characterized family included in the CAZy classification scheme, (iii) why CAZy does not cover all protein families related to glycans/glycoconjugates, and (iv) why CAZy does not transfer functional annotation to similar sequences. Finally, we present here a recent CAZy-associated tool, namely, the Polysaccharide Utilization Loci (PUL) predictor and database in Bacteroidetes species (Terrapon et al. 2015).
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Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.
2016Co-Authors: Otto Miettinen, Matthieu Hainaut, Robert Riley, Kerrie Barry, Daniel Cullen, Bernard Henrissat, Annele Hatakka, Ronald P. De Vries, Kristiina HildénAbstract:We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.
Jun Lin - One of the best experts on this subject based on the ideXlab platform.
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single phased white emitting ca3y gao 3 bo3 4 ce3 tb3 sm3 phosphors with high efficiency photoluminescence energy transfer and application in near uv pumped white leds
2018Co-Authors: Xiaoyong Huang, Jun LinAbstract:Abstract Novel single-phased white-emitting Ca3Y(GaO)3(BO3)4:Ce3+,Tb3+,Sm3+ phosphors with high-efficiency, were successfully synthesized via traditional high temperature solid-state reaction method. X-ray diffraction, luminescence spectroscopy, fluorescence decay time and fluorescent thermal stability tests have been used to characterize the as-prepared samples. The energy transfer among of Ce3+, Tb3+ and Sm3+ ions in Ca3Y(GaO)3(BO3)4 host have been studied in detail. The mechanisms of Ce3+ → Tb3+ and Ce3+ → Sm3+ energy transfer were demonstrated to be dipole-dipole interactions. The emission color of the obtained phosphors can be easily tuned by controlling the doping concentration ratios of Ce3+/Tb3+/Sm3+. Particularly, under the excitation at 340 nm, Ca3Y(GaO)3(BO3)4:0.01Ce3+,0.15Tb3+,0.01Sm3+ phosphor showed bright a white light with CIE coordinates of (0.2892, 0.2943) and internal quantum efficiency as high as 49.5%. By integrating this single-composition white-emitting Ca3Y(GaO)3(BO3)4:0.01Ce3+,0.15Tb3+,0.01Sm3+ phosphor with a 365 nm near-ultraviolet (NUV) light emitting diode (LED) chip, we successfully fabricated a prototype white LED (WLED) device, which exhibited high-brightness nearly ideal white light with CIE coordinates of (0.310, 0.330), color rendering index of 72.7 and a correlated color temperature of 6624 K. These results demonstrate that the proposed single-composition white-emitting Ca3Y(GaO)3(BO3)4:Ce3+,Tb3+,Sm3+ phosphors can serve as promising phosphors for the application of NUV-excited WLEDs.
Vicky Kelly - One of the best experts on this subject based on the ideXlab platform.
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Cary Environmental Monitoring Program Stream Hydrology Data: 1993-2018
2019Co-Authors: Vicky KellyAbstract:The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, and water pollution and streamwater hydrology. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2008 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org.Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org.
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Cary Environmental Monitoring Program Precipitation Chemistry Event-Based Data: 1984-2018
2019Co-Authors: Vicky KellyAbstract:The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, water pollution and streamwater hydrology. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2019 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org.Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org
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Cary Environmental Monitoring Program Stream Chemistry Data: 1985-2018
2019Co-Authors: Vicky KellyAbstract:The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, water pollution and streamwater hydrology. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2008 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org.Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org.
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Cary Environmental Monitoring Program Precipitation Chemistry Data: 1984-2017
2019Co-Authors: Vicky KellyAbstract:The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, water pollution and streamwater hydrology. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2008 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org.Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org.
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Cary Institute Environmental Monitoring Program Current Year Data
2019Co-Authors: Vicky KellyAbstract:The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, and water pollution and other streamwater chemistry. Our solar radiation monitoring includes diffuse and global photosynthetically active radiation (PAR), diffuse and global shortwave radiation, net radiation and UV. Long-term monitoring of solar radiation provides us with an understanding of atmospheric energy dynamics, which can affect natural and human systems. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2018 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org. Those wishing to publish data from Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact data manager Vicky Kelly, kellyv@caryinstitute.org.For complete data for previous years and for complete metadata, please see appropriate items for the Cary Institute Environmental Monitoring Program at https://caryinstitute.figshare.com/
Tengming Chen - One of the best experts on this subject based on the ideXlab platform.
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a novel single composition trichromatic white light ca3y gao 3 bo3 4 ce3 mn2 tb3 phosphor for uv light emitting diodes
2011Co-Authors: Chien Hao Huang, Tengming ChenAbstract:A novel single-composition white-emitting phosphor Ca3Y(GaO)3(BO3)4:Ce3+,Mn2+,Tb3+ has been synthesized by a high-temperature solid-state reaction. The spectral overlap between the emission band of Ce3+ and the excitation band of Mn2+, which supports the occurrence of the energy transfer from Ce3+ to Mn2+, has been studied and demonstrated to be a resonant type via a dipole−quadrupole mechanism. Because there was no spectral overlap between the emission spectra of Ce3+ and excitation band of Tb3+ in our study, no energy transfer from Ce3+ to Tb3+ was observed, indicating that Ce3+ and Tb3+ were coexcited. Through effective resonance-type energy transfer and coexcitation, the chromaticity coordinates of Ca3Y(GaO)3(BO3)4:Ce3+,Mn2+,Tb3+ phosphors can be tuned from (0.152, 0.061) for Ca3Y(GaO)3(BO3)4:Ce3+ to (0.562, 0.408) for Ca3Y(GaO)3(BO3)4:Mn2+, and eventually reaching (0.314, 0.573) for Ca3Y(GaO)3(BO3)4:Tb3+. A white light-emitting diode (LED) was fabricated by using the white-emitting single-composition...
Vincent Lombard - One of the best experts on this subject based on the ideXlab platform.
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the CAZy database the carbohydrate active enzyme CAZy database principles and usage guidelines
2017Co-Authors: Elodie Drula, Pedro M. Coutinho, Vincent Lombard, Bernard Henrissat, Nicolas TerraponAbstract:Carbohydrate-Active enZymes (CAZymes) assemble, breakdown, and modify glycans and glycoconjugates using their catalytic and binding modules (functional protein domains). The CAZy database offers since 1998 an online and continuously updated classification of CAZyme modules (Lombard et al. 2014). Each module family in the CAZy classification has been created based on experimentally characterized protein modules from the literature, and the families are populated by related module sequences from public protein sequence databases. Since no universal threshold allows the systematic classification of the various CAZyme families, CAZy annotations result from an expert combination of module modeling/calibration and human curation. CAZy annotations are made publicly available for all proteins released by GenBank (Benson et al. 2012), Swiss-Prot (Boutet et al. 2016) and the Protein Data Bank (PDB; http://www.rcsb.org; (Berman et al. 2000)). Further, functional and 3-D structural information, curated from the literature on a regular basis, constitute essential added values to the CAZy annotation. In this spirit, the display of ligand information from crystallographic complexes has been recently developed (Lombard et al. 2014). This chapter will guide the reader through the usage of CAZy to search enzyme annotations. It will also answer frequent questions such as (i) how to obtain CAZy annotations for a specific protein, a genome, or a metagenome, (ii) how to have a newly characterized family included in the CAZy classification scheme, (iii) why CAZy does not cover all protein families related to glycans/glycoconjugates, and (iv) why CAZy does not transfer functional annotation to similar sequences. Finally, we present here a recent CAZy-associated tool, namely, the Polysaccharide Utilization Loci (PUL) predictor and database in Bacteroidetes species (Terrapon et al. 2015).
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The carbohydrate-active enzymes database (CAZy) in 2013
2014Co-Authors: Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M. Coutinho, Bernard HenrissatAbstract:The Carbohydrate-Active Enzymes database (CAZy; http://www.CAZy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.
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expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
2013Co-Authors: Anthony Levasseur, Elodie Drula, Pedro M. Coutinho, Vincent Lombard, Bernard HenrissatAbstract:Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.CAZy.org ) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.
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the carbohydrate active enzymes database CAZy an expert resource for glycogenomics
2009Co-Authors: Brandi L Cantarel, Thomas Bernard, Pedro M. Coutinho, Corinne Rancurel, Vincent Lombard, Bernard HenrissatAbstract:The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.CAZy.org/.
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the carbohydrate active enzymes database CAZy an expert resource for glycogenomics
2009Co-Authors: Brandi L Cantarel, Thomas Bernard, Pedro M. Coutinho, Corinne Rancurel, Vincent Lombard, Bernard HenrissatAbstract:The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.CAZy.org/.