Firenze, Italy
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Blankenship S.M.,Genetics Section | Campbell M.R.,800 Trout Road | Hess J.E.,Columbia River Inter Tribal Fish Commission | Hess M.A.,Columbia River Inter Tribal Fish Commission | And 9 more authors.
Transactions of the American Fisheries Society | Year: 2011

It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k-means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal components corresponded to ancestral lineages of Sacramento redband trout O. m. stonei, coastal rainbow trout O. m. irideus, and interior Columbia River redband trout O. m. gairdneri. Genetic data were partitioned among primary aggregates (lower Columbia, middle-upper Columbia, and Snake rivers), and the magnitude of genetic divergence relative to genetic diversity was analyzed (per locus) to test for evidence of selection and subsequent signals of adaptation. Two loci showed higher divergence than expected by chance (i.e., positive selection); however, both of these loci were on the fringe of the 99% confidence level and are potential false positives. Genetic patterns were also significantly correlated with certain environmental and habitat parameters (e.g., precipitation), but the extent to which those correlations are causal as opposed to effectual remains unclear. Despite the remaining questions, these data provide a foundation formore detailed investigations of harvest, admixture, and introgression between hatcheryand natural-origin fish and differences in reproductive success among individuals as well as monitoring trends in productivity. © American Fisheries Society 2011.


Berta M.,Genetics section | Giovannelli A.,CNR Institute of Neuroscience | Sebastiani F.,GeneXpress Informatics Inc. | Camussi A.,Genetics section | Racchi M.L.,Genetics section
Plant Biology | Year: 2010

A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO2 assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit. © 2010 German Botanical Society and The Royal Botanical Society of the Netherlands.


Ciccacci C.,Genetics Section | Conigliaro P.,University of Rome Tor Vergata | Perricone C.,University of Rome La Sapienza | Rufini S.,Genetics Section | And 5 more authors.
Clinical and Experimental Immunology | Year: 2016

Rheumatoid arthritis (RA) is a systemic autoimmune disease resulting in chronic inflammation of the synovium and consequent cartilage and bone erosion. RA is associated strongly with the presence of rheumatoid factor (RF), and consists of clinical subsets of anti-citrullinated protein antibody (ACPA)-positive and -negative patients. This study was designed to evaluate whether relevant single nucleotide polymorphisms (SNPs) associated with RA and other autoimmune disorders are related to RF, ACPA and clinical phenotype in a cohort of biologic drugs naive Italian RA patients; 192 RA patients and 278 age-matched healthy controls were included. Clinical and laboratory data were registered. We analysed a total of 12 single nucleotide polymorphisms (SNPs) in signal transducer and activator of transcription-4 (STAT-4), interleukin (IL)-10, psoriasis susceptibility 1 candidate 1 (PSORS1C1), protein tyrosine phosphatase, non-receptor type 2 (PTPN2), endoplasmic reticulum aminopeptidase 1 (ERAP1), tumour necrosis factor receptor-associated 3 interacting protein 2 (TRAF3IP2) and microRNA 146a (MIR146A) genes by allelic discrimination assays. Case-control association studies and genotype/phenotype correlation analyses were performed. A higher risk to develop RA was observed for rs7574865 in the STAT-4 gene, while the rs1800872 in the IL-10 gene showed a protective effect. The presence of RF was associated significantly with rs1800872 variant in IL-10, while rs2910164 in MIR146A was protective. ACPA were associated significantly with rs7574865 in STAT-4. The SNP rs2233945 in the PSORS1C1 gene was protective regarding the presence of bone erosions, while rs2542151 in PTPN2 gene was associated with joint damage. Our results confirm that polymorphisms in STAT-4 and IL-10 genes confer susceptibility to RA. For the first time, we described that SNPs in PSORS1C1, PTPN2 and MIR146A genes were associated differently with a severe disease phenotype in terms of autoantibody status and radiographic damage in an Italian RA population. © 2016 British Society for Immunology


Turchi A.,Genetics section | Tamantini I.,IAO MAE | Camussi A.M.,Genetics section | Racchi M.L.,Genetics section
Plant Science | Year: 2012

Metallothioneins (MT) play an important role in heavy metal detoxification and homeostasis of intracellular metal ions in plant. In this study, two transgenic lines expressing MT type 2 gene (PsMT A1) from Pisum sativum, a regenerated non transformed line NT and clone AL22, selected as heavy metal tolerant, were characterized in presence of the heavy metals for the ability to accumulate zinc and copper and to activate antioxidative enzyme defences: superoxide dismutase, catalase, ascorbate peroxidase. The levels of expression of MT type 2 gene assessed by RT-qPCR confirmed the gene over-expression in transgenic lines and evidenced in NT and AL22 the up-regulation of gene transcription by zinc and copper. Transgenic poplar lines during heavy metal stress displayed increased ability to translocate and accumulate zinc and copper compared with NT and AL22. The antioxidant enzyme defence was differently activated in response to metals in the transgenic lines without a significant increase of ROS. These results suggested that PsMT A1 could play a role in ROS scavenging leading to enhanced metal tolerance and increased zinc and copper sequestration in root and leaf. © 2011 Elsevier Ireland Ltd.


PubMed | Genetics section
Type: Journal Article | Journal: Plant biology (Stuttgart, Germany) | Year: 2010

A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO(2) assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.


PubMed | Genetics section
Type: | Journal: Plant science : an international journal of experimental plant biology | Year: 2011

Metallothioneins (MT) play an important role in heavy metal detoxification and homeostasis of intracellular metal ions in plant. In this study, two transgenic lines expressing MT type 2 gene (PsMT(A1)) from Pisum sativum, a regenerated non transformed line NT and clone AL22, selected as heavy metal tolerant, were characterized in presence of the heavy metals for the ability to accumulate zinc and copper and to activate antioxidative enzyme defences: superoxide dismutase, catalase, ascorbate peroxidase. The levels of expression of MT type 2 gene assessed by RT-qPCR confirmed the gene over-expression in transgenic lines and evidenced in NT and AL22 the up-regulation of gene transcription by zinc and copper. Transgenic poplar lines during heavy metal stress displayed increased ability to translocate and accumulate zinc and copper compared with NT and AL22. The antioxidant enzyme defence was differently activated in response to metals in the transgenic lines without a significant increase of ROS. These results suggested that PsMT(A1) could play a role in ROS scavenging leading to enhanced metal tolerance and increased zinc and copper sequestration in root and leaf.

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