Analisi e gestione informatica di sequenze trascritte in organismi non-modello

2011/2012Il tema principale di questo lavoro di tesi è la discussione dei metodi che, mediante l’utilizzo di strumenti creati ad-hoc e di software di terze parti, hanno permesso analizzare sequenze trascritte di 5 organismi non-modello: Mytilus galloprovincialis, Ruditapes philippinarum, Latimeria menadoensis, Astacus leptodactylus e Procambarus clarkii.XXV Ciclo198

Action of larch bark in the regulation of cortisol induced stress in sheep

The effect of Larix decidua (LD) dietary administration on gene expression patterns has been evaluated in sheep under ACTH challenge. Experimental protocol was approved by local laws and regulations. Eighteen sheep at maintenance were allotted to 3 groups: CTR (negative control, without ACTH, and supplementation), ACTH (positive control, with ACTH, and without supplementation), LD (ACTH and 50 g/head/day of LD). ACTH was injected for 3 subsequent days to ACTH and LD groups and blood was sampled before (T0) and after 3 (T3) and 51 (T51) hours from the first injection. RNA extracted samples were pooled together within group and time of sampling. A custom oligoarray was synthesized using 24,384 35 -40mer probes designed from 12,194 UniGenes (NCBI) on a CombiMatrix 90K platform. Cy5 labelled samples were hybridized on the chip. Statistical analysis, performed with MeV software 4.1 (TIGR), allowed the identification of a set of genes which were up or down regulated as a consequence of ACTH treatment. Genes that resulted differentially expressed were annotated with HomoloGene system and data mining was performed with Babelomics v3.1 tool. Functional analysis showed that most of the differentially expressed genes belong to KEGG pathways involved in immune system response and signaling molecules and interaction. Larch administration was effective in counteracting the effect of ACTH injection on the inflammatory processes, restoring the physiological homeostasis

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.Agência financiadora Portuguese national funds from FCT-Foundation for Science and Technology: UID/Multi/04326/2016; European Regional Development Fund (FEDER): 22153-01/SAICT/2016; ALG-01-0145-FEDER-022121; ALG-01-0145-FEDER-022231; MAR2020 operational programme of the European Maritime and Fisheries Fund (project SARDI-NOMICS): MAR-01.04.02-FEAMP-0024; European Union's Horizon 2020 research and innovation programme: 654008info:eu-repo/semantics/publishedVersio

The eyestalk transcriptome of red swamp crayfish Procambarus clarkii

The red swamp crayfish (. Procambarus clarkii, Girard 1852) is among the most economically important freshwater crustacean species, and it is also considered one of the most aggressive invasive species worldwide. Despite its commercial importance and being one of the most studied crayfish species, its genomic and transcriptomic layout has only been partially studied. Illumina RNA-sequencing was applied to characterize the eyestalk transcriptome and identify its most characterizing genes. A collection of 83,170,732 reads from eyestalks was obtained using Illumina paired-end sequencing technology. A de novo assembly was performed with the Trinity assembly software generating 119,255 contigs (average length of 1007. bp) and identifying the first sequenced transcriptome in this species.The eyestalk is a major site for the production of neurohormones and controls a variety of physiological functions such as osmotic regulation, molting, epidermal color patterns and reproduction. Hence, its transcriptomic characterization is interesting and potentially instrumental to the elucidation of genes which have not been comprehensively described yet. Moreover, the availability of such a large amount of information supported the characterization of molecular families which have never been described before. The P. clarkii eyestalk transcriptome reported here provides a resource for improving the knowledge of the still incompletely defined neuroendocrinology of this species and represents an important source of data for all the interested carcinologists

RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum

Background The Mediterranean mussel Mytilus galloprovincialis is marine bivalve with a relevant commercial importance as well as a key sentinel organism for the biomonitoring of environmental pollution. Here we report the RNA sequencing of the mussel digestive gland, performed with the aim: a) to produce a high quality de novo transcriptome assembly, thus improving the genetic and molecular knowledge of this organism b) to provide an initial assessment of the response to paralytic shellfish poisoning (PSP) on a molecular level, in order to identify possible molecular markers of toxin accumulation. Results The comprehensive de novo assembly and annotation of the transcriptome yielded a collection of 12,079 non-redundant consensus sequences with an average length of 958 bp, with a high percentage of full-length transcripts. The whole-transcriptome gene expression study indicated that the accumulation of paralytic toxins produced by the dinoflagellate Alexandrium minutum over a time span of 5 days scarcely affected gene expression, but the results need further validation with a greater number of biological samples and naturally contaminated specimens. Conclusion The digestive gland reference transcriptome we produced significantly improves the data collected from previous sequencing efforts and provides a basic resource for expanding functional genomics investigations in M. galloprovincialis. Although not conclusive, the results of the RNA-seq gene expression analysis support the classification of mussels as bivalves refractory to paralytic shellfish poisoning and point out that the identification molecular biomarkers of PSP in the digestive gland of this organism is problematic

New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach.

Trebouxia is the most common lichen-forming genus of aero-terrestrial green algae and all its species are desiccation tolerant (DT). The molecular bases of this remarkable adaptation are, however, still largely unknown. We applied a transcriptomic approach to a common member of the genus, T. gelatinosa, to investigate the alteration of gene expression occurring after dehydration and subsequent rehydration in comparison to cells kept constantly hydrated. We sequenced, de novo assembled and annotated the transcriptome of axenically cultured T. gelatinosa by using Illumina sequencing technology. We tracked the expression profiles of over 13,000 protein-coding transcripts. During the dehydration/rehydration cycle c. 92 % of the total protein-coding transcripts displayed a stable expression, suggesting that the desiccation tolerance of T. gelatinosa mostly relies on constitutive mechanisms. Dehydration and rehydration affected mainly the gene expression for components of the photosynthetic apparatus, the ROS-scavenging system, Heat Shock Proteins, aquaporins, expansins, and desiccation related proteins (DRPs), which are highly diversified in T. gelatinosa, whereas Late Embryogenesis Abundant Proteins were not affected. Only some of these phenomena were previously observed in other DT green algae, bryophytes and resurrection plants, other traits being distinctive of T. gelatinosa, and perhaps related to its symbiotic lifestyle. Finally, the phylogenetic inference extended to DRPs of other chlorophytes, embryophytes and bacteria clearly pointed out that DRPs of chlorophytes are not orthologous to those of embryophytes: some of them were likely acquired through horizontal gene transfer from extremophile bacteria which live in symbiosis within the lichen thallus

Identification and Characterization of a Novel Family of Cysteine-Rich Peptides (MgCRP-I) from Mytilus galloprovincialis

We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis. These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling

CAESAR: Space Weather archive prototype for ASPIS

The project CAESAR (Comprehensive spAce wEather Studies for the ASPIS prototype Realization) is aimed to tackle all the relevant aspects of Space Weather (SWE) and realize the prototype of the scientific data centre for Space Weather of the Italian Space Agency (ASI) called ASPIS (ASI SPace Weather InfraStructure). This contribution is meant to bring attention upon the first steps in the development of the CAESAR prototype for ASPIS and will focus on the activities of the Node 2000 of CAESAR, the set of Work Packages dedicated to the technical design and implementation of the CAESAR ASPIS archive prototype. The product specifications of the intended resources that will form the archive, functional and system requirements gathered as first steps to seed the design of the prototype infrastructure, and evaluation of existing frameworks, tools and standards, will be presented as well as the status of the project in its initial stage.Comment: 4 pages, 2 figures, ADASS XXXII (2022) Proceeding

Parameter distributions for the drag-based modeling of CME propagation

In recent years, ensemble modeling has been widely employed in space weather to estimate uncertainties in forecasts. We here focus on the ensemble modeling of Coronal Mass Ejections (CME) arrival times and arrival velocities using a drag-based model, which is well-suited for this purpose due to its simplicity and low computational cost. Although ensemble techniques have previously been applied to the drag-based model, it is still not clear how to best determine distributions for its input parameters, namely the drag parameter and the solar wind speed. The aim of this work is to evaluate statistical distributions for these model parameters starting from a list of past CME-ICME events. We employ LASCO coronagraph observations to measure initial CME position and speed, and in situ data to associate them with an arrival date and arrival speed. For each event we ran a statistical procedure to invert the model equations, producing parameters distributions as output. Our results indicate that the distributions employed in previous works were appropriately selected, even though they were based on restricted samples and heuristic considerations. On the other hand, possible refinements to the current method are also identified, such as the dependence of the drag parameter distribution on the CME being accelerated or decelerated by the solar wind, which deserve further investigation

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution