Title |
CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems
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Published in |
BMC Genomics, August 2016
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DOI | 10.1186/s12864-016-2988-4 |
Pubmed ID | |
Authors |
Anne Abot, Gregory Arnal, Lucas Auer, Adèle Lazuka, Delphine Labourdette, Sophie Lamarre, Lidwine Trouilh, Elisabeth Laville, Vincent Lombard, Gabrielle Potocki-Veronese, Bernard Henrissat, Michael O’Donohue, Guillermina Hernandez-Raquet, Claire Dumon, Véronique Anton Leberre |
Abstract |
Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans. This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems. |
X Demographics
Geographical breakdown
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France | 1 | 33% |
Unknown | 2 | 67% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 3 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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France | 1 | 2% |
Unknown | 60 | 98% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 19 | 31% |
Student > Ph. D. Student | 9 | 15% |
Student > Bachelor | 7 | 11% |
Other | 5 | 8% |
Lecturer | 4 | 7% |
Other | 11 | 18% |
Unknown | 6 | 10% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 20 | 33% |
Biochemistry, Genetics and Molecular Biology | 16 | 26% |
Environmental Science | 5 | 8% |
Immunology and Microbiology | 4 | 7% |
Chemistry | 3 | 5% |
Other | 5 | 8% |
Unknown | 8 | 13% |