1,721,073 research outputs found
Il reddito d’impresa. Concetti strutturali, collegamenti sistematici e approfondimenti operativi
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A survey of mitochondrial evolution in Metazoa : large variability in little genomes
No full textThe animal mitochondrial genome (mtDNA) has been traditionally used as molecular marker for phylogenetic reconstructions but the study of the evolutionary history of this small genome can also help to unravel the hidden link between structural and functional genomic features. In this respect, the animal mtDNA can be regarded as a model in comparative genomics, whose use is also enhanced by the availability of complete sequences for about 2000 species. In spite of the biased taxon sampling, the analysis of the present mtDNA dataset is doubtless promising to reconstruct the evolutionary history of this entire genome in a wide phylogenetic range and to identify possible differences in its evolutionary trend among different lineages.
In order to carefully analyze the plethora of available mt sequences of Metazoa, we have developed a specialized mtDNA database, MitoZoa, collecting (nearly) complete mtDNA genomes whose annotations have been significantly corrected/improved using a semi-automatic reannotation pipeline. MitoZoa has been designed both to address comparative analyses of genomic features, such as gene order, non-coding regions and gene content, and to help comparisons at short evolutionary distances, such as in congeneric species. Here, we will briefly present the MitoZoa database and the preliminary results of our investigation on the mtDNA evolutionary dynamics in Metazoa: we have got insight into the variability of basic mitogenomic features, such as gene content, gene compactness, and base composition, and into the trend of gene order rearrangements in the main metazoan lineages. Especially in fast-evolving lineages, the same features have also been investigated in congeneric species, i.e. in closely-related species where saturation of evolutionary changes is unlikely to occur. Our data show that the mtDNA plasticity of Metazoa is higher that previously thought and that the mt evolutionary trend has changed several times, and sometimes dramatically, in the metazoan phylogenetic tree
Il trust “liberale” e l’imposta sulle donazioni (commento a Consiglio Nazionale del Notariato, Studio n. 80/2003/T).
No full textL'argomento viene approfondito nei seguenti aspetti: caratteristiche del trust e tributi indiretti, riconoscimento del trust tra le parti e nei confronti dei terzi, rilievi introduttivi; le "liberalità indirette" nella riforma imposta sulle donazioni, il riacquisto da parte del tributo della connotazione di "imposta d'atto" e la susseguente irrilevanza di tutte liberalità "non formalizzate"; il "trust liberale" tra formalità del negozio istitutivo e informalità di quelli dispositivi (Angelo Contrino); trust, libertà di forme e imposta di registro (Raffaello Lupi)
PROTEZIONE DELLO SCUDO FISCALE E TRATTAMENTO DETERIORE PER LE SOCIETA'
No full textAnche se lo scudo fiscale non era un condono, esso aveva delle ricadute oggettive che, inevitabilmente, avevano una portata oggettiva analoga, almeno su determinate fattispecie. Molte disponibilità all'estero, specie se riconducibili al piccolo capitalismo familiare, corrispondevano a ricchezza occultata «sopra la società», che non beneficia dello scudo fiscale del socio-dominus. Da una parte è la conferma che lo scudo fiscale non era un condono, dall'altra è la conferma della difficoltà del Fisco di intercettare la ricchezza occultata «sopra le società», da parte di chi ne è il «dominus». Se però si guarda isolatamente alle società rispetto ai loro soci si ha l'impressione di un trattamento peggiorativo. Che nel 2002 venne eliminato a posteriori attraverso un vero e proprio condono. È una prospettiva su cui discuteremo nei prossimi numeri
CONTROVERSIE PREVIDENZIALI COLLEGATE AD ACCERTAMENTI FISCALI
No full textSpesso un unico controllo sul reddito ha riflessi fiscali e previdenziali, ma le controversie potrebbero seguire binari processuali separati, tributario il primo e del lavoro il secondo. Sarebbe opportuno, trattandosi di valutare gli stessi eventi, unificare i due processi e la sede più naturale, per organizzazione e specificità di materia, sembrano essere le Commissioni tributarie. Non mancano del resto gli argomenti per conciliare questa attribuzione con la limitazione ai «tributi» della giurisdizione speciale, sia per la connessione con questioni tributarie, sia per la possibilità stessa di considerare oramai i contributi previdenziali come veri e propri tributi
Il trust alla prova dei regimi fiscali riferiti alle persone fisiche
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A combined approach for successful reannotation of animal mitochondrial tRNAs based on pattern-matching and tRNA-predictor programs
No full textMotivation.
Transfer RNAs encoded by the mitochondrial genome (mtDNA) of Metazoa present strong deviations from the classical cloverleaf secondary structure, including the loss or size variation of either D- or T-domain. In addition, some taxa show “bizarre” tRNA structures: nematodes possess unconventional mt-tRNAs lacking either the T or D stem (1); spiders (Araneae, Chelicerata) and gall midges (Cecidomiiydae, Insecta) have many “truncated” tRNAs, i.e. tRNAs lacking a well-paired aminoacyl stem, which can also lost the T-arm (2,3); annelids belonging to family Questidae have a full set of truncated tRNAs (4).
These peculiarities hamper the annotation of mt-tRNAs in mtDNA sequences, since conventional tRNA detection programs perform poorly (as tRNAscan-SE) or lead to the detection of a significant number of false positives (as Arwen) (5,6). Finally, mt-tRNA annotations of are affected by numerous errors in gene name, boundaries and strand definition occurring during the sequence submission to primary databases (7). In the effort to construct a curated database of complete mtDNAs of Metazoa, we have developed a specific pipeline including both pattern-matching and tRNA-predictor programs, aimed at automatically check/rectify the annotation of both standard and “bizarre” mt-tRNAs.
Methods.
The developed mt-tRNA reannotation pipeline analyses the single tRNA sequences through two different programs: PatSearch, a pattern-matching program (8); and Arwen, a mt-tRNA secondary structure predictor (6). Two modules, made of several home-made Python scripts, specifically parse the results of PatSearch and Arwen using several empirically-settled criteria.
As for PatSearch, two main tRNAs patterns were specifically set for each mt-tRNA category. These patterns are able to detect the overall tRNA secondary structure based on the identification of only the aminoacyl (AA) and anticodon (AC) arms: the first pattern assumes perfectly annotated tRNAs with correct limits and a single 3'-discriminant base in the AA stem, while the second pattern searches for tRNAs having incorrect boundaries. In addition, patterns looking for a perfect AC arm in the correct tRNA position were also defined in order to look for “truncated” tRNAs, only in taxa where such unusual tRNA structures are expected to be present (Araneae, Cecidomiiydae and Questidae). All mt-tRNA patterns assume the presence of canonical anticodon sequences.
In this pipeline, Arwen was preferred to tRNAscan-SE because it has a detection rate close to 100% for mt-tRNAs, however, given the high false positive rate, Arwen results were taken into account only for mt-tRNAs not identified by the PatSearch patterns. Arwen itself has the advantage to find tRNAs with unusual anticodons and uncommon secondary structures, moreover the program was run applying specific options and extending the original tRNA boundaries from 5 to 45 bp at both gene sides, using an incremental step of 5 or 15 bp. The extension of the original tRNA boundaries forced the program to identify mt-tRNAs having erroneous gene limits.
Results.
A total dataset of 42,617 mt-tRNA sequences collected in the MitoZoa database v2.0 (9) was analyzed by our pipeline: 95.9% mt-tRNAs were identified/corrected by the PatSearch module; 3.8% were identified/corrected only by the Arwen module; 0.3% of the total tRNAs were not identified at the end of the whole pipeline and correspond mainly to erroneously annotated tRNAs. Thus, our pipeline represents a reliable tool for improving the annotation quality of metazoan mt-tRNAs both in complete and partial mtDNA sequences, since it was able to resolve (i.e. correct or validate) the annotation of >99% of the analyzed sequences, taking into account either taxon-specific and secondary-structure peculiarities of tRNA genes.
In order to compare the resolving power and accuracy of the two-core modules of our pipeline, the PatSearch-confirmed tRNAs (42,617 minus the 184 “truncated” tRNAs) were re-analyzed by the Arwen module. The results were straightforward: only 0.06% mt-tRNAs were predicted with different gene name/strand by the PatSearch compared to the Arwen module (these cases will be fully discussed in the poster), while 1.5% mt-tRNAs identified by PatSearch were not found by the Arwen module. This is mainly due to the low detection rate of Arwen for tRNA-Ser(AGY), tRNA-Cys and nematode mt-tRNAs, which together correspond to 44% of the total tRNAs not identified by Arwen. Among the 184 “truncated” tRNAs, all sequences were found by the PatSearch-settled patterns, while only 64 tRNAs (34.8%) were identified by the Arwen module. These results demonstrate that adequate patterns describing the tRNA secondary structure outperforms a good tRNA predictor such as Arwen in the present mt-tRNA reannotation pipeline, and could be useful for the identification of tRNA-like structure.
Supplementary information
1.Watanabe, Y., Tsurui, H., Ueda, T., Furushima, R., Takamiya, S., Kita, K., Nishikawa, K. and Watanabe, K. (1994) J Biol Chem, 269, 22902-22906.
2.Beckenbach, A. and Joy, J. (2010) Genome Biology and Evolution, in press, 278-287.
3.Masta, S. and Boore, J. (2008) Mol Biol Evol, 25, 949-959.
4.Bleidorn, C., Hill, N., Erséus, C. and Tiedemann, R. (2009) Mol Phylogenet Evol., 52, 57-69.
5.Lowe, T.M. and Eddy, S.R. (1997) Nucleic Acids Res., 25, 955-964.
6.Laslett, D. and Canback, B. (2008) Bioinformatics., 24, 172-175.
7.Boore, J. (2006) OMICS, 10, 119-126.
8.Grillo G., Licciulli F., Liuni S., Sbisà E., Pesole G. (2003) Nucleic Acids Res. 31(13),3608-12.
9.Lupi, R., D'Onorio de Meo, P., Picardi, E., D'Antonio, M., Paoletti, D., Castrignanò, T., Pesole, G. and Gissi, C. (2010) Mitochondrion, 10, 192-199
[From cellular biology to molecular biology: Golgi apparatus from the discovery to nowadays].
No full textOn April the 9th 1898 Golgi presented the discovery of the Apparato Reticolare Interno or internal reticular apparatus to the Società Medico-Chirurgica in Pavia. The internal reticular apparatus was described as "a fine and elegant network within the cell body" of Purkinje cells. The discovery of this new intracellular structure can be considered a byproduct of Golgi studies devoted to the analysis of the nervous system histology. Golgi and his co-workers detected the internal reticular apparatus in many cell types and described the organelle pleiomorphism due to specific physiological or pathological conditions. However, the real existence of the apparatus was questioned until the organelle was finally identified by electron microscopy in 1954. At this point Golgi apparatus became an actual intracellular structure without any clear function. The involvement in cell secretion processes was verified by using biochemical and molecular investigations from the 1960s. Nowadays, Golgi apparatus is clearly known to be involved in different cell functions as growth, homeostasis and division. The correct execution of these functions lies on the ability to maintain an equilibrated balance between the proteins therein resident. Recently, Golgi apparatus has been involved also in human pathology as mutations in proteins localized in the organelle are linked to some hereditary disorders like the Lowe syndrome. Golgi apparatus has been debated since its discovery. From the Golgi milestones discussed here it is evident that controversies that have arisen were often resolved by information resulting from the application of new technical developments. Indeed the compound dynamic structure and the relevance in cell physiology and in human pathology render Golgi apparatus an open object for future studies. Overall, the history of the Golgi apparatus represents an excellent model not only to follow the transition of the study approaches from cellular biology to molecular cell biology but also to understand the current attention paid to integrate the molecular function and the organelle structure in order to explain what goes wrong in the context of human disease
Interessi passivi pagati dalla stabile organizzazione alla casa madre e capitalizzazione sottile
No full textLa residenza delle società e controllo tra schemi OCSE ed episodi giurisprudenziali interni
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