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ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data

O. Arnaiz, S. Cain, J. Cohen, L. Sperling
2007 Nucleic Acids Research  
ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia.  ...  Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the  ...  The Paramecium stock collection and genetic data were curated with the help of Janine Beisson and Françoise Ruiz (CGM, Gif-sur-Yvette).  ... 
doi:10.1093/nar/gkl777 pmid:17142227 pmcid:PMC1669747 fatcat:q3x6xgilmfhgfheeva5yfoaaxm

ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

O. Arnaiz, L. Sperling
2010 Nucleic Acids Research  
ParameciumDB is a community model organism database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia.  ...  Now ready for next-generation deep sequencing data and the genomes of other Paramecium species, this open-access resource is available at http://paramecium.cgm.cnrs-gif.fr.  ...  ParameciumDB is developed in the context of the CNRS European Research Group 'Paramecium Genome Dynamics and Evolution'.  ... 
doi:10.1093/nar/gkq918 pmid:20952411 pmcid:PMC3013783 fatcat:qxgffjoa7jelnmp4acfxyisrxa

GMODWeb: a web framework for the generic model organism database

Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein
2008 Genome Biology  
Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types.  ...  The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data.  ...  The authors wish to thank Stephen Ficklin and Meg Staton for sharing their experiences using Turnkey and GMODWeb at the Clemson University Genomics Institute.  ... 
doi:10.1186/gb-2008-9-6-r102 pmid:18570664 pmcid:PMC2481422 fatcat:ert5bsmtsbd73n6xgo26fuuxau

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Chengjie Fu, Jie Xiong, Wei Miao
2009 BMC Genomics  
Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under  ...  The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families  ...  Acknowledgements The authors thank Prof. Martin Gorovsky and Jody Bowen (University of Rochester) for generously sharing the microarray data and their critical review of the manuscript, Prof.  ... 
doi:10.1186/1471-2164-10-208 pmid:19409101 pmcid:PMC2691746 fatcat:y4ijtrzsljc5rmgkpsldw4bzna

C11orf70 mutations causing primary ciliary dyskinesia disrupt a conserved step in the intraflagellar transport-dependent assembly of multiple axonemal dyneins [article]

Mahmoud R. Fassad, Amelia Shoemark, Pierrick le Borgne, France Koll, Mitali Patel, Mellisa Dixon, Jane Hayward, Charlotte Richardson, Emily Frost, Lucy Jenkins, Thomas Cullup, Eddie M. K. Chung (+6 others)
2017 bioRxiv   pre-print
Fluorescently tagged C11orf70 in Paramecium and Chlamydomonas localises mainly in the cytoplasm with a small amount in the ciliary component, its abundance in the axoneme being IFT-dependant.  ...  We screened a cohort of affected individuals for disease-causing mutations using a targeted next generation sequencing panel and identified 2 unrelated families (3 affected children) with mutations in  ...  Acknowledgements We are very grateful to the families who participated in this study and thank the UK PCD Family  ... 
doi:10.1101/211953 fatcat:y46hinfiqvft7jrlwmmel72nai

Tetrahymena genome database Wiki: a community-maintained model organism database

N. A. Stover, R. S. Punia, M. S. Bowen, S. B. Dolins, T. G. Clark
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors would like to thank Mike Cherry, Stuart Miyasato, Gail Binkley and the staff at Saccharomyces Genome Database for maintaining TGD service during the transition to Bradley University  ...  The work of the Tetrahymena research community produces a sizable amount of data that can be used to improve the annotation of the genome.  ...  With these tasks completed we are now turning our attention to two goals: integrating new sources of data that will make the site more useful and convenient, and promoting use of the community annotation  ... 
doi:10.1093/database/bas007 pmid:22434841 pmcid:PMC3308163 fatcat:jdswubl2wzdh3fvccyulhiwkpm

ゾウリムシを用いた研究から明らかになった繊毛のエネルギー供給と運動調節機構
The molecular mechanisms of intraciliary energy-supply system and ciliary movements revealed by the studies on Paramecium cilia

Osamu Kutomi, Manabu Hori
2014 Gensei dobutsugaku zasshi  
Paramecium has long been used as a model organism for studying ciliary motility, because of its valuable experimental systems.  ...  Most motile cilia/flagella possess the inner structure called the axoneme with "9 + 2" pattern, in which the nine doublet microtubules surround two central singlet microtubules.  ...  Arnaiz, O., Cain, S., Cohen, J. and Sperling, L. (2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.  ... 
doi:10.18980/jjprotozool.47.1-2_13 fatcat:42ptex2vz5dntg4f4u57fwqkqu

Biochemical and regulatory aspects of DNA double-strand break repair

Julia Eileen Godau
2018
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res. 39, D632-D636 (2011). 38.  ...  Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. BMC Genomics 18, 483 (2017). 42. Lukaszewicz, A., Howard-Till, R.  ...  We further corroborated the importance of the FHTA sequence by showing that BRC4 16-mer peptides harboring a mirrored ATHF sequence display greatly reduced RAD51 binding affinity.  ... 
doi:10.5167/uzh-170542 fatcat:kovezqguv5fntbgz7ngrwbxmqe