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  • 1
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    Effects of atmospheric conditions on surface diffuse degassing (2013)
    Wiley
    Details
    Publication Date: 2013-01-03
    Description: [1]  Diffuse degassing through the soil is commonly observed in volcanic areas and monitoring of carbon dioxide flux at the surface can provide a safe and effective way to infer the state of activity of the volcanic system. Continuous measurement stations are often installed on active volcanoes such as Furnas (Azores archipelago), which features low temperature fumaroles, hot and cold CO 2 rich springs, and several diffuse degassing areas. As in other volcanoes, fluxes measured at Furnas are often correlated with environmental variables, such as air temperature or barometric pressure, with daily and seasonal cycles that become more evident when gas emission is low. In this work, we study how changes in air temperature and barometric pressure may affect the gas emission through the soil. The TOUGH2 geothermal simulator was used to simulate the gas propagation through the soil as a function of fluctuating atmospheric conditions. Then, a dual parameters study was performed to assess how the rock permeability and the gas source properties affect the resulting fluxes. Numerical results are in good agreement with the observed data at Furnas, and show that atmospheric variables may cause the observed daily cycles in CO 2 fluxes. The observed changes depend on soil permeability and on the pressure driving the upward flux.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-26
    Description: Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Atwell, Susanna -- Huang, Yu S -- Vilhjalmsson, Bjarni J -- Willems, Glenda -- Horton, Matthew -- Li, Yan -- Meng, Dazhe -- Platt, Alexander -- Tarone, Aaron M -- Hu, Tina T -- Jiang, Rong -- Muliyati, N Wayan -- Zhang, Xu -- Amer, Muhammad Ali -- Baxter, Ivan -- Brachi, Benjamin -- Chory, Joanne -- Dean, Caroline -- Debieu, Marilyne -- de Meaux, Juliette -- Ecker, Joseph R -- Faure, Nathalie -- Kniskern, Joel M -- Jones, Jonathan D G -- Michael, Todd -- Nemri, Adnane -- Roux, Fabrice -- Salt, David E -- Tang, Chunlao -- Todesco, Marco -- Traw, M Brian -- Weigel, Detlef -- Marjoram, Paul -- Borevitz, Justin O -- Bergelson, Joy -- Nordborg, Magnus -- GM057994/GM/NIGMS NIH HHS/ -- GM073822/GM/NIGMS NIH HHS/ -- GM078536/GM/NIGMS NIH HHS/ -- GM62932/GM/NIGMS NIH HHS/ -- P42ES007373/ES/NIEHS NIH HHS/ -- R01 GM057994/GM/NIGMS NIH HHS/ -- R01 GM057994-05A1/GM/NIGMS NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- R01 GM062932-05/GM/NIGMS NIH HHS/ -- R01 GM073822/GM/NIGMS NIH HHS/ -- R01 GM073822-01A1/GM/NIGMS NIH HHS/ -- R01 GM078536-01A1/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jun 3;465(7298):627-31. doi: 10.1038/nature08800. Epub 2010 Mar 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20336072" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*classification/*genetics ; Arabidopsis Proteins/genetics ; Flowers/genetics ; Genes, Plant/genetics ; Genetic Loci/genetics ; Genome, Plant/*genetics ; *Genome-Wide Association Study ; Genotype ; Immunity, Innate/genetics ; Inbreeding ; *Phenotype ; Polymorphism, Single Nucleotide/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-06-04
    Description: Plants can defend themselves against a wide array of enemies, from microbes to large animals, yet there is great variability in the effectiveness of such defences, both within and between species. Some of this variation can be explained by conflicting pressures from pathogens with different modes of attack. A second explanation comes from an evolutionary 'tug of war', in which pathogens adapt to evade detection, until the plant has evolved new recognition capabilities for pathogen invasion. If selection is, however, sufficiently strong, susceptible hosts should remain rare. That this is not the case is best explained by costs incurred from constitutive defences in a pest-free environment. Using a combination of forward genetics and genome-wide association analyses, we demonstrate that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6), underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains. A hyperactive ACD6 allele, compared to the reference allele, strongly enhances resistance to a broad range of pathogens from different phyla, but at the same time slows the production of new leaves and greatly reduces the biomass of mature leaves. This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055268/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055268/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Todesco, Marco -- Balasubramanian, Sureshkumar -- Hu, Tina T -- Traw, M Brian -- Horton, Matthew -- Epple, Petra -- Kuhns, Christine -- Sureshkumar, Sridevi -- Schwartz, Christopher -- Lanz, Christa -- Laitinen, Roosa A E -- Huang, Yu -- Chory, Joanne -- Lipka, Volker -- Borevitz, Justin O -- Dangl, Jeffery L -- Bergelson, Joy -- Nordborg, Magnus -- Weigel, Detlef -- F23-GM65032-1/GM/NIGMS NIH HHS/ -- GM057171/GM/NIGMS NIH HHS/ -- GM057994/GM/NIGMS NIH HHS/ -- GM073822/GM/NIGMS NIH HHS/ -- GM62932/GM/NIGMS NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- R01 GM062932-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jun 3;465(7298):632-6. doi: 10.1038/nature09083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520716" target="_blank"〉PubMed〈/a〉
    Keywords: *Alleles ; Ankyrins/genetics/metabolism ; Arabidopsis/*genetics/growth & development/metabolism/microbiology ; Arabidopsis Proteins/genetics/metabolism ; Biomass ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Fitness/*genetics ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Molecular Sequence Data ; Phenotype ; Plant Diseases/genetics/microbiology ; Plant Leaves/anatomy & histology/genetics/growth & development/parasitology ; Quantitative Trait Loci
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-20
    Description: Variation in the length of simple DNA triplet repeats has been linked to phenotypic variability in microbes and to several human disorders. Population-level forces driving triplet repeat contraction and expansion in multicellular organisms are, however, not well understood. We have identified a triplet repeat-associated genetic defect in an Arabidopsis thaliana variety collected from the wild. The Bur-0 strain carries a dramatically expanded TTC/GAA repeat in the intron of the ISOPROPYL MALATE ISOMERASE LARGE SUB UNIT1 (IIL1; At4g13430) gene. The repeat expansion causes an environment-dependent reduction in IIL1 activity and severely impairs growth of this strain, whereas contraction of the expanded repeat can reverse the detrimental phenotype. The Bur-0 IIL1 defect thus presents a genetically tractable model for triplet repeat expansions and their variability in natural populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sureshkumar, Sridevi -- Todesco, Marco -- Schneeberger, Korbinian -- Harilal, Ramya -- Balasubramanian, Sureshkumar -- Weigel, Detlef -- New York, N.Y. -- Science. 2009 Feb 20;323(5917):1060-3. doi: 10.1126/science.1164014. Epub 2009 Jan 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19150812" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*genetics/growth & development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Genes, Plant ; Genetic Variation ; *Introns ; Isomerases/*genetics/metabolism ; Molecular Sequence Data ; Phenotype ; Plant Leaves/growth & development ; RNA, Plant/genetics/metabolism ; Temperature ; *Trinucleotide Repeat Expansion ; Trinucleotide Repeats
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Effects of atmospheric conditions on surface diffuse degassing (2012)
    Wiley
    Details
    Publication Date: 2012-11-07
    Description: Diffuse degassing through the soil is commonly observed in volcanic areas and monitoring of carbon dioxide flux at the surface can provide a safe and effective way to infer the state of activity of the volcanic system. Continuous measurement stations are often installed on active volcanoes such as Furnas (Azores archipelago), which features low temperature fumaroles, hot and cold CO2 rich springs, and several diffuse degassing areas. As in other volcanoes, fluxes measured at Furnas are often correlated with environmental variables, such as air temperature or barometric pressure, with daily and seasonal cycles that become more evident when gas emission is low. In this work, we study how changes in air temperature and barometric pressure may affect the gas emission through the soil. The TOUGH2 geothermal simulator was used to simulate the gas propagation through the soil as a function of fluctuating atmospheric conditions. Then, a dual parameters study was performed to assess how the rock permeability and the gas source properties affect the resulting fluxes. Numerical results are in good agreement with the observed data at Furnas, and show that atmospheric variables may cause the observed daily cycles in CO2 fluxes. The observed changes depend on soil permeability and on the pressure driving the upward flux.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    The leap in the dark: Geological thoughts about an unpredictable planet (2017)
    Wiley
    Details
    Publication Date: 2017-04-21
    Description: We live on a dynamic planet that changes continuously. Most of the times, we are unaware of its restless motion, so slow that only satellites capture it. But the calm is only apparent, and we appreciate the entire magnitude of the forces at play when natural disasters strike. Earth Science explores how and when the quiet breaks, but we do not have access to the interior of the planet. We rely on indirect information to constrain complex processes that we cannot observe or reproduce in our laboratories. As a result, our knowledge is incomplete and our assessments are burden with unavoidable uncertainty. Should we not talk about it?
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    Pyroclastic flow hazard assessment at Vesuvius (Italy) by using numerical modeling. II. Analysis of flow variables (2002)
    Springer
    Details
    Publication Date: 2002-05-01
    Print ISSN: 0258-8900
    Electronic ISSN: 1432-0819
    Topics: Geosciences
    Published by Springer
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  • 8
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    Pyroclastic flow hazard assessment at Vesuvius (Italy) by using numerical modeling. I. Large-scale dynamics (2002)
    Springer
    Details
    Publication Date: 2002-05-01
    Print ISSN: 0258-8900
    Electronic ISSN: 1432-0819
    Topics: Geosciences
    Published by Springer
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  • 9
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    The L'Aquila trial (2015)
    Geological Society (of London)
    Details
    Publication Date: 2015-02-15
    Description: The first stage of the trial in L'Aquila (Italy) ended with a conviction of seven experts, convened by the head of Civil Protection on 31 March 2009, for multiple manslaughter and serious injuries. They were sentenced to six years in jail, perpetual interdiction from public office and a fine of several million euros to be paid to the victims of the earthquake of 6 April 2009 (moment magnitude 6.3) for having caused, by their negligent conduct, the death of 29 persons and the injury of several others. The verdict had a tremendous impact on the scientific community and on the way scientists deliver their expert opinions to decision makers and society. This paper analyses the scientific argumentations reported in the Verdict Motivations, where scientific data and results were largely debated and misused to demonstrate that they should have been considered as a tool to predict an impending large earthquake. Moreover, we show that the supposed message of reassurance was not generated at the experts’ meeting or by the official Istituto Nazionale di Geofisica e Vulcanologia reports. The media had a key role in conveying information during the seismic swarm, contributing to the risk perception. We stress that prevention actions based on seismic hazard knowledge are the best defence against earthquakes.
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
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  • 10
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    Time-lapse gravity inversion with an active time constraint (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-09
    Description: Traditional methods used to invert gravity data are generally based on smoothness as a regularizer and the time-lapse inversion of gravity data is traditionally based on sequential inversion. A smooth density model can be in contradiction with the known geology of the target and sequential time-lapse inversion may lead to the presence of artefacts in the sequence of tomograms due to the propagation of errors from the initial dataset and its associated tomogram. We propose a deterministic time-lapse algorithm to invert a sequence of gravity data combining two features: an image focusing technique and the use of a time-dependent regularizer using an Active Time Constrained (ATC) approach. These two features are included directly in the objective function to minimize. The ATC inversion of time-lapse gravity data is efficient in filtering out noise-contaminated data as long as the noise is not correlated over time. Our approach can also be used to incorporate prior information regarding the density model we want to retrieve. The forward solver is based on a commercial finite element solver with a high flexibility in meshing irregular domains, a feature that is important to include realistic topography from digital elevation maps, for instance, and to describe the density distribution of geological structures with complex geometries. We benchmark the accuracy of the forward modelling code using an analytical expression and test the effectiveness of the focusing algorithm. We show the advantage of our approach in the case of the water flooding of an oil reservoir in order to detect and monitor the position of the oil–water encroachment front. We also test the model against synthetic data describing the evolution of a hydrothermal system feed by a magmatic source and the collapse of a mine. In all these cases, the approach we follow is successful in monitoring density changes.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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