Dataset Information

Introducing IsoMad, a compilation of isotopic datasets for Madagascar.

ABSTRACT: We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.

SUBMITTER: Hixon SW

PROVIDER: S-EPMC11316086 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Introducing IsoMad, a compilation of isotopic datasets for Madagascar.

Hixon Sean W SW Fernandes Ricardo R Andriamahaihavana Antonin A Baden Andrea L AL Blanco Marina B MB Caulier Guillaume G Dammhahn Melanie M Eeckhaut Igor I Eppley Timothy M TM Frédérich Bruno B Ganzhorn Jörg U JU Garbaras Andrius A Gibson Dean D Goodman Steven M SM Irwin Mitchell M Kelley Elizabeth A EA Michel Loïc N LN Lepoint Gilles G Loudon James E JE Mittelheiser Laurent L Rakotondranary Jacques J Rasamisoa Delaïd C DC Rasolofonirina Richard R Ratovonamana Yedidya Y Razafindramanana Josia J Reisdorff Christoph C Sponheimer Matt M Terrana Lucas L Vasey Natalie N Crowley Brooke E BE

Scientific data 20240809 1

We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work ...[more]

PMID: 39122728

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Project description:Carbohydrate active enzymes (CAZymes) are pivotal in biological processes including energy metabolism, cell structure maintenance, signalling, and pathogen recognition. Bioinformatic prediction and mining of CAZymes improves our understanding of these activities and enables discovery of candidates of interest for industrial biotechnology, particularly the processing of organic waste for biofuel production. CAZy (www.cazy.org) is a high-quality, manually curated, and authoritative database of CAZymes that is often the starting point for these analyses. Automated querying and integration of CAZy data with other public datasets would constitute a powerful resource for mining and exploring CAZyme diversity. However, CAZy does not itself provide methods to automate queries, or integrate annotation data from other sources (except by following hyperlinks) to support further analysis. To overcome these limitations we developed cazy_webscraper, a command-line tool that retrieves data from CAZy and other online resources to build a local, shareable and reproducible database that augments and extends the authoritative CAZy database. cazy_webscraper's integration of curated CAZyme annotations with their corresponding protein sequences, up-to-date taxonomy assignments, and protein structure data facilitates automated large-scale and targeted bioinformatic CAZyme family analysis and candidate screening. This tool has found widespread uptake in the community, with over 35 000 downloads (from April 2021 to June 2023). We demonstrate the use and application of cazy_webscraper to: (i) augment, update and correct CAZy database accessions; (ii) explore the taxonomic distribution of CAZymes recorded in CAZy, identifying under-represented taxa and unusual CAZy class distributions; and (iii) investigate three CAZymes having potential biotechnological application for degradation of biomass, but lacking a representative structure in the PDB database. We describe in general how cazy_webscraper facilitates functional, structural and evolutionary studies to aid identification of candidate enzymes for further characterization, and specifically note that CAZy provides supporting evidence for recent expansion of the Auxiliary Activities (AA) CAZy family in eukaryotes, consistent with functions potentially specific to eukaryotic lifestyles.

Dataset Information

Introducing IsoMad, a compilation of isotopic datasets for Madagascar.

Publications

Introducing IsoMad, a compilation of isotopic datasets for Madagascar.

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