Biology subjects

Degli Esposti, D.

Publications and source records attributed to Degli Esposti, D..

3 recordsLinked to original sources

bioRxiv2025

Cadmium tolerance is associated with tissue-specific plasticity of metallothionein gene expression in Gammarus fossarum field populations

The metallothionein gene family codes for proteins involved in metal homeostasis and acute detoxification of non-essential toxic metal ions across the tree of life. We have previously documented increased cadmium (Cd) tolerance in field populations of the crustacean Gammarus fossarum exposed to chronic metallic contamination of geochemical origin. This tolerance is lost during maintenance of organisms in the laboratory, and is transmitted to offspring via parental effects. This study investigated whether the expression of the Cd-responsive metallothionein gene mt1 could be related to Cd-tolerance plasticity in G. fossarum. In eleven populations with different chronic Cd exposure history, we simultaneously assessed Cd-tolerance (mortality tests) and G. fossarum mt1 expression levels by RT-qPCR in the gills and caeca of adult males and in neonates. mt1 expression levels in the two organs were correlated to Cd-tolerance in field organisms and a loss of tolerance was observed in parallel with a decreased expression of mt1 in the caeca after maintenance in uncontaminated water. We also recorded a greater inducibility of mt1 expression in offspring of tolerant populations in the laboratory when re-exposed to Cd along with the bi-parental transmission of Cd-tolerance. These results suggest that the control of mt1 expression is involved in the plasticity of Cd-tolerance in gammarid populations with different histories of Cd exposure. Highlights- mt1 gene expression in the gills and in the hepatopancreatic caeca is associated with Cd tolerance in Gammarus fossarum populations. - Plasticity of G. fossarum mt1 gene expression is associated to loss of Cd tolerance. - Parental effect in Cd tolerance is supported by transgenerational control of mt1 expression, underlid by an increased induction of mt1 during Cd exposure.

evolutionary biology↗

bioRxiv2024

Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipod Gammarus fossarum

Metabolic pathways are targets of environmental contaminants underlying a large variability of toxic effects throughout biodiversity. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In order to improve the knowledge of the metabolism of sentinel species, in this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipod Gammarus fossarum. We revisited the assembly of RNA-seq data by de novo approaches drastically reducing RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs from G. fossarum males and females to identify organ-specific metabolic profiles. The G. fossarum metabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7,630 annotated enzymes, 2,610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. Our analysis shows organ-specific metabolic profiles, such as an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis. In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.

molecular biology↗

bioRxiv2023

Concomitant investigation of crustacean amphipods lipidome and metabolome during molting stage by Zeno SWATH Data-Independent Acquisition coupled with Electron Activated Dissociation and machine learning

BackgroundDIA (Data-Independent Acquisition) is a powerful technique in Liquid Chromatography coupled with high-resolution tandem Mass Spectrometry (LC-MS/MS) in metabolomics and lipidomics, for comprehensive profiling of molecules in biological samples. It provides unbiased coverage, improved reproducibility, and quantitative accuracy compared to Data-Dependent Acquisition (DDA). Combined with the Zeno trap and Electron-Activated Dissociation (EAD), DIA enhances data quality and structural elucidation compared to conventional fragmentation under CID. These tools were applied to study the lipidome and metabolome of the freshwater amphipod Gammarus fossarum, successfully discriminating stages and highlighting significant biological features. Despite being underused, DIA, along with the Zeno trap and EAD, holds great potential for advancing research in the omics field. ResultsDIA combined with the Zeno trap enhances detection reproducibility compared to conventional DDA, improving fragmentation spectra quality and putative identifications. LC coupled with Zeno-SWATH-DIA methods were used to study molecular changes in reproductive cycle of female gammarids. Multivariate data analysis including Principal Component Analysis and Partial Least Square Discriminant Analysis successfully identified statistically significant features responsible for group segregation. EAD fragmentation helped to identify unknown features and to confirm their molecular structure using fragmentation spectra DB annotation or machine learning. EAD database matching accurately annotated five glycerophospholipids, including the position of double bonds on fatty acid chain moieties. SIRIUS database predicted structures of unknown features based on experimental fragmentation spectra to compensate for database incompleteness. SignificanceReproducible detection of features and confident identification of putative compounds are pivotal stages within analytical pipelines. The DIA approach combined with Zeno pulsing and EAD synergistically enhances detection sensitivity while providing orthogonal fragmentation information, thereby facilitating a comprehensive and insightful exploration of pertinent biological molecules associated with the reproductive cycle of gammarids. The developed methodology holds great promises for identifying biomarkers of significance in the field of environmental assessment. HighlightsO_LIAdvancements in Data-Independent-Acquisition methods for lipidomics and metabolomics. C_LIO_LIZeno pulsing improves sensitivity in fragment detection and compound identification. C_LIO_LIComprehensive structure elucidation of lipids and metabolites using EAD fragmentation. C_LI

biochemistry↗