102 research outputs found
Detecting correlations among functional sequence motifs
No full textSequence motifs are words of nucleotides in DNA with biological functions, e.g. gene regulation. Identification of such words proceeds through rejection of Markov models on the expected motif frequency along the genome. Additional biological information can be extracted from the correlation structure among patterns of motif occurrences. In this paper a log-linear multivariate intensity Poisson model is estimated via expectation maximization on a set of motifs along the genome of E. coli K12. The proposed approach allows for excitatory as well as inhibitory interactions among motifs and between motifs and other genomic features like gene occurrences. Our findings confirm previous stylized facts about such types of interactions and shed new light on genome-maintenance functions of some particular motifs. We expect these methods to be applicable to a wider set of genomic features
On some properties of quasi-MV algebras and √′ quasi-MV algebras. Part II
No full textThe present paper is a sequel to Paoli F, Ledda A, Giuntini R, Freytes H (On some properties of QMV algebras and √′ QMV algebras, submitted). We provide two representation results for quasi-MV algebras in terms of MV algebras enriched with additional structure; we investigate the lattices of subvarieties and subquasivarieties of quasi-MV algebras; we show that quasi-MV algebras, as well as cartesian and flat √′ quasi-MV algebras, have the amalgamation property. © Springer-Verlag 2007.We gratefully acknowledge the precious information and insights we gathered from conversations or e-mail exchanges with Roberto Giuntini and Danica Jakubikova-Studenovska. We are especially indebted to Matthew Spinks for his extensive and detailed comments on a preliminary draft of the paper. The first author is partially supported by Grants MTM2004-03101 and TIN2004-07933-C03-02 from the Spanish Ministerio de Educación y Ciencia and Grant 2001SGR-00017 from the Generalitat de CatalunyaPeer Reviewe
Exploring the effect of vitamin D and DHA supplementation on the urine metabolome of preterm infants by 1H NMR-based metabolomics
No full textBackground and objectives:
Vitamin D and docosahexaenoic acid (DHA) insufficiency and deficiency could potentially have a great impact on health outcomes in preterm infant. Due to the importance of early
nutrition intervention in this population and given the lack of metabolomic studies concerning the supplementations effect on the metabolome of preterm infants, 44 premature infants were studied, divided in two groups, one receiving only vitamin D (DS) and the second both vitamin D and DHA (D-DHAS) supplementation. Two were the main objectives of the study: 1) to look at changes over time in the urinary metabolic profiles of infants before and over two months of supplementation; 2) to compare the urinary metabolome of the two groups after supplementation.
Methods:
1H NMR-based metabolomics approach was used to analyze urine samples obtained from preterm newborns at three different time points: at the time of hospital discharge and before supplementation (T0),
1 month (T1) and 2 months (T2) after the beginning of supplementation.
Results:
A clear temporal dynamics of the urinary metabolic profiles of preterm infants was highlighted by OPLS analysis. Both groups were characterized by growing levels of betaine, N,N-dimethylglycine, creatinine,
creatine and guanidinoacetate and diminishing levels of myo-inositol and hydroxyproline with increasing postmenstrual age (PMA). Additionally, for D-DHAS citrate and dimethylamine increased, while lactate decreased over time. OPLS-DA clearly discriminated the two groups after two months of supplementation. Compared to DS, D-DHAS group was characterized by higher levels of betaine, N,N-dimethylglycine, creatinine and
dimethylamine and lower amounts of lactate and myo-inositol.
Conclusions:
Metabolomic analysis of urine from the neonatal period could be a useful tool to understand metabolic processes linked to early nutrition and supplementation. According to
our results, vitamin D supplementation exerts in preterm newborns positive effects evaluated with urinary metabolomics. Moreover, it seems that
the supplementation with vitamin D and DHA exerts a higher antioxidant and protective action on newborns, and it could also positively affect the body fat composition
Sviluppo di un protocollo di estrazione del DNA da latte ovino finalizzato alla caratterizzazione del microbiota mediante NGS-based amplicon sequencing
No full textSheep’s milk is a complex and strategic matrix for the Mediterranean dairy sector, but its high fat and protein content makes the application of molecular methods challenging. Next-generation sequencing (NGS) techniques offer innovative perspectives for microbiota characterization, with impacts on food safety, traceability, and product valorization. However, the lack of standardized DNA extraction protocols limits the reproducibility and comparability of studies. A literature review (2015–2025) was therefore conducted to identify extraction protocols from ruminant milk. Among them, the Milk Bacterial DNA Isolation Kit was selected and applied to sheep’s milk samples from Sarda breed flocks in 10 farms located in the provinces of Grosseto and Viterbo. DNA yield and purity were assessed by spectrophotometry and agarose gel electrophoresis; in parallel, culture-based microbiological analyses were carried out for comparison, while data processing was performed using descriptive statistical tools. The kit provided optimal yields, including those for PCR. The analyses also revealed differences among farms in the two provinces, suggesting that environmental, management, and sanitary factors may influence the composition of the milk microbiota. The validated protocol proved effective and reproducible, laying the groundwork for future metagenomic studies and the application of NGS to support the sheep dairy supply chain
Distribution and evolution of short sequence tandem repeats in eukariotic genomes
No full textEls microsat el lits s on seq u encies d'ADN formades per repeticions en t andem de motius curts. Les curtes seq u encies repetides en t andem s on ubiq ues en els genomes dels eucariotes, tant en les regions codi cants com en les regions no codi cants. Aquestes seq u encies tenen un nivell molt elevat de polimor sme i de diverg encia interespec ca. Hem investigat si les dades obtingudes mitjan cant la seq uenciaci o de nova generaci o del Projecte Pilot dels 1000 Genomes s on utils per quanti car la variabilitat dels microsat el lits en les poblacions humanes i per descobrir nous loci hipot eticament implicats en malalties causades per l'expansi o de repeticions de trinucle otids. Hem analitzat la conservaci o ologen etica dels microsat el lits per entendre el rol que juga la selecci o en l'evoluci o dels microsat el lits. El primer estudi conclou que en els llinatges dels vertebrats, les repeticions en t andem d'amino acids estan m es conservades que altres seq u encies similars localitzades a les regions no codi cants. Aix o ens porta a concloure que l'evoluci o ha mantingut les repeticions a les regions codi cants de les prote nes. En una segona fase hem analitzat la conservaci o dels microsat el lits en diferents regions gen omiques, comparant-les amb la conservaci o dels microsat el lits a les regions interg eniques. Concloem que la selecci o no mant e nom es els microsat el lits als exons, sin o que tamb e a altres regions gen omiques.Microsatellites are DNA sequences formed by tandem repetition of short motifs. Short sequence tandem repeats are ubiquitous in eukaryotic genomes both in coding and non-coding regions. They show a very high level of polymophism and interspeci c divergence. We investigated the use of next generation sequencing data, from the 1000 Genomes Pilot Prjects, to quantify microsatellite variability in the human population and discover putative new loci involved in trinucleotide repeat expansion diseases. We analysed microsatellites phylogenetic conservation to learn about the role of selection in shaping microsatellite evolution. The rst study con- cluded that in vertebrate lineages amino acid tandem repeats were more conserved than similar sequences located in non-coding regions. This lead us to the conclusion that evolution was preserving repeats in protein-coding regions. In a second stage we analzed the conservation of microsatellites in di erent genomic regions, comparing them with the of microsatellite in inter- genic region. We concluded that selection was not preserving microsatellites only in exons but also in other genomic regions. 1Programa de doctorat en Biomedicin
A bosonic Weakly interacting massive particle as Dark Matter candidate
No full textLe attuali osservazioni cosmologiche concordano sul fatto che la maggior parte della materia che compone l'Universo non si accoppia ai fotoni e non è barionica. Decifrare la natura delle particelle che compongono questa cosiddetta materia oscura è una delle sfide che deve affrontare la fisica delle particelle. Sono state proposte molte particelle in grado dare una soluzione al problema e si spera che gli esperimenti presenti e futuri riescano a dirimere la questione.
Questa tesi si occupa di un modello che è stato recentemente proposto come estensione del Modello Standard, che permette di avere uno Higgs pesante, ma che può pure fornire una particella adatta a risolvere il problema della materia oscura. Questo modello prevede di aggiungere al Modello Standard un altro doppietto scalare, del tutto simile al doppietto di Higgs, che però non prende ed è protetto da una simmetria dall'interagire direttamente con i fermioni. Da quest'ultima caratteristica deriva il nome con cui ci si riferisce a questo secondo doppietto scalare: . Grazie alla simmetria , inoltre, la particella più leggera che compone il doppietto è stabile e appartiene alla famiglia delle Particelle Massive Debolmente Interagenti (WIMP).
Il fatto che non possa decadere rende la particella più leggera un valido candidato di materia oscura.
Richiedendo che tale particella sia la forma dominante di materia oscura si delimita la regione nello spazio dei parametri del doppietto inerte. Lo scopo della tesi è quello di determinare questa regione e corrispondentemente di studiare la rivelabilità della particella in esperimenti di ricerca diretta di materia oscura
Distribution and evolution of short sequence tandem repeats in eukariotic genomes
No full textEls microsat el lits s on seq u encies d'ADN formades per repeticions en
t andem de motius curts. Les curtes seq u encies repetides en t andem s on
ubiq ues en els genomes dels eucariotes, tant en les regions codi cants com
en les regions no codi cants. Aquestes seq u encies tenen un nivell molt elevat
de polimor sme i de diverg encia interespec ca.
Hem investigat si les dades obtingudes mitjan cant la seq uenciaci o de nova
generaci o del Projecte Pilot dels 1000 Genomes s on utils per quanti car la
variabilitat dels microsat el lits en les poblacions humanes i per descobrir
nous loci hipot eticament implicats en malalties causades per l'expansi o de
repeticions de trinucle otids.
Hem analitzat la conservaci o ologen etica dels microsat el lits per entendre
el rol que juga la selecci o en l'evoluci o dels microsat el lits. El primer
estudi conclou que en els llinatges dels vertebrats, les repeticions en t andem
d'amino acids estan m es conservades que altres seq u encies similars localitzades
a les regions no codi cants. Aix o ens porta a concloure que l'evoluci o
ha mantingut les repeticions a les regions codi cants de les prote nes. En
una segona fase hem analitzat la conservaci o dels microsat el lits en diferents
regions gen omiques, comparant-les amb la conservaci o dels microsat el lits
a les regions interg eniques. Concloem que la selecci o no mant e nom es els
microsat el lits als exons, sin o que tamb e a altres regions gen omiques.Microsatellites are DNA sequences formed by tandem repetition of short
motifs. Short sequence tandem repeats are ubiquitous in eukaryotic genomes
both in coding and non-coding regions. They show a very high level of
polymophism and interspeci c divergence.
We investigated the use of next generation sequencing data, from the
1000 Genomes Pilot Prjects, to quantify microsatellite variability in the
human population and discover putative new loci involved in trinucleotide
repeat expansion diseases.
We analysed microsatellites phylogenetic conservation to learn about
the role of selection in shaping microsatellite evolution. The rst study con-
cluded that in vertebrate lineages amino acid tandem repeats were more
conserved than similar sequences located in non-coding regions. This lead
us to the conclusion that evolution was preserving repeats in protein-coding
regions. In a second stage we analzed the conservation of microsatellites in
di erent genomic regions, comparing them with the of microsatellite in inter-
genic region. We concluded that selection was not preserving microsatellites
only in exons but also in other genomic regions.
1Programa de doctorat en Biomedicin
Immuno-histochemical study of ovine cystic echinococcosis (Echinococcus granulosus) shows predominant T cell infiltration in established cysts
No full textCorrection: High in vitro survival rate of sheep in vitro produced blastocysts vitrified with a new method and device (Journal of Animal Science and Biotechnology (2019) 10 (90) DOI: 10.1186/s40104-019-0390-1)
No full textIn the original publication of this article [1], the author point out an error in Fig. 3. The correct Fig. 3 is below. The publisher apologizes to the readers and authors for the inconvenience. The original publication has been corrected
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