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2. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy.

Author

Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cédric Berney, Lucie Bittner, Christophe Boutte, Gaétan Burgaud, Colomban de Vargas, Johan Decelle, Javier del Campo, John R. Dolan, Micah Dunthorn, Bente Edvardsen, Maria Holzmann, Wiebe H. C. F. Kooistra, Enrique Lara, Noan Le Bescot, Ramiro Logares, Frédéric Mahé, Ramon Massana, Marina Montresor, Raphael Morard, Fabrice Not, Jan Pawlowski, Ian Probert, Anne-Laure Sauvadet, Raffaele Siano, Thorsten Stoeck, Daniel Vaulot, Pascal Zimmermann, and Richard Christen

Published
2013
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3. Incidence and Outcome of Post-Transplant Cancer in Kidney Recipients with or without Pre-Transplant Malignancies

Author

Anita Hurni, Vanessa Banz, Lucienne Christen, Dusan Harmacek, Pascal Zimmermann, Daniel Sidler, Andrea Karolin, and Fabian Hauenstein

Subjects
medicine.medical_specialty, business.industry, Incidence (epidemiology), Cancer, Retrospective cohort study, 610 Medicine & health, General Medicine, medicine.disease, Single Center, Transplantation, surgical procedures, operative, Internal medicine, Cohort, medicine, business, Contraindication, Kidney transplantation
Abstract

Background: Previously, pre-existing cancers were considered a contraindication for kidney transplantation. Meanwhile, due to improved screening and treatment options, the prevalence of dialysis patients with cancer history is increasing. Potentially these patients could be eligible for kidney transplantation. Methods: Single center retrospective study, analyzing the incidence and outcome of de novo cancers in kidney transplant recipients with and without pre-existing cancer from 01.01.1981 through 31.12.2018. Results: The incidence of eligible transplant candidates with pre-existing malignancies increased over the last 40 years, primarily due to diagnosis of limited disease during the pre-transplant evaluations. Outcome is good with comparable graft and patient survival. Incidence of recurrent or secondary de novo cancers is low. The average annual incidence of de novo malignancy is 1 per 100 patient years in the post-transplant follow-up. In the last decades, the incidence of kidney cancers decreased, while lung cancers and post-transplant lymphoproliferative disorder (PTLD) increased. The outcome of malignant disease was poor, notably in patients with disseminated disease at presentation and mainly attributed to cancer-related death. Meanwhile, graft losses were rare after diagnosis of de novo malignancy. Conclusions: In summary, the incidence of pre-existing and de novo solid cancers increased within the last four decades in our transplant cohort. Patients with pre-existing cancers have an excellent outcome and – if well selected – should not be excluded from transplantation. Meanwhile, de novo cancers after transplantation are associated with poor outcome.

Published
2021

4. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Christophe Boutte, Raphael Morard, Gaëtan Burgaud, Micah Dunthorn, Pascal Zimmermann, David Bass, Noan Le Bescot, Laure Guillou, Fabrice Not, Bente Edvardsen, Enrique Lara, Dipankar Bachar, Colomban de Vargas, Thorsten Stoeck, Anne Laure Sauvadet, Marina Montresor, Jan Pawlowski, Cédric Berney, Daniel Vaulot, Maria Holzmann, Lucie Bittner, Ramon Massana, Johan Decelle, Javier del Campo, Wiebe H. C. F. Kooistra, Ramiro Logares, Richard Christen, Stéphane Audic, Frédéric Mahé, John R. Dolan, Raffaele Siano, Ian Probert, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Department of life sciences, The Natural History Museum [London] (NHM), Groupe Plancton Océanique, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Evolutionary Genetics, Stazione Zoologica Anton Dohrn (SZN), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of genetics and evolution, University of Geneva [Switzerland], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of ecology, Universität Kaiserslautern, Point Compétence Informatique, European Union [2008-6530, 287589], ANR (France), ANR Paralex (French), BIOMARKS, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Computational biology, medicine.disease_cause, Ribosome, DNA, Ribosomal, DNA sequencing, 03 medical and health sciences, Genetics, medicine, DNA Barcoding, Taxonomic, Gene, 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, 0303 health sciences, Internet, biology, 030306 microbiology, fungi, Intron, Protist, Eukaryota, High-Throughput Nucleotide Sequencing, Genes, rRNA, Articles, Ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, [SDE]Environmental Sciences, Eukaryote, Databases, Nucleic Acid, Cercozoa
Abstract

Laure Guillou ... et al. -- 8 pages, 1 figure, 1 table, The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists, The European Union’s Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7)

Published
2013

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