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Articles avec #organismes de laboratoire

The Copernicus Atmosphere Monitoring Service (CAMS)

24 Novembre 2016,

Publié par Bioécologie

The Copernicus Atmosphere Monitoring Service (CAMS) provides continuous data and information on atmospheric composition. The service describes the current situation, forecasts the situation a few days ahead, and analyses consistently retrospective data records for recent years.


The European amphioxus (Branchiostoma lanceolatum)

7 Octobre 2016,

Publié par Bioécologie

Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum).

Fuentes M1, Benito E, Bertrand S, Paris M, Mignardot A, Godoy L, Jimenez-Delgado S, Oliveri D, Candiani S, Hirsinger E, D'Aniello S, Pascual-Anaya J, Maeso I, Pestarino M, Vernier P, Nicolas JF, Schubert M, Laudet V, Geneviere AM, Albalat R, Garcia Fernandez J, Holland ND, Escriva H.

1Laboratoire Arago, UMR7628 CNRS, University Pierre and Marie Curie-Paris6 Banyuls sur Mer, F-66650, France.

The cephalochordate amphioxus (Branchiostoma sp.) is an important animal model for studying the evolution of chordate developmental mechanisms. Obtaining amphioxus embryos is a key step for these studies. It has been shown that an increase of 3-4 degrees C in water temperature triggers spawning of the European amphioxus (Branchiostoma lanceolatum) in captivity, however, very little is known about the natural spawning behavior of this species in the field. In this work, we have followed the spawning behavior of the European amphioxus during two spawning seasons (2004 and 2005), both in the field and in captivity. We show that animals in the field spawn approximately from mid-May through early July, but depending on the year, they show different patterns of spawning. Thus, even if temperature has a critical role in the induction of the spawning in captivity, it is not the major factor in the field. Moreover, we report some improvements on the methodology for inducing spawning in captivity (e.g. in maintenance, light cycle control and induction of spawning in a laboratory without running sea water system). These studies have important implications for amphioxus animal husbandry and for improving laboratory techniques to develop amphioxus as an experimental animal model.

Download the publication here

Global Soil Biodiversity Initiative

17 Juin 2016,

Publié par Bioécologie

The Global Soil Biodiversity Initiative was launched in September 2011 and is open to all those interested in developing a coherent platform for promoting the translation of expert knowledge on soil biodiversity into environmental policy and sustainable land management for the protection and enhancement of ecosystem services.

Global Soil Biodiversity Initiative

Model Organisms: yeast, Drosophila and C. elegans

30 Septembre 2014,

Publié par Bioécologie

Pour attraper les C. elegans (oeufs, larves, adultes), on utilise un fil de platine préalablement chauffé pour éviter toute contamination du milieu de culture par des micro-organismes.
Pour attraper les C. elegans (oeufs, larves, adultes), on utilise un fil de platine préalablement chauffé pour éviter toute contamination du milieu de culture par des micro-organismes.

This unique Science Education collection features three model organisms commonly used in life sciences research: S. cerevisiae (Baker’s Yeast), D. melanogaster (the fruit fly), and C. elegans (nematode roundworm). In addition to discussing the current and historical significance of these organisms, the collection includes concepts and methodology relating to how they are maintained and reproduce in the laboratory.

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California academy of sciences diatom collection

31 Juillet 2014,

Publié par Bioecologie

The CAS Diatom Collection Web Site is an ongoing project to present taxonomic information, images, records of collections, and references pertaining to diatoms. This work has been supported in part by grants BSR-9017609 and DEB-9505269 from the National Science Foundation.

Types Catalogue provides information on types in the CAS collection.

Hanna Database provides information on the Specimen, Samples, and Publication tables. The Specimen table contains 75,000 records of specimens that have been identified on slides. The Sample table contains detailed information on 29,000 samples accessioned in the Diatom Collection. The Publication table contains 12,000 bibliographic references.

Hanna Student Fellowship

Diatom identification resources
Currently, the project focuses on recent freshwater diatoms of the United States. In the future, it will include marine and fossil taxa with an expanded geographic range.

Introduction to Diatoms


Freshwater Diatom Identification and Information Resource includes images, keys, and a variety of collection, literature and distribution information to facilitate our understanding of freshwater diatom biodiversity, systematics, and evolution.

Catalogue of diatoms names 
The Catalogue of Diatom Names is a compilation of names of diatom genera, species and taxa at infraspecific ranks (64,000 names). It has been assembled during the past 12 years by staff at the California Academy of Sciences. It includes all scientific names of diatom genera, species, and taxa at infraspecific ranks, with authorship, date, place of publication, page of description, basionym or replaced name (if applicable), status (valid or invalid), and occasionally type information.

Web ressources
North American Diatom Symposium

Great Lakes Diatoms - Useful for images and information on freshwater diatoms.

Center for Algal Microscopy & Image Digitization - Bowling Green State University

Seaweed - Covers all aspects of seaweed and marine biology.

Paleolimnology and Diatom Home Pages - Indiana University. Links of interest to diatomists and paleolimnologists concerning professional announcements, journals, societies, and listservers.

The Loras College Freshwater Diatom Culture Collection - Diatom culture collection containing over 1,200 cultures at reasonable cost.

Index Nominum Algarum (INA). Bibiographia Phycologica Universalis (BPU) - The INA is a card file maintained by Paul Silva at the Herbarium of the University of California . It contains nearly 200,000 names of algae (in the broad sense). The BPU is a card file containing bibliographic references pertaining to algal taxonomy.

Index Nominum Genericorum (Plantarum) - A compilation of generic names published for all organisms covered by the International Code of Botanical Nomenclature.

Peter Bostock's Home Page - A site for translation of botanical Latin.

International Society of Diatom Research - A site for information about the society and its events.

UTEX, The Culture Collection of Algae at the University of Texas at Austin

The Farlow diatom Collection at Harvard University 

Other links from
Botany Dept, Univ Hawai'i at Manoa:

Diatoms, UC Berkeley Phytoplankton overview
The Diatom homepage (University of Indiana) Pictures of temperate diatoms
Experiments in phytoplankton growth: in the field and in the lab Phytoplankton ecology in Florida
Domoic acid as a toxin Red tides in Texas
What are red tides? Manatees linked to red tides
Dinoflagellates, UC Berkeley Global change and your health
Tropical dinoflagellates (University of Tsukuba) Coral bleaching;    Belizean reefs bleach

Caenorhabditis elegans: WormTox project

1 Août 2011,

Publié par JMB

Dans un précédent article, je présentais le programme américain Tox21 qui a pour objectif d’évaluer rapidement la toxicité de milliers de substances chimiques. Une des approches de ce programme est l’utilisation du vers Caenorhabditis elegans comme modèle animal pour mesurer la toxicité de ces substances. Cet organisme, qui adulte mesure 1 mm, est un modèle très intéressant car plusieurs travaux laissent penser que les réponses observés chez ce vers (e.g. expression de gènes,…) pourraient être similaires chez les organismes supérieurs. Ce projet, appelé WormTox, est dirigé par le chercheur Jonathan Freedman.

Pour plus d'informations (en anglais) :

* Boyd WA, McBride SJ, Rice JR, Snyder DW, Freedman JH (2010) A high-throughput method for assessing chemical toxicity using a Caenorhabditis elegans reproduction assay. Toxicol Appl Pharmacol, 245(2):153-9.

* NTP MediumThroughput C. elegans Screening Facility

* 8th World Congress on Alternatives and Animal Use in the Life Sciences (2011)


Caenorhabditis elegans: WormTox project

Caenorhabditis elegans : behavioral assays

20 Juillet 2011,

Publié par JMB

Caenorhabditis elegans (nematod)  is a good laboratory model to behavioral studies. In this publication, basic considerations for behavioral assays are very briefly examined. Both general considerations and admonitions relevant to C. elegans behavioral assays are included. Specific protocols for behavioral assays contributed by individual researchers follow this more general introduction.

Author: Hart, Anne C., ed. Behavior (July 3, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.87.1, http://www.wormbook.org/

Measuring Caenorhabditis elegans Life Span in 96 Well Microtiter Plates

18 Juillet 2011,

Publié par JMB

Caenorhabditis elegans is one of the principle models used to study aging because of its excellent genetics and short lifespan of three weeks. More recently, C.elegans has emerged as a model organism for phenotype based drug screens because of its small size and its ability to grow in microtiter plates.

This publication and video  presented an assay to measure C.elegans lifespan in 96 well microtiter plates. The assay was developed and successfully used to screen large libraries for molecules that extend C.elegans lifespan.

Screening of EPA’s ToxCast libraries using a C. elegans growth assay

17 Juillet 2011,

Publié par JMB

En juin 2011 s'est tenu à l'Université de Californie (Los Angeles, USA)  le " 18th International C. elegans Meeting ". Parmi toutes les présentations, je soulignerai ce poster (voir ci-dessous le résumé) en lien avec le sujet que j'ai abordé dans un précédent article : ici. 
Screening of EPA’s ToxCast libraries using a C. elegans growth assay.
Windy A. Boyd1, Majro V. Smith2, Julie R. Rice1, Jonathan H. Freedman1,3. 1) Biomolecular Screening Branch, National Toxicology Program, RTP, NC; 2) SRA International, RTP, NC; 3) Laboratory of Toxicology and Pharmacology, NIEHS, RTP, NC.

Tox21, an intergovernmental toxicology community, is exploring the use of high-throughput in vitro tests and alternative model organisms to screen the toxicity of large numbers of chemicals to prioritize toxicity testing in traditional toxicological models. As part of this effort, the U.S. EPA compiled collections of chemicals known as the ToxCast Phase I and II libraries. The Phase I library contains 309 unique compounds, mainly pesticide active ingredients with well-characterized mammalian toxicities. The Phase II library contains 676 unique chemicals including failed drugs, food additives, and industrial products. Toxicity assays in 96-well plate format have been developed for C. elegans including reproduction, growth, and feeding using the COPAS Biosort. In the growth assay, the change in size from L1 - L4 is measured after 48-h exposures. The Phase I library was screened for effects on growth and development at seven concentrations. Chemical activity was evaluated using half-maximal effective concentrations (EC50s) and lowest effective concentrations (LECs). A total of 67 EC50s and 173 LECs were estimated. In order to rank chemical potency of all compounds, an activity score was devised based on decreased size at each concentration and steepness of negative concentration-response trends. Activity scores of 0 were classified as inactive, 1 as inconclusive, and 2 - 9 as active with chemical potencies increasing with score values. Overall, 64% of the chemicals were classified as active. The 67 EC50s were negatively related to activity scores, as a low EC50 and a high activity score both indicated toxicity. Furthermore, these same compounds had activity scores of at least 3, suggesting that the activity score is a good indicator of chemical potency. The most active compounds affected growth at all concentrations. These were primarily insecticides including several avermectins, compounds designed to control parasitic nematodes. Activity scores were also compared to mammalian endpoints including chronic, sub-chronic, cancer, developmental and reproductive toxicity in mice, rats, and rabbits. In general, the most active chemicals in the C. elegan.

Session Title: Physiology: Aging and stress (Poster)Program Number: 225A

More informations: The National Toxicology Program (NTP) WormTox

The Toxicology in the 21st Century (Tox21) : un robot pour évaluer la toxicité des substances chimiques

17 Juillet 2011,

Publié par JMB

Au sein de nos sociétés modernes, des dizaines de milliers de substances chimiques (molécules organiques, métaux, radionucléides, nanoparticules,...) sont actuellement en circulation et des centaines de nouvelles substances sont introduites chaque année. Elles font partie de notre quotidien : on peut les retrouver dans des produits ménagers, des désodorisants, des peintures, des déchets industriels, des pesticides, des aliments, et in fine  dans les sols, les cours d'eau, l'air,... Aussi surprenant que cela puisse paraitre, les risques de toxicité pour l'Homme et l'environnement n'ont été évalués que pour seulement 10 % de ces substances. De plus, il reste encore beaucoup à découvrir concernant l'évaluation de ces substances en mélange. En effet, il est par exemple connu qu'une substance puisse ne pas être - ou peu - toxique, mais par contre, en présence d'une autre substance, cette toxicité peut être démultipliée. Sachant qu'il existe des milliers de substances existantes, et des nouvelles chaque année, le nombre de combinaisons possibles - et donc d'effets toxiques potentiels-  est faramineux. Comment évaluer la toxicité de ces milliers de substances, en mélange ou non, pour l'Homme et l'environnement ? 

En 2005, aux USA, un programme de recherche,  "The Toxicology in the 21st Century", fut mis en place pour apporter des réponses à cette question. A ce jour,  quatre agences gouvernementales (the National Institute of Environmental Health Sciences, the Environmental Protection Agency,  the Food and Drug Administration, and the National Institutes of Health Chemical Genomics Center)  sont impliquées dans ce projet de recherche. Une des approches adoptée est le construction d'un robot automatisé pour tester la toxicité de milliers de substances très rapidement et à moindre coût. En simplifiant, le principe est le suivant : une infime quantité de substance est déposée dans des minuscules puits (ces puits constituent une plaque) où se trouve des cellules (par exemple des cellules de foie  humain, de poisson,...qui sont cultivées au laboratoire). Ces cellules peuvent être modifiées pour émettre une lumière fluorescente si la substance est toxique. Toutes ces plaques sont manipulées par un bras robotique. Tous le système est automatisé. Ainsi, il est possible de tester la toxicité de milliers de substances par jour. Par ailleurs, cette méthode évite d'utiliser des animaux vertébrés (poissons, rats, lapins, ....). A travers cette démarche, il est possible d'obtenir rapidement une première estimation de la toxicité des substances chimiques pour par la suite approfondir les investigations.

Voici une vidéo qui présente ce robot en action :


Pour en savoir plus : 

United State Environmental Protection Agency

The CompTox Program

Department of Health and Human Services