scholarly journals Promising potential of high-throughput molecular phenotyping of freshwater fishes for environmental assessment

2020 ◽  
Author(s):  
Maud Mouchet ◽  
Julie Leloup ◽  
Aurelie Bonin ◽  
Alison Gallet ◽  
BENJAMIN MARIE
Keyword(s):  
High Throughput ◽  
Environmental Assessment ◽  
High Resolution Mass Spectrometry ◽  
Perca Fluviatilis ◽  
Ecological Indicators ◽  
Rapid Expansion ◽  
Lepomis Gibbosus ◽  
Environmental Constraints ◽  
Intestine Microbiome ◽  
Molecular Phenotyping

The recent democratisation of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g. epigenomics, transcriptomics, proteomics, metabolomics, as well as microbiome metabarcoding), that now represent innovative perspectives for environmental assessments. Indeed, when developed for ecologically relevant species, these emerging omics analyses may present valuable alternatives for the development of novel generations of ecological indicators, that in turn could provide early warnings of eco(toxico)logical impairments. This pilot study investigates the bio-indicative potential of different multi-metric tools based on different high-throughput molecular phenotyping approaches (i.e. metabarcoding of the intestine microbiome, and liver metabolomics by nuclear magnetic resonance (NMR) and liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) on two sentinel fish species (Perca fluviatilis and Lepomis gibbosus) from a set of eight water bodies of the peri-urban area of Paris (France). We show that the LC-MS metabolome dataset allows remarkably clear separation of individuals according to the species but also according to their respective sampling lakes. Interestingly, the similar variations of Perca and Lepomis metabolomes occur locally indicating that local environmental constraints drive the observed metabolome variations beyond their obvious genetic differences. Thus, the development of such reliable molecular phenotyping for environmental monitoring constitutes a promising and innovative bio-indicative tool for environmental assessment.

scholarly journals Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping

2018 ◽  
Vol 69 (2) ◽  
pp. 321-333.e3 ◽  
Author(s):  
Philipp A. Jaeger ◽  
Lilia Ornelas ◽  
Cameron McElfresh ◽  
Lily R. Wong ◽  
Randolph Y. Hampton ◽  
...  
Keyword(s):  
High Throughput ◽  
Molecular Phenotyping

scholarly journals Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges

2019 ◽  
Vol 21 (9) ◽  
pp. 1426-1445 ◽  
Author(s):  
Emma L. Schymanski ◽  
Nancy C. Baker ◽  
Antony J. Williams ◽  
Randolph R. Singh ◽  
Jean-Pierre Trezzi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Environmental Exposure ◽  
Environmental Assessment ◽  
Medical Information ◽  
High Resolution Mass Spectrometry ◽  
High Resolution Mass ◽  
Disciplinary Perspective ◽  
Interactive Resources ◽  
Resolution Mass

A multi-disciplinary perspective on connecting chemistry, exposure and medical information to “neurotoxicity” for mass spectrometry-based environmental assessment, including multiple interactive resources for readers to use and explore.

scholarly journals First Occurrence of Eustrongylides spp. (Nematoda: Dioctophymatidae) in a Subalpine Lake in Northwest Italy: New Data on Distribution and Host Range

2020 ◽  
Vol 17 (11) ◽  
pp. 4171 ◽  
Author(s):  
Vasco Menconi ◽  
Maria Vittoria Riina ◽  
Paolo Pastorino ◽  
Davide Mugetti ◽  
Serena Canola ◽  
...  
Keyword(s):  
Host Range ◽  
Fish Species ◽  
Ictalurus Punctatus ◽  
Micropterus Salmoides ◽  
Perca Fluviatilis ◽  
Freshwater Ecosystems ◽  
Lepomis Gibbosus ◽  
Exact Test ◽  
Subalpine Lake ◽  
The Mean

The genus Eustrongylides includes nematodes that infect fish species and fish-eating birds inhabiting freshwater ecosystems. Nematodes belonging to the genus Eustrongylides are potentially pathogenic for humans; infection occurs after the consumption of raw or undercooked fish. In the two-year period 2019–2020, a total of 292 fish belonging to eight species were examined for the occurrence of Eustrongylides spp. from Lake San Michele, a small subalpine lake in northwest Italy. The prevalence of infestation was 18.3% in Lepomis gibbosus, 16.7% in Micropterus salmoides, and 10% in Perca fluviatilis. The other five fish species (Ameiurus melas, Ictalurus punctatus, Squalius cephalus, Carassius carassius, and Scardinius erythrophthalmus) were all negative for parasite presence. There were no significant differences in prevalence between the three fish species (Fisher’s exact test; p = 0.744). The mean intensity of infestation ranged from 1 (M. salmoides and P. fluviatilis) to 1.15 (L. gibbosus), and the mean abundance ranged from 0.1 (P. fluviatilis) to 0.28 (L. gibbosus). There were significant differences in the infestation site between the four muscle quadrants (anterior ventral, anterior dorsal, posterior ventral, and posterior dorsal) and the visceral cavity (Kruskal–Wallis test; p = 0.0008). The study findings advance our knowledge about the distribution and host range of this parasite in Italy.

High-throughput simultaneous quantitation of multi-analytes in tobacco by flow injection coupled to high-resolution mass spectrometry

Talanta ◽  
2018 ◽  
Vol 190 ◽  
pp. 363-374 ◽  
Author(s):  
Samuel Kaiser ◽  
Jailson C. Dias ◽  
Jorge A. Ardila ◽  
Frederico L.F. Soares ◽  
Marcelo C.A. Marcelo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
High Throughput ◽  
Flow Injection ◽  
High Resolution Mass Spectrometry ◽  
High Resolution Mass ◽  
Resolution Mass

scholarly journals Quantification and Identification of Post-Translational Modifications Using Modern Proteomics

2021 ◽  
pp. 225-235
Author(s):  
Anja Holtz ◽  
Nathan Basisty ◽  
Birgit Schilling
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
High Throughput ◽  
High Resolution Mass Spectrometry ◽  
Label Free ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Lysine Residues ◽  
Detailed Protocol ◽  
Resolution Mass

AbstractPost-translational modifications (PTMs) occur dynamically, allowing cells to quickly respond to changes in the environment. Lysine residues can be targeted by several modifications including acylations (acetylation, succinylation, malonylation, glutarylation, and others), methylation, ubiquitination, and other modifications. One of the most efficient methods for the identification of post-translational modifications is utilizing immunoaffinity enrichment followed by high-resolution mass spectrometry. This workflow can be coupled with comprehensive data-independent acquisition (DIA) mass spectrometry to be a high-throughput, label-free PTM quantification approach. Below we describe a detailed protocol to process tissue by homogenization and proteolytically digest proteins, followed by immunoaffinity enrichment of lysine-acetylated peptides to identify and quantify relative changes of acetylation comparing different conditions.

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