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  • 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
  • 04.02. Exploration geophysics
  • Chromatin and Epigenetics
  • JSTOR Archive Collection Business II
  • Textbook of informatics
  • Oxford University Press  (44)
  • Springer  (21)
  • Wiley  (10)
  • AGU  (6)
  • American Chemical Society (ACS)
Schlagwörter
Erscheinungszeitraum
  • 1
    Publikationsdatum: 2021-06-14
    Beschreibung: Southwestern Sicily is an area of infrequent seismic activity; however, some studies carried out in the archaeological Selinunte site suggest that, between the fourth century BC and the early Middle Ages, probably at least two earthquakes strucked this area with enough energy to damage and cause the collapse and kinematics of much of the architecture of Selinunte. Take into account that, in 2008, a noninvasive archaeological prospection and traditional data gathering methods along the Acropolis north fortifications were carried out. Following these first studies, after about 10 years, a new geophysical campaign was carried out. This second campaign benefited from the application of modern technologies for the acquisition and processing of the point cloud data on the northern part of the Acropolis, like terrestrial laser scanning and unmanned aerial vehicle photogrammetry. In this paper, we present the application of these techniques and a strategy for their integration for the 3D modelling of buildings and cultural heritages. We show how the integration of data acquired independently by these two techniques is an added value able to overcome the intrinsic limits of the individual techniques. The application to Selinunte's Acropolis allowed it to highlight and measure with high accuracy fractures, dislocation, inclinations of walls, depressions of some areas and other interesting observations, which may be important starting points for future investigations.
    Beschreibung: Published
    Beschreibung: 153-165
    Beschreibung: 2IT. Laboratori analitici e sperimentali
    Beschreibung: JCR Journal
    Schlagwort(e): 3D reconstruction ; archaeological survey ; digital elevation model ; Selinunte Archaeological Park ; terrestrial laser scanning ; unmanned aerial vehicle photogrammetry ; 05.04. Instrumentation and techniques of general interest ; 04.02. Exploration geophysics ; 05.02. Data dissemination ; 05.06. Methods
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2023-10-13
    Beschreibung: This study focuses on two weak points of the present procedure to carry out microzoning study in near-field areas: (1) the Ground Motion Prediction Equations (GMPEs), commonly used in the reference seismic hazard (RSH) assessment; (2) the ambient noise measurements to define the natural frequency of the near surface soils and the bedrock depth. The limitations of these approaches will be discussed throughout the paper based on the worldwide and Italian experiences performed after the 2009 L’Aquila earthquake and then confirmed by the most recent 2012 Emilia Romagna earthquake and the 2016–17 Central Italy seismic sequence. The critical issues faced are (A) the high variability of peak ground acceleration (PGA) values within the first 20–30 km far from the source which are not robustly interpolated by the GMPEs,(B) at the level 1 microzoning activity, the soil seismic response under strong motion shaking is characterized by microtremors’ horizontal to vertical spectral ratios (HVSR) according to Nakamura’s method. This latter technique is commonly applied not being fully compliant with the rules fixed by European scientists in 2004, after a 3-year project named Site EffectS assessment using AMbient Excitations (SESAME). Hereinafter, some “best practices” from recent Italian and International experiences of seismic hazard estimation and microzonation studies are reported in order to put forward two proposals: (a) to formulate site-specific GMPEs in near-field areas in terms of PGA and (b) to record microtremor measurements following accurately the SESAME advice in order to get robust and repeatable HVSR values and to limit their use to those geological contests that are actually horizontally layered.
    Beschreibung: Published
    Beschreibung: id 11
    Beschreibung: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Beschreibung: JCR Journal
    Schlagwort(e): earthquake ; site effects ; 04.06. Seismology ; 04.02. Exploration geophysics
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2020-07-08
    Beschreibung: The response of continental forelands to subduction and collision is a widely investigated topic in geodynamics. The deformation occurring within a foreland shared by two opposite‐verging chains, however, is uncommon and poorly understood. The Apulia Swell in the southern end of the Adria microplate (Africa‐Europe plate boundary, central Mediterranean Sea) represents one of these cases, as it is the common foreland of the SW verging Albanides‐Hellenides and the NE verging Southern Apennines merging into the SSE verging Calabrian Arc. We investigated the internal deformation of the Apulia Swell using multiscale geophysical data: multichannel seismic profiles recording up to 12‐s two‐way time (TWT) for a consistent image of the upper crust; high‐resolution multichannel seismic profiles, high‐resolution multibeam bathymetry, and CHIRP profiles acquired by R/V OGS Explora to constrain the Quaternary geological record. The results of our analyses characterize the geometry of the South Apulia Fault System (SAFS), a 100‐km‐long and 12‐km‐wide structure attesting an extensional (and possibly transtensional) response of the foreland to the two contractional fronts. The SAFS consists of two NW‐SE right‐stepping master faults and several secondary structures. The SAFS activity spans from the Early Pleistocene through the Holocene, as testified by the bathymetric and high‐resolution seismic data, with long‐term slip rates in the range of 0.2–0.4 mm/yr. Considering the position within an area with few or none other active faults in the surroundings, the dimension, and the activity rates, the SAFS can be a candidate causative fault of the 20 February 1743, M 6.7, earthquake.
    Beschreibung: Italian Ministry for Education, University, and Research (MIUR), Premiale 2014 D. M. 291 03/05/2016.
    Beschreibung: Published
    Beschreibung: e2020TC006116
    Beschreibung: 2T. Deformazione crostale attiva
    Beschreibung: 2TR. Ricostruzione e modellazione della struttura crostale
    Beschreibung: JCR Journal
    Schlagwort(e): active tectonics ; apulia ; south apulia fault system ; 1743 earthquake ; marine geology ; stable continental region ; ionian sea ; active faults ; subsurface geology ; seismic interpretation ; 04.04. Geology ; 04.07. Tectonophysics ; 04.02. Exploration geophysics
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2016-06-21
    Beschreibung: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2016-07-09
    Beschreibung: Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity, it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila . Here, we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress possible toxic effects of Dam. In addition, we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. These new DamID tools will be valuable for the mapping of binding patterns of chromatin proteins in Drosophila tissues and especially in cell lineages.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2016-09-03
    Beschreibung: Nucleosomes, the fundamental subunits of eukaryotic chromatin, are organized with respect to transcriptional start sites. A major challenge to the persistence of this organization is the disassembly of nucleosomes during DNA replication. Here, we use complimentary approaches to map the locations of nucleosomes on recently replicated DNA. We find that nucleosomes are substantially realigned with promoters during the minutes following DNA replication. As a result, the nucleosomal landscape is largely re-established before newly replicated chromosomes are partitioned into daughter cells and can serve as a platform for the re-establishment of gene expression programmes. When the supply of histones is disrupted through mutation of the chaperone Caf1, a promoter-based architecture is generated, but with increased inter-nucleosomal spacing. This indicates that the chromatin remodelling enzymes responsible for spacing nucleosomes are capable of organizing nucleosomes with a range of different linker DNA lengths.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2016-09-20
    Beschreibung: DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological information such as biological networks has been proven to be powerful in identifying disease-associated genes in both gene expression studies and genome-wide association studies (GWAS) but has been under studied in EWAS. Although recent studies have noticed that there are differences in methylation variation in different groups, only a few existing methods consider variance signals in DNA methylation studies. Here, we present a network-assisted algorithm, NEpiC, that combines both mean and variance signals in searching for differentially methylated sub-networks using the protein–protein interaction (PPI) network. In simulation studies, we demonstrate the power gain from using both the prior biological information and variance signals compared to using either of the two or neither information. Applications to several DNA methylation datasets from the Cancer Genome Atlas (TCGA) project and DNA methylation data on hepatocellular carcinoma (HCC) from the Columbia University Medical Center (CUMC) suggest that the proposed NEpiC algorithm identifies more cancer-related genes and generates better replication results.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2016-08-20
    Beschreibung: To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2016-02-20
    Beschreibung: Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to ‘phasing’ off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 10
    Publikationsdatum: 2016-02-20
    Beschreibung: The Illumina HumanMethylation450 BeadChip is increasingly utilized in epigenome-wide association studies, however, this array-based measurement of DNA methylation is subject to measurement variation. Appropriate data preprocessing to remove background noise is important for detecting the small changes that may be associated with disease. We developed a novel background correction method, ENmix, that uses a mixture of exponential and truncated normal distributions to flexibly model signal intensity and uses a truncated normal distribution to model background noise. Depending on data availability, we employ three approaches to estimate background normal distribution parameters using (i) internal chip negative controls, (ii) out-of-band Infinium I probe intensities or (iii) combined methylated and unmethylated intensities. We evaluate ENmix against other available methods for both reproducibility among duplicate samples and accuracy of methylation measurement among laboratory control samples. ENmix out-performed other background correction methods for both these measures and substantially reduced the probe-design type bias between Infinium I and II probes. In reanalysis of existing EWAS data we show that ENmix can identify additional CpGs, and results in smaller P -value estimates for previously-validated CpGs. We incorporated the method into R package ENmix , which is freely available from Bioconductor website.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 11
    Publikationsdatum: 2016-05-20
    Beschreibung: Epigenetic modifications of histone tails play an essential role in the regulation of eukaryotic transcription. Writer and eraser enzymes establish and maintain the epigenetic code by creating or removing posttranslational marks. Specific binding proteins, called readers, recognize the modifications and mediate epigenetic signalling. Here, we present a versatile assay platform for the investigation of the interaction between methyl lysine readers and their ligands. This can be utilized for the screening of small-molecule inhibitors of such protein–protein interactions and the detailed characterization of the inhibition. Our platform is constructed in a modular way consisting of orthogonal in vitro binding assays for ligand screening and verification of initial hits and biophysical, label-free techniques for further kinetic characterization of confirmed ligands. A stability assay for the investigation of target engagement in a cellular context complements the platform. We applied the complete evaluation chain to the Tudor domain containing protein Spindlin1 and established the in vitro test systems for the double Tudor domain of the histone demethylase JMJD2C. We finally conducted an exploratory screen for inhibitors of the interaction between Spindlin1 and H3K4me3 and identified A366 as the first nanomolar small-molecule ligand of a Tudor domain containing methyl lysine reader.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 12
    Publikationsdatum: 2016-04-08
    Beschreibung: The brain is built from a large number of cell types which have been historically classified using location, morphology and molecular markers. Recent research suggests an important role of epigenetics in shaping and maintaining cell identity in the brain. To elucidate the role of DNA methylation in neuronal differentiation, we developed a new protocol for separation of nuclei from the two major populations of human prefrontal cortex neurons—GABAergic interneurons and glutamatergic (GLU) projection neurons. Major differences between the neuronal subtypes were revealed in CpG, non-CpG and hydroxymethylation (hCpG). A dramatically greater number of undermethylated CpG sites in GLU versus GABA neurons were identified. These differences did not directly translate into differences in gene expression and did not stem from the differences in hCpG methylation, as more hCpG methylation was detected in GLU versus GABA neurons. Notably, a comparable number of undermethylated non-CpG sites were identified in GLU and GABA neurons, and non-CpG methylation was a better predictor of subtype-specific gene expression compared to CpG methylation. Regions that are differentially methylated in GABA and GLU neurons were significantly enriched for schizophrenia risk loci. Collectively, our findings suggest that functional differences between neuronal subtypes are linked to their epigenetic specification.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 13
    Publikationsdatum: 2016-04-21
    Beschreibung: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a key technique in chromatin research. Although heavily applied, existing ChIP-seq protocols are often highly fine-tuned workflows, optimized for specific experimental requirements. Especially the initial steps of ChIP-seq, particularly chromatin shearing, are deemed to be exceedingly cell-type-specific, thus impeding any protocol standardization efforts. Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (NEXSON: Nuclei EXtraction by SONication) that is highly effective across various organisms, cell types and cell numbers. The described method has the potential to replace complex cell-type-specific, but largely ineffective, nuclei isolation protocols. By including NEXSON in ChIP-seq workflows, we completely eliminate the need for extensive optimization and sample-dependent adjustments. Apart from this significant simplification, our approach also provides the basis for a fully standardized ChIP-seq and yields highly reproducible transcription factor and histone modifications maps for a wide range of different cell types. Even small cell numbers (~10 000 cells per ChIP) can be easily processed without application of modified chromatin or library preparation protocols.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 14
    Publikationsdatum: 2016-12-01
    Beschreibung: The study of changes in protein–DNA interactions measured by ChIP-seq on dynamic systems, such as cell differentiation, response to treatments or the comparison of healthy and diseased individuals, is still an open challenge. There are few computational methods comparing changes in ChIP-seq signals with replicates. Moreover, none of these previous approaches addresses ChIP-seq specific experimental artefacts arising from studies with biological replicates. We propose THOR, a Hidden Markov Model based approach, to detect differential peaks between pairs of biological conditions with replicates. THOR provides all pre- and post-processing steps required in ChIP-seq analyses. Moreover, we propose a novel normalization approach based on housekeeping genes to deal with cases where replicates have distinct signal-to-noise ratios. To evaluate differential peak calling methods, we delineate a methodology using both biological and simulated data. This includes an evaluation procedure that associates differential peaks with changes in gene expression as well as histone modifications close to these peaks. We evaluate THOR and seven competing methods on data sets with distinct characteristics from in vitro studies with technical replicates to clinical studies of cancer patients. Our evaluation analysis comprises of 13 comparisons between pairs of biological conditions. We show that THOR performs best in all scenarios.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 15
    Publikationsdatum: 2016-12-04
    Beschreibung: Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 16
    facet.materialart.
    Unbekannt
    Oxford University Press
    Publikationsdatum: 2016-01-09
    Beschreibung: Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 17
    Publikationsdatum: 2020-02-24
    Beschreibung: The results of a detailed seismic microzonation study performed at Canazei (Trentino—Northern Italy) are here presented. We investigated the local seismic response of this small village using a Level 3 seismic microzonation, the most accurate according to the Italian Code of Seismic Microzonation. This method consists of gradual steps of knowledge to consider different aspects of the amplification phenomena. A multidisciplinary approach has been performed, including a local geological study, geophysical investigations, geotechnical characterization of lithologies and numerical analyses. The obtained elastic response spectra were compared to the spectra prescribed by the Italian Building Code. Our results show the geologic and geophysical subsoil heterogeneities, responsible for different local seismic responses in terms of acceleration spectra and amplification factors.
    Beschreibung: Published
    Beschreibung: 1085-1089
    Beschreibung: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Beschreibung: reserved
    Schlagwort(e): Seismic microzonation ; Response spectra ; Amplification factor ; Canazei ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: book chapter
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  • 18
    Publikationsdatum: 2015-12-16
    Beschreibung: Many cancers comprise heterogeneous populations of cells at primary and metastatic sites throughout the body. The presence or emergence of distinct subclones with drug-resistant genetic and epigenetic phenotypes within these populations can greatly complicate therapeutic intervention. Liquid biopsies of peripheral blood from cancer patients have been suggested as an ideal means of sampling intratumor genetic and epigenetic heterogeneity for diagnostics, monitoring and therapeutic guidance. However, current molecular diagnostic and sequencing methods are not well suited to the routine assessment of epigenetic heterogeneity in difficult samples such as liquid biopsies that contain intrinsically low fractional concentrations of circulating tumor DNA (ctDNA) and rare epigenetic subclonal populations. Here we report an alternative approach, deemed DREAMing (Discrimination of Rare EpiAlleles by Melt), which uses semi-limiting dilution and precise melt curve analysis to distinguish and enumerate individual copies of epiallelic species at single-CpG-site resolution in fractions as low as 0.005%, providing facile and inexpensive ultrasensitive assessment of locus-specific epigenetic heterogeneity directly from liquid biopsies. The technique is demonstrated here for the evaluation of epigenetic heterogeneity at p14 ARF and BRCA1 gene-promoter loci in liquid biopsies obtained from patients in association with non-small cell lung cancer (NSCLC) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN), respectively.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 19
    facet.materialart.
    Unbekannt
    Oxford University Press
    Publikationsdatum: 2015-12-16
    Beschreibung: Bisulfite sequencing is a key methodology in epigenetics. However, the standard workflow of bisulfite sequencing involves heat and strongly basic conditions to convert the intermediary product 5,6-dihydrouridine-6-sulfonate (dhU6S) (generated by reaction of bisulfite with deoxycytidine (dC)) to uracil (dU). These harsh conditions generally lead to sample loss and DNA damage while milder conditions may result in incomplete conversion of intermediates to uracil. Both can lead to poor recovery of bisulfite-treated DNA by the polymerase chain reaction (PCR) as either damaged DNA and/or intermediates of bisulfite treatment are poor substrate for standard DNA polymerases. Here we describe an engineered DNA polymerase (5D4) with an enhanced ability to replicate and PCR amplify bisulfite-treated DNA due to an ability to bypass both DNA lesions and bisulfite intermediates, allowing significantly milder conversion conditions and increased sensitivity in the PCR amplification of bisulfite-treated DNA. Incorporation of the 5D4 DNA polymerase into the bisulfite sequencing workflow thus promises significant sensitivity and efficiency gains.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 20
    Publikationsdatum: 2015-02-18
    Beschreibung: The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture in conjunction with super-SILAC quantification to carry out an unbiased high-throughput analysis of the composition of protein complexes that bind to histone H3K9/S10 and H3K27/S28 methyl-phospho modifications. The accurate quantification allowed us to perform Weighted correlation network analysis (WGCNA) to obtain a systems-level view of the histone H3 histone tail interactome. The analysis reveals the underlying modularity of the histone reader network with members of nuclear complexes exhibiting very similar binding signatures, which suggests that many proteins bind to histones as part of pre-organized complexes. Our results identify a novel complex that binds to the double H3K9me3/S10ph modification, which includes Atrx, Daxx and members of the FACT complex. The super-SILAC approach allows comparison of binding to multiple peptides with different combinations of modifications and the resolution of the WGCNA analysis is enhanced by maximizing the number of combinations that are compared. This makes it a useful approach for assessing the effects of changes in histone modification combinations on the composition and function of bound complexes.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 21
    Publikationsdatum: 2015-07-12
    Beschreibung: We present a capture-based approach for bisulfite-converted DNA that allows interrogation of pre-defined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 22
    Publikationsdatum: 2015-07-12
    Beschreibung: Androgen receptor (AR) variants (AR-Vs) expressed in prostate cancer (PCa) lack the AR ligand binding domain (LBD) and function as constitutively active transcription factors. AR-V expression in patient tissues or circulating tumor cells is associated with resistance to AR-targeting endocrine therapies and poor outcomes. Here, we investigated the mechanisms governing chromatin binding of AR-Vs with the goal of identifying therapeutic vulnerabilities. By chromatin immunoprecipitation and sequencing (ChIP-seq) and complementary biochemical experiments, we show that AR-Vs display a binding preference for the same canonical high-affinity androgen response elements (AREs) that are preferentially engaged by AR, albeit with lower affinity. Dimerization was an absolute requirement for constitutive AR-V DNA binding and transcriptional activation. Treatment with the bromodomain and extraterminal (BET) inhibitor JQ1 resulted in inhibition of AR-V chromatin binding and impaired AR-V driven PCa cell growth in vitro and in vivo . Importantly, this was associated with a novel JQ1 action of down-regulating AR-V transcript and protein expression. Overall, this study demonstrates that AR-Vs broadly restore AR chromatin binding events that are otherwise suppressed during endocrine therapy, and provides pre-clinical rationale for BET inhibition as a strategy for inhibiting expression and chromatin binding of AR-Vs in PCa.
    Schlagwort(e): Chromatin and Epigenetics
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 23
    Publikationsdatum: 2015-12-02
    Beschreibung: DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Recent developments in whole genome bisulfite sequencing (WGBS) technology have enabled genome-wide measurements of DNA methylation at single base pair resolution. Many experiments have been conducted to compare DNA methylation profiles under different biological contexts, with the goal of identifying differentially methylated regions (DMRs). Due to the high cost of WGBS experiments, many studies are still conducted without biological replicates. Methods and tools available for analyzing such data are very limited. We develop a statistical method, DSS-single, for detecting DMRs from WGBS data without replicates. We characterize the count data using a rigorous model that accounts for the spatial correlation of methylation levels, sequence depth and biological variation. We demonstrate that using information from neighboring CG sites, biological variation can be estimated accurately even without replicates. DMR detection is then carried out via a Wald test procedure. Simulations demonstrate that DSS-single has greater sensitivity and accuracy than existing methods, and an analysis of H1 versus IMR90 cell lines suggests that it also yields the most biologically meaningful results. DSS-single is implemented in the Bioconductor package DSS.
    Schlagwort(e): Chromatin and Epigenetics
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 24
    Publikationsdatum: 2015-11-17
    Beschreibung: Sequencing DNA fragments associated with proteins following in vivo cross-linking with formaldehyde (known as ChIP-seq) has been used extensively to describe the distribution of proteins across genomes. It is not widely appreciated that this method merely estimates a protein's distribution and cannot reveal changes in occupancy between samples. To do this, we tagged with the same epitope orthologous proteins in Saccharomyces cerevisiae and Candida glabrata , whose sequences have diverged to a degree that most DNA fragments longer than 50 bp are unique to just one species. By mixing defined numbers of C. glabrata cells (the calibration genome) with S. cerevisiae samples (the experimental genomes) prior to chromatin fragmentation and immunoprecipitation, it is possible to derive a quantitative measure of occupancy (the occupancy ratio – OR) that enables a comparison of occupancies not only within but also between genomes. We demonstrate for the first time that this ‘internal standard’ calibration method satisfies the sine qua non for quantifying ChIP-seq profiles, namely linearity over a wide range. Crucially, by employing functional tagged proteins, our calibration process describes a method that distinguishes genuine association within ChIP-seq profiles from background noise. Our method is applicable to any protein, not merely highly conserved ones, and obviates the need for the time consuming, expensive, and technically demanding quantification of ChIP using qPCR, which can only be performed on individual loci. As we demonstrate for the first time in this paper, calibrated ChIP-seq represents a major step towards documenting the quantitative distributions of proteins along chromosomes in different cell states, which we term biological chromodynamics.
    Schlagwort(e): Chromatin and Epigenetics
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  • 25
    Publikationsdatum: 2015-08-18
    Beschreibung: Stochastic epigenetic changes drive biological processes, such as development, aging and disease. Yet, epigenetic information is typically collected from millions of cells, thereby precluding a more precise understanding of cell-to-cell variability and the pathogenic history of epimutations. Here we present a novel procedure for directly detecting epimutations in DNA methylation patterns using single-cell, locus-specific bisulfite sequencing (SLBS). We show that within gene promoter regions of mouse hepatocytes the epimutation rate is two orders of magnitude higher than the mutation rate.
    Schlagwort(e): Chromatin and Epigenetics
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 26
    Publikationsdatum: 2014-11-28
    Beschreibung: Genome-wide assessment of protein–DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify ‘hyper ChIPable regions’ as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 27
    Publikationsdatum: 2014-05-01
    Beschreibung: DNA methylation is an important epigenetic modification that has essential roles in cellular processes including gene regulation, development and disease and is widely dysregulated in most types of cancer. Recent advances in sequencing technology have enabled the measurement of DNA methylation at single nucleotide resolution through methods such as whole-genome bisulfite sequencing and reduced representation bisulfite sequencing. In DNA methylation studies, a key task is to identify differences under distinct biological contexts, for example, between tumor and normal tissue. A challenge in sequencing studies is that the number of biological replicates is often limited by the costs of sequencing. The small number of replicates leads to unstable variance estimation, which can reduce accuracy to detect differentially methylated loci (DML). Here we propose a novel statistical method to detect DML when comparing two treatment groups. The sequencing counts are described by a lognormal-beta-binomial hierarchical model, which provides a basis for information sharing across different CpG sites. A Wald test is developed for hypothesis testing at each CpG site. Simulation results show that the proposed method yields improved DML detection compared to existing methods, particularly when the number of replicates is low. The proposed method is implemented in the Bioconductor package DSS.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
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  • 28
    Publikationsdatum: 2014-04-03
    Beschreibung: Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.
    Schlagwort(e): Chromatin and Epigenetics
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    Publiziert von Oxford University Press
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  • 29
    Publikationsdatum: 2014-04-03
    Beschreibung: Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered 〉70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation ( r 2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 30
    Publikationsdatum: 2014-09-17
    Beschreibung: Three-dimensional organization of chromatin is fundamental for transcriptional regulation. Tissue-specific transcriptional programs are orchestrated by transcription factors and epigenetic regulators. The RUNX2 transcription factor is required for differentiation of precursor cells into mature osteoblasts. Although organization and control of the bone-specific Runx2-P1 promoter have been studied extensively, long-range regulation has not been explored. In this study, we investigated higher-order organization of the Runx2-P1 promoter during osteoblast differentiation. Mining the ENCODE database revealed interactions between Runx2-P1 and  Supt3h promoters in several non-mesenchymal human cell lines. Supt3h is a ubiquitously expressed gene located within the first intron of Runx2 . These two genes show shared synteny across species from humans to sponges. Chromosome conformation capture analysis in the murine pre-osteoblastic MC3T3-E1 cell line revealed increased contact frequency between Runx2-P1 and Supt3h promoters during differentiation. This increase was accompanied by enhanced DNaseI hypersensitivity along with RUNX2 and CTCF binding at the Supt3h promoter. Furthermore, interplasmid-3C and luciferase reporter assays showed that the Supt3h promoter can modulate Runx2-P1 activity via direct association. Taken together, our data demonstrate physical proximity between Runx2-P1 and Supt3h promoters, consistent with their syntenic nature. Importantly, we identify the Supt3h promoter as a potential regulator of the bone-specific Runx2-P1 promoter .
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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  • 31
    Publikationsdatum: 2014-11-12
    Beschreibung: Understanding the role of a given transcription factor (TF) in regulating gene expression requires precise mapping of its binding sites in the genome. Chromatin immunoprecipitation-exo, an emerging technique using exonuclease to digest TF unbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with near-single nucleotide resolution. Although ChIP-exo promises deeper insights into transcription regulation, no dedicated bioinformatics tool exists to leverage its advantages. Most ChIP-seq and ChIP-chip analytic methods are not tailored for ChIP-exo, and thus cannot take full advantage of high-resolution ChIP-exo data. Here we describe a novel analysis framework, termed MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. The MACE workflow consists of four steps: (i) sequencing data normalization and bias correction; (ii) signal consolidation and noise reduction; (iii) single-nucleotide resolution border peak detection using the Chebyshev Inequality and (iv) border matching using the Gale-Shapley stable matching algorithm. When applied to published human CTCF, yeast Reb1 and our own mouse ONECUT1/HNF6 ChIP-exo data, MACE is able to define TFBSs with high sensitivity, specificity and spatial resolution, as evidenced by multiple criteria including motif enrichment, sequence conservation, direct sequence pileup, nucleosome positioning and open chromatin states. In addition, we show that the fundamental advance of MACE is the identification of two boundaries of a TFBS with high resolution, whereas other methods only report a single location of the same event. The two boundaries help elucidate the in vivo binding structure of a given TF, e.g. whether the TF may bind as dimers or in a complex with other co-factors.
    Schlagwort(e): Chromatin and Epigenetics
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    Thema: Biologie
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  • 32
    Publikationsdatum: 2013-04-02
    Beschreibung: DNA methylation is one of the most important epigenetic alterations involved in the control of gene expression. Bisulfite sequencing of genomic DNA is currently the only method to study DNA methylation patterns at single-nucleotide resolution. Hence, next-generation sequencing of bisulfite-converted DNA is the method of choice to investigate DNA methylation profiles at the genome-wide scale. Nevertheless, whole genome sequencing for analysis of human methylomes is expensive, and a method for targeted gene analysis would provide a good alternative in many cases where the primary interest is restricted to a set of genes. Here, we report the successful use of a custom Agilent SureSelect Target Enrichment system for the hybrid capture of bisulfite-converted DNA. We prepared bisulfite-converted next-generation sequencing libraries, which are enriched for the coding and regulatory regions of 174 ADME genes (i.e. genes involved in the metabolism and distribution of drugs). Sequencing of these libraries on Illumina’s HiSeq2000 revealed that the method allows a reliable quantification of methylation levels of CpG sites in the selected genes, and validation of the method using pyrosequencing and the Illumina 450K methylation BeadChips revealed good concordance.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 33
    Publikationsdatum: 2013-12-07
    Beschreibung: The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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  • 34
    Publikationsdatum: 2013-10-19
    Beschreibung: Methylation-specific fluorescence in situ hybridization (MeFISH) was developed for microscopic visualization of DNA methylation status at specific repeat sequences in individual cells. MeFISH is based on the differential reactivity of 5-methylcytosine and cytosine in target DNA for interstrand complex formation with osmium and bipyridine-containing nucleic acids (ICON). Cell nuclei and chromosomes hybridized with fluorescence-labeled ICON probes for mouse major and minor satellite repeats were treated with osmium for crosslinking. After denaturation, fluorescent signals were retained specifically at satellite repeats in wild-type, but not in DNA methyltransferase triple-knockout (negative control) mouse embryonic stem cells. Moreover, using MeFISH, we successfully detected hypomethylated satellite repeats in cells from patients with immunodeficiency, centromeric instability and facial anomalies syndrome and 5-hydroxymethylated satellite repeats in male germ cells, the latter of which had been considered to be unmethylated based on anti-5-methylcytosine antibody staining. MeFISH will be suitable for a wide range of applications in epigenetics research and medical diagnosis.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 35
    Publikationsdatum: 2013-01-20
    Beschreibung: Genomic deletions induced by imprecise excision of transposons have been used to disrupt gene functions in Drosophila . To determine the excision properties of Tol2 , a popular transposon in zebrafish, we took advantage of two transgenic zebrafish lines Et(gata2a:EGFP)pku684 and Et(gata2a:EGFP)pku760 , and mobilized the transposon by injecting transposase mRNA into homozygous transgenic embryos. Footprint analysis showed that the Tol2 transposons were excised in either a precise or an imprecise manner. Furthermore, we identified 1093-bp and 1253-bp genomic deletions in Et(gata2a:EGFP)pku684 founder embryos flanking the 5' end of the original Tol2 insertion site, and a 1340-bp deletion in the Et(gata2a:EGFP)pku760 founder embryos flanking the 3' end of the insertion site. The mosaic Et(gata2a:EGFP)pku684 embryos were raised to adulthood and screened for germline transmission of Tol2 excision in their F 1 progeny. On average, ~42% of the F 1 embryos displayed loss or altered EGFP patterns, demonstrating that this transposon could be efficiently excised from the zebrafish genome in the germline. Furthermore, from 59 founders, we identified one that transmitted the 1093-bp genomic deletion to its offspring. These results suggest that imprecise Tol2 transposon excision can be used as an alternative strategy to achieve gene targeting in zebrafish.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
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  • 36
    Publikationsdatum: 2013-08-28
    Beschreibung: Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which detects two proteins in close vicinity (~30 nm). The specificity of the method [designated as imaging of a combination of histone modifications (iChmo)] was confirmed by positive signals from H3K4me3/acetylated H3K9, H3K4me3/RNA polymerase II and H3K9me3/H4K20me3, and negative signals from H3K4me3/H3K9me3. Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination of repressive histone marks in tissue samples. The application of iChmo to samples with heterogeneous cell population and tissue samples is expected to clarify unknown biological and pathological significance of various combinations of epigenetic modifications.
    Schlagwort(e): Chromatin and Epigenetics
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    Thema: Biologie
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  • 37
    Publikationsdatum: 2013-03-13
    Beschreibung: Nucleosome positioning on the chromatin strand plays a critical role in regulating accessibility of DNA to transcription factors and chromatin modifying enzymes. Hence, detailed information on nucleosome depletion or movement at cis -acting regulatory elements has the potential to identify predicted binding sites for trans -acting factors. Using a novel method based on enrichment of mononucleosomal DNA by bacterial artificial chromosome hybridization, we mapped nucleosome positions by deep sequencing across 250 kb, encompassing the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene. CFTR shows tight tissue-specific regulation of expression, which is largely determined by cis -regulatory elements that lie outside the gene promoter. Although multiple elements are known, the repertoire of transcription factors that interact with these sites to activate or repress CFTR expression remains incomplete. Here, we show that specific nucleosome depletion corresponds to well-characterized binding sites for known trans -acting factors, including hepatocyte nuclear factor 1, Forkhead box A1 and CCCTC-binding factor. Moreover, the cell-type selective nucleosome positioning is effective in predicting binding sites for novel interacting factors, such as BAF155. Finally, we identify transcription factor binding sites that are overrepresented in regions where nucleosomes are depleted in a cell-specific manner. This approach recognizes the glucocorticoid receptor as a novel trans -acting factor that regulates CFTR expression in vivo .
    Schlagwort(e): Chromatin and Epigenetics
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  • 38
    Publikationsdatum: 2013-11-02
    Beschreibung: Here, we describe an approach to isolate native chromatin sections without genomic engineering for label-free proteomic identification of associated proteins and histone post-translational modifications. A transcription activator-like (TAL) protein A fusion protein was designed to recognize a unique site in the yeast GAL1 promoter. The TAL-PrA fusion enabled chromatin affinity purification (ChAP) of a small section of native chromatin upstream from the GAL1 locus, permitting mass spectrometric (MS) identification of proteins and histone post-translational modifications regulating galactose-induced transcription. This TAL-ChAP-MS approach allows the biochemical isolation of a specific native genomic locus for proteomic studies and will provide for unprecedented objective insight into protein and epigenetic mechanisms regulating site-specific chromosome metabolism.
    Schlagwort(e): Chromatin and Epigenetics
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  • 39
    Publikationsdatum: 2020-10-26
    Beschreibung: One of the main objectives of the ITACA (ITalian ACcelerometric Archive) strong motion database, promoted by the Italian Department of Civil Protection, was to improve the characterization of the recording sites from a geological and geophysical point of view and to provide their seismic classification according to the seismic norms pertinent to Italy, namely the Eurocode 8 and the National Technical Norms for Constructions. A standard format to summarize the available information for the recording stations was first produced, in terms of a technical report dynamically linked to the database, i.e., some of the relevant information is automatically updated when the corresponding fields of the database are modified. Then, an important activity of collection, qualification and synthesis of available data was carried out, especially for stations that recorded the strongest earthquakes in Italy in the last 40 years, and for which a relevant number of studies have been published. In spite of this activity, among the more than 700 strong motion stations present in the ITACA database, only a limited number of them could be characterized by quantitative information on subsurface soil properties. For this reason, a dual seismic site classification criterion was implemented, either based on the standard Vs,30 scheme, or, in the absence of such information, based on an expert opinion supported by shallow geology maps, mostly at 1:100,000 scale, and when available on the H/V ratios calculated on recordings. Owing to the relevance in the Italian geographic and morphological context, a special care was also given to the topographic classification of stations, based on suitable criteria developed within a GIS environment.
    Beschreibung: Published
    Beschreibung: 1779-1796
    Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): ITACA database ; Strong motion station ; General characterization ; Site classification ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 05. General::05.02. Data dissemination::05.02.02. Seismological data ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 40
    Publikationsdatum: 2017-04-04
    Beschreibung: In this paper we investigate nature and properties of narrow-band, transient seismic signals observed by a temporary array deployed in the Val Tiberina area (central Apennines, Italy). These signals are characterized by spindle-shaped, harmonic waveforms with no clear S-wave arrivals. The first portion of the seismograms exhibits a main frequency peak centred at 4.5 Hz, while the spectrum of the slowly decaying coda is peaked at about 2 Hz. Events discrimination is performed using a matched-filtering technique, resulting in a set of 2466 detections spanning the 2010 January–March time interval. From a plane-wave-fitting procedure, we estimate the kinematic properties of signals pertaining to a cluster of similar events. The repetition of measurements over a large number of precisely aligned seismograms allows for obtaining a robust statistics of horizontal slownesses and propagation azimuths associated with the early portion of the waveforms. The P-wave arrival exhibits horizontal slownesses around 0.1 s km−1, thus suggesting waves impinging at the array almost vertically. Separately, we use traveltimes measured at a sparse network to derive independent constraints on epicentral location. Ray parameters and azimuths are calibrated using slowness measurements from a local, well-located earthquake. After this correction, the joint solution from traveltime inversion and array analysis indicates a source region spanning the 1–3 km depth interval. Considerations related to the source depth and energy, and the occurrence rate which is not related to the daily and weekly working cycles, play against a surface, artificial source. Instead, the close resemblance of these signals to those commonly observed in volcanic environments suggest a source mechanism related to the resonance of a fluid–filled fracture, likely associated with instabilities in the flux of pressurized CO2.
    Beschreibung: Published
    Beschreibung: 918-928
    Beschreibung: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): Fracture and flow ; Earthquake source observations ; Interface waves ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 41
    Publikationsdatum: 2017-04-04
    Beschreibung: This paper describes the analyses of the single-station ambient-vibration measurements performed on the Italian accelerometric network to detect site resonance phenomena potentially affecting earthquake recordings. The use of low cost, high quality microtremor measurement can be helpful to discriminate among soil classes, since several classification schemes based on resonance frequencies were proposed in the last decades. Operatively, in the framework of the Italian Strong Motion Database project (DPC-INGV 2007–2009 S4; http://esse4.mi.ingv.it), soil resonance frequencies have been evaluated from more than 200 ambient vibration measurements in correspondence of accelerometric stations included in ITACA (http://itaca.mi.ingv.it/ItacaNet/). The noise recordings have been analyzed using the same numerical protocol in order to standardize the results. Particular attention has been paid to evaluate the quality of measurements and to develop an on-purpose mathematical tool to automatically estimate the peaks in the horizontal-to-vertical spectral ratio (HVSR) curve. The reliability of the resonance frequencies from HVSR has been tested by comparing estimates provided by independent methods (modeling or earthquake recordings). The test confirmed the reliability of the microtremor HVSR for assessing the resonance frequencies of the examined sites.
    Beschreibung: Published
    Beschreibung: 1821-1838
    Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): Ambient vibration measurements ; Strong motion database ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 42
    Publikationsdatum: 2012-06-28
    Beschreibung: Bromodeoxyuridine (5-bromo-2'-deoxyuridine, BrdU) is a halogenated nucleotide of low toxicity commonly used to monitor DNA replication. It is considered a valuable tool for in vitro and in vivo studies, including the detection of the small population of neural stem cells (NSC) in the mammalian brain. Here, we show that NSC grown in self-renewing conditions in vitro , when exposed to BrdU, lose the expression of stem cell markers like Nestin, Sox2 and Pax6 and undergo glial differentiation, strongly up-regulating the astrocytic marker GFAP. The onset of GFAP expression in BrdU exposed NSC was paralleled by a reduced expression of key DNA methyltransferases (DNMT) and a rapid loss of global DNA CpG methylation, as we determined by our specially developed analytic assay. Remarkably, a known DNA demethylating compound, 5-aza-2'-deoxycytidine (Decitabine), had similar effect on demethylation and differentiation of NSC. Since our key findings apply also to NSC derived from murine forebrain, our observations strongly suggest more caution in BrdU uses in stem cells research. We also propose that BrdU and its related substances may also open new opportunities for differentiation therapy in oncology.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 43
    Publikationsdatum: 2012-06-28
    Beschreibung: In Escherichia coli , the SeqA protein binds specifically to GATC sequences which are methylated on the A of the old strand but not on the new strand. Such hemimethylated DNA is produced by progression of the replication forks and lasts until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemimethylated DNA covered by SeqA follows the replication fork. We show that this is, indeed, the case by using global ChIP on Chip analysis of SeqA in cells synchronized regarding DNA replication. To assess hemimethylation, we developed the first genome-wide method for methylation analysis in bacteria. Since loss of the SeqA protein affects growth rate only during rapid growth when cells contain multiple replication forks, a comparison of rapid and slow growth was performed. In cells with six replication forks per chromosome, the two old forks were found to bind surprisingly little SeqA protein. Cell cycle analysis showed that loss of SeqA from the old forks did not occur at initiation of the new forks, but instead occurs at a time point coinciding with the end of SeqA-dependent origin sequestration. The finding suggests simultaneous origin de-sequestration and loss of SeqA from old replication forks.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 44
    Publikationsdatum: 2012-08-23
    Beschreibung: Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult to mimic in vitro . However, different studies have yielded widely discrepant predictions, and so it remains uncertain how to make the measurements accurately. To establish a benchmark we measured binding of the transcription factor p53 to chromatin by three approaches: fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and single-molecule tracking (SMT). Using new procedures to analyze the SMT data and to guide the FRAP and FCS analysis, we show how all three approaches yield similar estimates for both the fraction of p53 molecules bound to chromatin (only about 20%) and the residence time of these bound molecules (~1.8 s). We also apply these procedures to mutants in p53 chromatin binding. Our results support the model that p53 locates specific sites by first binding at sequence-independent sites.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 45
    Publikationsdatum: 2012-09-27
    Beschreibung: DNA methylation plays a key role in epigenetic regulation of eukaryotic genomes. Hence the genome-wide distribution of 5-methylcytosine, or the methylome, has been attracting intense attention. In recent years, whole-genome bisulfite sequencing (WGBS) has enabled methylome analysis at single-base resolution. However, WGBS typically requires microgram quantities of DNA as well as global PCR amplification, thereby precluding its application to samples of limited amounts. This is presumably because bisulfite treatment of adaptor-tagged templates, which is inherent to current WGBS methods, leads to substantial DNA fragmentation. To circumvent the bisulfite-induced loss of intact sequencing templates, we conceived an alternative method termed Post-Bisulfite Adaptor Tagging (PBAT) wherein bisulfite treatment precedes adaptor tagging by two rounds of random primer extension. The PBAT method can generate a substantial number of unamplified reads from as little as subnanogram quantities of DNA. It requires only 100 ng of DNA for amplification-free WGBS of mammalian genomes. Thus, the PBAT method will enable various novel applications that would not otherwise be possible, thereby contributing to the rapidly growing field of epigenomics.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 46
    Publikationsdatum: 2012-11-04
    Beschreibung: The mammalian thymine DNA glycosylase (TDG) is implicated in active DNA demethylation via the base excision repair pathway. TDG excises the mismatched base from G:X mismatches, where X is uracil, thymine or 5-hydroxymethyluracil (5hmU). These are, respectively, the deamination products of cytosine, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). In addition, TDG excises the Tet protein products 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) but not 5hmC and 5mC, when paired with a guanine. Here we present a post-reactive complex structure of the human TDG domain with a 28-base pair DNA containing a G:5hmU mismatch. TDG flips the target nucleotide from the double-stranded DNA, cleaves the N -glycosidic bond and leaves the C1' hydrolyzed abasic sugar in the flipped state. The cleaved 5hmU base remains in a binding pocket of the enzyme. TDG allows hydrogen-bonding interactions to both T/U-based (5hmU) and C-based (5caC) modifications, thus enabling its activity on a wider range of substrates. We further show that the TDG catalytic domain has higher activity for 5caC at a lower pH (5.5) as compared to the activities at higher pH (7.5 and 8.0) and that the structurally related Escherichia coli mismatch uracil glycosylase can excise 5caC as well. We discuss several possible mechanisms, including the amino-imino tautomerization of the substrate base that may explain how TDG discriminates against 5hmC and 5mC.
    Schlagwort(e): Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 47
    Publikationsdatum: 2017-04-04
    Beschreibung: During 2007–2008, three CO2 flux surveys were performed on El Chichón volcanic lake, Chiapas, Mexico, with an additional survey in April 2008 covering the entire crater floor (including the lake). The mean CO2 flux calculated by sequential Gaussian simulation from the lake was 1,190 (March 2007), 730 (December 2007) and 1,134 g m−2 day−1 (April 2008) with total emission rates of 164±9.5 (March 2007), 59±2.5 (December 2007) and 109±6.6 t day−1 (April 2008). The mean CO2 flux estimated from the entire crater floor area was 1,102 g m−2 day−1 for April 2008 with a total emission rate of 144±5.9 t day−1. Significant change in CO2 flux was not detected during the period of survey, and the mapping of the CO2 flux highlighted lineaments reflecting the main local and regional tectonic patterns. The 3He/4He ratio (as high as 8.1 RA) for gases in the El Chichón crater is generally higher than those observed at the neighbouring Transmexican Volcanic Belt and the Central American Volcanic Arc. The CO2/3He ratios for the high 3He/4He gases tend to have the MORB-like values (1.41×109), and the CO2/3He ratios for the lower 3He/4He gases fall within the range for the arc-type gases. The high 3He/4He ratios, the MORB-like CO2/3He ratios for the high 3He/4He gases and high proportion of MORB-CO2 (M=25 ±15%) at El Chichón indicate a greater depth for the generation of magma when compared to typical arc volcanoes.
    Beschreibung: Published
    Beschreibung: 423-441
    Beschreibung: 2.4. TTC - Laboratori di geochimica dei fluidi
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): El Chichon ; CO2 soil flux ; Crater Lake ; Gas geochemistry ; He-C isotopes ; Fumarolic and bubbling gases ; Tectonics ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.05. Geomagnetism::04.05.08. Instruments and techniques ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 48
    Publikationsdatum: 2017-04-03
    Beschreibung: After an earthquake, rapid, real-time assessment of hazards such as ground shaking and tsunami potential is important for early warning and emergency response. Tsunami potential depends on sea floor displacement, which is related to the length, L, width, W, mean slip, D, and depth, z, of earthquake rupture. Currently, the primary discriminant for tsunami potential is the centroid-moment tensor magnitude, MwCMT, representing the seismic potency LWD, and estimated through an indirect, inversion procedure. The obtained MwCMT and the implied LWD value vary with the depth of faulting, assumed earth model and other factors, and is only available 30 min or more after an earthquake. The use of more direct procedures for hazard assessment, when available, could avoid these problems and aid in effective early warning. Here we present a direct procedure for rapid assessment of earthquake tsunami potential using two, simple measures on P-wave seismograms – the dominant period on the velocity records, Td, and the likelihood that the high-frequency, apparent rupture-duration, T0, exceeds 50-55 sec. T0 can be related to the critical parameters L and z, while Td may be related to W, D or z. For a set of recent, large earthquakes, we show that the period-duration product TdT0 gives more information on tsunami impact and size than MwCMT and other currently used discriminants. All discriminants have difficulty in assessing the tsunami potential for oceanic strike-slip and back-arc or upper-plate, intraplate earthquake types. Our analysis and results suggest that tsunami potential is not directly related to the potency LWD from the “seismic” faulting model, as is assumed with the use of the MwCMT discriminant. Instead, knowledge of rupture length, L, and depth, z, alone can constrain well the tsunami potential of an earthquake, with explicit determination of fault width, W, and slip, D, being of secondary importance. With available real-time seismogram data, rapid calculation of the direct, period- duration discriminant can be completed within 6-10 min after an earthquake occurs and thus can aid in effective and reliable tsunami early warning.
    Beschreibung: In press
    Beschreibung: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): Earthquake dynamics ; Earthquake source observations ; Seismic monitoring ; Body waves ; Early warning ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 49
    Publikationsdatum: 2017-04-04
    Beschreibung: In this work we present and discuss the results of ambient seismic noise analyses computed at four sites where seismic stations, managed by the INGV (Italian Institute for Geophysics and Vulcanology) and the DPC (Italian Department of Civil Protection), are installed inside buildings. The experiments were performed considering different types of installation: sensor located at the bottom of a school, directly installed on rock (case 1); sensor located at the bottom of a medieval fortress, built on an isolate hill, directly installed on rock (case 2); sensor installed on the foundations of a medieval fortress, built on an isolate hill (case 3); sensor installed on the foundations of a school, built on alluvial deposits (case 4). Since recent works proposed the use of spectral ratio techniques to study the dynamic characterization of buildings, ambient seismic-noise measurements were performed for each site close to the stations (at the base of the structures), at the top of the structures and outside the buildings. In order to check the source of vibrations both horizontal to vertical spectral ratio (HVNR) and standard spectral ratio (SSR) techniques were applied. For all stations the results from ambient seismic noise were compared to those obtained from earthquakes (HVSR). In order to detect preferential directions of amplification, for each site average HVNRs and HVSRs were computed considering one azimuth for each set of 5°. We obtain different results for different types of installation: in cases 1 and 2, where the sensors are directly installed on rock, the vibrations of the structure do not affect the noise measures performed close to the stations, which show flat HVNR in the whole frequency range: in both cases the eigenfrequency of the building is given by the HVNR calculated from the measures performed at the top of the structure. In cases 3 and 4, where the sensors are installed on the foundations of the considered structures, both the amplification peaks between 5 and 9 Hz (case 3) and between 5.5 and 7 Hz (case 4) include the contribution of the free oscillations of the buildings. In particular, in case 4, HVNRs performed outside building highlight possible soil–structure resonance effects in case of an earthquake.
    Beschreibung: Published
    Beschreibung: 723-738
    Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): site effect ; soil-structure interaction ; spectral ratio techniques ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 50
    Publikationsdatum: 2017-04-04
    Beschreibung: The necessity of a dense network in Northern Italy started from the lack of available data after the occurrence of the 24th November 2004, Ml 5.2, Salò earthquake. Since 2006, many efforts have been made by the INGV (Italian National Institute for Geophysic and Vulcanology), Department of Milano-Pavia (hereinafter INGV MI-PV), to improve the strong-motion monitoring of the Northern Italy regions. This activity led to the installation of a strong-motion network composed by 20 accelerometers, 4 coupled with 20-bits Lennartz Mars88 recorders, 12 coupled with 24-bits Reftek 130 recorders and 4 coupled with 24-bits Gaia2 recorders. The network allow us to reduce, in the area under study, the average inter-distances between strong-motion stations from about 40 km (at November 2004) to 15 km. At present the network includes nine 6-channels stations where velocity sensors work together the strong-motion ones. The data transmission is assured by modem-gsm, with the exception of four stations that send data in real time through a TCP/IP protocol. In order to evaluate different site responses, the stations have been installed both in free field and near (or inside) public buildings, located in the center of small villages. From June 2006 to December 2008 a dataset of 94 events with local magnitude range from 0.7 to 5.1 has been collected. An ad hoc data-processing system have been created in order to provide, after each recorded event, engineering parameters such as peak ground acceleration (PGA) and velocity (PGV), response spectra (SA and PSV), Arias and Housner intensities. Data dissemination is achieved through the web site http://rais.mi.ingv.it, while the waveforms are distributed through the Italian strong motion database (http://itaca.mi.ingv.it).
    Beschreibung: Published
    Beschreibung: 1091-1104
    Beschreibung: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): North Italy ; Strong motion station ; Data acquisition system ; Seismic networks ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 51
    Publikationsdatum: 2017-04-04
    Beschreibung: A new method of macroseismic surveys, based on voluntary collaboration through the Internet, has been running at the Istituto Nazionale di Geofisica e Vulcanologia (INGV) since July 2007. The macroseismic questionnaire is addressed to a single non-specialist; reported effects are statistically analysed to extrapolate a probabilistic estimate of Mercalli Cancani Sieberg and European Macroseismic Scale intensities for that observer. Maps of macroseismic intensity are displayed online in almost real time and are continuously updated when new data are made available. For densely inhabited zones, we have received reports of felt effects for even very small events (M=2). Six earthquakes are presented here, showing the ability of the method to give fast and interesting results. The effects reported in questionnaires coming from three towns are carefully analysed and assigned intensities are compared with those derived from traditional macroseismic surveys, showing the reliability of our web-based method.
    Beschreibung: Published
    Beschreibung: 1.11. TTC - Osservazioni e monitoraggio macrosismico del territorio nazionale
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): Earthquakes ; Macroseismic intensity ; Questionnaire ; Macroseismic effects ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 52
    Publikationsdatum: 2017-04-04
    Beschreibung: Experimental data and numerical modelling were used to study the effect of local geology on the seismic response of the Catania area. The town extends on a marly clays bedrock and terraced deposits made up by coastal sands and alluvial conglomerates. This sedimentary substratum is deeply entrenched by paleo-valleys filled by lava flows and pyroclastics. Available borehole data and elastic parameters were used to reconstruct a geotechnical model in order to perfome 1D numerical modeling. Seismic urban scenarios were simulated considering destructive (Mw = 7.0), strong (Mw = 6.2) and moderate (Mw = 5.7) earthquakes to assess the shaking level of the different outcropping formations. For each scenario seven real accelerograms were selected from the European Strong Motion Database to assess the expected seismic input at the bedrock. PGA and spectral acceleration at different periods were obtained in the urban area through the equivalent linear numerical code EERA, and contour maps of different levels of shaking were drawn. Standard and horizontal-to-vertical spectral ratios were achieved making use of a dataset of 172 seismic events recorded at ten sites located on the main outcropping lithotypes. Spectral ratios inferred from earthquake data were compared with theoretical transfer functions. Both experimental and numerical results confirm the role of the geological and morphologic setting of Catania. Amplification of seismic motion mainly occurs in three different stratigraphic conditions: (a) sedimentary deposits mainly diffused in the south of the study area; (b) spots of soft sediments surrounded by lava flows; (c) intensely fractured and scoriaceous basaltic lavas.
    Beschreibung: In press
    Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Scenario earthquake ; 1D modelling ; PGA values ; Earthquake records ; spectral ratios ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.09. Waves and wave analysis
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 53
    Publikationsdatum: 2017-04-04
    Beschreibung: During local and regional earthquakes, an evident amplification of horizontal ground motion is observed at two seismological stations near the Tremestieri fault, on the southeastern flank of Mt. Etna volcano. Rotated-component spectral ratios show a narrow spectral peak around 4-Hz along a N40°E direction. A conventional polarization analysis using the eigenvectors of the covariance matrix confirms the very stable directional effect enhancing the approximately NE-SW elongation of the horizontal ground motion in the fault zone. The effect is evident during the entire seismogram and independent of source backazimuth as well as distance and depth of earthquakes. The same polarization is observed in ambient noise as well. This consistency allowed us to use microtremors for checking ground motion polarization along and across the Tremestieri fault zone with a high spatial resolution. The result is a stable polarization of horizontal motion in the entire area, interesting a broad frequency band. To check whether this ground motion property is recurrent and understand a possible relationship with fault strike, faulting style, or orientation of fractures, ambient noise was recorded on other mapped faults of the Mt. Etna area, the Moscarello, Acicatena and Pernicana faults. The latter, in particular, is characterized by different strike and faulting style. A systematic tendency of ambient noise to be polarized is found in all of the faults. A picture emerges where normal faults of the eastern flank show a E-W to NE-SW polarization that changes on the Pernicana fault, which develops approximately E-W and is characterized by a prevailing NW-SE to NS polarization. Directions of polarization were never parallel to the fault strike. Moreover, polarization persists too far away from the fault trace, excluding an effect limited to a narrow low velocity zone hosted between harder wall rocks. Both these observations rule out an interpretation in terms of fault-trapped waves. The cause of observed polarizations will be the subject of future studies. However, the consistency with recent results of velocity anisotropy in a part of the investigated area suggests a possible role of attenuation anisotropy on horizontal amplitude variations versus azimuth.
    Beschreibung: Published
    Beschreibung: B10306
    Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): polarization ; fault zones ; Etna volcano ; microtremors ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.06. Seismology::04.06.09. Waves and wave analysis ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 54
    Publikationsdatum: 2017-04-04
    Beschreibung: The spatial pattern of the b value of the frequency-magnitude relation has been analyzed using gridding techniques beneath Mount Etna, Italy. A regional data set of 2900 events with Md (duration magnitude) 1.5 up to 15 km depth occurring between August 1999 and December 2005 has been used. Two regions with an abnormally high b value have been found, one centered beneath the southern part of the Valle del Bove, above the 6 km below sea level (bsl) deep basement, and the other beneath the summit region 2 km bsl east of the Central Craters. We can infer that these high b value anomalies are regions of increased crack density, and/or high pore pressure, related to the presence of nearby magma storage. This interpretation is supported by all the available geophysical evidence, such as tomographic studies and geodetic deformation measurements. The data set has also been subdivided into five periods, corresponding to different phases of volcanic activity: 2001 preeruption, 2001 eruptive, 2002–2003 preeruption, 2002–2003 eruptive, and 2002–2003 posteruption. The minimum magnitude of completeness, Mc, and the b value were computed for each period. A volume of anomalously high b values can be observed in each of these periods (except for the 2002–2003 preeruption interval). This approach has allowed the detection of the transient presence of magmatic intrusions during the various periods evaluated.
    Beschreibung: Published
    Beschreibung: B12303
    Beschreibung: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Beschreibung: 4.3. TTC - Scenari di pericolosità vulcanica
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): b value ; Mount Etna ; frequency-magnitude relation ; magmatic intrusions ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 55
    Publikationsdatum: 2017-04-04
    Beschreibung: We report unprecedented observations of long-period (LP) seismicity in non-volcanic setting. Our data are from the Central-Northern sector of the Apennine chain, Italy. For this area, intense CO2 circulation of mantle origin has been documented by either groundwater composition and borehole measurements. We perform waveform correlation and stacking to obtain reliable epicenter estimates. Following Chouet's crack model, we find that both the quality factor and dominant frequency of LP oscillations are consistent with the sustained resonance of a wet crack filled by a water-CO2 mixture.
    Beschreibung: Published
    Beschreibung: L12303
    Beschreibung: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): Long-period events ; apennines ; fluids ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 56
    Publikationsdatum: 2017-04-04
    Beschreibung: We detect seismic wave velocity changes at Mt. Vesuvius, using doublets and the Coda Wave Interferometry method. The high sensitivity of multiply scattered coda waves to temporal changes in the medium allows us to detect velocity variation smaller than 0.4%. We use 17 doublets, some of them grouped in families of multiplets, spanning January 1996 to December 1999. Data show a systematic increase in velocity from 1996 to end- September 1999, followed by a rapid drop in velocity. This drop immediately precedes a sustained swarm of VT-type earthquakes, including the 9th October 1999 M = 3.6 event, the largest in the region since at least 1972. We propose a long term fluid pressurization followed by influx as a possible causative mechanism.
    Beschreibung: Published
    Beschreibung: L06306
    Beschreibung: reserved
    Schlagwort(e): NONE ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 57
    Publikationsdatum: 2017-04-04
    Beschreibung: The Institute for Geophysics at Hamburg University and the Research Center for Marine Geoscience (GEOMAR) of Kiel University have developed new, wideband ocean bottom seismic stations for long-term, deep sea deplyments of up to 1 year.
    Beschreibung: Published
    Beschreibung: 309-315
    Beschreibung: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Beschreibung: open
    Schlagwort(e): Ocean Bottom Seismometer ; Tyrrhenian Sea ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 58
    facet.materialart.
    Unbekannt
    Springer
    In:  London, Springer, vol. 13, no. 3, pp. 632 pp., (ISBN-10: 1-84628-053-2, ISBN-13:978-1-84628-053-5, eISBN 1-84628-054-0, xx + 591 pp. + CD-ROM)
    Publikationsdatum: 2006
    Schlagwort(e): Textbook of informatics ; Handbook of informatics ; compiler ; computing ; FTN ; GFZ ; M ; 06.0186 ; 000444331
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  • 59
    Publikationsdatum: 2017-04-04
    Beschreibung: Source and Qp parameters were estimated from the inversion of first arrival P waveform durations of about 300 microearthquakes recorded at a digital seismic network operating in southeastern Sicily. The average risetime and pulse width at each station do not show large differences, allowing us to exclude significant differential attenuation site effects. A first Qp estimate was obtained by applying the classical risetime method, under the assumption of a point-like source time function. In order to investigate the effect of directivity due to the finiteness of seismic sources, new nonlinear relationships, based on a circular crack model rupturing at a constant velocity, were numerically built. These relationships were used to formulate a nonlinear inverse method for retrieving source (radius, dip, and strike of the circular crack) and Qp parameters from the inversion of risetime and pulse width data. The application of the method produced a better fit of the observed data and a Qp value higher than that obtained by applying the risetime method. The discrepancy between the different Q estimates may be due to a trade-off among source dimension and Qp, as we inferred from a test on a subset of low-magnitude events (Ml ≤ 2.5). A good agreement with independent estimates of fault plane solutions, as inferred from P polarities and S polarizations, was found. The estimated stress drops are generally very low (0.1–10 bars). This suggests that the background seismic activity in southeastern Sicily is related to fault segments and/or weakened zones where great stress accumulations are hindered.
    Beschreibung: Published
    Beschreibung: 1-14
    Beschreibung: partially_open
    Schlagwort(e): source and Qp parameters ; risetime ; pulse width ; attenuation ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.02. Earthquake interactions and probability ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 60
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    Wiley
    In:  Chichester, 2nd ed., xvii + 517 pp., Wiley, vol. 5, no. 22, pp. 662-664, (ISBN 0-470-87000-1 (HB), ISBN 0-470-87001-X (PB))
    Publikationsdatum: 2005
    Schlagwort(e): GIS ; Textbook of informatics ; Textbook of geography ; geography ; management ; policy
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  • 61
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    Springer
    In:  Berlin, Heidelberg, New York, Springer, vol. 4, no. 85, pp. 175, (ISBN 3-540-24988-5)
    Publikationsdatum: 2005
    Schlagwort(e): Textbook of informatics ; Earthquake hazard ; Earthquake risk ; Tsunami(s) ; Proceedings of a conference ; INSPIRE ; OpenGIS ; GIS ; floods ; landslides ; storms ; geography ; Delft ; GFZ ; M ; 06.0234 ; 000303921
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  • 62
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    Springer
    In:  Geo-Information for Disaster Management, Berlin, Heidelberg, New York, Springer, vol. 12, pp. 323-336, (ISBN 3-540-24988-5)
    Publikationsdatum: 2005
    Schlagwort(e): Textbook of informatics ; Earthquake hazard ; Earthquake risk ; Tsunami(s) ; Proceedings of a conference ; Earthquake ; Indonesia ; Geodesy
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    Wiley
    In:  New York - 2nd ed., 372 pp., Wiley, vol. 1, pp. 225, (ISBN 0-471-32192-3)
    Publikationsdatum: 1999
    Schlagwort(e): Textbook of geography ; Textbook of informatics ; GIS
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    Wiley
    In:  Chichester, 292 pp., Wiley, vol. 45, pp. ii + 37 pp. + 35 figs. + 4 tabs., (ISBN 0-471-95596-5)
    Publikationsdatum: 1998
    Schlagwort(e): Textbook of informatics ; FTN90 ; Gegenueberstellung ; der ; beiden ; Programmiersprachen ; PIK ; Potsdam
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    Springer
    In:  Berlin, Springer, vol. 15, no. Publ. No. 12, pp. 585, (ISBN 1-85233-708-7)
    Publikationsdatum: 1989
    Schlagwort(e): Textbook of informatics ; Textbook of mathematics ; Chaotic behaviour
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  • 66
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    Springer
    In:  Berlin, Springer, vol. 96, pp. 225, (ISBN 0-471-95596-5)
    Publikationsdatum: 1986
    Schlagwort(e): COS ; gra ; Textbook of informatics
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  • 67
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    Springer
    In:  New York, Springer, vol. 113, no. XVI:, pp. 1-14, (ISBN 1-56670-263-3)
    Publikationsdatum: 1972
    Schlagwort(e): Transformations ; squ ; Textbook of informatics ; Textbook of mathematics
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  • 68
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    Oxford University Press | JSTOR
    Online: 1.1986 – (older than 6 years)
    Verlag: Oxford University Press , JSTOR
    Print ISSN: 0257-3032
    Digitale ISSN: 1564-6971
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Springer | JSTOR
    Online: 1(1).1991 – (older than 4 years)
    Verlag: Springer , JSTOR
    Print ISSN: 0938-2259
    Digitale ISSN: 1432-0479
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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  • 70
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    Wiley | JSTOR | formerly Oxford University Press (OUP)
    Online: 10(1).1988 –
    Vormals: Illinois Agricultural Economics; North Central Journal of Agricultural Economics; Review of Agricultural Economics  (1961–2009)
    Verlag: Wiley , JSTOR , formerly Oxford University Press (OUP)
    Print ISSN: 0191-9016 , 1058-7195 , 2040-5790
    Digitale ISSN: 1467-9353 , 2040-5804
    Thema: Land- und Forstwirtschaft, Gartenbau, Fischereiwirtschaft, Hauswirtschaft , Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Springer | Palgrave Macmillan | International Monetary Fund | JSTOR
    Online: 44.1997 –
    Verlag: Springer , Palgrave Macmillan , International Monetary Fund , JSTOR
    Print ISSN: 0020-8027 , 1020-7635 , 2041-4161
    Digitale ISSN: 1564-5150 , 2041-417X
    Thema: Wirtschaftswissenschaften
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    Oxford University Press | JSTOR
    Online: 1.1985 – (older than 8 years)
    Verlag: Oxford University Press , JSTOR
    Print ISSN: 8756-6222
    Digitale ISSN: 1465-7341
    Thema: Rechtswissenschaft , Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Springer | JSTOR
    Online: 1.1982 – (older than 4 years)
    Verlag: Springer , JSTOR
    Print ISSN: 0167-4544
    Digitale ISSN: 1573-0697
    Thema: Philosophie , Wirtschaftswissenschaften
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    Online: 1.2003 – (older than 6 years)
    Verlag: Oxford University Press , JSTOR
    Print ISSN: 1542-4766
    Digitale ISSN: 1542-4774
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Oxford University Press | JSTOR
    Online: 1.1986 – (older than 6 years)
    Verlag: Oxford University Press , JSTOR
    Print ISSN: 0258-6770
    Digitale ISSN: 1564-698X
    Thema: Wirtschaftswissenschaften
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    Oxford University Press | JSTOR
    Online: 1.1985 – (older than 6 years)
    Verlag: Oxford University Press , JSTOR
    Print ISSN: 0266-4658
    Digitale ISSN: 1468-0327
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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  • 77
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    Wiley | JSTOR
    Online: 78.1976 – (older than 6 years)
    Verlag: Wiley , JSTOR
    Print ISSN: 0347-0520
    Digitale ISSN: 1467-9442
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Springer | JSTOR
    Online: 1(1).1988 – (older than 4 years)
    Verlag: Springer , JSTOR
    Print ISSN: 0933-1433
    Digitale ISSN: 1432-1475
    Thema: Sociologie , Wirtschaftswissenschaften
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    Springer | JSTOR
    Online: 4.1968 – (older than 4 years)
    Verlag: Springer , JSTOR
    Print ISSN: 0048-5829
    Digitale ISSN: 1573-7101
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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    Springer | JSTOR
    Online: 2(1).2001 – (older than 4 years)
    Verlag: Springer , JSTOR
    Print ISSN: 1618-7598
    Digitale ISSN: 1618-7601
    Thema: Medizin , Wirtschaftswissenschaften
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    Wiley | Financial Management Association International | JSTOR
    Online: 1(1).1972 – (older than 4 years)
    Verlag: Wiley , Financial Management Association International , JSTOR
    Print ISSN: 0046-3892
    Digitale ISSN: 1755-053X
    Thema: Wirtschaftswissenschaften
    Schlagwort(e): JSTOR Archive Collection Business II
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