In this thesis RNA-sequencing tools are applied on some representatives of the antarctic trophic chain exposed to a non lethal temperature increase, as to understand and model their response to the increase in temperature expected to happen in this decade, in order to extend eventual functional conclusions to other temperate stenotherm organisms such as those living at extreme depths. RNA-sequencing consists in a set of powerful and sensible tools that allow qualitative and quantitative measurements in gene expression, pairing molecular analyses with state-of-the-art statistics and computer science. The aforementioned sensitivity, in synergy with a proper experimental design, allowed studying not only the response to a temperature increase, but also to the experimental condition itself (i.e. stabling of wild animals in tanks). The notothenioid fish Trematomus bernacchii (from which muscle, gills and brain were sampled), the scallop Adamussium colbecki (from which gills, mantle and digestive gland were sampled), the amphipod Pseudorchomene plebs and the tardigrade Acutuncus antarcticus are the models of choice of this work. In particular T. bernacchii was the most responsive of the bunch, specially in the brain tissues, where the temperature (+1.5°C increase) induced upregulation of genes involved in immune response and inflammatory state after 7 days of exposure. After 20 days of heat exposure many pathways related to synapse function and structure were altered, suggesting an on-going profound alterations in the tissue, which may also be the result of the combined effect of heat and the impossibility to avoid it in captivity. Even more profound effects were observed in the response to time in experimental tanks, as an important shift in gene expression was observed in the brain, suggesting profound changes in the neural pathways, including those involved in specific stress perception. The scallop A. colbecki did not show significant change in gene expression patterns in response to heat, but a small change was observed in the digestive gland after 20 days of experimental captivity, showing alterations in genes whose functions are mainly involved in feeding ability. Samples from the amphipod P. plebs were challenging to prepare and to analyze, as many were lost due to unfreezing during transport. Moreover the presence of a bycatch of Eusirus cf. giganteus juvenile and an high degree of parasitism from a dinoflagellate of the genus Hematodinium in all samples made it impossible to study the response of the amphipod to a warmer environment. Nevertheless, the transcriptomic data allowed the identification of an high expression of hemocyanin in E. giganteus suggesting a possible cold adaptation trait, the classification of our samples as a Orchomenid cryptic species, and the first identification of active Hematodinium parasitism in the antarctic ocean. Finally the tardigrade A. antarcticus displayed a striking sample variability, that may underlie an never described genomic variability and/or an high level of heterozygosity. This fact reduced the number of samples in the differential expression analysis, which nevertheless showed a response to short term exposure to heat with a pattern proportional to temperature in terms of fold changes of gene expression levels. The differentially expressed genes suggested that mitochondrial oxidative metabolism increased and hinted the activation of pathways related to resistance forms typical of the Tardigrada phylum. Such a response was not observed in a long term exposure to the higher temperatures, suggesting that the changes observed in short term are compensatory. ​

Risposta trascrittomica di metazoi antartici al riscaldamento ambientale

GRECO, SAMUELE
2022

Abstract

In this thesis RNA-sequencing tools are applied on some representatives of the antarctic trophic chain exposed to a non lethal temperature increase, as to understand and model their response to the increase in temperature expected to happen in this decade, in order to extend eventual functional conclusions to other temperate stenotherm organisms such as those living at extreme depths. RNA-sequencing consists in a set of powerful and sensible tools that allow qualitative and quantitative measurements in gene expression, pairing molecular analyses with state-of-the-art statistics and computer science. The aforementioned sensitivity, in synergy with a proper experimental design, allowed studying not only the response to a temperature increase, but also to the experimental condition itself (i.e. stabling of wild animals in tanks). The notothenioid fish Trematomus bernacchii (from which muscle, gills and brain were sampled), the scallop Adamussium colbecki (from which gills, mantle and digestive gland were sampled), the amphipod Pseudorchomene plebs and the tardigrade Acutuncus antarcticus are the models of choice of this work. In particular T. bernacchii was the most responsive of the bunch, specially in the brain tissues, where the temperature (+1.5°C increase) induced upregulation of genes involved in immune response and inflammatory state after 7 days of exposure. After 20 days of heat exposure many pathways related to synapse function and structure were altered, suggesting an on-going profound alterations in the tissue, which may also be the result of the combined effect of heat and the impossibility to avoid it in captivity. Even more profound effects were observed in the response to time in experimental tanks, as an important shift in gene expression was observed in the brain, suggesting profound changes in the neural pathways, including those involved in specific stress perception. The scallop A. colbecki did not show significant change in gene expression patterns in response to heat, but a small change was observed in the digestive gland after 20 days of experimental captivity, showing alterations in genes whose functions are mainly involved in feeding ability. Samples from the amphipod P. plebs were challenging to prepare and to analyze, as many were lost due to unfreezing during transport. Moreover the presence of a bycatch of Eusirus cf. giganteus juvenile and an high degree of parasitism from a dinoflagellate of the genus Hematodinium in all samples made it impossible to study the response of the amphipod to a warmer environment. Nevertheless, the transcriptomic data allowed the identification of an high expression of hemocyanin in E. giganteus suggesting a possible cold adaptation trait, the classification of our samples as a Orchomenid cryptic species, and the first identification of active Hematodinium parasitism in the antarctic ocean. Finally the tardigrade A. antarcticus displayed a striking sample variability, that may underlie an never described genomic variability and/or an high level of heterozygosity. This fact reduced the number of samples in the differential expression analysis, which nevertheless showed a response to short term exposure to heat with a pattern proportional to temperature in terms of fold changes of gene expression levels. The differentially expressed genes suggested that mitochondrial oxidative metabolism increased and hinted the activation of pathways related to resistance forms typical of the Tardigrada phylum. Such a response was not observed in a long term exposure to the higher temperatures, suggesting that the changes observed in short term are compensatory. ​
GIULIANINI, PIERO GIULIO
GERDOL, MARCO
34
2020/2021
Settore BIO/05 - Zoologia
Università degli Studi di Trieste
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11368/3030493
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