Mitochondrial Inheritance, Mito-nuclear Coevolution, and Sex-associated Genes in Bivalve Molluscs: Transcriptomics and Molecular Evolution

Bivalvia represents an ancient taxon including around 25,000 living species that have adapted to a wide range of environmental conditions, and show a great diversity in body size, shell shapes, and anatomic structure. Bivalves are characterized by highly variable genome sizes and extremely high levels of heterozygosity, which obstacle complete and accurate genome assemblies and hinder further genomic studies. Moreover, some bivalve species presented a stable evolutionary exception to the strictly maternal inheritance of mitochondria, namely doubly uniparental inheritance (DUI), making these species a precious model to study mitochondrial biology. During my PhD, I focused on a DUI species, the Manila clam Ruditapes philippinarum, and my work was two-folded. First, taking advantage of a newly assembled draft genome and a large RNA-seq dataset from different tissues of both sexes, I investigated 1) the role of gene expression and alternative splicing in tissue differentiation; 2) the relationship across tissue specificity, regulatory network connectivity, and sequence evolution; 3) sexual contrasting genetic markers potentially associated with sexual differentiation. The detailed information for this part is in Chapter 2. Second, using the same RNA-seq data, I investigated how nuclear oxidative phosphorylation (OXPHOS) genes coordinate with two divergent mitochondrial genomes in DUI species (mito-nuclear coordination and coevolution). To address this question, I compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of R. philippinarum in Chapter 3. To my knowledge, this thesis represents the first study exploring the role of alternative splicing in tissue differentiation, and the first study analyzing both transcriptional regulation and sequence evolution to investigate the coordination of OXPHOS genes in bivalves.

Genes involved in germline regulative pathways in metazoa: an integrative approach to investigate a key feature of animal biology

In Metazoa, the germline represents the cell lineage devoted to transmission of genetic heredity across generations. Its functions intuitively evoke the crucial roles that it plays in the development of a new organism and in the evolution of the species. Germline establishment is tightly tied to animal multicellularity itself, in which the complex differentiation of cell lineages is favoured by the confinement of totipotency in specific cell populations. In the present thesis, I addressed the subject of germline characterization in animals through different approaches, in an attempt to cover different sides and scales. First, I investigated the extent and nature of shared differentially transcribed molecular factors in 10 different species germline-related lineages. I observed that newly evolved genes are less likely to be involved in germline-related mechanisms and that the mostly shared transcriptional signal across the species considered was the upregulation of genes associated to proper DNA replication, instead of the expected transcriptional and post-transcriptional regulation, that apparently have a higher level of lineage-specificity. I then focused on the evolutionary history of Tudor domain containing proteins, a gene family that underwent germline-associated expansions in animals. Using data from 24 holozoan phyla, I could confirm the previously proposed evolution of the Tudor domain secondary structure. Also, I associated lineage-specific family reductions and expansions to peculiar genomic dynamics and to the evolution of germline-associated piRNA pathway of retrotransposon silencing. Lastly, I characterized and investigated the expression of the Tudor protein TDRD7 in the clam Ruditapes philippinarum. Through immunolocalization, I could compare its expression profiles in gametogenic specimens to the previously characterized germline marker vasa. Combining results with literature, I proposed that, in this species, TDRD7 is involved in the assembly of germ granules, i.e. cytoplasmic structures associated to germline differentiation in virtually all animals, but whose assemblers can be taxon specific.

Bycatch and discard issues in the Adriatic demersal fisheries

Commercial fisheries exploiting the demersal resources of Western Adriatic Sea produce high bycatch and discard rates; the most important are bottom trawls, hydraulic dredges and passive nets. The five papers here published assess these fisheries’ impacts and investigate the potential of specific solutions to promote more sustainable exploitation. Papers I, II, III focused on bottom trawl fishery. Paper I compared the catch performance of the two legal codends by accounting for the entire species community in trawl catches. 50% of the catch in weight and 80% in count numbers consisted of discarded species, highlighting the severe impact of this fishery. Paper II estimated the selectivity of experimental codend having meshes turned 90° (T90) and of traditional diamond mesh codend with same mesh size. The T90 codend improved the size selection for all the target species. Paper III investigated the use of T90 meshes in the extension piece together with a reduction in mesh number at extension circumference. Results revealed that both these changes applied in the extension piece did not improve the selectivity of the main target species. Paper IV focused on hydraulic dredge fishery targeting the striped venus clam by assessing the clams’ size selection process operated by the dredge. 25% of the clams caught were not size selected due to clogging phenomenon in the dredge. The clam length with 50% retention probability was 18.9 mm, highlighting that the additional size selection process of sorting sieve is necessary to land only the legal clams >22 mm. Paper V compared the catch performance of innovative fish pots and of traditional trammel net. A similar catch efficiency between the two gears for the commercial portion was observed, while the trammel net produced significantly more discards in terms of species number and weight. All the results are discussed in fisheries management perspective.

Caratterizzazione di SiPM in ambiente criogenico per il far detector di DUNE

DUNE (Deep Underground Neutrino Experiment) è un esperimento internazionale attualmente in costruzione al laboratorio Fermilab in Illinois, Stati Uniti. Il suo scopo sarà quello di studiare alcuni dei fenomeni e quesiti aperti che riguardano i neutrini: particelle debolmente interagenti facenti parte del Modello Standard. In particolare DUNE intende studiare il fenomeno dell'oscillazione di sapore dei neutrini, osservare neutrini provenienti da supernove e stelle di neutroni per studiarne la formazione e ricercare l'eventuale decadimento dei protoni. L'esperimento sarà formato da due siti sperimentali distanti circa 1300 km tra loro: il Near Detector situato a Fermilab ed il Far Detector, situato al Sanford Underground Research Facility (SURF) in South Dakota. Questa tesi è rivolta in particolare al sistema di fotorivelazione del Far Detector, che utilizza fotomoltiplicatori al silicio (Silicon Photomultipliers, o SiPM). Questi dispositivi dovranno funzionare in condizioni criogeniche in argon liquido, perciò è stata avviata un'intensiva campagna di test volta alla caratterizzazione e validazione dei sensori che saranno montati nell'apparato. La sezione INFN di Bologna è coinvolta in questa campagna e dovrà testare una parte dei SiPM destinati all'impiego in DUNE. A tale scopo è stato realizzato, nei laboratori INFN, un sistema per il test di tali dispositivi in criogenia su larga scala. L'attività di tesi ha previsto la caratterizzazione di diversi SiPM sia a temperatura ambiente sia in criogenia e l'analisi delle distribuzioni statistiche dei parametri di diversi campioni di SiPM.

Submesoscale features in regions with different baroclinic deformation radius

In questo studio, un modello nidificato "child" ad alta risoluzione (risoluzione 1/48°) è ottenuto attraverso la piattaforma SURF. Il modello "child" è ottenuto tramite "downscaling" dei campi medi giornalieri dal modello globale "parent" (1/12°). Questo permette di osservare le caratteristiche della sottomesoscala in due regioni dell'oceano Atlantico settentrionale, Azzorre e Bermuda, dal 4 al 12 gennaio 2021. Questa tesi si propone di condurre un'analisi preliminare della relazione fra il raggio di deformazione baroclino e l'esordio dell'attività di sottomesoscala, nelle regioni di interesse. A questo scopo, vengono effettuati molti confronti fra i campi risultanti dal "parent" e dal "child". In particolare, ci concentriamo sulla Mixed-Layer Instability (MLI) studiata attraverso variabili come la Mixed-Layer Depth (MLD), la vorticità relativa, le velocità orizzontali e verticali, l'energia cinetica e la frequenza di Brunt-Vaisala. Dai risultati, mentre il modello "parent" sembra inadeguato, quello "child" è in grado di rilevare la MLI e la presenza di filamenti e scie topografiche in entrambe le regioni, riproducendo meglio le correnti orizzontali e verticali alla sottomesoscala. Ciò fornisce una connessione tra mesoscala e sottomesoscala: mentre nelle Azzorre la MLI sembra svolgere un ruolo chiave nella ristratificazione della colonna d'acqua, lo stesso non sembra nelle Bermuda dove i vortici di mesoscala sono più ampi, influendo maggiormente sulla stratificazione verticale. Qui, i processi di ristratificazione sembrerebbero correlati alle mesoscale piuttosto che alle sottomesoscale. La MLI giocherebbe comunque un ruolo nella generazione di correnti alla sottomesoscala, insieme ad altri processi come la frontogenesi e le scie topografiche. In conclusione, il valore del raggio di deformazione baroclino non sembra influenzare l'attivazione dei processi di sottomesoscala, mentre sembrerebbe determinare l'importanza della MLI nel processo di ristratificazione.