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Risposta trascrittomica di metazoi antartici al riscaldamento ambientale
No full textIn 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.
Independent acquisition of short insertions at the RIR1 site in the spike N‐terminal domain of the SARS‐CoV‐2 BA.2 lineage
Full text linkAlthough the major SARS‐CoV‐2 omicron lineages share over 30 non‐synonymous substitutions in the spike glycoprotein, they show several unique mutations that were acquired after their ancestral split. One of the most intriguing mutations associated with BA.1 is the presence of the inserted tripeptide Glu‐Pro‐Glu within the N‐terminal domain, at a site that had previously independently acquired short insertions in several other SARS‐CoV‐2 lineages. Although the functional implications of the small nucleotide sequences found at this insertion hotspot, named RIR1, are still unclear, we have previously hypothesized that they may play a compensatory role in counterbalancing minor fitness deficits associated with other co‐occurring spike non‐synonymous mutations. Here we show that similar insertion events have independently occurred at RIR1 at least 20 times in early 2022 within the BA.2 lineage, being occasionally associated with significant community transmission. One of these omicron sublineages, characterized by a Ser‐Gly‐Arg insertion in position 212, has been responsible of over 4,000 documented covid‐19 cases worldwide between January and July 2022, for the most part concentrated in Denmark, where it reached a national prevalence close to 4% (10% in the Nordjylland region) in mid‐May. Although the concurrent spread of the BA.2.12.1, BA.4 and BA.5 lineages led to the rapid decline of this BA.2 sublineage, the independent acquisition of several other RIR1 insertions on a BA.2 genomic background suggests that these events may provide a slight fitness advantage. Therefore, we they should be carefully monitored in the upcoming months in other emerging omicron‐related lineages, including BA.5. This article is protected by copyright. All rights reserve
Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves
Full text linkC1q-domain-containing (C1qDC) proteins are rapidly emerging as key players in the innate immune response of bivalve mollusks. Growing experimental evidence suggests that these highly abundant secretory proteins are involved in the recognition of microbe-associated molecular patterns, serving as lectin-like molecules in the bivalve proto-complement system. While a large amount of functional data concerning the binding specificity of the globular head C1q domain and on the regulation of these molecules in response to infection are quickly accumulating, the genetic mechanisms that have led to the extraordinary lineage-specific expansion of the C1qDC gene family in bivalves are still largely unknown. The analysis of the chromosome-scale genome assembly of the Eastern oyster Crassostrea virginica revealed that the 476 oyster C1qDC genes, far from being uniformly distributed along the genome, are located in large clusters of tandemly duplicated paralogs, mostly found on chromosomes 7 and 8. Our observations point out that the evolutionary process behind the development of a large arsenal of C1qDC lectin-like molecules in marine bivalves is still ongoing and likely based on an unequal crossing over
Molecular Diversity of Mytilin-Like Defense Peptides in Mytilidae (Mollusca, Bivalvia)
Full text linkThe CS-αβ architecture is a structural scaffold shared by a high number of small, cationic, cysteine-rich defense peptides, found in nearly all the major branches of the tree of life. Although several CS-αβ peptides involved in innate immune response have been described so far in bivalve mollusks, a clear-cut definition of their molecular diversity is still lacking, leaving the evolutionary relationship among defensins, mytilins, myticins and other structurally similar antimicrobial peptides still unclear. In this study, we performed a comprehensive bioinformatic screening of the genomes and transcriptomes available for marine mussels (Mytilida), redefining the distribution of mytilin-like CS-αβ peptides, which in spite of limited primary sequence similarity maintain in all cases a well-conserved backbone, stabilized by four disulfide bonds. Variations in the size of the alpha-helix and the two antiparallel beta strand region, as well as the positioning of the cysteine residues involved in the formation of the C1–C5 disulfide bond might allow a certain degree of structural flexibility, whose functional implications remain to be investigated. The identification of mytilins in Trichomya and Perna spp. revealed that many additional CS-αβ AMPs remain to be formally described and functionally characterized in Mytilidae, and suggest that a more robust scheme should be used for the future classification of such peptides with respect with their evolutionary origi
Bivalves Present the Largest and Most Diversified Repertoire of Toll-Like Receptors in the Animal Kingdom, Suggesting Broad-Spectrum Pathogen Recognition in Marine Waters
Full text link21 pages, 10 figures.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial LicenseToll-like receptors (TLRs) are the most widespread class of membrane-bound innate immune receptors, responsible of specific pathogen recognition and production of immune effectors through the activation of intracellular signaling cascades. The repertoire of TLRs was analyzed in 85 metazoans, enriched on molluscan species, an underrepresented phylum in previous studies. Following an ancient evolutionary origin, suggested by the presence of TLR genes in Anthozoa (Cnidaria), these receptors underwent multiple independent gene family expansions, the most significant of which occurred in bivalve molluscs. Marine mussels (Mytilus spp.) had the largest TLR repertoire in the animal kingdom, with evidence of several lineage-specific expanded TLR subfamilies with different degrees of orthology conservation within bivalves. Phylogenetic analyses revealed that bivalve TLR repertoires were more diversified than their counterparts in deuterostomes or ecdysozoans. The complex evolutionary history of TLRs, characterized by lineage-specific expansions and losses, along with episodic positive selection acting on the extracellular recognition domains, suggests that functional diversification might be a leading evolutionary force. We analyzed a comprehensive transcriptomic data set from Mytilus galloprovincialis and built transcriptomic correlation clusters with the TLRs expressed in gills and in hemocytes. The implication of specific TLRs in different immune pathways was evidenced, as well as their specific modulation in response to different biotic and abiotic stimuli. We propose that, in a similar fashion to the remarkable functional specialization of vertebrate TLRs, the expansion of the TLR gene family in bivalves attends to a functional specification motivated by the biological particularities of these organisms and their living environmentThis research was funded by Ministerio de Ciencia e Innovación (PID2021-124955OB-I00) and by Agencia Galega de Innovación (IN607B 2022/13). A.S. was supported by a Spanish AEI/EU-FSE predoctoral contract PRE2019-090760Peer reviewe
Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome
Full text linkCaudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs
Congeria in the Dinaric Karst: conservation and scientific study of a unique cave-dwelling bivalve genus
Full text linkCongeria, one of the few extant genera of cave-dwelling bivalve mollusks, is endemic to the Dinaric Karst and currently comprises three distinct species with highly fragmented distributions, facing serious threats of extinction. Here we highlight the unique life history traits exhibited by Congeria and discuss the potential of ongoing and future scientific research in addressing the critical challenges associated with its conservation. The subterranean waters of the Karst represent a highly stable yet vulnerable ecosystem that has been significantly impacted by human activities over the past few decades. Hydrotechnical projects have notably reduced water flow to underground habitats that are essential for the reproduction and survival of Congeria, leading to habitat loss and severe population declines in several areas. These challenges, together with water pollution, intensive agriculture and tourism, are projected to cause further population decreases in the coming decades, exacerbated by inadequate regulatory measures and our limited understanding of the biology of these bivalves. Scientific advancements, which include the recently completed sequencing of the genome of C. kusceri, have the potential to provide critical insights into previously unexplored aspects of Congeria biology, unveiling the molecular mechanisms underlying its adaptive success in this challenging environment. Such research may offer a platform for an improved understanding of the factors underpinning the adaptation of Congeria to the subterranean environments and a comprehensive assessment of the genetic health, demographic history and resilience of the three extant species in the face of habitat alterations
First de novo transcriptome analysis of the Antarctic springtail Cryptopygus terranovus (Collembola: Isotomidae) following mid-term heat exposure
Full text linkGlobal human activities, such as greenhouse emissions and pollution, are promoting global
warming, environmental changes and biodiversity reduction. Pristine environments such as those of
Antarctica are not immune to these phenomena, as is noticeable from the increasing pace of the
temperature shift registered within the continent in recent decades. In this study, we describe the first
de novo transcriptome analysis of the endemic Antarctic springtail (= collembolan) Cryptopygus
terranovus and we evaluate its global gene expression response following a mid-term exposure of
20 days to 18°C. Expression data are compared with wild specimens sampled from their native
environment to outline the molecular mechanisms triggered by the thermal exposure. Although
individual plasticity in transcript modulation is assessed, several pathways appear to be differentially
modulated in springtails subjected to the heat treatment vs wild specimens. Through enrichment
analysis, we show that protein catabolism, fatty acid metabolism and a sexual response characterized
by spermatid development are induced, while carbohydrate consumption, lipid catabolism and tissue
development are downregulated in treated samples compared to control
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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