Heavy metal load and effects on biochemical properties in urban soils of a medium-sized city, Ancona, Italy

none6noUrban soils are often mixed with extraneous materials and show a high spatial variability that determine great differences from their agricultural or natural counterparts. The soils of 18 localities of a medium-sized city (Ancona, Italy) were analysed for their main physicochemical and biological properties, and for chromium (Cr), copper (Cu), cobalt (Co), lead (Pb), nickel (Ni), zinc (Zn), and mercury (Hg) total content, distribution among particle-size fractions, and extractability. Because of the absence of thresholds defining a hot spot for heavy metal pollution in urban soils, we defined a “threshold of attention” (ToA) for each heavy metal aiming to bring out hot spot soils where it is more impellent to intervene to mitigate or avoid potential environmental concerns. In several city locations, the soil displayed sub-alkaline pH, large contents of clay-size particles, and higher TOC, total N, and available P with respect to the surrounding rural areas, joined with high contents of total heavy metals, but low availability. The C biomass, basal respiration, qCO2, and enzyme activities were compared to that detected in the near rural soils, and results suggested that heavy metals content has not substantially compromised the soil ecological services. We conclude that ToA can be considered as a valuable tool to highlight soil hot spots especially for cities with a long material history and, for a proper risk assessment in urban soils, we suggest considering the content of available heavy metals (rather than the total content) and soil functions.openSerrani D.; Ajmone-Marsan F.; Corti G.; Cocco S.; Cardelli V.; Adamo P.Serrani, D.; Ajmone-Marsan, F.; Corti, G.; Cocco, S.; Cardelli, V.; Adamo, P

Single Nucleotide Polymorphisms in collagen genes and association with skin quality trait

AbstractLivestock skin is largely employed in the manufacturing of clothing and shoes, sector in which Italy is a world leader. To sustain Italian products against foreign competition in the globalization era particular attention is to be focus on product quality. Here we investigate the association of SNP mutations in genes coding for collagen proteins present in animal skin with a number of phisico-chemical parameters influencing skin quality for the tanning industry.Skin and blood were sampled from 73 Italian Friesian and Italian Brown bovines and from 43 Bergamasca and Sarda ovines, classified by sex and age. Skins were characterised for a set of chemico-physical parameters (thickness, density, humidity, protein content, ashes, lipid content, hydrossi-proline and DNA content).Regions of the collagen type I, III and IV were screened for SNP discovery in the two species by sequencing a set of reference animals. In bovine 15 polymorphisms were identified: (2 in collagen type I, 9 in collagen type III alp..

Traceability of the PGI product "Vitellone Bianco dell'Appennino Centrale" by SNP markers

AbstractTraceability of meat has become a key aspect of food-quality assurance and a priority for EU countries, to meet consumer demand for comprehensive and integrated food safety policies. In this context, the traceability of animals and animal products at the breed level might play a key role as it would enable the certification of regional products linked to particular breeds. Technologies based on DNA analysis have the potential to achieve this goal bypassing the large scale and systematic biological sampling necessary for individual fingerprinting.The objective of this work was to test the power of a SNP panel to trace PGI "Vitellone Bianco dell'Appennino Centrale", a product linked to three breeds: Chianina, Marchigiana and Romagnola.A total of 180 unrelated animals belonging to PGI-allowed breeds (Chianina n=22; Romagnola n=22; and Marchigiana n=22) and PGI-not allowed breeds (Piemontese n=22, Maremmana n=24, Italian Red Pied n=24, Italian Brown n=22, Italian Friesian n=22) were sampled and genoty..

Developing Lockdown Policies

Hardly a week passes without reading or hearing about a school being locked down because of concerns for the safety of students, teachers, and staff. The increasing number of events that prompt lockdowns presents a sad commentary about today’s world. Aware of the very real possibility of threats of violence on campus, district leaders must ensure that they have current policies that cover the safety and risk management issues associated with imposed lockdowns

Molecular characterization of the Montecristo feral goats in the Mediterranean context

The Montecristo wild goat is an endangered feral population occurring on the homonymous island in the Tuscan Archipelago since a long time. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project on the Italian mainland, respectively. Diversity levels, gene flow, population structure and relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, highlighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, Neighbour-network and population structure analyses clearly separated the insular nucleus from all other breeds, but also the two Montecristo populations from each other. Treemix software analysis pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs Of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time, and highlighted a noticeable differentiation between the two nuclei. This evidence can serve as a starting point to implement marker-assisted conservation plans for the endangered Montecristo feral goat

The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions

The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed\u2019s main purpose is to produce milk and meat, but is peculiar for its involvement in the \u201cBatailles de Ch\ue8vres,\u201d a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed

Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

The Montecristo wild goat is an endangered feral population that has been on the homony-mous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project. Diversity levels, gene flow, population structure, and genetic relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, high-lighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, network, and population structure analyses clearly separated the insular nucleus from all other breeds, including the population of Montecristo goats from the mainland. Moreover, admixture and gene flow analyses pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent extensive inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time and highlighted a noticeable differentiation between the two nuclei

A genome-wide perspective on the population structure of Italian cattle breeds

Despite the growing diffusion of cosmopolite specialized breeds, several autochthonous populations are still farmed in Italy. The aim of this study was to provide a high-resolution picture of the genome-wide diversity and population structure of Italian local cattle breeds using medium-density genome-wide SNP markers. After data editing, the dataset included 800 samples from 32 breeds that were genotyped for 31,013 SNPs. For several breeds we observed a low level of polymorphism and genetic diversity that confirmed threat of extinction. Shared ancestry, admixture events, and reticulations observed on the phylogenetic tree between some breeds, all suggest high levels of gene flow. Clear clusters and relationships between breeds that originated from the same geographical area were detected. However, in spite of the complex admixture history, many of the local Italian cattle breeds have retained unique identities and are clearly differentiated breeds. Differences in their origin, in climate characteristics of farming areas, the genetic isolation, and the inbreeding can be the main reasons for such differentiation. This study represents the first exhaustive genome-wide analysis of Italian cattle diversity. The results largely agreed with the breeding history of the Italian cattle breeds. The population structure and the low genetic diversity presented here for several breeds should be evaluated in adopting conservation strategies. Thus, efforts should be made to improve genetic diversity in these breeds. Control of inbreeding, breeding stations development and improvement of recording system are strategies to conserve these breeds under in situ conservation situation, and in this context, genomic information may play a crucial role for the preservation and management of these populations

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Background: Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results: We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions: These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations