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San Michele Mondovì, Italy

Falda M.,University of Padua | Fontana P.,Edmund Machinery Foundation | Barzon L.,University of Padua | Toppo S.,University of Padua | Lavezzo E.,University of Padua
Bioinformatics | Year: 2014

The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because of the impact they may have in recent molecular biology applications. keeSeek is able to find absent sequences with primer-like features, which can be used as unique labels for exogenously inserted DNA fragments to recover their exact position into the genome using PCR techniques. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers. KeeSeek has been implemented in C++ and CUDA (Compute Unified Device Architecture) to work in a General-Purpose Computing on Graphics Processing Units (GPGPU) environment.Availability and implementation: Freely available under the Q Public License at http://www.medcomp.medicina.unipd.it/main-site/doku.php?id=keeseek. © 2014 The Author. Source

Migliaccio F.,CNR Institute of Agro-environmental and Forest Biology | Tassone P.,CNR Institute of Agro-environmental and Forest Biology | Fortunati A.,Edmund Machinery Foundation
American Journal of Botany | Year: 2013

Although publications on circumnutation of the aerial parts of fl owering plants are numerous and primarily from the time between Darwin (1880) and the 1950s, reports on circumnutation of roots are scarce. With the introduction of modern molecular biology techniques, many topics in the plant sciences have been revitalized; among these is root circumnutation. The most important research in this area has been done on Arabidopsis thaliana, which has roots that behave differently from those of many other plants; roots grown on inclined agar dishes produce a pattern of half waves slanted to one side. When grown instead on horizontally set dishes, the roots grow in loops or in tight right-handed coils that are characterized by a tight torsion to the left-hand. The roots of the few plants that differ from Arabidopsis and have been similarly tested do not present such patterns, because even if they circumnutate generally in a helical pattern, they subsequently straighten. Research on plants in space or on a clinostat has allowed the testing of these roots in a habitat lacking gravity or simulating the lack. Recently, molecular geneticists have started to connect various root behaviors to specifi c groups of genes. For example, anomalies in auxin responses caused by some genes can be overcome by complementation with wild-type genes. Such important studies contribute to understanding the mechanisms of growth and elongation, processes that are only superfi cially understood. © 2013 Botanical Society of America. Source

Spinelli R.,CNR Tree and Timber Institute | Nati C.,CNR Tree and Timber Institute | Pari L.,Italian Agricultural Research Council | Mescalchin E.,Edmund Machinery Foundation | Magagnotti N.,CNR Tree and Timber Institute
Applied Energy | Year: 2012

Vineyards cover about eight millions of hectares worldwide and their annual pruning generates a large amount of ligno-cellulosic biomass, potentially available for industrial and energy use. Commercial pruning residue harvesters are now available, which may allow cost-effective recovery. The study aimed at determining the quantity and the quality of pruning residues potentially derived from vineyard management. Data were obtained from 17 fields in Northern and Central Italy. Fields were harvested with seven different machines. The experimental design adapted to the necessities of field trials, but was adequate for testing the main sources of variability. Net residue yield varies around 1 oven dry tonne per hectare, with minor differences between grape varietals and harvesting technologies. Losses are still high, and are generally related to ineffective management techniques. Moisture content at harvest varies between 40% and 45%, whereas the higher heating value is slightly lower than that of forest fuels. Comminuted vineyard residues are unsuitable for firing residential boilers, due to the frequent presence of oversize and/or undersize particles. The application of pesticides does not result in any significant contamination with noxious chemicals, because these products are almost completely weathered before residues are recovered. In wine-producing regions, the recovery of vineyard pruning residue may represent a substantial source of industrial bio-fuel. © 2011 Elsevier Ltd. Source

Latte L.D.,University of Padua | Bortolin F.,University of Padua | Rota-Stabelli O.,Edmund Machinery Foundation | Fusco G.,University of Padua | Bonato L.,University of Padua
ZooKeys | Year: 2015

Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcod­ing gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia. ©Laura Del Latte et al. Source

Foggi B.,University of Florence | Lastrucci L.,University of Siena | Geri F.,University of Siena | Rocchini D.,Edmund Machinery Foundation
Landscape Research | Year: 2015

The Mediterranean region is a major hotspot of biodiversity. However, over the last 50 to 100 years, this area has suffered dramatic changes in human pressure that has led to significant landscape changes resulting in a recovery of the vegetation cover to one of higher biomass. A multi-temporal vegetation analysis of Giannutri Island, based on inspection of a 50-year series of vegetation maps (1958–2008), shows an increase in high maquis and Juniperus-thickets positively correlated with a decrease in open and low maquis. The increase of high maquis and Juniperus-thickets shows two distinct types of strategies in their advancement: the first increases its coverage with new patches arising some distance away from one another, while Juniperus-thickets expand from the margins. These two behaviour types may be correlated to a different pressure from thrushes (Turdus spp.) their disperser found on the island. The few patches of Quercus ilex woodland have remained constant due to the absence in Giannutri of its principal disperser: the jay (Garrulus glandarius). Based on this it would be impossible to take into consideration the Potential Natural Vegetation (PNV) concept in addressing conservation activities on an island like Giannutri. © 2014, Landscape Research Group Ltd. Source

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