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Mele G.,CNR Institute of Agricultural Biology and Biotechnology
BMC Bioinformatics | Year: 2016

Background: The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting enhancers and silencers have key roles in controlling gene transcription. The genomic era allowed the transition from single gene analysis to the investigation of full transcriptomes. This transition increased the complexity of the analyses and the difficulty in the interpretation of the results. In this context, there is demand for new tools aimed at the creation of gene networks that can facilitate the interpretation of Next Generation Sequencing (NGS) data. Results: Arabidopsis Motif Scanner (AMS) is a Windows application that runs on local computers. It was developed to build gene networks by identifying the positions of cis-regulatory elements in the model plant Arabidopsis thaliana and by providing an easy interface to assess and evaluate gene relationships. Its major innovative feature is to combine the cis-regulatory element positions, NGS and DNA Chip Arrays expression data, Arabidopsis annotations and gene interactions for the identification of gene networks regulated by transcription factors. In studies focused on transcription factors function, the software uses the expression data and binding site motifs in the regulative gene regions to predict direct target genes. Additionally, AMS utilizes DNA-protein and protein-protein interaction data to facilitate the identification of the metabolic pathways regulated by the transcription factor of interest. Conclusions: Arabidopsis Motif Scanner is a new tool that helps researchers to unravel gene relations and functions. In fact, it facilitates studies focused on the effects and the impact that transcription factors have on the transcriptome by correlating the position of cis-acting elements, gene expression data and interactions. © 2016 Mele. Source

Puccinelli E.,CNR Institute of Clinical Physiology | Gervasi P.G.,CNR Institute of Clinical Physiology | Longo V.,CNR Institute of Agricultural Biology and Biotechnology
Current Drug Metabolism | Year: 2011

The pig has been used as an important animal model for human studies because of its similarity in size, physiology and disease development. However, in contrast to the extensive data available on the cytochrome P450 (CYP) system for humans and rodents, the data related to pig are limited because of, among others, the presence of intra-species differences (domestic pigs and minipigs). The knowledge of the CYP superfamily in a given experimental animal is crucial for pharmacological and toxicological tests in developing drugs and for understanding the metabolic pathways of toxicants and carcinogens. In addition, information on the CYP system in pigs is important since it plays a dominant role in the metabolism of veterinary drugs, whose residues remain in the porcine tissues which are food for humans. The aim of the present review is to examine - in the liver and extrahepatic tissues of pig - our current knowledge of the xenobioticmetabolizing CYPs belonging to families 1-4, in terms of drug metabolism, substrate specificity, inhibition, gene expression and receptor- driven regulation, in comparison with human data. It is hoped, furthermore, that this review may stimulate research on the porcine drug-metabolizing enzymes in order to evaluate the hypothesis whereby pig data may better reflect human drug metabolism and toxicity than those obtained from the traditional non-rodent models. © 2011 Bentham Science Publishers Ltd. Source

Stella A.,CNR Institute of Agricultural Biology and Biotechnology | Ajmone-Marsan P.,Catholic University of the Sacred Heart | Lazzari B.,Parco Tecnologico Padano | Boettcher P.,International Atomic Energy Agency
Genetics | Year: 2010

The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals. The validity of this approach was confirmed by obtaining extremely large CLLs at the sites of causative variation for polled (BTA1) and black-coat-color (BTA18) phenotypes. Across the 30 bovine chromosomes, 699 putative selection signatures were detected. The largest CLL was on BTA6 and corresponded to KIT, which is responsible for the piebald phenotype present in four of the five dairy breeds. Potassium channel-related genes were at the site of the largest CLL on three chromosomes (BTA14, -16, and -25) whereas integrins (BTA18 and -19) and serine/arginine rich splicing factors (BTA20 and -23) each had the largest CLL on two chromosomes. On the basis of the results of this study, the application of population genomics to farm animals seems quite promising. Comparisons between breed groups have the potential to identify genomic regions influencing complex traits with no need for complex equipment and the collection of extensive phenotypic records and can contribute to the identification of candidate genes and to the understanding of the biological mechanisms controlling complex traits. Copyright © 2010 by the Genetics Society of America. Source

Longo V.,CNR Institute of Agricultural Biology and Biotechnology | Gervasi P.G.,CNR Institute of Clinical Physiology | Lubrano V.,CNR Institute of Neuroscience
Food and Chemical Toxicology | Year: 2011

The protective effect of a powder of grain (Lisosan G) against cisplatin-induced toxicity in rats was studied. Male rats were fed with Lisosan G before injection of cisplatin and four days later they were killed and blood was collected along with hepatic, renal and testicular tissues. The results showed that cisplatin treatment increased plasma blood urea nitrogen, creatinine and hydrogen peroxide and decreased cytochrome P450 content in renal and hepatic tissues. It also reduced the plasmatic testosterone level and caused a depletion of testicular 17α-progesterone hydroxylase activity. In the group fed with Lisosan G and treated with cisplatin blood urea nitrogen and creatinine returned to the control level indicating a protective effect of Lisosan G. It was also observed that the ones fed with Lisosan G were able to attenuate the decrease in the P450-dependent activities and the activities of antioxidant enzymes as well. Lisosan G protected the testicular 17α-progesterone hydroxylase activity and increased the plasma testosterone level compared to animals treated only with cisplatin. Our results showed a protective effect of Lisosan G against the cisplatin induced toxicity. The protective effect of Lisosan G could be associated mainly with the attenuation of the oxidative stress and the preservation in antioxidant enzymes. © 2010 Elsevier Ltd. Source

Vidoz M.L.,SantAnna School of Advanced Studies | Loreti E.,CNR Institute of Agricultural Biology and Biotechnology | Mensuali A.,SantAnna School of Advanced Studies | Alpi A.,University of Pisa | Perata P.,SantAnna School of Advanced Studies
Plant Journal | Year: 2010

Soil flooding, which results in a decline in the availability of oxygen to submerged organs, negatively affects the growth and productivity of most crops. Although tomato (Solanum lycopersicum) is known for its sensitivity to waterlogging, its ability to produce adventitious roots (ARs) increases plant survival when the level of oxygen is decreased in the root zone. Ethylene entrapment by water may represent the first warning signal to the plant indicating waterlogging. We found that treatment with the ethylene biosynthesis inhibitor aminoethoxyvinylglycine (AVG) and the auxin transport inhibitor 1-naphthylphthalamic acid (NPA) resulted in a reduction of AR formation in waterlogged plants. We observed that ethylene, perceived by the Never Ripe receptor, stimulated auxin transport. In a process requiring the Diageotropica gene, auxin accumulation in the stem triggered additional ethylene synthesis, which further stimulated a flux of auxin towards to the flooded parts of the plant. Auxin accumulation in the base of the plant induces growth of pre-formed root initials. This response of tomato plants results in a new root system that is capable of replacing the original one when it has been damaged by submergence. © 2010 Blackwell Publishing Ltd. Source

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