Biomedical subjects

Roberto Marangoni

Publications and source records attributed to Roberto Marangoni.

6 recordsLinked to original sources

PubMed2007

TAMGeS: a Three-array Method for Genotyping of SNPs by a dual-colour approach.

BACKGROUND: Many of the most effective high-throughput protocols for SNP genotyping employ microarrays. Genotypes are assessed by comparing the signal intensities that derive from the hybridization of different allele-specific probes labelled either by using four fluorescent dyes, one for each base, or by using only two dyes and investigating the polymorphic alleles two by two on separate arrays. The employment of only two dyes makes it possible to use a dual-laser scanner, which has the advantage of being present in every microarray laboratory. However, this protocol may present some drawbacks. To infer all the six possible genotypes it is necessary to compare signals from two arrays, but this comparison not always is successful. A number of systematic errors in the experimental protocol, in fact, may differently affect signal intensities on separate arrays. Here we present TAMGeS (Three-Array Method for Genotyping of SNPs), an exhaustive method for SNP genotyping through SBE (Single Base Extension) and dual-colour microarrays, which makes the comparison of signals on distinct arrays reliable by using a third array and a data handling method for signal normalization based on bilinear regression theory. RESULTS: We tested the effectiveness of the proposed method by evaluating the results obtained from the direct comparison of the two arrays or by applying TAMGeS, both on experimental and synthetic data. With synthetic data, TAMGeS reduced the frequency of errors by an order of magnitude, when the incidence of systematic errors was not negligible. With the experimental data, produced by genotyping 25 SNPs in 437 subjects, TAMGeS reduced the percentage of missing genotypes from 54% (Two-Array Method) to 14.5%. Allelic and genotypic call rates were 99.3% and 99.5%, respectively. The normalization procedure takes into account also systematic errors, which can be generated by a time-delayed assay, thus making the protocol more flexible. CONCLUSION: TAMGeS represents an innovative method, which proved to be very effective in producing reliable SNP genotyping data by dual-colour microarrays. The requirement of a third array is well balanced by the strong enhancement in data quality and by the greater flexibility of the experimental protocol.

Base Sequence↗

PubMed2006

A compression-based approach for coding sequences identification. I. Application to prokaryotic genomes.

Most of the gene prediction algorithms for prokaryotes are based on Hidden Markov Models or similar machine-learning approaches, which imply the optimization of a high number of parameters. The present paper presents a novel method for the classification of coding and non-coding regions in prokaryotic genomes, based on a suitably defined compression index of a DNA sequence. The main features of this new method are the non-parametric logic and the costruction of a dictionary of words extracted from the sequences. These dictionaries can be very useful to perform further analyses on the genomic sequences themselves. The proposed approach has been applied on some prokaryotic complete genomes, obtaining optimal scores of correctly recognized coding and non-coding regions. Several false-positive and false-negative cases have been investigated in detail, which have revealed that this approach can fail in the presence of highly structured coding regions (e.g., genes coding for modular proteins) or quasi-random non-coding regions (e.g., regions hosting non-functional fragments of copies of functional genes; regions hosting promoters or other protein-binding sequences). We perform an overall comparison with other gene-finder software, since at this step we are not interested in building another gene-finder system, but only in exploring the possibility of the suggested approach.

Algorithms↗

PubMed2003

Effect of preillumination on photomotile responses of the marine ciliate Fabrea salina.

Fabrea salina is a marine ciliate that shows photomotile responses such as positive phototaxis and a step-down photophobic reaction. We found that preilluminated F. salina cells show a phototactic response significantly greater than that of dark-adapted cells when exposed to the same phototactic light stimulus. In particular, positive phototaxis is strongly enhanced by preillumination. This enhancement effect depends on the preillumination light irradiance, on the total preillumination dose, and on the duration of the dark interval between preillumination and the phototaxis measurement. Our results show that the determining factor is the total preillumination dose given to the sample. The enhancement effect shows an asymptotic behavior over a certain range of energy values (10-200 W/m2). Further, the effect is transient; after 120 s in the dark, the cells lose any memory of the preillumination, independent of the preillumination energy received. These results are tentatively discussed in terms of light-driven membrane potential or membrane channel conductances.

Animals↗

PubMed2002

A method for prediction of accessible sites on an mRNA sequence for target selection of hammerhead ribozymes.

Hammerhead ribozymes are short RNA molecules endowed with endoribonucleolytic activity. Their use as molecular tools for specific inhibition of gene translation is affected by many factors including the target accessibility. A method for the prediction of accessible target sites for hammerhead ribozymes within a given RNA sequence is described. This method maps all putative NUH cleavage sites (N = A, C, G, U and H = A, C, U) and picks out short flanking regions as the binding domain for the corresponding ribozyme. The probabilistic level of unfolding, accessibility score (AS), is then calculated for each target region on the basis of a comparison of all folding structures obtained for the target RNA and arranged according to the Boltzmann's distribution. At the end, a series of imposed limits gives the best target sequences endowed with highly probable accessibility and with a potentially active catalytic structure of the hammerhead sequence. A successive experimental approach to verify the effective accessibility of selected targets was used. For that, antisense oligonucleotides addressed to the coding region of bcl2 mRNA were synthesized and administered to the MCF7 human cell line. The inhibition of gene expression, as measured by western analysis of the BCL2 protein, demonstrated that all target sites selected on the basis of their putative accessibility were actually sensitive to antisense treatments while the inaccessible ones were not. The application of this target discovery method to ribozyme design is proposed in order to satisfy a crucial condition.

Algorithms↗

PubMedDate not supplied

Biological weighting function of the UV-B-induced impairment of phototaxis in the freshwater ciliate Ophryoglena flava.

We determined the biological weighting function (BWF) of the effect of UV radiation on phototaxis of the freshwater, histophagous ciliate Ophryoglena flava. Dose-effect curves were measured by exposing the cells to 12 different irradiation regimens obtained with two different levels of UV-B radiation and by using six filters with cutoff wavelengths ranging from 280 to 335 nm. The results show that there are significant damages to phototaxis at the doses used and that the effect increases when the cutoff is shifted toward short wavelengths. The data were used to calculate the BWF of phototaxis impairment by applying a nonlinear fit procedure. The BWF thus obtained decays exponentially with increasing wavelength in agreement with similar findings reported in the literature for other systems.

Animals↗

PubMedDate not supplied

Effects of UV-B irradiation on a marine microecosystem.

Purpose of this work was to study the effect of UV irradiation on a microecosystem consisting of several interacting species. The system chosen was of a hypersaline type, where all the species present live at high salt concentration; it comprises different bacteria; a producer, the photosynthetic green alga Dunaliella salina; and a consumer, the ciliated protozoan Fabrea salina, which form a complete food chain. We were able to establish the initial conditions that give rise to a self-sustaining microecosystem, stable for at least 3 weeks. We then determined the effect of UV irradiation on this microecosystem under laboratory-controlled conditions, in particular by measuring the critical UV exposure for the two main components of the microecosystem (algae and protozoa) under UV-B irradiances comparable to those of solar irradiation. In our experiments, we varied irradiance, total dose and spectral composition of the actinic light. The critical doses at irradiances of the order of 56 kJ/m(2) (typical average daily irradiance in a sunny summer day in Pisa), measured for each main component of the microecosystem (algae and ciliates), turned out to be around 70 kJ/m(2) for ciliates and 50 kJ/m(2) for D. salina. By exposing microecosystems to daily UV-B irradiances of the order of 8 kJ/m(2) (typical average daily irradiance in a sunny winter day in Pisa), we found no effect at total doses of the order of the critical doses at high irradiances, showing that the reciprocity law does not hold. We have also measured a preliminary spectral-sensitive curve of the UV effects, which shows an exponential decay with wavelength.

Animals↗