PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity

Background: Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking. Results: We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module. Conclusions: PhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data

Thermal anomalies and fluid geochemistry framework in occurrence of the 2000-2001 Nizza Monferrate seismic sequence (northern Italy): Episodic changes in the fault zone heat flow or chemical mixing phenomena?

International audienceThe paper discusses the correlation between the heating of shallow groundwater over a 10 × 20 km wide area close to the town of Nizza Monferrato (Piemonte Region, Northern Italy) and the concomitant local seismic sequences during the period August 2000 ? July 2001. The first seismic sequence started on 21 August 2000 with a Ml = 5.2 earthquake. Within few hours, the local authorities received calls alerting that the groundwater temperature rose from 10 to 30°C in many shallow wells. Our geochemical experimental data and the geological-seismotectonic framework do not allow the hypothesis of simple fluid mixing between the thermal reservoir of Acqui Terme and the Nizza-Monferrato shallow groundwater to explain the observed thermal anomalies. On the other hand, we invoke more complex processes such as frictional heating, mechano-chemistry, fault-valve mechanism, adiabatic decompression and hydrogeologically driven heat flow i.e., thermal effects due to variations of basin-scale permeability field. All these processes are able to transmit heat to the surface and to generate a transient incremental heat flow better than the mass transfer occurring typically when fluids from different reservoirs mix

Soil-gas survey of liquefaction and collapsed caves during the Emilia seismic sequence

Immediately after the 20th May 2012 Mw 5.9 main shock Emilia earthquake and during the seismic sequence of May-June, 2012, geochemical field investigations were carried out into the epicentral area. This paper provides preliminary soils measurements of CO2 and CH4 performed on widespread liquefactions and ground fractures, occurred after the main shock. Soil gas concentrations and flux measurements on some collapsed caves, already studied in 2008, were repeated again during the seismic sequence of 2012. Observations related to gap forming between buildings and sidewalk, damage of roads, tilting of electricity poles, sand eruption from a well and settlement of ground are also presented

A Multidisciplinary Approach to Earthquake Research: Implementation of a Geochemical Geographic Information System for the Gargano Site, Southern Italy

A priority task for correct environmental planning is to evaluate Natural Hazards, especially in highly populated areas. In particular, thorough investigations based on different Earth Science techniques must be addressed for the Seismic Hazard Assessment (SHA) in tectonically active areas. Not only the management but also the multidisciplinary analysis of all the SHA-related data sets is best performed using a Geographic Information System. In this paper we show how a researchoriented GIS is built and used in a practical case. The Geochemical Geographic Information System (G2IS) was developed and applied to the Gargano promontory (southern Italy) in the framework of an EC research project, the Geochemical Seismic Zonation (GSZ) Project. This multidisciplinary – multiscaling powerful tool is described in its structure, updating procedures and manipulation techniques. Preliminary results are presented on the detection of geochemically active fault zones and their correlation with remote sensing data and other evidences of seismogenic structures.Published255-278JCR Journalreserve

Feasibility study (I stage) of CO2 geological storage by ECBM tecniques in the Sulcis Coal Province (SW Sardinia).

An ECBM feasibility study started for the Sulcis Coal Province (SW Sardinia, Italy): available geochemical, structural-geology, stratigraphic and reservoir engineering considerations as well as the newly gathered experimental data are discussed, including: fluid geochemistry (major and minor elements, dissolved gases, C and He isotopic ratios) of different strata/reservoir, coal composition and experimental data on CO2/CH4 adsorption-desorption on coal. A MapInfo GIS structure was built up including stratigraphic, geo-structural, hydro-geochemical, coal-compositional and environmental-impact information as well as the CO2 sources location and typology. Despite preliminary, these data highlighted both the challenging positive and negative aspects of the Sulcis Coal Province versus the exploitation of the ECBM technique. The most important objective of this phase I of the project is the selection of the best Sulcis ECBM test-pilot site, which will be followed (Phase II-2007) by the choice of a scaled up site and possibly by a future network (Phase III-2008). CO2 geological storage and CH4 production potentials in Sulcis have been grossly evaluated as a whole, in the frame of the Sardinia region CO2 sources, including the coal-fired power plants, both existent and foreseen (hundreds of millions of tonnes of CO2 are possible to be stored underground in the next decades).UnpublishedTrondheim, Norway4.4. Scenari e mitigazione del rischio ambientaleope

Feasibility study (I stage) of CO2 geological storage by ECBM tecniques in the Sulcis Coal Province (SW Sardinia).

An ECBM feasibility study started for the Sulcis Coal Province (SW Sardinia, Italy): available geochemical, structural-geology, stratigraphic and reservoir engineering considerations as well as the newly gathered experimental data are discussed, including: fluid geochemistry (major and minor elements, dissolved gases, C and He isotopic ratios) of different strata/reservoir, coal composition and experimental data on CO2/CH4 adsorption-desorption on coal. A MapInfo GIS structure was built up including stratigraphic, geo-structural, hydro-geochemical, coal-compositional and environmental-impact information as well as the CO2 sources location and typology. Despite preliminary, these data highlighted both the challenging positive and negative aspects of the Sulcis Coal Province versus the exploitation of the ECBM technique. The most important objective of this phase I of the project is the selection of the best Sulcis ECBM test-pilot site, which will be followed (Phase II-2007) by the choice of a scaled up site and possibly by a future network (Phase III-2008). CO2 geological storage and CH4 production potentials in Sulcis have been grossly evaluated as a whole, in the frame of the Sardinia region CO2 sources, including the coal-fired power plants, both existent and foreseen (hundreds of millions of tonnes of CO2 are possible to be stored underground in the next decades)

Contribution of Rare and Low-Frequency Variants to Multiple Sclerosis Susceptibility in the Italian Continental Population

Genome-wide association studies identified over 200 risk loci for multiple sclerosis (MS) focusing on common variants, which account for about 50% of disease heritability. The goal of this study was to investigate whether low-frequency and rare functional variants, located in MS-established associated loci, may contribute to disease risk in a relatively homogeneous population, testing their cumulative effect (burden) with gene-wise tests. We sequenced 98 genes in 588 Italian patients with MS and 408 matched healthy controls (HCs). Variants were selected using different filtering criteria based on allelic frequency and in silico functional impacts. Genes showing a significant burden (n = 17) were sequenced in an independent cohort of 504 MS and 504 HC. The highest signal in both cohorts was observed for the disruptive variants (stop-gain, stop-loss, or splicing variants) located in EFCAB13, a gene coding for a protein of an unknown function (p < 10–4). Among these variants, the minor allele of a stop-gain variant showed a significantly higher frequency in MS versus HC in both sequenced cohorts (p = 0.0093 and p = 0.025), confirmed by a meta-analysis on a third independent cohort of 1298 MS and 1430 HC (p = 0.001) assayed with an SNP array. Real-time PCR on 14 heterozygous individuals for this variant did not evidence the presence of the stop-gain allele, suggesting a transcript degradation by non-sense mediated decay, supported by the evidence that the carriers of the stop-gain variant had a lower expression of this gene (p = 0.0184). In conclusion, we identified a novel low-frequency functional variant associated with MS susceptibility, suggesting the possible role of rare/low-frequency variants in MS as reported for other complex diseases

Groundwater of Rome

This paper describes the contents of the new Hydrogeological Map of the City of Rome (1:50,000 scale). The map extends to the entire municipality (1285 km2) and is based on both the most recent scientific studies on the groundwater field and new survey activities carried out in order to fill the data gaps in several areas of the examined territory. The map is the result of a combination of different urban groundwater expertise and Geographic Information System (GIS)-based mapping performed using the most recent available data and has been produced with the intention of furnishing the City of Rome with the most recent and updated information regarding groundwater

Continuous in situ measurements of volcanic gases with a diode-laser-based spectrometer: CO2 and H2O concentration and soil degassing at Vulcano (Aeolian islands: Italy)

We report on a continuous-measurement campaign carried out in Vulcano (Aeolian islands, Sicily), devoted to the simultaneous monitoring of CO2 and H2O concentrations. The measurements were performed with an absorption spectrometer based on a semiconductor laser source emitting around a 2-μm wavelength. The emitted radiation was selectively absorbed by two molecular ro-vibrational transitions specific of the investigated species. Data for CO2 and H2O concentrations, and CO2 soil diffusive flux using an accumulation chamber configuration, were collected at several interesting sampling points on the island (Porto Levante beach- PLB, Fossa Grande Crater – FOG- and Valley of Palizzi, PAL). CO2/H2O values, measured on the ground, are very similar (around 0.019 (± 0.006)) and comparable to the previous discrete detected values of 0.213 (Fumarole F5-La Fossa crater rim) and 0.012 (Fumarole VFS – Baia Levante beach) obtaid during the 1977–1993 heating phase of the crater fumaroles

Expanded phenotype of AARS1-related white matter disease.

Purpose Recent reports of individuals with cytoplasmic transfer RNA (tRNA) synthetase-related disorders have identified cases with phenotypic variability from the index presentations. We sought to assess phenotypic variability in individuals with AARS1-related disease. Methods A cross-sectional survey was performed on individuals with biallelic variants in AARS1. Clinical data, neuroimaging, and genetic testing results were reviewed. Alanyl tRNA synthetase (AlaRS) activity was measured in available fibroblasts. Results We identified 11 affected individuals. Two phenotypic presentations emerged, one with early infantile–onset disease resembling the index cases of AARS1-related epileptic encephalopathy with deficient myelination (n = 7). The second (n = 4) was a later-onset disorder, where disease onset occurred after the first year of life and was characterized on neuroimaging by a progressive posterior predominant leukoencephalopathy evolving to include the frontal white matter. AlaRS activity was significantly reduced in five affected individuals with both early infantile–onset and late-onset phenotypes. Conclusion We suggest that variants in AARS1 result in a broader clinical spectrum than previously appreciated. The predominant form results in early infantile–onset disease with epileptic encephalopathy and deficient myelination. However, a subgroup of affected individuals manifests with late-onset disease and similarly rapid progressive clinical decline. Longitudinal imaging and clinical follow-up will be valuable in understanding factors affecting disease progression and outcome