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  • Evolution  (686)
  • phosphorus  (681)
  • 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
  • 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring
  • Cultural Heritage
  • Springer  (1,373)
  • American Geophysical Union  (12)
  • Copernicus  (7)
  • Institute of Electrical and Electronics Engineers (IEEE)
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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers a comprehensive overview of the role and potential of microorganisms in the degradation and preservation of cultural materials (e.g. stone, metals, graphic documents, textiles, paintings, glass, etc.). Microorganisms are a major cause of deterioration in cultural artefacts, both in the case of outdoor monuments and archaeological finds. This book covers the microorganisms involved in biodeterioration and control methods used to reduce their impact on cultural artefacts. Additionally, the reader will learn more about how microorganisms can be used for the preservation and protection of cultural artefacts through bio-based and eco-friendly materials. New avenues for developing methods and materials for the conservation of cultural artefacts are discussed, together with concrete advances in terms of sustainability, effectiveness and toxicity, making the book essential reading for anyone interested in microbiology and the preservation of cultural heritage.
    Keywords: Microbiology ; Cultural Heritage ; Microbial Ecology ; Microbial Genetics and Genomics ; Enzymology ; Applied Microbiology ; Microbial Genetics ; Industrial Microbiology ; Open Access ; Restoration ; Conservation ; Biodeterioration ; Bioweathering ; Bioremediation ; Biocleaning ; Biotechnology ; Green Chemistry ; Fungi ; Bacteria ; Artwork ; Antimicrobial protection ; Biocides ; Microbiology (non-medical) ; Cultural studies ; Social & cultural history ; Ecological science, the Biosphere ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCC Cultural studies ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 3
    Publication Date: 2021-04-07
    Description: The flow of ground water in a buried permeable paleochannel can be observed at the ground surface through its self-potential signature. We apply this method to delineate the Saint-Ferréol paleo-channel of the Rhone River located in Camargue, in the South East of France. Negative potentials, 30 mV (reference taken outside the paleochannel),are associated with ground water flow in this major sand-filled channel (500 m wide). Electrical resistivity is primarily controls by the salinity of the pore water. Electrical resistivity tomography and in situ sampling show the salinity of the water inside the paleo-channel is ten times smaller by comparison with the pore water of the surrounding sediments. Combining electrical resistivity surveys, self-potential data, and a minimum of drilling information, a 3-D reconstruction of the architecture of the paleo-channel is obtained showing the usefulness of this methodology for geomorphological reconstructions in this type of coastal environment.
    Description: - Observatoire de Recherche en Environnement (ORE)
    Description: Published
    Description: L07401
    Description: partially_open
    Keywords: Self-potential ; electrical resistivity tomography ; hydrogeology ; tomography ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 03. Hydrosphere::03.02. Hydrology::03.02.02. Hydrological processes: interaction, transport, dynamics ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 04. Solid Earth::04.02. Exploration geophysics::04.02.04. Magnetic and electrical methods ; 04. Solid Earth::04.06. Seismology::04.06.07. Tomography and anisotropy ; 05. General::05.02. Data dissemination::05.02.04. Hydrogeological data
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 4
    Publication Date: 2021-06-07
    Description: The diagnosis of the conservation state of monumental structures from constraints to the spatial distribution of their physical properties on shallow and inner materials represents one of the key objectives in the application of non-invasive techniques. In situ, CRP and 3D ultrasonic tomography can provide an effective coverage of stone materials in space and time. The intrinsic characteristics of the materials that make up a monumental structure and affect the two properties (i.e., reflectivity, longitudinal velocity) through the above methods substantially differ. Consequently, the content of their information is mainly complementary rather than redundant. In this study we present the integrated application of different non-destructive techniques i.e., Close Range Photogrammetry (CRP), and low frequency (24 KHz) ultrasonic tomography complemented by petrographycal analysis based essentially on Optical Microscopy (OM). This integrated methodology has been applied to a Carrara marble column of the Basilica of San Saturnino, in Byzantine-Proto-Romanesque style, which is part of the Paleo Christian complex of the V-VI century. This complex also includes the adjacent Christian necropolis in the square of San Cosimo in the city of Cagliari, Sardinia, Italy. The column under study is made of bare material dating back probably to the first century A.D., it was subjected to various traumas due to disassembly and transport to the site, including damage caused by the close blast of a WWII fragmentation bomb. High resolution 3D modelling of the studied artifact was computed starting from the integration of proximal sensing techniques such as CRP based on Structure from Motion (SfM), with which information about the geometrical anomalies and reflectivity of the investigated marble column surface was obtained. On the other hand, the inner parts of the studied body were successfully inspected in a non-invasive way by computing the velocity pattern of the ultrasonic signal through the investigated materials using 3D ultrasonic tomography. This technique gives information on the elastic properties of the material related with mechanical properties and a number of factors, such as presence of fractures, voids, and flaws. Extracting information on such factors from the elastic wave velocity using 3D tomography provides a non-invasive approach to analyse the property changes of the inner material of the ancient column. The integrated application of in situ CRP and ultrasonic techniques provides a full 3D high resolution model of the investigated artifact. This model enhanced by the knowledge of the petrographic characteristics of the materials, improves the diagnostic process and affords reliable information on the state of conservation of the materials used in the construction processes of the studied monumental structure. The integrated use of the non-destructive techniques described above also provides suitable data for a possible restoration and future preservation.
    Description: Copernicus
    Description: Published
    Description: On line
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Keywords: Cultural Heritage ; Monumental Structures ; Non-Destructive Testing ; Close Range Photogrammetry ; 3D Ultrasonic Tomography ; High resolution 3D modelling ; Restoration ; Conservation ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Abstract
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  • 5
    Publication Date: 2017-04-04
    Description: The recent eruption of Mount Etna (July 2001) offered the opportunity to analyze magma-derived volatiles emitted during preand syn-eruptive phases, and to verify whether their composition is affected by changes in volcanic dynamics. This paper presents the results of analyses of F, Cl and S in the volcanic plume collected by filter-packs, and interprets variations in the composition based on contrasting solubility in magmas. A Rayleigh-type degassing mechanism was used to fit the acquired data and to estimate Henryâ s solubility constant ratios in Etnean basalt. This model provided insights into the dynamics of the volcano. Abundances of sulfur and halogens in eruptive plumes may help predict the temporal evolution of an ongoing effusive eruption.
    Description: -Gruppo Nazionale per la Vulcanologia.
    Description: Published
    Description: 1559
    Description: partially_open
    Keywords: magmatic degassing ; acidic gases ; plume chemistry ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 6
    Publication Date: 2017-04-04
    Description: Six hundred and sixty-seven water samples were collected from public drinking water supplies in Sicily and analysed for electric conductivity and for their Cl-, Br- and F- contents. The samples were, as far as possible, collected evenly over the entire territory with an average sampling density of about one sample for every 7600 inhabitants. The contents of Cl- and Br-, ranging between 5.53 and 1302 mg/l and between 〈 0.025 and 4.76 mg/l respectively, correlated well with the electric conductivity, a parameter used as a proxy for water salinity. The highest values were found both along the NW and SE coasts, which we attributed to seawater contamination, and in the central part of Sicily, which we attributed to evaporitic rock dissolution. The fluoride concentrations ranged from 0.023 to 3.28 mg/l, while the highest values (only 3 exceeding the maximum admissible concentration of 1.5 mg/l) generally correlated either with the presence in the area of crystalline (volcanic or metamorphic) or evaporitic rocks or with contamination from hydrothermal activity. Apart from these limited cases of exceeding F- levels, the waters of public drinking water supplies in Sicily can be considered safe for human consumption for the analysed parameters. Some limited concern could arise from the intake of bromide-rich waters (about 3% exceeding 1 mg/l) because of the potential formation of dangerous disinfection by-products.
    Description: Published
    Description: 303-313
    Description: 4.4. Scenari e mitigazione del rischio ambientale
    Description: JCR Journal
    Description: reserved
    Keywords: drinking water quality ; fluoride ; bromide ; chloride ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2017-04-04
    Description: Methane plays an important role in the Earth’s atmospheric chemistry and radiative balance being the second most important greenhouse gas after carbon dioxide. Methane is released to the atmosphere by a wide number of sources, both natural and anthropogenic, with the latter being twice as large as the former (IPCC, 2007). It has recently been established that significant amounts of geological methane, produced within the Earth’s crust, are currently released naturally into the atmosphere (Etiope, 2004). Active or recent volcanic/geothermal areas represent one of these sources of geological methane. But due to the fact that methane flux measurements are laboratory intensive, very few data have been collected until now and the contribution of this source has been generally indirectly estimated (Etiope et al., 2007). The Greek territory is geodynamically very active and has many volcanic and geothermal areas. Here we report on methane flux measurements made at two volcanic/geothermal systems along the South Aegean volcanic arc: Sousaki and Nisyros. The former is an extinct volcanic area of Plio-Pleistocene age hosting nowadays a low enthalpy geothermal field. The latter is a currently quiescent active volcanic system with strong fumarolic activity due to the presence of a high enthalpy geothermal system. Both systems have gas manifestations that emit significant amounts of hydrothermal methane and display important diffuse carbon dioxide emissions from the soils. New data on methane isotopic composition and higher hydrocarbon contents point to an abiogenic origin of the hydrothermal methane in the studied systems. Measured methane flux values range from –48 to 29,000 (38 sites) and from –20 to 1100 mg/mˆ2/d (35 sites) at Sousaki and Nisyros respectively. At Sousaki measurement sites covered almost all the degassing area and the diffuse methane output can be estimated in about 20 t/a from a surface of about 10,000 mˆ2. At Nisyros measurements covered the Stephanos and Kaminakia areas, which represent only a part of the entire degassing area. The two areas show very different methane degassing pattern with latter showing much higher flux values. Methane output can be estimated in about 0.25 t/a from an area of about 30,000 mˆ2 at Stephanos and about 1 t/a from an area of about 20,000 mˆ2 at Kaminakia. The total output from the entire geothermal system of Nisyros probably should not exceed 2 t/a.
    Description: Published
    Description: Vienna, Austria
    Description: 4.5. Studi sul degassamento naturale e sui gas petroliferi
    Description: open
    Keywords: methane output ; diffuse degassing ; volcanic/hydrothermal systems ; Greece ; 01. Atmosphere::01.01. Atmosphere::01.01.03. Pollution ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2017-04-04
    Description: A biomonitoring survey, above tree line level, using two endemic species (Senecio aethnensis and Rumex aethnensis) was performed on Mt. Etna, in order to evaluate the dispersion and the impact of volcanic atmospheric emissions. Samples of leaves were collected in summer 2008 from 30 sites in the upper part of the volcano (1500- 3000 m a.s.l). Acid digestion of samples was carried out with a microwave oven, and 44 elements were analyzed by using plasma spectrometry (ICP-MS and ICP-OES). The highest concentrations of all investigated elements were found in the samples collected closest to the degassing craters, and in the downwind sector, confirming that the eastern flank of Mt. Etna is the most impacted by volcanic emissions. Leaves collected along two radial transects from the active vents on the eastern flank, highlight that the levels of metals decrease one or two orders of magnitude with increasing distance from the source. This variability is higher for volatile elements (As, Bi, Cd, Cs, Pb, Sb, Tl) than for more refractory elements (Al, Ba, Sc, Si, Sr, Th, U). The two different species of plants do not show significant differences in the bioaccumulation of most of the analyzed elements, except for lanthanides, which are systematically enriched in Rumex leaves. The high concentrations of many toxic elements in the leaves allow us to consider these plants as highly tolerant species to the volcanic emissions, and suitable for biomonitoring researches in the Mt. Etna area.
    Description: Published
    Description: Vienna, Austria
    Description: 4.4. Scenari e mitigazione del rischio ambientale
    Description: open
    Keywords: Mt. Etna ; biomonitoring ; Trace elements ; 01. Atmosphere::01.01. Atmosphere::01.01.03. Pollution ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: Etna volcano, Italy, hosts one of the major groundwater systems of the island of Sicily. Waters circulate within highly permeable fractured, mainly hawaiitic, volcanic rocks. Aquifers are limited downwards by the underlying impermeable sedimentary terrains. Thickness of the volcanic rocks generally does not exceed some 300 m, preventing the waters to reach great depths. This is faced by short travel times (years to tens of years) and low thermalisation of the Etnean groundwaters. Measured temperatures are, in fact, generally lower than 25 °C. But the huge annual meteoric recharge (about 0.97 kmˆ3) with a high actual infiltration coefficient (0.75) implies a great underground circulation. During their travel from the summit area to the periphery of the volcano, waters acquire magmatic heat together with volcanic gases and solutes through water-rock interaction processes. In the last 20 years the Etnean aquifers has been extensively studied. Their waters were analysed for dissolved major, minor and trace element, O, H, C, S, B, Sr and He isotopes, and dissolved gas composition. These data have been published in several articles. Here, after a summary of the obtained results, the estimation of the magmatic heat flux through the aquifer will be discussed. To calculate heat uptake during subsurface circulation, for each sampling point (spring, well or drainage gallery) the following data have been considered: flow rate, water temperature, and oxygen isotopic composition. The latter was used to calculate the mean recharge altitude through the measured local isotopic lapse rate. Mean recharge temperatures, weighted for rain amount throughout the year, were obtained from the local weather station network. Calculations were made for a representative number of sampling points (216) including all major issues and corresponding to a total water flow of about 0.315 kmˆ3/a, which is 40% of the effective meteoric recharge. Results gave a total energy output of about 140 MW/a the half of which is ascribable to only 13 sampling points. These correspond to the highest flow drainage galleries with fluxes ranging from 50 to 1000 l/s and wells with pumping rates from 70 to 250 l/s. Geographical distribution indicates that, like magmatic gas leakage, heat flow is influenced by structural features of the volcanic edifice. The major heat discharge through groundwater are all tightly connected either to the major regional tectonic systems or to the major volcanic rift zones along which the most important flank eruptions take place. But rift zones are much more important for heat upraise due to the frequent dikes injection than for gas escape because generally when dikes have been emplaced the structure is no more permeable to gases because it becomes sealed by the cooling magma.
    Description: Published
    Description: Vienna, Austria
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: open
    Keywords: groundwaters ; volcanic surveillance ; water chemistry ; dissolved gases ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-04
    Description: Constraining fluxes of volcanic bromine and iodine to the atmosphere is important given the significant role these species play in ozone depletion. However, very few such measurements have been made hitherto, such that global volcanic fluxes are poorly constrained. Here we extend the data set of volcanic Br and I degassing by reporting the first measurements of bromine and iodine emissions from Mount Etna. These data were obtained using filter packs and contemporaneous ultraviolet spectroscopic SO2 flux measurements, resulting in time-averaged emission rates of 0.7 kt yr 1 and 0.01 kt yr 1 for Br and I, respectively, from April to October 2004, from which we estimate global Br and I fluxes of order 13 (range, 3â 40) and 0.11 (range, 0.04â 6.6) kt yr 1. Observed changes in plume composition highlight the coherent geochemical behavior of HCl, HF, HBr, and HI during magmatic degassing, and strong fractionation of these species with respect to SO2.
    Description: Published
    Description: Q08008
    Description: partially_open
    Keywords: bromine and iodine in volcanic gases ; halogen atmospheric chemistry ; volcanic degassing ; volcanic plumes ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 11
    Publication Date: 2017-04-04
    Description: A new method for extracting dissolved gases in natural waters has been developed and tested, both in the laboratory and in the field. The sampling device consists of a polytetrafluroethylene (PTFE) tube (waterproof and gas permeable) sealed at one end and connected to a glass sample holder at the other end. The device is pre-evacuated and subsequently dipped in water, where the dissolved gases permeate through the PTFE tube until the pressure inside the system reaches equilibrium. A theoretical model describing the time variation in partial gas pressure inside a sampling device has been elaborated, combining the mass balance and ‘‘Solution-Diffusion Model’’ which describes the gas permeation process through a PTFE membrane). This theoretical model was used to predict the temporal evolution of the partial pressure of each gas species in the sampling device. The model was validated by numerous laboratory tests. The method was applied to the groundwater of Vulcano Island (southern Italy). The results suggest that the new sampling device could easily extract the dissolved gases from water in order to determine their chemical and isotopic composition.
    Description: - European Social Fund.
    Description: Published
    Description: Q09005
    Description: partially_open
    Keywords: dissolved gases ; helium isotope ; PTFE membrane ; Vulcano Island ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.07. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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  • 12
    Publication Date: 2017-04-04
    Description: Ground-based measurements of volcanic sulfur dioxide fluxes are important indicators of volcanic activity, with application in hazard assessment, and understanding the impacts of volcanic emissions upon the environment and climate. These data are obtained by making traverses underneath the volcanic plume a few kilometers from source with an ultraviolet spectrometer, measuring integrated SO2 concentrations across the plume’s cross section, and multiplying by the plume’s transport speed. However, plume velocities are usually derived from ground-based anemometers, located many kilometers from the traverse route and hundreds of meters below plume altitude, complicating the experimental design and introducing large flux (can be 〉100%) errors. Here we present the first report of a single instrument capable of (accurate) volcanic SO2 flux measurements. This device records integrated SO2 concentrations and plume heights during traverses. Between traverses, two in-plume SO2 time series are measured from underneath the plume with the instrument, corresponding to zenith and inclined (user-specified angle from vertical in the direction of the volcano) fields of view, respectively. The distance between the points of intersection of the two views with the plume is found on the basis of the determined plume height, and the two signals are cross-correlated to determine the lag between them, enabling accurate derivation of the wind speed. We present flux data (with errors ±12%) obtained in this way at Mt. Etna during July 2004.
    Description: Published
    Description: Q02003
    Description: partially_open
    Keywords: DOAS ; volcanic SO2 emissions. ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 13
    Publication Date: 2017-04-04
    Description: Volcanoes represent an important natural source of several trace elements to the atmosphere. For some species (e.g., As, Cd, Pb and Se) they may be the main natural source and thereby strongly influencing geochemical cycles from the local to the global scale. Mount Etna is one of the most actively degassing volcanoes in the world, and it is considered to be, on the long-term average, the major atmospheric point source of many environmental harmful compounds. Their emission occurs either through continuous passive degassing from open-conduit activity or through sporadic paroxysmal eruptive activity, in the form of gases, aerosols or particulate. To estimate the environmental impact of magma-derived trace metals and their depositions processes, rainwater and snow samples were collected at Mount Etna area. Five bulk collectors have been deployed at various altitudes on the upper flanks around the summit craters of the volcano; samples were collected every two week for a period of one year and analyzed for the main chemical-physical parameters (electric conductivity and pH) and for major and trace elements concentrations. Chemical analysis of rainwater clearly shows that the volcanic contribution is always prevailing in the sampling site closest to the summit crater (about 1.5 km). In the distal sites (5.5-10 km from the summit) and downwind of the summit craters, the volcanic contribution is also detectable but often overwhelmed by anthropogenic or other natural (seawater spray, geogenic dust) contributions. Volcanic contribution may derive from both dry and wet deposition of gases and aerosols from the volcanic plume, but sometimes also from leaching of freshly emitted volcanic ashes. In fact, in our background site (7.5 km in the upwind direction) volcanic contribution has been detected only following an ash deposition event. About 30 samples of fresh snow were collected in the upper part of the volcano, during the winters 2006 and 2007 to estimate deposition processes at high altitude during cold periods. Some of the samples were collected immediately after a major explosive event from the summit craters to understand the interaction between snow and fresh erupted ash. Sulphur, Chlorine and Fluorine, are the major elements that prevailingly characterize the volcanic contribution in atmospheric precipitation on Mount Etna, but high concentrations of many trace elements are also detected in the studied samples. In particular, bulk deposition samples display high concentration of Al, Fe, Ti, Cu, As, Rb, Pb, Tl, Cd, Cr, U and Ag, in the site most exposed to the volcanic emissions: median concentration values are about two orders of magnitude higher than those measured in our background site. Also in the snow samples the volcanic signature is clearly detectable and decreases with distance from the summit craters. Some of the analysed elements display very high enrichment values with respect to the average crust and, in the closest site to the summit craters, also deposition values higher than those measured in polluted urban or industrial sites.
    Description: Published
    Description: Vienna, Austria
    Description: 4.5. Degassamento naturale
    Description: open
    Keywords: Mt. Etna ; trace elements ; rainwater ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 03. Hydrosphere::03.03. Physical::03.03.01. Air/water/earth interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters
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  • 14
    Publication Date: 2017-04-04
    Description: From December 2002 to July 2003, Stromboli volcano was characterized by a new effusive stage of eruption after a period of extraordinary strombolian activity. Signals recorded in two continuous monitoring stations during the eruption, which have already been presented in very recent papers, evidenced anomalies in the CO2 flux just before the onset of the eruption. A more detailed analysis carried out on the data subset acquired during the eruption, integrated by daily field observations of the scientific personnel working at the volcanological observatory in Stromboli, showed that CO2 flux and soil temperature are strictly related to volcanic events. Furthermore, the relative minima and maxima of the two parameters showed a strong correlation with wind speed and direction. This fact was especially true at the summit station, whereas at the coastal sites seasonal and meteorological effects masked the volcanic signal. The analysis of the wind data, particularly the relationships between wind speed and direction, air and soil temperature, and local circulation of atmospheric air masses revealed that during the eruption, in the summit area of Stromboli air movements were not only related to atmospheric circulation but were also significantly affected, and in certain cases caused, by volcanic activity. This conclusion was reached by observing several anomalies, such as the discrepancies in the wind direction between the two stations, higher air temperatures at the summit site, and inversion of direction for wind before and after the reopening of the conduit in a major explosion on 5 April 2003. The relationships found between volcanic activity, soil temperatures, CO2 fluxes, and wind speed and direction indicate that soil temperature measurements, in an open conduit volcano such as in this case, could be used to monitor the level of volcanic activity, along with CO2 flux. Furthermore, the possible volcanic origin of a peculiar type of air circulation identified in the summit area of Stromboli suggests that the separation between volcanic and atmospheric signals might not be obvious, requiring monitoring over a wide area, rather than a single location.
    Description: Published
    Description: Q12001
    Description: partially_open
    Keywords: carbon dioxide flux ; continuous monitoring ; soil temperature ; wind ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 15
    Publication Date: 2017-04-04
    Description: We present the first regional map of CO2 Earth degassing from a large area (most of central and south Italy) derived from the carbon of deep provenance dissolved in the main springs of the region. The investigation shows that a globally significant amount of deeply derived CO2 (10% of the estimated global CO2 emitted from subaerial volcanoes) is released by two large areas located in western Italy. The anomalous flux of CO2 suddenly disappears in the Apennine in correspondence to a narrow band where most of seismicity concentrates. Here, at depth, the gas accumulates in crustal traps generating CO2 overpressurized reservoirs which induce seismicity.
    Description: Published
    Description: 1-4
    Description: partially_open
    Keywords: Carbon dioxide ; Central Italy ; Southern Italy ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
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  • 16
    Publication Date: 2017-04-04
    Description: Improving the constraints on the atmospheric fate and depletion rates of acidic compounds persistently emitted by non-erupting (quiescent) volcanoes is important for quantitatively predicting the environmental impact of volcanic gas plumes. Here, we present new experimental data coupled with modelling studies to investigate the chemical processing of acidic volcanogenic species during tropospheric dispersion. Diffusive tube samplers were deployed at Mount Etna, a very active open-conduit basaltic volcano in eastern Sicily, and Vulcano Island, a closed-conduit quiescent volcano in the Aeolian Islands (northern Sicily). Sulphur dioxide (SO2), hydrogen sulphide (H2S), hydrogen chloride (HCl) and hydrogen fluoride (HF) concentrations in the volcanic plumes (typically several minutes to a few hours old) were repeatedly determined at distances from the summit vents ranging from 0.1 to ~10 km, and under different environmental conditions. At both volcanoes, acidic gas concentrations were found to decrease exponentially with distance from the summit vents (e.g., SO2 decreases from ~10,000 μg/m3 at 0.1 km from Etna’s vents down to ~7 _μg/m3 at ~10km distance), reflecting the atmospheric dilution of the plume within the acid gas-free background troposphere. Conversely, SO2/HCl, SO2/HF, and SO2/H2S ratios in the plume showed no systematic changes with plume aging, and fit source compositions within analytical error. Assuming that SO2 losses by reaction are small during short-range atmospheric transport within quiescent (ash-free) volcanic plumes, our observations suggest that, for these short transport distances, atmospheric reactions for H2S and halogens are also negligible. The one-dimensional model MISTRA was used to simulate quantitatively the evolution of halogen and sulphur compounds in the plume of Mt. Etna. Model predictions support the hypothesis of minor HCl chemical processing during plume transport, at least in cloud-free conditions. Larger variations in the modelled SO2/HCl ratios were predicted under cloudy conditions, due to heterogeneous chlorine cycling in the aerosol phase. The modelled evolution of the SO2/H2S ratios is found to be substantially dependent on whether or not the interactions of H2S with halogens are included in the model. In the former case, H2S is assumed to be oxidized in the atmosphere mainly by OH, which results in minor chemical loss for H2S during plume aging and produces a fair match between modelled and measured SO2/H2S ratios. In the latter case, fast oxidation of H2S by Cl leads to H2S chemical lifetimes in the early plume of a few seconds, and thus SO2 to H2S ratios that increase sharply during plume transport. This disagreement between modelled and observed plume compositions suggests that more in-detail kinetic investigations are required for a proper evaluation of H2S chemical processing in volcanic plumes.
    Description: Published
    Description: 1441-1450
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 4.5. Degassamento naturale
    Description: JCR Journal
    Description: open
    Keywords: Mt. Etna ; volcanic gas plumes ; tropospheric processing ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
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  • 17
    Publication Date: 2017-04-04
    Description: Volcanic and geothermal areas are one of the major natural sources of H2S to the atmosphere. Its environmental impact is often the main cause of the opposition to the development of geothermal energy exploitation programs. In this paper we analyze the air concentrations and dispersion pattern of naturally emitted H2S at the geothermal area of Sousaki (Corinthia, Greece). Measurements, made with a network of passive samplers, evidence a rapid decrease of concentration values away from the emission points. The fact that the decrease is more pronounced in the summer with respect to the winter indicates that it is not only due to a dilution effect, but also to redox reactions favoured by higher temperatures and intense sunlight typical of the summer period.
    Description: Published
    Description: 1723-1728
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: Hydrogen sulphide ; Environmental impact of volcanic activity ; Gas hazard ; Passive samplers ; 01. Atmosphere::01.01. Atmosphere::01.01.03. Pollution ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 18
    Publication Date: 2017-04-04
    Description: Active volcanoes are thought to be important contributors to the atmospheric mercury (Hg) budget, and this chemical element is one of the most harmful atmospheric pollutants, owing to its high toxicity and long residence time in ecosystems. There is, however, considerable uncertainty over the magnitude of the global volcanic Hg flux, since the existing data on volcanogenic Hg emissions are sparse and often ambiguous. In an attempt to extend the currently limited dataset on volcanogenic Hg emissions, we summarize the results of Hg flux measurements at seven active open-conduit volcanoes; Stromboli, Asama, Miyakejima, Montserrat, Ambrym, Yasur, and Nyiragongo.. Data from the domebuilding Soufriere Hills volcano are also reported. Using our determined mercury to SO2 mass ratios in tandem with the simultaneously-determined SO2 emission rates, we estimate that the 7 volcanoes have Hg emission rates ranging from 0.2 to 18 t yr-1 (corresponding to a total Hg flux of ~41 t·yr-1). Based on our dataset and previous work, we propose that a Hg/SO2 plume ratio ~10-5 is bestrepresentative of gas emissions from quiescent degassing volcanoes. Using this ratio, we infer a global volcanic Hg flux from persistent degassing of ~95 t·yr-1
    Description: Published
    Description: 497-510
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Volcanogenic mercury ; Mercury ; Volcanic plume ; Mercury flux ; Mercury inventories ; Atmospheric mercury ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 19
    Publication Date: 2017-04-04
    Description: Here, we report the first continuous data of geochemical parameters acquired directly from the active summit crater of Vulcano. This approach provides a means to better investigate deep geochemical processes associated with the degassing system of Vulcano Island. In particular, we report on soil CO2 fluxes from the upper part of Vulcano, a closed-conduit volcano, from September 2007 to October 2010. Large variations in the soil CO2 and plume SO2 fluxes (order of magnitude), coinciding with other discontinuous geochemical parameters (CO2 concentrations in fumarole gas) and physical parameters (increase of shallow seismic activity and fumarole temperatures) have been recorded. The results from this work suggest new prospects for strengthening geochemical monitoring of volcanic activity and for improving the constraints in the construction of a “geochemical model”, this being a necessary condition to better understand the functioning of volcanic systems.
    Description: Published
    Description: 1859-1863
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: 1R. Reti di monitoraggio e Osservazioni
    Description: JCR Journal
    Description: restricted
    Keywords: Vulcano Island ; Geochemical monitoring ; CO2 flux ; CO2 fumaroles ; SO2 flux ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
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  • 20
    Publication Date: 2017-04-03
    Description: Total CO2 output from fumaroles, soil gas, bubbling gas discharges and water dissolved gases discharged from the island, was estimated for Vulcano island, Italy. The CO2 emission from fumaroles from the La Fossa summit crater was estimated from the SO2 crater output, while CO2 discharged through diffuse soil emission was quantified on the basis of 730 measurements of CO2 fluxes from the soil of the island, performed by using the accumulation chamber method. The results indicate an overall output of ≅500 t/day of CO2 from the island. The main contribution to the total CO2 output comes from the summit area of the La Fossa cone (453 t/day), with 362 t/day from crater fumaroles and 91 t/day from crater soil degassing. The release of CO2 from peripheral areas is ≅20 t/day by soil degassing (Palizzi and Istmo areas mainly), an amount comparable to both the contribution of water dissolved CO2 (6 t/day), as well as to seawater bubbling CO2 (4 t/day measured in the Istmo area). Presented data (September 2007) refer to a period of moderate solphataric activity, when the fumaroles temperature were 450°C and gas/water molar ratio of fumaroles was up to 0.16. The calculated total CO2 emission allows the estimation of the mass release and related thermal energy from the volcanic-hydrothermal system.
    Description: Published
    Description: Q02012
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: restricted
    Keywords: CO2 flux, SO2 flux, Vulcano island ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
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  • 21
    Publication Date: 2017-04-04
    Description: We investigated the structure and evolution of the 2010 Eyjafjallajökull volcanic cloud and its dispersal over Iceland and Europe integrating satellite multispectral images and numerical simulations. Data acquired by Medium Resolution Imaging Spectrometer (MERIS)and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) have been analyzed to quantify the cloud extent and composition. The VOL-CALPUFF dispersal code was applied to reconstruct the transient and 3-D evolution of the cloud. Source parameters estimated on the base of available a posteriori volcanological data sets have been used. Quantitative comparisons between satellite retrievals and modeling results were performed for two selected instants of time during the first and third eruptive phases on a regional scale. Sensitivity of the model to initial volcanological conditions has been analyzed at continental scale. Several complex non intuitive features of cloud dynamics have been highlighted and strengths and limitations of the adopted methods identified. The main findings are: the level of quantitative agreement between satellite observations and numerical results depends on ash cloud composition (particle sizes and concentration) with better agreement for smaller particles and higher concentrations; the agreement between observations and modeling outcomes also depends on the temporal stability of volcanological conditions and the complexity of the meteorological wind field; the irregular dispersion of ash, as reconstructed from satellite data and numerical modeling, can be well explained by the different response of particle sizes to strong vertical wind-shear, and by resuspension processes acting at ground level; eruptive source conditions are the main source of uncertainty in modeling, especially during an ongoing crisis and at long-range scales.
    Description: Published
    Description: 4729–4747
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Volcanic ash cloud ; Satellite retrieval ; Numerical modelling ; Eyjafjallajokull ; Ash dispersal and deposition ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
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  • 22
    Publication Date: 2017-04-04
    Description: We present the results of laboratory experiments on the aggregation and disaggregation of colliding volcanic ash particles. Ash particles of different composition and size 〈90 µm were held in turbulent suspension and filmed in high speed while colliding, aggregating, and disaggregating, forming a growing layer of electrostatically bound particles along a vertical plate. At room conditions and regardless of composition, 60–80% of the colliding particles smaller than 32 µm remained aggregated. In contrast, aggregation of particles larger than 63 µm was negligible, and, when a layer formed, periods when disaggregation (mainly by collisions or drag) exceeded aggregation occurred twice as frequently than for smaller particles. An empirical relationship linking the aggregation index, i.e., the effective fraction of aggregated particles surviving disaggregation, to the mean particle collision kinetic energy is provided. Our results have potential implications on the dynamics of volcanic plumes and ash mobility in the environment.
    Description: INGV-DPC project V1 “Probabilistic evaluation of volcanic hazard”; EU Seventh Programme FP7 “MED-SUV” grant agreement 308665
    Description: Published
    Description: 1068–1075
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 2IT. Laboratori sperimentali e analitici
    Description: JCR Journal
    Description: restricted
    Keywords: volcanic ash ; disaggregation ; experimental modeling ; volcanic plumes ; aggregation processes ; colliding particles ; sticking rate ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 23
    Publication Date: 2019-03-26
    Description: Abstract. When combined, the three-dimensional imaging of different physical properties of architectural monumen- tal structures acquired through different methodologies can highlight with efficiency the characteristics of the stone building materials. In this work, we compound high res- olution Digital Color Images (DCI) and Terrestrial Laser Scanner (TLS) data for a dense 3-D reconstruction of an ancient pillar in a nineteenth century building in the town of Cagliari, Italy. The TLS technique was supported by a digital photogrammetry survey in order to obtain a natural color texturized 3-D model of the studied pillar. Geometri- cal anomaly maps showing interesting analogies were com- puted both from the 3-D model derived from the TLS ap- plication and from the high resolution 3-D model detected with the photogrammetry. Starting from the 3-D reconstruc- tion from previous techniques, an acoustic tomography in a sector of prior interest of the investigated architectural ele- ment was planned and carried out. The ultrasonic tomogra- phy proved to be an effective tool for detecting internal decay or defects, locating the position of the anomalies and estimat- ing their sizes, shapes, and characteristics in terms of elastic- mechanical properties. Finally, the combination of geophysi- cal and petrographical data sets represents a powerful method for understanding the quality of the building stone materials in the shallow and inner parts of the investigated architectural structures.
    Description: Regione Autonoma della Sardegna (RAS) (Sardinian Autonomous Region), Regional Law 7th August 2007, no. 7, Promotion of scientific research and technological innovation in Sardinia (Italy).
    Description: Published
    Description: 57-62
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Architectural monumental structures ; Structural Diagnosis ; Digital Color Images ; 3D Terrestrial Laser Scanner ; Acoustic tomography ; Petrographical data ; 3D Modeling ; Cultural Heritage ; Architectural Elements ND Diagnosis
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  • 24
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 7 (2006): Q12007, doi:10.1029/2006GC001290.
    Description: New multibeam and side-scan sonar surveys of Fernandina volcano and the geochemistry of lavas provide clues to the structural and magmatic development of Galápagos volcanoes. Submarine Fernandina has three well-developed rift zones, whereas the subaerial edifice has circumferential fissures associated with a large summit caldera and diffuse radial fissures on the lower slopes. Rift zone development is controlled by changes in deviatoric stresses with increasing distance from the caldera. Large lava flows are present on the gently sloping and deep seafloor west of Fernandina. Fernandina's submarine lavas are petrographically more diverse than the subaerial suite and include picrites. Most submarine glasses are similar in composition to aphyric subaerially erupted lavas, however. These rocks are termed the “normal” series and are believed to result from cooling and crystallization in the subcaldera magma system, which buffers the magmas both thermally and chemically. These normal-series magmas are extruded laterally through the flanks of the volcano, where they scavenge and disaggregate olivine-gabbro mush to produce picritic lavas. A suite of lavas recovered from the terminus of the SW submarine rift and terraces to the south comprises evolved basalts and icelandites with MgO = 3.1 to 5.0 wt.%. This “evolved series” is believed to form by fractional crystallization at 3 to 5 kb, involving extensive crystallization of clinopyroxene and titanomagnetite in addition to plagioclase. “High-K” lavas were recovered from the southwest rift and are attributed to hybridization between normal-series basalt and evolved-series magma. The geochemical and structural findings are used to develop an evolutionary model for the construction of the Galápagos Platform and better understand the petrogenesis of the erupted lavas. The earliest stage is represented by the deep-water lava flows, which over time construct a broad submarine platform. The deep-water lavas originate from the subcaldera plumbing system of the adjacent volcano. After construction of the platform, eruptions focus to a point source, building an island with rift zones extending away from the adjacent, buttressing volcanoes. Most rift zone magmas intrude laterally from the subcaldera magma chamber, although a few evolve by crystallization in the upper mantle and deep crust.
    Description: This work was supported by the National Science Foundation grants OCE0002818 and EAR0207605 (D.G.), OCE0002461 (D.J.F. and M.K.), OCE9811504 (D.J.F. and M.R.P.), and EAR0207425 (K.H.) and WHOI postdoctoral support for Soule.
    Keywords: Rift zone ; Magmatic ; Evolution ; Galapagos
    Repository Name: Woods Hole Open Access Server
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  • 25
    Publication Date: 2017-04-04
    Description: In this paper, in an attempt to reveal possible changes connected to natural or anthropogenic causes, the main results of hydrogeochemical monitoring carried out at Mount Etna are evaluated. We report on the salinity contents of the groundwaters that flow in fractured volcanics, which make up the flanks of the volcano. These waters, analyzed for major ion chemistry, were sampled regularly from 1994 to 2004. Basing on nonparametric Sen’s slope estimator, time series of groundwater composition reveal that the salinity of most of the Etnean aquifers increased by 0.5% to 3.5% each year during this period. This change in the water chemistry is clearly referable to the overexploitation of the aquifers. This increasing trend needs to be inverted urgently; otherwise, it will cause a shortage of water in the near future, because the maximum admissible concentration of salinity for drinking water will be exceeded.
    Description: Published
    Description: 431-446
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: restricted
    Keywords: Hydrochemistry ; Salinization ; Over-abstraction ; Groundwater monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.02. Hydrological processes: interaction, transport, dynamics ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.06. Water resources ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters
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  • 26
    Publication Date: 2017-04-04
    Description: Natural precipitation and water samples from passive devices were collected at Mt. Vesuvius and Vulcano Island, Italy, during the period 2004–2006, in order to investigate its possible interactions with fumarolic gases. Evidence of chemical reactions between fumarolic fluids and rain samples before and after its deposition into the sampling devices was found at Vulcano Island. Very low pH values (down to 2.5) and significant amounts of chlorine and sulfate (up to 22 mEq/l) were measured at sampling points located close to the fumarolic field. In contrast, anthropogenic contributions and/or dissolution of aerosols (both maritime and continental) influence the chemistry of rainwaters at Mt. Vesuvius, which show inter-annual variations that are highly consistent with those recorded at the coastal site at Vulcano Island. Chemistry of waters directly exposed to fumarolic fluids may then give useful information about its temporal evolution, holding the signal of the ‘‘maximum’’ chemical event occurred in the meanwhile. In addition, the observation of the health status of vegetation colonizing the immediate surroundings of the fumarolic fields, due to its strong dependence on the interactions with these fluids, may work as a possible biomarker of volcanic activity.
    Description: Published
    Description: 159-171
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: restricted
    Keywords: Precipitation ; Fumarole ; Vesuvius ; Vulcano ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects
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  • 27
    Publication Date: 2024-05-09
    Description: We carried out a combined geophysical and gas-geochemical survey on an active fault strand along the North-Anatolian Fault (NAF) system in the Gulf of İzmit (eastern Sea of Marmara), providing for the first time in this area data on the distribution of methane (CH4) and other gases dissolved in the bottom seawater, as well as the CH4 isotopic composition. Based on high-resolution morphobathymetric data and chirp-sonar seismic reflection profiles we selected three areas with different tectonic features associated to the NAF system, where we performed visual and instrumental seafloor inspections, including in-situ measurements of dissolved CH4, and sampling of the bottom water. Starting from background values of 2-10 nM, methane concentration in the bottom seawater increases abruptly up to 20 nM over the main NAF trace. CH4 concentration peaks up to ~120 nM were detected above mounds related probably to gas and fluids expulsion. Methane is microbial (δ13CCH4: -67.3 and -76 ‰ vs. VPDB), and was found mainly associated with pre- Holocene deposits topped by a 10-20 m thick draping of marine mud. The correlation between tectonic structures and gas-seepages at the seafloor suggests that the NAF in the Gulf of İzmit could represent a key site for long-term combined monitoring of fluid exhalations and seismicity to assess their potential as earthquake precursors.
    Description: Published
    Description: Q10018
    Description: 1.8. Osservazioni di geofisica ambientale
    Description: JCR Journal
    Description: restricted
    Keywords: submarine ; gas seepage ; active fault ; Marmara sea ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring
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  • 28
    Electronic Resource
    Electronic Resource
    Springer
    Acta biotheoretica 33 (1984), S. 35-50 
    ISSN: 1572-8358
    Keywords: Evolution ; falsification ; Darwinism ; philosophy of science
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called “the theory of common descent”), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.
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  • 29
    Electronic Resource
    Electronic Resource
    Springer
    Acta biotheoretica 35 (1986), S. 77-106 
    ISSN: 1572-8358
    Keywords: Evolution ; nonequilibrium thermodynamics ; boundary conditions models ; initial conditions models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.
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  • 30
    ISSN: 1572-8358
    Keywords: Animal cognition ; Evolution ; Representation ; Computation ; Significance ; Phenomenology ; Autonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A distinction is made between two definitions of animal cognition: the one most frequently employed in cognitive sciences considers cognition as extracting and processing information; a more phenomenologically inspired model considers it as attributing to a form of the outside world a significance, linked to the state of the animal. The respective fields of validity of these two models are discussed along with the limitations they entail, and the questions they pose to evolutionary biologists are emphasized. This is followed by a presentation of a general overview of what might be the study of the evolution of knowledge in animals.
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  • 31
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    Journal of applied electrochemistry 29 (1999), S. 1171-1176 
    ISSN: 1572-8838
    Keywords: alloys ; cyclic voltammetry ; electrodeposition ; electroless deposition ; nickel ; phosphorus ; zinc
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Notes: Abstract Electroless Ni–Zn–P alloy deposition from a sulphate bath, containing sodium hypophosphite as reducer, was investigated. To increase the plating rate, the deposition parameters were optimized. The effect of process parameters (T, pH and [Zn2+]) on the plating rate and deposit composition was examined and it was found that the presence of zinc in the bath has an inhibitory effect on the alloy deposition. As a consequence, the percentage of zinc in the electroless Ni–Zn–P alloys never reaches high values. Using cyclic voltammetry the electrodeposition mechanism of Ni–Zn–P alloys was investigated. It was observed that the zinc deposition inhibits the nickel discharge and, as a consequence, its catalytic activity on hypophosphite oxidation. It was also found that increase in temperature or pH leads to the deposition of nickel rich alloys.
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  • 32
    ISSN: 1572-8854
    Keywords: Octahedral ; phosphorus ; chloride
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    Topics: Geosciences , Physics
    Notes: Abstract The title compound [P(tpp)Cl2]+Cl− crystallizes in the space group P21/n witha=10.701(2),b=24.860(2),c=14.799(2), β=94.24(2)°,Z=4. The phosphorus atom has an octahedral coordination geometry formed by the four nitrogen atoms (Np) of the porphyrinato group and the two chloride ions. The average phosphorus-chloride distance is 2.150(1) Å, with phosphorus situated 0.006 Å below the porphyrin ring.
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  • 33
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    Journal of applied electrochemistry 27 (1997), S. 1198-1206 
    ISSN: 1572-8838
    Keywords: alloy ; amorphous ; anomalous ; hydrogen ; iron ; nickel ; phosphorus ; plating
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Notes: Abstract In this study we have investigated the electrodeposition of amorphous iron–nickel–phosphorus alloys from a sulfate electrolyte. Fe-Ni alloys are known to exhibit an ’anomalous‘ type of plating behaviour in which deposition of the less noble metal is favoured. We have found that the codeposition of phosphorus from hypophosphite in the electrolyte led to a reversal to a ’normal‘ behaviour. This reversal was due both to the suppression of iron and enhancement of nickel partial currents. The overall deposition process is dominated by the hydrogen evolution reaction. This is exacerbated by the low pH needed to codeposit sufficient phosphorus to achieve an amorphous structure.
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  • 34
    ISSN: 1572-8838
    Keywords: alloys ; electroless ; microstructure ; morphology ; nickel ; phosphorus ; zinc
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Notes: Abstract Electroless Ni–Zn–P alloy coatings were obtained on an iron substrate from a sulfate bath at various pH values. The effects of changes in bath pH on alloy composition, morphology, microstructure and corrosion resistance were studied. Scanning electron microscopy was performed to observe the morphological change of the deposits with bath pH. Coating crystallinity was investigated by grazing incidence asymmetric Bragg X-ray diffraction and transmission electron microscopy. A transition from an amorphous to polycrystalline structure was observed on increasing the bath alkalinity, and thus decreasing the phosphorus content of the alloys. A single crystalline phase corresponding to face-centred-cubic nickel was identified in the alloys obtained from a strong alkaline solution. An increase in zinc percentage up to 23% in the deposits does not change the f.c.c. nickel crystalline structure. Corrosion potential and polarization resistance measurements indicated that the corrosion resistance of electroless Ni–Zn–P alloys depends strongly on the microstructure and chemical composition. The deposits obtained at pH 9.0–9.5 and with 11.4–12.5% zinc and 11.8–11.2% phosphorous exhibited the best corrosion resistance.
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  • 35
    ISSN: 1572-879X
    Keywords: selective catalytic reduction ; nitric oxide reduction ; phosphorus ; acid property
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    Topics: Chemistry and Pharmacology
    Notes: Abstract To examine the influence of phosphorus on the commercial V2O5(WO3)/TiO2 SCR catalyst, measurements were carried out by means of infrared and Raman spectroscopy, XPS, and NO reduction measurement as a function of phosphorus loading. Phosphorus added to the catalyst was found to disperse well over the catalyst without a significant agglomeration up to 5 wt% P2O5 addition. The number of the hydroxyl groups bonded to the vanadium and titanium species decreased readily with increasing amount of phosphorus. Correspondingly, the hydroxyl groups bonded to the phosphorus species were formed. NH3 adsorbed on both hydroxyl groups bonded to vanadium and phosphorus as ammonium ions, implying that the P–OH groups formed are also responsible for the Brønsted acidity. The NO reduction activity was found to be decreased with increasing amount of phosphorus; however, the influence of phosphorus was relatively small irrespective of the large amount of phosphorus addition. The deactivation might be caused by the change in the nature of the surface hydroxyl groups as Brønsted acid sites. Phosphorus species might partially wrap the surface V=O and W=O groups, which might also contribute to the deactivation.
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  • 36
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    Monatshefte für Chemie 125 (1994), S. 1033-1039 
    ISSN: 1434-4475
    Keywords: Prebiotic peptide formation ; Evolution ; Clay catalysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Fähigkeit von Tonmineralien der Montmorillonitklasse zur Katalyse von Peptidbildungsreaktionen aus Aminosäuren in wäßriger Lösung wurde am Beispiel von Glyzin und Kupfer sowie Kalzium und Morillonit untersucht. Experimente mit Verdampfungszyklen haben gezeigt, daß kleinere Mengen von Di- und Tripeptiden aus der Aminosäure gebildet werden. Die weitere Polymerisation von Dipeptiden hingegen scheint wesentlich leichter in diesem Reaktionssystem zu verlaufen als der Anfangsschritt der Bildung des Dipeptides. Eine mögliche Rolle von Tonmineralien in der präbiotischen Peptidevolution kann daher in der Verlängerung von Peptidketten gesehen werden. Kupferionen in der Tonmatrix zeigen keinerlei Vorteile gegenüber den üblichen Kalziumionen, die in natürlichem Montmorillonit vorkommen.
    Notes: Summary The ability of montmorillonite clay minerals for catalyzing peptide formation from amino acids in aqueous solution has been investigated using glycine and Cu2+ and Ca2+ containing montmorillonites as reaction systems. Evaporation cycle experiments showed that minor amounts of di- and tripeptide are formed from the amino acid. Further polymerization of dipeptide, however, seems to be more favoured by this reaction system than the initial step of dipeptide formation, and a possible role of clays in prebiotic peptide evolution could be seen therefore in the prolongation of peptide chains. Cu2+ ions in the clay matrix did not show any advantage over the usual Ca2+ ions embedded in natural montmorillonite.
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  • 37
    ISSN: 1433-4909
    Keywords: Key words Thermococcus ; Pyrococcus ; Thermophilic ; Phosphofructokinase ; Evolution ; ADP ; Glycolysis ; ATP
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    Topics: Biology
    Notes: Abstract The ADP-dependent phosphofructokinase (PFK) from Thermococcus zilligii has been purified 950 fold; it had a specific activity of 190 U mg−1. The enzyme required Mg2+ ions for optimal activity and was specific for ADP. The forward reaction kinetics were hyperbolic for both cosubstrates (pH optimum of 6.4), and the apparent K m values for ADP and fructose-6-phosphate were 0.6 mM (apparent V max of 243 U mg−1) and 1.47 mM (apparent V max of 197 U mg−1), respectively. Significantly, the enzyme is indicated to be nonallosteric but was slightly activated by some monovalent cations including Na+ and K+. The protein had a subunit size of 42.2 kDa and an estimated native molecular weight of 66 kDa (gel filtration). Maximal reaction rates for the reverse reaction were attained at pH 7.5–8.0, and the apparent K m values for fructose-1,6-bisphosphate and AMP were 0.56 mM (apparent V max of 2.9 U mg−1) and 12.5 mM, respectively. The biochemical characteristics of this unique ADP-dependent enzymatic activity are compared to ATP and pyrophosphate-dependent phosphofructokinases.
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  • 38
    ISSN: 1433-4909
    Keywords: Key wordsNatronomonas pharaonis ; Natronobacteria ; Archaea ; Serine protease ; Chymotrypsinogen ; Evolution
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    Topics: Biology
    Notes: Abstract A protease of a molecular mass of approximately 30 kDa was isolated and purified from the haloalkaliphilic archaeon Natronomonas (formerly Natronobacterium) pharaonis. The enzyme hydrolyzed synthetic peptides, preferentially at the carboxyl terminus of phenylalanine or leucine, as well as large proteins. Hydrolysis occurred over the range of pH from 6 to 12, with an optimum at pH 10. The temperature optimum was 61°C. The enzyme was nearly equally active over the range of salt concentration from 0.5 to 4 M (NaCl or KCl). A strong cross-reaction with a polyclonal antiserum against human chymotrypsin was observed. Enzymatic activity was inhibited by typical serine protease inhibitors. There was significant homology between N-terminal and internal sequences from autolytic fragments and the sequence of bovine chymotrypsinogen B; the overall amino acid composition was similar to that of vertebrate chymotrypsinogens. Evidence for a zymogen-like processing of the protease was obtained. Cell extracts from other halobacteria exhibited similar proteolytic activity and immunoreactivity. The data suggested a widespread distribution of a chymotrypsinogen B-like protease among halo- and haloalkaliphilic Archaea.
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  • 39
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    Aquatic sciences 53 (1991), S. 263-272 
    ISSN: 1420-9055
    Keywords: Lake ecosystem ; chl-a ; phosphorus ; nitrogen ; river flow ; thermocline ; simulation model ; multiple regression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The management variables which primarily affect phytoplankton biomass (as chl-a) in Lake Mjøsa, Norway, are total phosphorus loading (TP) and the timing and volume of water through flow (by active storage reservoirs). The response of the lake to changes in these factors is studied using a simulation model of the lake ecosystem. Chl-a responses from both observed data and the simulated results are extracted by multiple regression. Results show that decreasing TP load decreases chl-a, but less at low TP levels (〈 10 mg TP · m−3). There is also a certain time period for peak river flow which gives the least yield of chl-a per unit TP. This time period occurs in early summer (i.e., around June 10) if the total phosphorus load is low, and later if the load is high. Both observations and simulation results show that a high water flow increases chl-a at low epilimnion depths (〈 15 m), but that the same high water flow decreases chl-a when epilmnion is deep.
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  • 40
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    Aquatic sciences 52 (1990), S. 199-220 
    ISSN: 1420-9055
    Keywords: Eutrophication ; lake management ; phosphorus ; ecosystem ; chlorophyll-a ; mathematical modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We compare results of a new model for predicting the short term inter annual changes in chlorophyll-a (chl-a) in lakes after reductions in total phosphorus (TP) to predictions made by least squares regression models. In the new method, slopes of chl-a/TP graphs (both axes in mg · m−3) are depicted in frequency diagrams and used to extract information on the expected, short term chl-a/TP response. The short term response for nine shallow (〈 10 m deep) and nutrient rich lakes to changes in TP was found to be: Chl-a = 0.49 · TP + 17.3, and for nine deep, P-limited lakes: Chl-a = 0.08 · TP + 3.5. If the TP-reduction is known to be greater than 10 mg · m−3, the expected slope increases to 0.58 for shallow lakes and to 0.26 for deep lakes. The slope, 0.58, is 8% lower than the slope for the long term response calculated by regression for the shallow lakes. For deep lakes the slope, 0.26, is 2 to 3 times higher than that calculated by regression, indicating that reductions in TP for deep lakes give greater effects than least squares regression equations suggest. We have also calculated the reduction in TP which will give about 80% probability that a reduction in chl-a will be observed next year. For shallow, P-limited lakes this reduction is about 30 mg · m−3 (5% of average initial in-lake TP concentration), and for deep lakes about 14 mg · m−3 (35% of average initial in-lake TP concentration).
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  • 41
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    Aquatic sciences 52 (1990), S. 256-268 
    ISSN: 1420-9055
    Keywords: Vertical mixing ; stratification ; phosphorus ; Lake Constance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Depth variable vertical eddy diffusion coefficients for heat (K z) were calculated from continuously measured temperature profiles in Überlinger See (western part of Lake Constance). The temperatures were averaged over vertical intervals of 10 m yielding 14 discrete values (maximum depth of Überlinger See: 147 m). A linear fit from 10 June to 29 September 1987 was used to smooth the significant temperature fluctuations caused by internal seiches of Lake Constance. Assuming horizontal homogeneity for the smoothed data the Gradient-Flux-Method was applied to compute vertical diffusion coefficientsK z at different depths using the depth variable volumes and surfaces of the 14 layers. The resulting mean diffusion coefficients for the period from June to September are 0.04 cm2/s near the thermocline and up to 0.8 cm2/s in deeper strata (accuracy: ± 50%). It is shown that horizontal mixing between Überlinger See and Obersee (main lake) alters the computation ofK z by less than 50%. A relationship betweenK z and stability (Brunt-Väisälä) frequencyN is found which corresponds well to the theory of internal wave induced turbulence. Combining the diffusion coefficients with measured phosphorus profiles, a phosphorus flux from the hypolimnion to the epilimnion of (0.7 ± 0.4) mg P m−2 d−1 was calculated, corresponding to about 20% of the average external loading per area of Lake Constance in 1986.
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  • 42
    ISSN: 1420-9055
    Keywords: Sediment ; interstitial water ; phosphorus ; iron ; persulfate digestion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It is shown that sorption of orthophosphate to iron compounds, formed during persulfate digestion, can cause a significant underestimation of total dissolved phosphorus in interstitial waters rich in iron and poor in phosphorus. Labelling the samples with carrier free32PO4 before digestion allows to correct for these losses.
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  • 43
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    Cellular and molecular life sciences 41 (1985), S. 1080-1082 
    ISSN: 1420-9071
    Keywords: Evolution ; evolutionary rate ; stasis ; brain ; encephalization ; body size ; fitness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Constant evolutionary rates are possible only in verylarge populations, where natural selection does not exhaust varition because mutation supplies fresh variability. In a small population where a small number of genes influence an integrated system like brain and body size which have an allometric relationship, variation is removed rapidly under natural selection, This occurs even when the final fitness of the population is not optimal.
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  • 44
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    Cellular and molecular life sciences 43 (1987), S. 202-205 
    ISSN: 1420-9071
    Keywords: Evolution ; substrate specificity ; serological homologies ; flavone biosynthesis ; Silene ; glycosyltransferases
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The variation in flavone glycosylation patterns inSilene is the result of the expression of six genetic loci, which control either the presence of allozymes differing in substrate specificity or isozymes regulated differently during development. Serological studies showed that at least three of these six loci are evolutionarily related. The genetic mechanisms leading to these complicated variation patterns and the role of this polymorphism for the plant in its interaction with the environment are discussed.
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  • 45
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    Journal for general philosophy of science 21 (1990), S. 309-328 
    ISSN: 1572-8587
    Keywords: Evolution ; evolutionäre Erkenntnistheorie ; Organismus ; Autonomie ; Abbildungskritik
    Source: Springer Online Journal Archives 1860-2000
    Topics: Philosophy , Nature of Science, Research, Systems of Higher Education, Museum Science
    Notes: Summary The concept of evolutionary epistemology has been critically discussed by philosophers who have mainly pointed to unacceptable philosophical tenets (cf. Vittorio Hösle, this Journal, Vol. 19 (1988), pp. 348–377). However, as most philosophers are extremely reluctant to critically treat the biological theories on which the ideas of evolutionary epistemology are based, the invalid concepts of adaption escaped their critical scrutiny. Therefore the influence of preconceived biological theories on the biological basis of evolutionary epistemology and the distorting consequences on the philosophical level could not be elaborated. The following context sketches a new view of organismic reasoning and its impact on evolutionary aspects of epistemology. The basic theorem of adaptation is shown to be unacceptable and invalid if organisms are conceived as autonomous entities which can only evolve according to their specific internal organismic properties.
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  • 46
    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
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    Topics: Biology , Medicine
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  • 47
    ISSN: 1432-1211
    Keywords: Key words NRAMP ; Fish ; Carp ; Evolution ; Expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The mouse Lsh/Ity/Bcg locus regulates natural resistance to intracellular pathogens, and the Nramp1 gene was isolated as its candidate. Nramp is part of a small family of at least two genes, Nramp1 and Nramp2. In the present study, a full-length cDNA for carp NRAMP has been isolated and characterized. Nucleotide and predicted amino acid sequence analysis indicate that the carp NRAMP encodes a 548 amino acid membrane protein with 12 putative transmembrane domains, two N-linked glycosylation sites, and an evolutionarily conserved consensus transport motif. The peptide sequence identity among carp and human NRAMP2 is 78%, and 65% with human NRAMP1. Reverse transcription-polymerase chain reaction revealed that carp NRAMP is ubiquitously expressed. Phylogenetic analysis, using neigbor-joining, showed that the carp NRAMP protein clustered together with mammalian NRAMP2 proteins.
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  • 48
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    Immunogenetics 50 (1999), S. 301-308 
    ISSN: 1432-1211
    Keywords: Key words T-cell receptors ; Variable region genes ; Evolution ; Phylogeny ; Diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes.
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  • 49
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    Immunogenetics 50 (1999), S. 329-335 
    ISSN: 1432-1211
    Keywords: Key words Marsupials ; Light chains ; Variable regions ; IGK ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A full-length and several partial cDNAs encoding IGK light chains from the marsupial South American opossum, Monodelphis domestica, were isolated and characterized. Using these clones as a starting point, the expressed IGKV repertoire was sampled by anchored polymerase chain reaction using an IGKC-specific primer. Based on nucleotide sequences of twenty unique, expressed IGKV-J combinations, there are at least four IGKV families and two J segments. Southern blot analysis revealed each IGK-V family contains multiple gene segments totaling at least thirty-five IGKV in the opossum genome. No evidence for particular, recurrent IGKV-J combinations in the opossum IGK repertoire was seen, rather the V-J combinations appeared random and diverse. Each of the four IGKV families appear more closely related to V segments from placental mammals than to each other, suggesting the duplication of the IGKV families prior to the separation of marsupials and placental mammals more than one-hundred-million years ago. Overall, the complexity of opossum light chain V segments appears greater than that found in the heavy chain, and light chains are likely to contribute significantly to Ig diversity in this species.With this report, the homologues encoding all three classes of eutherian Ig chains, IGH, IGL, and IGK, have been described in a non-placental mammal.
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  • 50
    ISSN: 1432-1211
    Keywords: Key words MHC ; MIC ; Nonhuman primates ; Evolution
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    Topics: Biology , Medicine
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  • 51
    ISSN: 1432-1211
    Keywords: Key words Antigen presentation ; Autoimmune disease ; Evolution ; MHC ; Self peptides
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    Topics: Biology , Medicine
    Notes: Abstract  Comparison of peptides eluted from human class I and class II major histocompatibility complex (MHC) molecules and the proteins from which they are derived (source proteins) revealed that class I MHC bind peptides derived from proteins that are highly conserved, hydrophilic, and universally expressed, while the peptides themselves are hydrophobic and even more conserved than their source proteins. In contrast, source proteins for class II-bound peptides were not significantly more conserved than a random sample of proteins. Class II-bound peptides were generally more conserved than their source proteins but were significantly less conserved than class I-bound peptides. The characteristics of class I-bound peptides can probably be explained by the selectivity of processing and transport of peptides for binding by class I, while the relative lack of selectivity of peptide binding for class II may explain the high incidence of autoimmune diseases associated with alleles of these molecules.
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  • 52
    ISSN: 1432-1211
    Keywords: Key words iNOS ; Fish ; Parasite ; Evolution ; Transcription
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    Topics: Biology , Medicine
    Notes: Abstract  Using an oligonucleotide primer based on a partial goldfish inducible nitric oxide synthase (iNOS) sequence, a complete carp iNOS cDNA was isolated from an activated carp phagocyte cDNA library. Nucleotide and predicted amino acid sequence analysis indicate that carp iNOS encodes a 1127-amino acid protein with 57% sequence identity to human iNOS. Like mammalian NOSs, carp iNOS protein contains putative binding sites for heme, tetrahydrobiopterin, calmodulin, flavine mononucleotide, flavine adenine dinucleotide, and NADPH. Phylogenetic analysis, using neighbor joining, showed that the carp iNOS protein clustered together with the other vertebrate iNOS proteins. Inducibility of carp iNOS was confirmed by reverse transcription-polymerase chain reaction after stimulation of carp phagocytes with lipopolysaccharide or the protozoan blood flagellate Trypanoplasma borreli. These stimulators produced high amounts of nitric oxide that were toxic for T. borreli in vitro. The nuclear transciption factor NF-κB was shown to play a role in the induction of iNOS transcription.
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  • 53
    ISSN: 1432-1211
    Keywords: Key words HLA ; Patr class I molecules ; Evolution ; Polymorphism ; AIDS
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Human immunodefiency virus (HIV) poses a major threat to humankind. And though, like humans, chimpanzees are susceptible to HIV infection, they are considered to be resistant to the development of the acquired immune deficiency syndrome (AIDS). Little is known about major histocompatibility complex (MHC) class I diversity in chimpanzee populations and, moreover, whether qualitative aspects of Patr class I molecules may control resistance to AIDS. To address these questions, we assayed MHC class I diversity in a West African chimpanzee population and in some animals from other subspecies of chimpanzee. Application of different techniques allowed the detection of 17 full-length Patr-A, 19 Patr-B, and 10 Patr-C alleles. All Patr-A alleles cluster only into the HLA-A1/A3/A11 family, which supports the idea that chimpanzees have experienced a reduction in their repertoire of A locus alleles. The Patr-B alleles do not cluster in the same lineages as their human equivalents, due to frequent exchange of polymorphic sequence motifs. Furthermore, polymorphic motifs may have been exchanged between Patr-A and Patr-B loci, resulting in convergence. With regard to evolutionary stability, the Patr-C locus is more similar to the Patr-A locus than it is to the Patr-B locus. Despite the relatively low number of animals analyzed, humans and chimpanzees were ascertained as sharing similar degrees of diversity at the contact residues constituting the B and F pockets in the peptide-binding side of MHC class I molecules. Our results indicate that within a small sample of a West African chimpanzee population, a high degree of Patr class I diversity is encountered. This is in agreement with the fact that chimpanzees display more mitochondrial DNA variation than humans. In addition, population analyses demonstrated that particular Patr-B molecules, with the capacity to bind conserved HIV-1 epitopes, are characterized by high gene frequencies. These findings have important implications for evaluating immune responses in HIV vaccine studies and, more importantly, may help in understanding the relative resistance of chimpanzees to AIDS.
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  • 54
    ISSN: 1432-1211
    Keywords: Key words HLA genes ; IgV genes ; Evolution ; Gene conversion ; Sheep ileal Peyer's patch
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    Topics: Biology , Medicine
    Notes: Abstract  Polymorphic sequence variation in the peptide-binding domains of MHC class I molecules appears to have been driven largely by the constructive action of natural selection on the specificity of the peptide-binding groove. Similar features are displayed by the variable domains of immunoglobulins generated in the sheep ileal Peyer's patch, but in this case there is evidence that the action of a targeted hypermutator acting on a selected substrate rather than antigen-driven selection is responsible for the pattern of variation in the system. Such a hypermutator acting in the germ line would not only mimic the action of natural selection but also, by convergent mutation, generate similar patterns of variation in unrelated alleles that could be interpreted as evidence for short-tract gene conversion. We analyzed human class I MHC alleles in the light of these data, but failed to find evidence of the action of a similar hypermutator. A search for other mutationally driven patterns of variation also failed, even in hypervariable residues from parsimonious phylogenies. Single-nucleotide variation at these residues is also frequent in recent allelic variants, but the data are as consistent with short-tract gene conversion as with base mutation. We conclude that the patterns of allelic variation in MHC molecules are not driven by mutational pressure, but rather by conventional mutational processes, accompanied by short-tract gene conversion and intense natural selection.
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    Immunogenetics 51 (2000), S. 587-590 
    ISSN: 1432-1211
    Keywords: Key words J chain ; Immunoglobulin ; Amphibian ; Evolution ; Comparative immunology
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    Immunogenetics 51 (2000), S. 606-609 
    ISSN: 1432-1211
    Keywords: Key words MHC ; Evolution ; Primate ; Callithrix ; Callicebus
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    Immunogenetics 49 (1999), S. 295-302 
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex ; Class II ; Antigen processing ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family.
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  • 58
    ISSN: 1432-1211
    Keywords: Key words Mhc ; Class II A ; Cichlid ; Fish ; Evolution
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  • 59
    ISSN: 1432-1211
    Keywords: Key words Beta2-microglobulin ; Evolution ; Sturgeon ; cDNA ; Genomic
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  • 60
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    Mycorrhiza 4 (1993), S. 1-4 
    ISSN: 1432-1890
    Keywords: Tropics ; Mycotrophy ; Spore dispersal ; Community composition ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This article introduces reports concerning the occurrence of mycorrhizae on epiphytes in Costa Rica, Ethiopia, Venezuela, Malaysia, and Mexico. Association of vesicular-arbuscular mycorrhizal fungi with the roots of epiphytes is not well known. Vesicular-arbuscular mycorrhizal fungi (VAM) do occur in the canopy, but are uncommon except in certain sites and host taxa. Occurrence of VAM on epiphytes may be constrained by mineral nutrient availability and spatial heterogeneity in the canopy. Nevertheless, epiphytes present unique opportunities to study influences of mycorrhizae on vascular plant community composition and on the evolution of mycorrhizal associations.
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    Mycorrhiza 10 (2000), S. 145-149 
    ISSN: 1432-1890
    Keywords: Keywords Arbuscular mycorrhiza ; Pteridophyte ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The percentage of arbuscular mycorrhizal pteridophytes among 256 pteridophyte species distributed in Yunnan (southwest China) was found to be lower than that in angiosperms. In the pteridophytes, the occurrence of arbuscular mycorrhizas was low in sporophytes of fern-allies and leptosporangiates, whereas in the eusporangiates it was relatively high. From the standpoint of mycotrophism, the evolutionary trend in the Filicineae may be from constantly mycorrhizal to facultative mycorrhizal and finally to nonmycorrhizal plants.
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  • 62
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    Biology and fertility of soils 9 (1990), S. 110-118 
    ISSN: 1432-0789
    Keywords: Kuehneltiella terricola gen. nov., sp. nov. ; Soil ciliates ; Colpodidae ; Systematics ; Evolution ; Australia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The morphology and biology of the colpodid ciliate Kuehneltiella terricola gen. nov., sp. nov. has been investigated using living organisms, various silver impregnation methods, and scanning electron microscopy. The new species has been isolated in soil from central Australia and might be endemic to this continent. The new genus Kuehneltiella differs from its nearest relative, Bresslaua, in having a right oral polykinetid composed of a single row of dikinetids. A reinvestigation of Lynn's slides of Bresslaua insidiatrix showed that, contrary to the statement of Lynn (1979), this species has a typic colpodid right oral polykinetid, i.e., composed of many short, disordered kineties. A brief review of the literature suggests that simple, single-rowed, right oral polykinetids are apomorphic in the colpodids s. str. Further, this special character has obviously evolved independently several times within the class Colpodea and even within the colpodids s. str. An illustrated key to the genera of the family Colpodidae is provided.
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  • 63
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    Biology and fertility of soils 9 (1990), S. 95-100 
    ISSN: 1432-0789
    Keywords: Assulina-Valkanovia ; Testacea ; Polymorphism ; Genotypes ; Evolution ; Spruce forest ; Sphagnum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The taxonomy and evolution of the Assulina-Valkanovia complex were investigated in a spruce forest soil which included a Sphagnum plot (GDR, Thuringia). In both habitats Assulina muscorum occurred in two colour forms (brown and colourless) and four shapes. A quantified phenospectrum from Assulina muscorum was obtained. The four shapes were distributed differently between the brown and the colourless forms in Sphagnum and soil. The shell measurements showed statistically significant differences between the brown and the colourless forms. Even between the two brown populations there were some significant differences. Each of the four shape types of brown and of colourless Assulina can be kept in clonal cultures for some time. However, without selection, single cultures eventually revert to mixed types. The four shape types show different degrees of stability. These colour and shape forms are genotypes, which can also occur for short periods in the natural habitats. The brown populations in Sphagnum and in the soil were dominated by different shape types during the period of investigation. Valkanovia elegans cannot be distinguished from Assulina muscorum type 4, but Valkanovia can inhabit both upper and lower soil horizons, whereas Assulina and its forms lives exclusively in the upper horizon (litter). Valkanovia from the lower horizon is constant in clonal culture. The conclusion of the present investigation is that there are stable and unstable constellations within a changeable genome, which give asexual groups both a taxonomic structure and a continuum of forms. Selection can increase stability, by polygenic control of features.
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  • 64
    ISSN: 1432-0789
    Keywords: Key words Phosphorus dynamics ; Olsen ; phosphorus ; Soil phosphorus fractions ; Manure ; Soybean-wheat rotation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  Soil P availability and efficiency of applied P may be improved through an understanding of soil P dynamics in relation to management practices in a cropping system. Our objectives in this study were to evaluate changes in plant-available (Olsen) P and in different inorganic P (Pi) and organic P (P0) fractions in soil as related to repeated additions of manure and fertilizer P under a soybean-wheat rotation. A field experiment on a Typic Haplustert was conducted from 1992 to 1995 wherein the annual treatments included four rates of fertilizer P (0, 11, 22 and 44 kg ha–1 applied to both soybean and wheat) in the absence and presence of 16 t ha–1 of manure (applied to soybean only). With regular application of fertilizer P to each crop the level of Olsen P increased significantly and linearly through the years in both manured and unmanured plots. The mean P balance required to raise Olsen P by 1 mg kg–1 was 17.9 kg ha–1 of fertilizer P in unmanured plots and 5.6 kg ha–1 of manure plus fertilizer P in manured plots. The relative sizes of labile [NaHCO3-extractable Pi (NaHCO3-Pi) and NaHCO3-extractable P0 (NaHCO3-P0)], moderately labile [NaOH-extractable Pi (NaOH-Pi) and NaOH-extractable P0 (NaOH-P0)] and stable [HCl-extractable P (HCl-P) and H2SO4/H2O2-extractable P (resisual-P)] P pools were in a 1 : 2.9 : 7.6 ratio. Application of fertilizer P and manure significantly increased NaHCO3-Pi and -P0 and NaOH-Pi, and -P0 fractions and also total P. However, HCl-P and residual-P were not affected. The changes in NaHCO3-Pi, NaOH-Pi and NaOH-P0 fractions were significantly correlated with the apparent P balance and were thought to represent biologically dynamic soil P and act as major sources and sinks of plant-available P.
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  • 65
    ISSN: 1432-0819
    Keywords: Key wordsZoned magma body ; Chemical variation ; ash-flow sheets ; Tephra sequence ; Differentiation ; time constraints ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract The Rainier Mesa ash-flow is a large (1200 km3), 11.6 My old, chemically zoned unit that ranges in composition from 55 to 76% SiO2– one of the largest chemical ranges ever observed in a large volume ash-flow sheet. Two chemical trends occur in this sheet, a low silica (55–66% SiO2) and a high silica (〉66% SiO2) trend. Ninety per cent of the Rainier Mesa sheet occurs in the high silica trend. Immediately beneath the Rainier Mesa sheet is a thick tephra sequence. The chemical variation of this sequence is nearly equivalent to the high silica portion of the Rainier Mesa ash-flow sheet (about 66–78% SiO2). Throughout the tephra sequence numerous small ash-flow layers occur, and each ash-flow layer is chemically zoned from more evolved at the base to less evolved at the top. This is consistent with having been erupted from a zoned magma body. The lowest silica tephra units are at the base of the sequence and the highest silica units are at the top – that is, the large-scale chemical trend of the entire sequence is opposite to that of the individual ash-flow layers. These ash-flow layers are of very small volume. The tephra sequence provides a unique record of the incremental development of the zoned, high silica portion of the Rainier Mesa magma body.
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    Bulletin of volcanology 59 (1997), S. 161-170 
    ISSN: 1432-0819
    Keywords: Key words Structure ; Evolution ; Uplift ; Geodetic modeling ; Alban Hills
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  The Alban Hills, a Quaternary volcanic center lying west of the central Apennines, 15–25 km southeast of Rome, last erupted 19 ka and has produced approximately 290 km3 of eruptive deposits since the inception of volcanism at 580 ka. Earthquakes of moderate intensity have been generated there at least since the Roman age. Modern observations show that intermittent periods of swarm activity originate primarily beneath the youngest features, the phreatomagmatic craters on the west side of the volcano. Results from seismic tomography allow identification of a low-velocity region, perhaps still hot or partially molten, more than 6 km beneath the youngest craters and a high-velocity region, probably a solidified magma body, beneath the older central volcanic construct. Thirty centimeters of uplift measured by releveling supports the contention that high levels of seismicity during the 1980s and 1990s resulted from accumulation of magma beneath these craters. The volume of magma accumulation and the amount of maximum uplift was probably at least 40×106 m3 and 40 cm, respectively. Comparison of newer levelings with those completed in 1891 and 1927 suggests earlier episodes of uplift. The magma chamber beneath the western Alban Hills is probably responsible for much of the past 200 ka of eruptive activity, is still receiving intermittent batches of magma, and is, therefore, continuing to generate modest levels of volcanic unrest. Bending of overburden is the most likely cause of the persistent earthquakes, which generally have hypocenters above the 6-km-deep top of the magma reservoir. In this view, the most recent uplift and seismicity are probably characteristic and not precursors of more intense activity.
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    Current genetics 17 (1990), S. 223-227 
    ISSN: 1432-0983
    Keywords: Orotidine-5′-phosphate decarboxylase ; Cephalosporium acremonium ; Recombinant DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned the Cephalosporium acremonium pyr4 gene by cross-hybridization with the equivalent gene from Neurospora crassa, the closest relative from which this gene is available. The C. acremonium pyr4 gene complements an E. coli pyrF mutant lacking orotidine-5′-phosphate decarboxylase (OMPdecase), and most probably does not contain introns. Maxicell analysis in E. coli shows that it encodes a 46 kDa polypeptide. The C. acremonium OMPdecase contains a highly conserved pentadecapeptide characteristic for this category of enzyme. Extensive sequence comparison suggests an important role of this region in enzymatic activity.
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  • 68
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the genes encoding te largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might from the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage. RNA polymerase I, however, arises separately from the eubacterial β′ lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.
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  • 69
    ISSN: 1432-0983
    Keywords: psbA ; Cyanelle ; Cyanophora paradoxa ; Evolution ; Sequence analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The psbA gene is part of the reaction center of photosystem II in cyanobacteria and the plastids of higher plants. Its primary sequence is highly conserved among all species investigated so far and its sequence shows homologies with the L and M subunits of the reaction center of photosynthetic bacteria. We have analyzed the psbA homolog from a eukaryotic alga, Cyanophora paradoxa, where the gene is encoded on cyanelle DNA. These cyanelles are surrounded by a murein sacculus and resemble cyanobacteria in many other characteristics, although they are genuine organelles that functionally replace plastids. Analysis of the gene revealed a psbA protein identical in length (360 codons) with the cyanobacterial counterpart. The overall sequence identity is, however, more pronounced between cyanelle psbA and the shorter (353 amino acids) psbA product found in higher plants. These data strongly support the postulated bridge position of cyanelles between chloroplasts and free-living cyanobacteria.
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    Current genetics 10 (1986), S. 931-941 
    ISSN: 1432-0983
    Keywords: T. aestivum ; Chloroplast DNA ; Repeat DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Low-stringency hybridisation between recombinant plasmids representing the complete T. aestivum chloroplast genome has revealed small repeated DNA segments dispersed through the molecule. Thirty-two repeated DNA segments were detected, and they could be divided into 12 unrelated sets; no repeat was detected as multiple copies. The longest of the small repeats mapped just within the large inverted repeat in spinach and mung-bean ctDNAs. It was found to have been duplicated after the divergence of a cereal progenitor to generate a third, dispensible copy, 0.2 kbp downstream of rbcL. In maize at least, this copy has also become integrated, with rbcL, in the mitochondrial genome. Another of the repeats is thought to have mediated a chloroplast DNA inversion (Howe 1985). Thus the diverse collection of small repeats probably represents some consequences and causes of past recombination events as well as a mechanism for further intramolecular ctDNA recombination. Their possible significance in the restructuring and evolution of chloroplast genomes is discussed.
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  • 71
    ISSN: 1432-0983
    Keywords: Wheat chloroplast DNA ; Repeated sequences ; Ribosomal protein genes ; Evolution
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    Topics: Biology
    Notes: Summary Some dispersed repeated sequences and their flanking regions from wheat and maize ctDNAs have been characterized. Two sets of wheat ctDNA repeats were found to be the chloroplast ribosomal protein genesrpl2 andrpl23, plus nonfunctional segments of them, designatedrpl2′ andrpl23′. Pairwise comparisons were made between the wheatrp123 andrpl23′, and the maizerp123′ sequences. The precise patterns of homology suggest that the divergence of the wheat and maize nonfunctional (rpl23′) sequences is being retarded by nonreciprocal recombination, biased by selection for individuals with functional (rpl23) sequences. The implied involvement of these sequences in mechanisms of homologous recombination, and therefore in the creation and spread of new ctDNA variants, is discussed.
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    Current genetics 15 (1989), S. 99-106 
    ISSN: 1432-0983
    Keywords: Yeast ; Isoleucyl-tRNA synthetase ; Isoleucine ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The isoleucyl-tRNA synthetase gene (ILS1) from the yeast Saccharomyces cerevisiae was cloned and sequenced. This gene was initially cloned because it cross-hybridizated to what is now presumed to be the isoleucyl-tRNA synthetase gene (cupC) from the protozoan Tetrahymena hhermophila. The ILS1 gene was determined to be 1,072 amino acids in length. A comparison with a recently published sequence of ILS1 1 from another laboratory (Englisch et al. 1987) was made and differences noted. Two promoter elements were detected, one for general amino acid control and one for constitutive transcription. A heat shock protein (hsp70) gene (probably SSA3) was found 237 by upstream from the ILS1 translation start site. The ILS1 amino acid sequence was compared to isoleucyl-tRNA synthetases from other organisms, as well as to valyl-, leucyl- and methionyl-tRNA synthetases. Regions of conservation between these enzymes were found.
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    Current genetics 15 (1989), S. 221-229 
    ISSN: 1432-0983
    Keywords: Chloroplast DNA ; Chlorophyll a/c alga ; Evolution ; Ribosomal operon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are almost no data describing chloroplast genome organization in chromophytic (chlorophyll a/c) plants. In this study chloroplast ribosomal operon placement and gene organization has been determined for the golden-brown alga Olisthodiscus luteus. Ribosomal RNA genes are located on the chloroplast DNA inverted repeat structure. Nucleotide sequence analysis, demonstrated that in contrast to the larger spacer regions in land plants, the 16S–23S rDNA spacer of O. luteus is only 265 by in length. This spacer contains tRNAIle and tRNAAla genes which lack introns and are separated by only 3 bp. The sequences of the tRNA genes and 16S and 23S rDNA termini flanking the spacer were examined to determine homology between O. luteus, chlorophytic plant chloroplast DNA, and prokaryotes.
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  • 74
    ISSN: 1432-0983
    Keywords: Comparative restriction site mapping ; Gene mapping ; Deletions and additions ; Chloroplast genome ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The chloroplast genomes from the interfertile green algae Chlamydomonas eugametos and C. moewusii have been compared in their overall sequence organization. Physical mapping of Aval, BstEII and EcoRI restriction sites on the C. moewusii chloroplast genome revealed that this 292 kilobase-pair (kbp) genome is 49 kbp larger than the C. eugametos genome. Heterologous fragment hybridizations indicated the same order of common sequence elements on the two algal genomes. Almost all of the 49 kbp size difference is accounted for by the presence of two large extra sequences in C. moewusii: a 21 kbp sequence in the inverted repeat and a 5.8 kbp sequence in the single copy-region bordering the 16S ribosomal RNA (rRNA) genes. In addition to these two major deletion/addition differences, 42 restriction site and fragment length differences (ranging from 100 to 500 base pairs) were mapped on the two algal genomes. Surprisingly, the greatest density of these differences was found to be confined within the inverted repeat, one of the most conserved regions of land plant chloroplast genomes.
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  • 75
    ISSN: 1432-0983
    Keywords: Physarum polycephalum ; rRNA ; Sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA (SSU rRNA) gene has been determined. Sequence data indicate that the mature 19S SSU rRNA is 1,964 nucleotides long. A complete secondary structure model for P. polycephalum SSU rRNA has been constructed on the basis of the Escherichia coli 16S rRNA model and data from comparative analyses of 28 different eukaryotic sequences. A “four-helix” model is presented for the central domain variable region. This model can be applied both to vertebrate and most lower eukaryotic SSU rRNAs. The increased size of P. polycephalum SSU rRNA relative to the smaller SSU rRNAs from such other lower eukaryotes, as Dictyostelium, Tetrahymena or Saccharomyces is due mainly to three G+C-rich insertions found in two regions known to be of variable length in eukaryotes. In a phylogenetic tree constructed from pairwise comparisons of eukaryotic SSU rRNA sequences, the acellular myxomycete P. polycephalum is seen to diverge before the appearance of the cellular mycomycete Dictyostelium discoideum.
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  • 76
    ISSN: 1432-0983
    Keywords: Cyanophora paradoxa ; Ferredoxin-NADP+-oxidoreductase ; Protein-import ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cyanophora paradoxa is an important model organism for the study of the transition from endocytobiontic cyanobacteria to factual eukaryotic cell organelles. The cyanelles of these organisms possess cyanobacterial, as well as plastidic, characteristics. Although the transfer of cyanellar proteins from cytosolic into cyanellar space has been shown, the process of translocation of a known protein across the peptidoglycan layer and the envelope membranes has not been characterized. In this study we demonstrate that a specific and obligate cyanelle protein —Ferredoxin-NADP+-oxidoreductase (FNR) — is coded on the nuclear genome, synthesized on 80S ribosomes and transported from the eukaryotic cell compartment into the cyanelles of Cyanophora paradoxa, an original intracellular host-guest relation. These results indicate a gene transfer from guest to host genome and support the view that, in spite of their cyanobacterial origin, cyanelles have been evolved to cell organelles comparable to plastids.
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  • 77
    ISSN: 1432-0983
    Keywords: Evolution ; Sequence comparison ; RUBISCO ; Transit peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have isolated and characterized a full-length cDNA clone encoding the precursor of the small subunit (pSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) from the green alga, Chlamydomonas moewusii. Comparison with the C. reinhardtii rbcS1 gene sequence reveals that both small subunit (SS) coding regions are 75% homologous and that their predicted mature polypeptide chains are each composed of 140 amino acids. In contrast, their transit peptides appear to be divergent. We also show that transcription of the C. moewusii rbcS gene(s) which generates a 1,230 and a 930 base mRNA species are light-stimulated/or accumulated during the light period of the cell cycle. Finally, the SS polypeptide sequences of fifteen different photosynthetic organisms are compared; this analysis reveals at least five well-conserved polypeptide domains.
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    Journal of molecular evolution 5 (1975), S. 187-197 
    ISSN: 1432-1432
    Keywords: Evolution ; Cytochrome C ; Substitution ; Covarion ; Monte-Carlo Simulations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A statistical analysis aimed at obtaining some informations on a possible correlation between simultaneous amino acid substitutions is proposed. This method is applied to a set of cytochromes C, at the level of tandem and triple substitutions separated along the peptide chain by 1 to 15 peptide bonds. Monte-Carlo simulations are performed and the results are compared. We find a significant occurence of three adjacent amino acid substitutions in which the first replacement requires a two nucleotide substitution. A possible explanation of this fact is proposed on the basis of covarions.
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  • 79
    ISSN: 1432-1432
    Keywords: Evolution ; κ-Casein ; Cytochrome b ; Artiodactyla ; Ruminantia ; Caprinae ; Capricornis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences for the κ-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine κ-casein gene; they were applicable for the amplification of the κ-casein genes from the 13 species in the Ruminantia except exon 2 of the lesser mouse deer. These results permitted an easy phylogenetic analysis based on the sequences of an autosomal gene. A phylogenetic tree was constructed from the mature K-casein sequences and compared with the tree of the cytochrome b genes which were sequenced from the same individuals. The Cervidae (sika deer, Cervus nippon) were separated from the branch of the Bovidae on the tree of κ-casein genes with a relatively high confidence level of the bootstrap analysis, but included in the branch of the Bovidae on the tree of cytochrome b genes. The κ-casein tree indicated a monophyly of the subfamily Caprinae, although the internal branches were uncertain in the Caprinae. The tree based on the nucleotide sequences of cytochrome b genes clearly showed the relationships of the closely related species in the genus Capricornis consisting of serow (C. smatorensis), Japanese serow (C. crispus), and Formosan serow (C. swinhoei). These results would be explained by the difference of resolving power between the κ-casein and the cytochrome b sequences.
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    Journal of molecular evolution 7 (1976), S. 133-149 
    ISSN: 1432-1432
    Keywords: 5S rRNA ; Nucleotide Sequence Homology ; Evolution ; Mutation Frequencies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of ‘costs’ for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and proto-sequence reconstructions are done for a large number of different con-figurations of mutation costs. Examination of the family of curves of total replacements inferred versus the ratio of transitions/trans-versions inferred, each curve corresponding to a given number of in-sertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutation.
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  • 81
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    Journal of molecular evolution 43 (1996), S. 399-404 
    ISSN: 1432-1432
    Keywords: Asarum ; Dioscorea ; Angiosperms ; Evolution ; Legumins ; Seed proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms.
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  • 82
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    Journal of molecular evolution 43 (1996), S. 685-689 
    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
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  • 83
    ISSN: 1432-1432
    Keywords: Alleles ; Evolution ; Gene conversion ; Introns ; Nematode
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    Topics: Biology
    Notes: Abstract Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
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  • 84
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    Journal of molecular evolution 5 (1975), S. 47-55 
    ISSN: 1432-1432
    Keywords: Gene Duplication ; Dipeptides ; Posterior Pituitary Peptide ; Evolution ; Protein Sequence
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    Topics: Biology
    Notes: Summary We have compiled the dipeptide frequencies in 100 known protein sequences. We suggest that dipeptides which occur with low frequencies can be used to locate proteins where partial gene duplication may have taken place. The 48 residue sequence of posterior pituitary peptide contains two Cys Trp pairs. The adjacent portions of the sequence are compatible with a partial gene duplication in the evolutionary history of posterior pituitary peptide.
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  • 85
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    Journal of molecular evolution 6 (1975), S. 309-320 
    ISSN: 1432-1432
    Keywords: Aminoacyl Transfer ; Amino Acid Adenylate ; Imidazole Catalysis ; Evolution ; Peptide
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    Topics: Biology
    Notes: Summary Imidazole catalysis of phenylalanyl transfer from phenylalanine adenylate anhydride to the hydroxyl groups of homopolyribonucleotides was investigated as a chemical model of the biochemical aminoacylation of tRNA. Imidazole catalyzed transfer of phenylalanine to poly (U) increases from pH 6.5 to 7.7 and decreases above pH 7.7. At pH 7.7 approximately 10% of the phenylalanyl residues are transferred to poly (U). At pH 7.1, transfer to poly (U) was five times as great as to poly (A) and transfer to a poly (A) poly (U) double helix was negligible. At pH 7.1 approximately 45 mole percent linkages to poly (U) were monomeric phenylalanine; the remainder of the linkages were peptides of phenylalanine. The number of linkages and their lability to base and neutral hydroxylamine indicates that phenylalanine and its peptides are attached as esters to the 2′ hydroxyl groups throughout poly (U) and the 2′ (3) hydroxyl groups at the terminus of poly (U). These results do model the contemporary process of aminoacyl transfer to tRNA and continue to suggest that a histidine residue is in the active site of aminoacyl-tRNA-synthetases.
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  • 86
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    Journal of molecular evolution 7 (1976), S. 111-131 
    ISSN: 1432-1432
    Keywords: Crustacea ; Evolution ; Repeated DNA ; Molecular Hybridization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of data obtained from molecular hybridization of3H-labeled repetitious DNA has been utilized to reconstruct the broad outlines of phylogenetic relationships among decapod Crustacea. This molecular reconstruction agrees reasonably well with the paleontological record, and with other schemes obtained by comparative morphological and serological approaches. Preliminary evidence is in line with the hypothesis that continuous addition of new repeated sequence families to the genome over long periods of time may in part account for the correlation observed between percent repetitious DNA hybridized and divergence time. It is tentatively concluded that a core of DNA base sequence homology has been highly conserved throughout the evolution of theCrustacea. Demonstration of inter-species sequence homology has important implications to models which relegate a genetic regulatory function to repeated DNAs.
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  • 87
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    Journal of molecular evolution 7 (1976), S. 185-195 
    ISSN: 1432-1432
    Keywords: Evolution ; Randomicity ; Counter-Example
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    Notes: Summary Specific counter-examples are derived theoretically to the hypothesis that a random amino acid composition signifies a random evolutionary process.
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  • 88
    ISSN: 1432-1432
    Keywords: Bacilli, 16S rRNA ; Phylogeny ; Thermophile ; Evolution ; Oligonucleotide Fingerprint
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    Topics: Biology
    Notes: Summary Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500–3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease. These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms,Bacillus subtilis, B.pumilus andB.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.
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  • 89
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    Journal of molecular evolution 6 (1975), S. 149-163 
    ISSN: 1432-1432
    Keywords: Electrophoretic Detectability ; Neutral Mutation Theory ; Evolution ; Mutation Rates
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    Topics: Biology
    Notes: Summary Routine electrophoretic surveys for genetic variation in natural populations depend primarily upon detecting differences in the net charge carried by a protein. We have calculated the proportion of base substitutions which would yield an electrophoretically detectable mutant protein, and the relative mutation rates among different charge classes, under a variety of simplifying assumptions. These calculations indicate that: (i) only 25 per cent of all single base mutations would lead to a charge change on a protein molecule. (ii) five distinct classes of electrophoretic variants can be generated from a specified protein by single base substitutions. (iii) the relative mutation rates differ markedly among the different charge classes which can be generated by single base substitutions. The estimates of the proportion of electrophoretically detectable mutant proteins and relative mutation rates among charge classes were relatively robust to changes in assumptions concerned with the kind and site of base substitutions and the amino acid composition of the protein.
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  • 90
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    Journal of molecular evolution 8 (1976), S. 79-94 
    ISSN: 1432-1432
    Keywords: Histones ; Evolution ; Prokaryotes ; Lower Eukaryotes ; Higher Eukaryotes
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    Topics: Biology
    Notes: Summary The occurrence of basic chromosomal proteins in lower eukaryotes provides a useful approach to the study of histone evolution and function in higher eukaryotes. The histones of higher plants and animals are very similar and some are nearly identical, suggesting a high degree of evolutionary conservation within this group of proteins. However, a literature survey reveals that in the lower eukaryotes the histone situation is quite variable. The ciliates, and the true and cellular slime molds possess basic chromosomal proteins that are very similar to the histones of higher plants and animals. Various other lower eukaryotes possess basic chromosomal proteins that resemble at least some of the major histone fractions, and some microorganisms possess basic chromosomal proteins that bear little or no relationship to higher plant and animal histones. Since histones play a major role in the control of gene expression and the maintenance of chromosome structure in higher organisms, the evolution of these proteins represents a major change in the packaging of DNA and the mode of regulating gene expression in eukaryotes.
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  • 91
    ISSN: 1432-1432
    Keywords: Evolution ; Expression patterns ; α-Amylase ; Glucose repression ; Starch induction ; Intra- and interspecific variation ; Drosophila ; Gene expression ; Regulatory genes
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    Topics: Biology
    Notes: Abstract Intraspecific variation of α-amylase activity in D. melanogaster and D. immigrans, which is distantly related to D. melanogaster, and interspecific variation of α-amylase activity in 18 Drosophila species were examined. The amount of intraspecific variation of α-amylase activities measured in terms of coefficient of variation in D. melanogaster and D. immigrans was one-half and one-tenth or less, respectively, of the interspecific variation in 18 Drosophila species. We also surveyed the response patterns of α-amylase activity to dietary carbohydrates at the larval and adult stages. The levels of α-amylase activity depended on both repression by dietary glucose (glucose repression) and induction by dietary starch (starch induction). In general, our data suggest that glucose repression was conserved among species at both stages while starch induction was mainly observed in larvae, although the degree of the response depended on species. In D. lebanonensis lebanonensis and D. serrata, larvae expressed electrophoretically different α-amylase variants (isozymes) from those of adult flies. These results may suggest that the regulatory systems responsible both for the response to environment and developmental expression are different among species in Drosophila.
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  • 92
    ISSN: 1432-1432
    Keywords: Soybean ; Ferritin ; Plant-animal ; Monocotyledons ; Dicotyledons ; Plastid ; Gene organization ; Evolution ; Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ferritin, a protein widespread in nature, concentrates iron −1011−1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soy-bean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
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  • 93
    ISSN: 1432-1432
    Keywords: Evolution ; Multigene family ; Recombination ; Trypanosome ; Variant surface glycoprotein
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    Topics: Biology
    Notes: Abstract The surface of the parasitic protozoanTrypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome ofT. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 by downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.
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  • 94
    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
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  • 95
    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
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  • 96
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    Journal of molecular evolution 8 (1976), S. 387-388 
    ISSN: 1432-1432
    Keywords: Nitrate Respiration ; Fermentation ; Energy Metabolism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary E. Broda's recent argument against our concept that nitrate respiration antedated oxygen respiration is criticized.
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  • 97
    ISSN: 1432-1432
    Keywords: Evolution ; Repetitive DNA ; SI Nuclease ; Sequence Organization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The organization of repetitive and single copy DNA sequences in sea urchin DNA has been examined with the single strand specific nuclease Sl fromAspergillus. Conditions and levels of enzyme were established so that single strand DNA was effectively digested while reassociated divergent repetitive duplexes remained enzyme resistant. About 25% of sea urchin DNA reassociates with repetitive kinetics to form Sl resistant duplexes of two distinct size classes derived from long and short repetitive sequences in the sea urchin genome. Fragments 2,000 nucleotides long were reassociated to Cot 20 and subjected to controlled digestion with Sl nuclease. About half of the resistant duplexes (13% of the DNA) are short, with a mode size of about 300 nucleotide pairs. This class exhibits significant sequence divergence, and principally consists of repetitive sequences which were interspersed with single copy sequences. About one-third of the long duplexes (4% of the DNA) are reduced in size after extensive Sl nuclease digestion to about 300 nucleotide pairs. About two-thirds of the long resistant duplexes (8% of the DNA) remains long after extensive SI nuclease digestion. These long reassociated duplexes are precisely base paired. The short duplexes are imprecisely paired with a melting temperature about 9°C below that of precisely paired duplexes of the same length. The relationship between length of repetitive duplex and precision of repetition is confirmed by an independent method and has been observed in the DNA of a number of species over a wide phylogenetic area.
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  • 98
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    Journal of molecular evolution 9 (1977), S. 131-158 
    ISSN: 1432-1432
    Keywords: Parvalbumins ; Evolution ; Maximum parsimony ; Troponin-C ; Myosin alkali light chain
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic trees requiring the lowest sum of nucleotide replacements and gene duplicative events were constructed from the amino acid sequence data on ten gnathostome parvalbumins (PAR) and two related myofibrillar proteins troponin-C (TNC) and myosin alkali-light-chain (ALC). The origin and differentiation of the structural domains within these proteins were also investigated by the maximum parsimony method and by an alignment statistic for identifying evolutionarily related protein sequences. The results suggest, in agreement with the Weeds-McLachlan model, that tandem duplications in a precursor gene caused a primordial one-domain polypeptide (consisting of two helices with a calcium binding region in between) to double and then quadruple in size. Duplications of the gene coding for this four domain (I–II–III–IV) protein in an early metazoan, pre-gnathostome lineage gave rise to the separate loci for TNC, ALC, and PAR. TNC, which alone retained the Ca-binding function in each of its four domains, evolved much more slowly than either the ALC or PAR lineages. In the PAR lineage the I–II–III–IV structure was degraded, presumably by a partial gene deletion, to the II–III–IV structure during descent to the gnathostome ancestor of parvalbumins. Also during this period the mid region in domain II lost its Ca-binding function and, as it did so, evolved at an accelerated rate over other regions, a pattern indicative of positive selection for a change in function. In turn, from the gnathostome ancestor to the present, the mid regions of domains III and IV, which each retained Ca-bindung function, evolved much more slowly than other regions, a pattern indicative of stabilizing selection for preservation of function. Between the gnathostome and teleost-tetrapod ancestor a gene duplication separated the parvalbumins into anα-lineage and aβ-lineage. During this early vertebrate period PAR genes evolved at the extremely fast rate of 89 nucleotide replacements per 100 codons per 108 years (i.e. 89 NR %), but from the teleost-tetrapod ancestor to the present, bothα- andβ-PAR lineages evolved at a much slower rate, about 8 NR %. The use ofβ-parvalbumins as phylogenetic markers was complicated by presumptive evidence that paralogous (i.e. duplication dependent) gene lineages occur within this group. As a final point, in the genealogy of TNC, ALC, and PAR lineages, a non-random pattern of nucleotide replacements was observed between the reconstructed ancestral and descendant mRNA sequences. The pattern was similar to that observed for other protein genealogies and seems to reflect a bias in the genetic code for guanine to adenine and adenine to guanine transitions (especially at the first nucleotide position of the RNA codons) to produce amino acid substitutions which are compatible with the preservation of protein three-dimensional structure.
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  • 99
    ISSN: 1432-1432
    Keywords: Histone H1° ; 3′ untranslated region ; Slippage ; Sequence simplicity ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site.
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  • 100
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    Journal of molecular evolution 6 (1975), S. 61-76 
    ISSN: 1432-1432
    Keywords: 5S ribosomal RNA ; Translation ; Evolution ; Molecular Architecture ; Conformational Changes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An extensive comparative analysis of the available primary sequence data on 5S rRNA has been made. A universal secondary structure is presented for procaryotic 5S rRNA which contains four helical regions. Eucaryotic 5S rRNAs are found to have only three of these helices and thus have a somewhat different architecture. In addition, a highly conserved segment of more than thirty nucleotides is identified in the 5′ half of the procaryotic molecule. This segment includes the oligonucleotide-CGAAC- which presumably binds to the t-RNA “common” sequence-GTΨCG-. Among the eucaryotes, the plants display a procaryotic nature in this region, but no eucaryote has the sequence -CGAAC- in this segment. A functional role for the procaryotic 5S rRNA molecule is discussed in which it is envisioned to undergo conformational change, i.e., coiling and uncoiling of one of the helices, which can result in a cyclic interaction of the 5S rRNA molecule with two t-RNA molecules. A general principle also emerges: the natural rotational motion inherent in coiling and uncoiling of nucleic acid helices can be converted quite simply to linear mechanical motion.
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