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G. Kass-simon - One of the best experts on this subject based on the ideXlab platform.
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The two nerve rings of the hypostomal nervous system of Hydra Vulgaris—an immunohistochemical analysis
Cell and Tissue Research, 2016Co-Authors: L. A. Hufnagel, G. Kass-simonAbstract:In Hydra Vulgaris , physiological and pharmacological evidence exists for a hypostomal circumferential neuro-effector pathway that initiates ectodermal pacemaker activity at tentacular-hypostomal loci coordinating body and tentacle contractions. Here, we describe an ectodermal nerve ring that runs below and between the tentacles, and an anti-GABA_B receptor antibody-labeled ring coincident with it. The location of this ring is consistent with the physiology of the hypostomal pacemaker systems of Hydra. We also describe a distally located, ectodermal ring of nerve fibers that is not associated with anti-GABA_B receptor antibody labeling. The neurites and cell bodies of sensory cells contribute to both rings. The location of the distal ring and its sensory cell neurites suggests an involvement in the behavior of the mouth. Between the two rings is a network of anastomosing sensory and ganglion cell bodies and their neurites. Phase contrast, darkfield, and antibody-labeled images reveal that the mouth of Hydra comprises five or six epithelial folds whose endoderm extensively labels with anti-GABA_B receptor antibody, suggesting that endodermal metabotrobic GABA receptors are also involved in regulating mouth behavior.
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The two nerve rings of the hypostomal nervous system of Hydra Vulgaris-an immunohistochemical analysis.
Cell and tissue research, 2016Co-Authors: Linda A. Hufnagel, G. Kass-simonAbstract:In Hydra Vulgaris, physiological and pharmacological evidence exists for a hypostomal circumferential neuro-effector pathway that initiates ectodermal pacemaker activity at tentacular-hypostomal loci coordinating body and tentacle contractions. Here, we describe an ectodermal nerve ring that runs below and between the tentacles, and an anti-GABAB receptor antibody-labeled ring coincident with it. The location of this ring is consistent with the physiology of the hypostomal pacemaker systems of Hydra. We also describe a distally located, ectodermal ring of nerve fibers that is not associated with anti-GABAB receptor antibody labeling. The neurites and cell bodies of sensory cells contribute to both rings. The location of the distal ring and its sensory cell neurites suggests an involvement in the behavior of the mouth. Between the two rings is a network of anastomosing sensory and ganglion cell bodies and their neurites. Phase contrast, darkfield, and antibody-labeled images reveal that the mouth of Hydra comprises five or six epithelial folds whose endoderm extensively labels with anti-GABAB receptor antibody, suggesting that endodermal metabotrobic GABA receptors are also involved in regulating mouth behavior.
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Extraocular spectral photosensitivity in the tentacles of Hydra Vulgaris.
Comparative biochemistry and physiology. Part A Molecular & integrative physiology, 2015Co-Authors: Stephanie L. Guertin, G. Kass-simonAbstract:Abstract Previous electrophysiological studies on the cnidarian Hydra Vulgaris have shown that Hydra have a highly developed and specific photoresponse despite their lack of any structure recognizable as a traditional photoreceptor. In an effort to identify the site of Hydra's photoreceptors, we recorded extracellularly from single excised tentacles and from ablated hypostomes lacking tentacles in absolute darkness and during exposure to light of various wavelengths. During recording, after an initial period of absolute darkness, tentacles or hypostomes were exposed to light from 450 nm to 600 nm, red, and white light. Exposure to light caused a change in the pattern and frequency of impulses in the tentacles that varied with color. The number of large tentacle pulses (TPs) increased at 550 and 600 nm relative to darkness, whereas the number of small tentacle pulses (STPs) tended to decrease in 500 nm light. Impulse frequency was significantly different among the different wavelengths. In addition to bursts of tentacle contraction pulses, long trains of pulses were observed. A change in lighting caused a switch from bursting to trains or vice versa. In contrast to excised tentacles, no change in electrical activity was seen in ablated hypostomes at any of the wavelengths relative to each other or relative to darkness. These results indicate that isolated tentacles can distinguish among and respond to various colors across the visible spectrum and suggest that electromagnetic information is transmitted from the tentacles to the hypostome where it may be integrated by the hypostomal nervous system, ultimately contributing to Hydra's photoreceptive behavior.
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Extraocular spectral photosensitivity in the tentacles of Hydra Vulgaris Part A Molecular & integrative physiology
Comparative Biochemistry and Physiology, 2015Co-Authors: Stephanie L. Guertin, G. Kass-simonAbstract:Previous electrophysiological studies on the cnidarian Hydra Vulgaris have shown that Hydra have a highly developed and specific photoresponse despite their lack of any structure recognizable as a traditional photoreceptor. In an effort to identify the site of Hydra's photoreceptors, we recorded extracellularly from single excised tentacles and from ablated hypostomes lacking tentacles in absolute darkness and during exposure to light of various wavelengths. During recording, after an initial period of absolute darkness, tentacles or hypostomes were exposed to light from 450nm to 600nm, red, and white light. Exposure to light caused a change in the pattern and frequency of impulses in the tentacles that varied with color. The number of large tentacle pulses (TPs) increased at 550 and 600nm relative to darkness, whereas the number of small tentacle pulses (STPs) tended to decrease in 500nm light. Impulse frequency was significantly different among the different wavelengths. In addition to bursts of tentacle contraction pulses, long trains of pulses were observed. A change in lighting caused a switch from bursting to trains or vice versa. In contrast to excised tentacles, no change in electrical activity was seen in ablated hypostomes at any of the wavelengths relative to each other or relative to darkness. These results indicate that isolated tentacles can distinguish among and respond to various colors across the visible spectrum and suggest that electromagnetic information is transmitted from the tentacles to the hypostome where it may be integrated by the hypostomal nervous system, ultimately contributing to Hydra's photoreceptive behavior.
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Nematocyst discharge in Hydra Vulgaris: Differential responses of desmonemes and stenoteles to mechanical and chemical stimulation.
Comparative biochemistry and physiology. Part A Molecular & integrative physiology, 2010Co-Authors: A. A. Scappaticci, Fhyzeedon Kahn, G. Kass-simonAbstract:The effects of mechanical and chemical stimulation on desmoneme and stenotele discharge in Hydra Vulgaris were quantified, in situ, in isolated tentacles and single tentacles with attached hypostomes. Cnidocils of desmonemes and stenoteles were stimulated 24h after tentacle ablation. Single impacts with maximum calculated forces of 3.7x10(-3) to 3.8x10(-2) Newtons were delivered by piezoelectrically-driven glass capillary probes. Video analysis revealed that desmonemes discharged at forces of 3.7x10(-3)N; stenoteles required forces of 1.9x10(-2)N. Desmonemes not directly stimulated discharged if another desmoneme was adequately stimulated; the effect was carried through to at least two adjacent battery cells. Tentacles responded to desmoneme stimulation, by bending at the stimulation site. These findings imply afferent excitatory pathways between nematocytes onto other nematocytes and myonemes. Locomotory nematocysts (atrichous isorhizas) discharged only in hypostome-attached tentacles contacting a substrate; desmonemes and stenoteles did not discharge during substrate attachment, implying differential neuronal inhibition. At low concentrations, bath-applied mucin, a prey-associated glycosylated protein, lowered desmoneme and stenotele firing thresholds, abolishing the force dose-dependency in stenoteles, and allowing them to discharge at previously below threshold forces. At higher concentrations, mucin inhibited discharge, suggesting an involvement in prey-induced feeding inhibition.
Mario Rosario Guarracino - One of the best experts on this subject based on the ideXlab platform.
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An Atlas of annotations of Hydra Vulgaris transcriptome.
BMC bioinformatics, 2016Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario GuarracinoAbstract:RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's Vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra Vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra Vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .
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An Atlas of annotations of Hydra Vulgaris transcriptome
BMC Bioinformatics, 2016Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario GuarracinoAbstract:Background RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Results Starting from a previous work, Transcriptator, we present the Atlas of Hydra’s Vulgaris , an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra Vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Conclusion Atlas , as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra Vulgaris exposed to the distinct experimental treatments. Web resource URL http://www-labgtp.na.icar.cnr.it/Atlas .
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An Atlas of annotations of Hydra Vulgaris
2016Co-Authors: Kumar Parijat Tripathi, Mario Rosario GuarracinoAbstract:Background: RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Results: Starting from a previous work, Transcriptator, we present the Atlas of Hydra’s Vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra Vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Conclusion: Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra Vulgaris exposed to the distinct experimental treatments.
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hvdbase a web resource on Hydra Vulgaris transcriptome
International Conference on Bioinformatics and Biomedical Engineering, 2015Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Valentina Scuotto, Mario Rosario GuarracinoAbstract:The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quantification, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra Vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, and from which it is possible to have access and download all the information related to 15,522 transcripts. The study includes different functional annotations coming from 19 repositories, conveniently grouped by type, such as: i. Pathway: BBID, BioCarta, KEGG, Panther; ii. Domain: COG-Ontology, Interpro, PIR Superfamily, SMART, PFam; iii. Protein Interaction: BIND, MINT, UCSF-TFBS; iv. GO: GO-Term Cellular Components, GO-Term Biological Processes, GO-Term Molecular Functions; v. Miscellaneous: OMIM, EC Number, SP-PIR Keywords, UP-SEQ features. The easily-accessible nature of HvDBase makes this resource a valuable tool for rapidly retrieve knowledges at transcript level as well as useful to inspect differential expression of protein-coding genes in Hydra Vulgaris transcriptome in the contex to the different experimental condition. Web resource URL: http://www-labgtp.na.icar.cnr.it/HvDBase
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IWBBIO (2) - HvDBase : A Web Resource on Hydra Vulgaris Transcriptome
Bioinformatics and Biomedical Engineering, 2015Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Valentina Scuotto, Mario Rosario GuarracinoAbstract:The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quantification, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra Vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, and from which it is possible to have access and download all the information related to 15,522 transcripts. The study includes different functional annotations coming from 19 repositories, conveniently grouped by type, such as: i. Pathway: BBID, BioCarta, KEGG, Panther; ii. Domain: COG-Ontology, Interpro, PIR Superfamily, SMART, PFam; iii. Protein Interaction: BIND, MINT, UCSF-TFBS; iv. GO: GO-Term Cellular Components, GO-Term Biological Processes, GO-Term Molecular Functions; v. Miscellaneous: OMIM, EC Number, SP-PIR Keywords, UP-SEQ features. The easily-accessible nature of HvDBase makes this resource a valuable tool for rapidly retrieve knowledges at transcript level as well as useful to inspect differential expression of protein-coding genes in Hydra Vulgaris transcriptome in the contex to the different experimental condition. Web resource URL: http://www-labgtp.na.icar.cnr.it/HvDBase
Claus Fütterer - One of the best experts on this subject based on the ideXlab platform.
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Fluctuations and differential contraction during regeneration of Hydra Vulgaris tissue toroids
New Journal of Physics, 2013Co-Authors: Michael Krahe, Iris Wenzel, Kao-nung Lin, Julia Fischer, Joseph Goldmann, Markus Kästner, Claus FüttererAbstract:We studied regenerating bilayered tissue toroids dissected from Hydra Vulgaris polyps and relate our macroscopic observations to the dynamics of force-generating mesoscopic cytoskeletal structures. Tissue fragments undergo a specific toroid–spheroid folding process leading to complete regeneration towards a new organism. The time scale of folding is too fast for biochemical signalling or morphogenetic gradients, which forced us to assume purely mechanical self-organization. The initial pattern selection dynamics was studied by embedding toroids into hydro-gels, allowing us to observe the deformation modes over longer periods of time. We found increasing mechanical fluctuations which break the toroidal symmetry, and discuss the evolution of their power spectra for various gel stiffnesses. Our observations are related to single-cell studies which explain the mechanical feasibility of the folding process. In addition, we observed switching of cells from a tissue bound to a migrating state after folding failure as well as in tissue injury. We found a supra-cellular actin ring assembled along the toroid's inner edge. Its contraction can lead to the observed folding dynamics as we could confirm by finite element simulations. This actin ring in the inner cell layer is assembled by myosin-driven length fluctuations of supra-cellular F-actin bundles (myonemes) in the outer cell layer.
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Fluctuations and symmetry breaking during regeneration of Hydra Vulgaris tissue toroids
arXiv: Biological Physics, 2012Co-Authors: Michael Krahe, Iris Wenzel, Kao-nung Lin, Julia Fischer, Claus FüttererAbstract:While much is known in single cell mechanics, the mechanics of regeneration of naturally grown tissues and cell assemblies is largely unexplored. We found a symmetry breaking scenario accompanied by shape fluctuations in dissected regenerating Hydra Vulgaris tissue tori. A subsequent folding and merging process leads finally to a regenerating spheroid. These phenomena are related to the dynamics of fluorescent beta- and trans-cellular alpha-actin structures. By embedding the tissues in a hydro-gel the fluctuations could be studied over a longer period of time. The power spectrum of the torus-fluctuations shows a non-trivial energy distribution dynamics depending on the gel stiffness. During the transition, many higher modes where found but in the end the 2nd mode wins in most cases. The toroid builds up an uniform alpha-actin ring along the inner edge of the torus. We found this ring in the inner cellular layer to be responsible for the force generation destabilizing the toroid shape. This actin structure is presumably controlled by the more stable alpha-actin structure of the outer cell-layer. beta-actin, in contrast, seems not to be involved actively. Only when cells switch from the tissue bound state to the individual migrating state, which can be triggered mechanically, this actin isoform was found to become important. We describe structure and dynamics of both actin systems during the folding and tissue merging process finally leading to a spheroid - the inevitable initial state for regeneration.
David Pascoe - One of the best experts on this subject based on the ideXlab platform.
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A comparison of metal accumulation by the cnidarian Hydra Vulgaris directly from water or through contaminated prey and effects upon reproduction and regeneration
2007Co-Authors: Wanchamai Karntanut, David PascoeAbstract:Karntanut, W. and Pascoe, D. A comparison of metal accumulation by the cnidarian Hydra Vulgaris directly from water or through contaminated prey and effects upon reproduction and regeneration
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Do pharmaceuticals affect freshwater invertebrates? A study with the cnidarian Hydra Vulgaris
Chemosphere, 2003Co-Authors: David Pascoe, Wanchamai Karntanut, Carsten Theodor MullerAbstract:Pharmaceuticals enter natural waters through sewage effluent and landfill leachates and present an unknown risk to aquatic species including freshwater invertebrates. In this study the acute and chronic toxicity of 10 drugs, commonly prescribed in the UK i.e. ibuprofen, paracetamol, acetylsalicylic acid, amoxicillin, bendroflumethiazide, furosemide, atenolol, diazepam, digoxin, amlodipine were assessed using the cnidarian Hydra Vulgaris. In a 7 day exposure period there were no effects on survival at concentrations up to 1.0 mg l−1 and after 17 days neither feeding nor bud formation were adversely affected. However the ability of dissected polyps to regenerate a hypostome, tentacles and foot was inhibited by diazepam, digoxin and amlodipine at 10 μg l−1. It is suggested that other drugs targeted at mammalian receptor systems may also affect aquatic invertebrates although it is unlikely, at their low environmental concentrations, that those examined in this study actually present a risk.
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Toxicity of 17α-Ethinylestradiol and Bisphenol A to the Freshwater Cnidarian Hydra Vulgaris
Archives of environmental contamination and toxicology, 2002Co-Authors: David Pascoe, Kathleen Carroll, W. Karntanut, Matthew M. WattsAbstract:Estrogens and estrogen mimics that enter the environment are known to present a serious threat to the development and reproduction of vertebrates by disrupting their normal endocrine function. There is also concern that such chemicals may be damaging to invertebrates. In this study, Hydra Vulgaris, a member of the Cnidaria, an evolutionarily primitive group of invertebrates present before the divergence of the protostomes and deuterostomes, was exposed to the synthetic estrogen 17alpha-ethinylestradiol (EE2) and bisphenol A (BPA), both of which are known to be estrogenic in fish. Effects on polyp survival, structure, and regeneration (and sexual reproduction for EE2) were examined and mortality was recorded at high concentrations, with 96-h LC(50)s of 3.8 mg/L and 6.9 mg/L for EE2 and BPA, respectively. The structure and physiology of polyps was adversely affected at concentrations greater than 58 microg/L EE2 and 42 microg/L BPA. There was a concentration-related inhibition of regeneration above 150 microg/L EE2 and 460 microg/L BPA. Sexual reproduction was only impaired at 500 microg/L EE2. These results clearly suggest that the signaling processes necessary for the control and regulation of cell movement and differentiation during normal development, regeneration, and sexual reproduction in H. Vulgaris are not disrupted by estrogenic pollutants at low environmentally relevant concentrations.
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A comparison of methods for measuring acute toxicity to Hydra Vulgaris.
Chemosphere, 2000Co-Authors: Wanchamai Karntanut, David PascoeAbstract:The freshwater coelenterate Hydra Vulgaris (Pallas) is a common component of freshwater ecosystems and is sensitive to a range of pollutants. It can be cultured easily in the laboratory to provide large numbers of test animals and can be used in simple, cost effective bioassays of both acute, sub-acute and chronic toxicity. This study, using the heavy metals: copper, cadmium and zinc, aimed to compare two methods of assessing acute toxicity. The first method was based upon a conventional determination of LC50s while the second involved an evaluation, using a scoring procedure, of progressive changes in structure and proved to have a number of advantages compared with a simple LC50. These include the potential to help explain mechanisms of toxicity and to examine the ability of animals to recover from pollutant-induced damage.
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THE ROLE OF Hydra Vulgaris (PALLAS) IN ASSESSING THE TOXICITY OF FRESHWATER POLLUTANTS
Water Research, 1998Co-Authors: Matthew J. Beach, David PascoeAbstract:Abstract The freshwater coelenterate Hydra Vulgaris is an important component of freshwater ecosystems, and this study aimed to establish its value as an indicator of pollutants entering freshwater. The toxicity of the heavy metals copper, cadmium and zinc was assessed using both acute lethal and sub-lethal responses. Techniques involving the identification and large-scale culture of Hydra were also examined. The acute lethal toxicity of copper, cadmium and zinc was measured by determining 24-h, 48-h, 72-h and 96-h LC50 values and the sub-lethal effects assessed using a feeding test. The feeding test examined toxic effects on the normal responses of Hydra to the presence of the prey provided, neonate Daphnia magna (Strauss). Results of this study demonstrated that H. Vulgaris (Pallas) is a suitable species for evaluating the toxicity of freshwater pollutants and can be used successfully to rank toxicants in order of potential hazard. It can be cultured easily in the laboratory to provide large numbers of test animals and can be used in simple, cost-effective bioassays of both acute and sub-acute toxicity. © 1998 Elsevier Science Ltd. All rights reserved
Daniela Evangelista - One of the best experts on this subject based on the ideXlab platform.
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An Atlas of annotations of Hydra Vulgaris transcriptome
BMC Bioinformatics, 2016Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario GuarracinoAbstract:Background RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Results Starting from a previous work, Transcriptator, we present the Atlas of Hydra’s Vulgaris , an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra Vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Conclusion Atlas , as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra Vulgaris exposed to the distinct experimental treatments. Web resource URL http://www-labgtp.na.icar.cnr.it/Atlas .
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An Atlas of annotations of Hydra Vulgaris transcriptome.
BMC bioinformatics, 2016Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario GuarracinoAbstract:RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's Vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra Vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra Vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .
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hvdbase a web resource on Hydra Vulgaris transcriptome
International Conference on Bioinformatics and Biomedical Engineering, 2015Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Valentina Scuotto, Mario Rosario GuarracinoAbstract:The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quantification, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra Vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, and from which it is possible to have access and download all the information related to 15,522 transcripts. The study includes different functional annotations coming from 19 repositories, conveniently grouped by type, such as: i. Pathway: BBID, BioCarta, KEGG, Panther; ii. Domain: COG-Ontology, Interpro, PIR Superfamily, SMART, PFam; iii. Protein Interaction: BIND, MINT, UCSF-TFBS; iv. GO: GO-Term Cellular Components, GO-Term Biological Processes, GO-Term Molecular Functions; v. Miscellaneous: OMIM, EC Number, SP-PIR Keywords, UP-SEQ features. The easily-accessible nature of HvDBase makes this resource a valuable tool for rapidly retrieve knowledges at transcript level as well as useful to inspect differential expression of protein-coding genes in Hydra Vulgaris transcriptome in the contex to the different experimental condition. Web resource URL: http://www-labgtp.na.icar.cnr.it/HvDBase
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IWBBIO (2) - HvDBase : A Web Resource on Hydra Vulgaris Transcriptome
Bioinformatics and Biomedical Engineering, 2015Co-Authors: Daniela Evangelista, Kumar Parijat Tripathi, Valentina Scuotto, Mario Rosario GuarracinoAbstract:The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quantification, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra Vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, and from which it is possible to have access and download all the information related to 15,522 transcripts. The study includes different functional annotations coming from 19 repositories, conveniently grouped by type, such as: i. Pathway: BBID, BioCarta, KEGG, Panther; ii. Domain: COG-Ontology, Interpro, PIR Superfamily, SMART, PFam; iii. Protein Interaction: BIND, MINT, UCSF-TFBS; iv. GO: GO-Term Cellular Components, GO-Term Biological Processes, GO-Term Molecular Functions; v. Miscellaneous: OMIM, EC Number, SP-PIR Keywords, UP-SEQ features. The easily-accessible nature of HvDBase makes this resource a valuable tool for rapidly retrieve knowledges at transcript level as well as useful to inspect differential expression of protein-coding genes in Hydra Vulgaris transcriptome in the contex to the different experimental condition. Web resource URL: http://www-labgtp.na.icar.cnr.it/HvDBase
