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  • Physiology & Biochemistry  (57)
  • 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous  (33)
  • Oxford University Press  (57)
  • Elsevier  (33)
  • 2015-2019  (59)
  • 2005-2009  (31)
  • 1945-1949
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  • 2015-2019  (59)
  • 2005-2009  (31)
  • 1945-1949
  • 2010-2014  (7)
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  • 1
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    Mechanisms for ground-surface fracturing and incipient slope failure associated with the 2001 eruption of Mt. Etna, Italy: analysis of ephemeral field data (2008)
    Elsevier
    Details
    Publication Date: 2020-11-26
    Description: During the July^August 2001 eruption of Mt. Etna development of extensional fractures/faults and grabens accompanied magma intrusion and subsequent volcanic activity. During the first days of the eruption, we performed an analysis of attitude, displacement and propagation of fractures and faults exposed on the ground surface in two sites, Torre del Filosofo and Valle del Leone, located along the same fracture system in the region surrounding the Valle del Bove depression on the eastern flank of Mt. Etna. Fractures and faults formed as the consequence of a shallow intruding dyke system that fed the several volcanic centres developed along the fracture system. The investigated sites differ in slope attitude and in geometrical relationships between fractures and slopes. In particular, the fracture system propagated parallel to the gentle slope (67‡ dip) in the Torre del Filosofo area, and perpendicular to the steep slope (V25‡ dip) in the Valle del Leone area. In the Torre del Filosofo area, slight graben subsidence and horizontal extension of the ground surface by about 3 m were recorded. In the Valle del Leone area, extensional faulting forming a larger and deeper graben with horizontal extension of the ground surface by about 10 m was recorded. For the Valle del Leone area, we assessed a downhill dip of 14‡ for the graben master fault at the structural level beneath the graben where the fault dip shallows. These results suggest that dyke intrusion at Mount Etna, and particularly in the region surrounding the Valle del Bove depression, may be at the origin of slope failure and subsequent slumps where boundary conditions, i.e. geometry of dyke, slope dip and initial shear stress, amongst others, favour incipient failures.
    Description: Published
    Description: 281-294
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: dykes ; extensional fractures ; grabens ; slope failures ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 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::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    The late Pleistocene pyroclastic deposits of the Campanian Plain: New insights into the explosive activity of Neapolitan volcanoes (2008)
    Elsevier
    Details
    Publication Date: 2020-12-21
    Description: The lithological and compositional characteristics of eighteen different pyroclastic deposits of Campanian origin, dated between 125 cal ky BP and 22 cal ky BP, were described. The pyroclastic deposits were correlated among different outcrops mainly located on the Apennine slopes that border the southern Campanian Plain. They were grouped in two main stratigraphic and chronologic intervals of regional significance: a) between Pomici di Base (22.03 cal ky BP; Somma–Vesuvius) and Campanian Ignimbrite (39 cal ky BP; Campi Flegrei) eruptions; and b) older than Campanian Ignimbrite eruption. Three new 14C AMS datings support the proposed correlations. Six eruptions were attributed to the Pomici di Base- Campanian Ignimbrite stratigraphic interval, while twelve eruptions are older than Campanian Ignimbrite. Of the studied deposits two originated from Ischia island, five are related to Campi Flegrei, and three to Somma– Vesuvius. Two eruptions have an uncertain correlation with Somma–Vesuvius or Campi Flegrei, while six eruptions remain of uncertain source. Minimum volumes of five eruptions were assessed, ranging between 0.5 km3 and 4 km3. Two of the studied deposits were correlated with Y-3 and X-5 tephra layers, which are widely dispersed in the central Mediterranean area. The new stratigraphic and chronologic data provide an upgraded chrono-stratigraphy for the explosive activity of Neapolitan volcanoes in the period between 125 and 22 cal ky BP.
    Description: Published
    Description: 19–48
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: reserved
    Keywords: Neapolitan volcanoes ; late Pleistocene ; explosive eruptions ; Somma–Vesuvius ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 3
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    Evidence of thermal-driven processes triggering the 2005–2014 unrest at Campi Flegrei caldera (2015)
    Elsevier | Elsevier Science Limited
    Details
    Publication Date: 2021-05-12
    Description: An accelerating process of ground deformation that began 10 years ago is currently affecting the Campi Flegrei caldera. The deformation pattern is here explained with the overlapping of two processes: short time pulses that are caused by injection of magmatic fluids into the hydrothermal system; and a long time process of heating of the rock. The short pulses are highlighted by comparison of the residuals of ground deformation (fitted with an accelerating polynomial function) with the fumarolic CO2/CH4 and He/CH4 ratios (which are good geochemical indicators of the arrival of magmatic gases). The two independent datasets show the same sequence of five peaks, with a delay of ∼200 days of the geochemical signal with respect to the geodetic signal. The heating of the hydrothermal system, which parallels the long-period accelerating curve, is inferred by temperature–pressure gas geoindicators. Referring to a recent interpretation that relates variations in the fumarolic inert gas species to open system magma degassing, we infer that the heating is caused by enrichment in water of the magmatic fluids and by an increment in their flux. Heating of the rock caused by magmatic fluids can be a central factor in triggering unrest at calderas.
    Description: Published
    Description: 58-67
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Campi Flegrei Caldera ; hydrothermal system ; ground deformation ; magmatic fluids ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Crustal residence times of explosive phonolite magmas: U–Th ages of magmatic Ca-Garnets of Mt. Somma-Vesuvius (Italy) (2008)
    Elsevier
    Details
    Publication Date: 2021-06-16
    Description: Assessing the residence times of phonolite magmas in the shallow crust contributes to the understanding of explosive volcanic systems. Estimations of that by dating the residence time of a mineral in a melt was difficult in the past, because e.g. of the lack of evidence for the co-genetic character of the crystals dated. Here we present an estimate for the residence time of a phonolite magma feeding the Pomici di Mercato Plinian eruption (8890±90 cal years BP) of Mt. Somma-Vesuvius (Southern Italy), employing U–Th disequilibrium dating of unzoned Ca-rich phenocrystic magmatic garnets. Based on combined textural, geochemical, and Sr- O isotope evidence, these garnets can be identified as co-genetic with their host phonolites. Furthermore, experimental and petrological data suggest that Ca-garnets can be a liquidus phase in highly differentiated phonolite magmas of Mercato. A whole-rock–glass–garnet U–Th isochron gives a crystallisation age for the Ca-rich garnets of 14,400±1100 a (2σ). This implies a Ca-garnet residence time of 5510±1100 years (2σ) in the Mercato phonolite melt prior to eruption and provides one of the first robust estimates of how long explosive phonolite magma has resided in the shallow crust before eruption. Calculations of magma cooling rates and settling velocities of the Ca-garnets confirm that garnet-bearing phonolite can remain liquid and the garnets remain suspended in a magma chamber for as long as 5510 years before the time of eruption. Processes which may have disturbed the U–Th isotope systematic of the samples, such as assimilation, recharge or surface alteration can be ruled out.
    Description: Published
    Description: 293-301
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: Uranium ; Thorium ; U–Th isotopes ; Somma-Vesuvius ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Magma dynamics at mid-ocean ridges by noble gas kinetic fractionation: Assessment of magmatic ascent rates (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Despite its impact in understanding oceanic crust formation and eruptive styles of related volcanism, magma dynamics at midocean ridges are poorly known. Here, we propose a new method to assess ascent rates of mid-ocean ridge basalt (MORB) magmas, as well as their pre- and sin-eruptive dynamics. It is based on the idea that a rising magma can reach a variable degree of both CO2 supersaturation in melt and kinetic fractionation among noble gases in vesicles in relation to its ascent rate through the crust. To quantify the relationship, we have used a model of multicomponent bubble growth in MORB melts, developed by extending the single-component model of Proussevitch and Sahagian [A.A. Proussevitch, D.L. Sahagian, Dynamics and energetics of bubble growth in magmas: analytical formulation and numerical modeling, J. Geophys. Res. 103 (1998), 18223–18251.] to CO2–He–Ar gas mixtures. After proper parameterization, we have applied it to published suites of data having the required features (glasses from Pito Seamount and mid-Atlantic ridges). Our results highlight that the investigated MORB magmas display very different ranges of ascent rates: slow rises of popping rock forming-magmas that cross the crust (0.01–0.5 m/s), slightly faster rates of energetic effusions (0.1–1 m/s), up to rates of 1–10 m/s which fall on the edge between lava effusion and Hawaiian activity. Inside a single plumbing system, very dissimilar magma dynamics highlight the large differences in compressive stress of the oceanic crust on a small scale. Constraints on how the systems of ridges work, as well as the characteristics of the magmatic source, can also be obtained. Our model shows how measurements of both the dissolved gas concentration in melt and the volatile composition of vesicles in the same sample are crucial in recognizing the kinetic effects and definitively assessing magma dynamics. An effort should be made to correctly set the studied samples in the sequence of volcanic submarine deposits where they are collected. Enhanced knowledge of a number of physical properties of gas-bearing MOR magmas is also required, mainly noble gas diffusivities, to describe multicomponent bubble growth at a higher confidence level.
    Description: Published
    Description: 138-158
    Description: JCR Journal
    Description: reserved
    Keywords: Bubble growth; ; MORB; ; Noble gas; ; Kinetic fractionation; ; Modeling ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 6
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    Viscosity and glass transition temperature of hydrous float glass (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Viscosity of water-bearing float glass (0.03–4.87 wt% H2O) was measured in the temperature range of 573–1523 K and pressure range of 50–500 MPa using a parallel plate viscometer in the high viscosity range and the falling sphere method in the low viscosity range. Melt viscosity depends strongly on temperature and water content, but pressure up to 500 MPa has only minor influence. Consistent with previous studies on aluminosilicate compositions we found that the effect of dissolved water is most pronounced at low water content, but it is still noticeable at high water content. A new model for the calculation of the viscosities as a function of temperature and water content is proposed which describes the experimental data with a standard deviation of 0.22 log units. The depression of the glass tran- sition temperature Tg by dissolved water agrees reasonably well with the prediction by the model of Deubener [J. Deubener, R. Mu¨ ller, H. Behrens, G. Heide, J. Non-Cryst. Solids 330 (2003) 268]. Using water speciation measured by near-infrared spectroscopy we infer that although the effect of OH groups in reducing Tg is larger than that of H2O molecules, the difference in the contribution of both species is smaller than predicted by Deubener et al. (2003). Compared to alkalis and alkaline earth elements the effect of protons on glass fragility is small, mainly because of the relatively low concentration of OH groups (max. 1.5 wt% water dissolved as OH) in the glasses.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: Glass transition ; Pressure effects ; FTIR measurements ; Alkali silicates ; Silicates ; Soda-lime-silica ; Fragility ; Viscosity ; Water in glass ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 7
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    Experimental determination of permeability of Neapolitan Yellow Tuff. (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: This paper presents and discusses the measurement of permeability of Neapolitan Yellow Tuff (NYT) samples obtained in the framework of a study concerning the phenomenon of bradyseism, i.e. the slow vertical movement of soil, in the Campi Flegrei caldera (Campania—Italy). Measurements have been performed under isothermal, non-isothermal and transient non-isothermal conditions using a specifically designed apparatus. Results of measurements of porosity of different samples are also reported. Experimental results in isothermal conditions show that the volume flux through the samples changes linearly with applied pressure. The values of permeability obtained turn out to be independent of the temperature and pressure gradients applied to the samples. This result is consistent with the fact that the permeability is a characteristic of the porous medium, and as such is not affected by temperature and pressure variation, at least in the range examined. The permeability values measured in our laboratories agree quite well with the ones measured in situ by the Agenzia Generale Italiana Petroli (AGIP) during a geothermal exploration of the Campi Flegrei area in 1980. An interesting, still unexplained phenomenon has been detected during transient phases when both pressure and temperature gradients were applied to the samples. The phenomenon consists in an enhancement of volume flux due to heat flux in the transient phase. The extra volume-flux disappears once the steady temperature gradient is reached.
    Description: Published
    Description: 125-136
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: reserved
    Keywords: Campi Flegrei ; hydrothermal systems; ; resurgent calderas ; porous media ; hydraulic permeability ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Hydrothermal fluid circulation and its effect on caldera unrest (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: This paper focuses on the role that hydrothermal systems may play in caldera unrest. Changes in the fluid chemistry, temperature, and discharge rate of hydrothermal systems are commonly detected at the surface during volcanic unrest, as hydrothermal fluids adjust to changing subsurface conditions. Geochemical monitoring is carried out to observe the evolving system conditions. Circulating fluids can also generate signals that affect geophysical parameters monitored at the surface. Effective hazard evaluation requires a proper understanding of unrest phenomena and correct interpretation of their causes. Physical modeling of fluid circulation allows quantification of the evolution of a hydrothermal system, and hence evaluation of the potential role of hydrothermal fluids during caldera unrest. Modeling results can be compared with monitoring data, and then contribute to the interpretation of the recent caldera evolution. This paper: 1) describes the main features of hydrothermal systems; 2) briefly reviews numerical modeling of heat and fluid flow through porous media; 3) highlight the effects of hydrothermal fluids on unrest processes; and 4) describes some model applications to the Phlegrean Fields caldera. Simultaneous modeling of different independent parameters has proved to be a powerful tool for understanding caldera unrest. The results highlight the importance of comprehensive conceptual models that incorporate all the available geochemical and geophysical information, and they also stress the need for high-quality, multi-parameter monitoring and modeling of volcanic activity.
    Description: Accepted
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: open
    Keywords: hydrothermal activity ; caldera unrest ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 9
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    Volumetric observations during paroxysmal eruptions at Mount Etna: pressurized drainage of a shallow chamber or pulsed supply? (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The October 17 to November 5, 1999, eruption of Mount Etna’s Bocca Nuova crater emplaced a V15U106 m3 flow field. The eruption was characterized by 11 paroxysmal events during which intense Strombolian and lava fountain activity fed vigorous channelized PaPa flows at eruption rates of up to 120 m3 s31. Each paroxysm lasted between 75 and 450 min, and was separated by periods of less intense Strombolian activity and less vigorous (610 m3 s31) effusion. Ground-based, satellite- and model-derived volumetric data show that the eruption was characterized by two periods during which eruption rates and cumulative volume showed exponential decay. This is consistent with a scenario whereby the system was depressurized during the first eruptive period (October 17^23), repressurized during an October 24 pause, and then depressurized again during the second period (October 25^28). The imbalance between the erupted and supplied volumes mean that the two periods involved the collection of 1.5^5.7U106 m3 and 1.2^ 3.6U106 m3, respectively, or an increase in the time-averaged supply to 11.6^13.6 m3 s31 and 12.5^14.9 m3 s31. Two models are consistent with the observed episodic fountaining, derived volumetric trends and calculated volume imbalance: a magma collection model and a pulsed supply model. In the former case, depressurization of a shallow reservoir cause the observed volumetric trends and foam collapse at the reservoir roof powers fountaining. In the pulsing case, variations in magma flux account for pressurization^depressurization and supply the excess volume. Increases in rise rate and volatile flux, coupled with rapid exsolution during ascent, trigger fountaining. Limiting equations that define critical foam layer volumes and magma rise rates necessary for Hawaiian-style fountaining favor the latter model.
    Description: Published
    Description: 79-95
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: reserved
    Keywords: Etna ; lava fountaining ; eruption rates ; lava channel ; foam layers ; rise rates ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.01. Earth Interior::04.01.05. Rheology ; 04. Solid Earth::04.02. Exploration geophysics::04.02.99. General or miscellaneous ; 04. Solid Earth::04.02. Exploration geophysics::04.02.05. Downhole, radioactivity, remote sensing, and other methods ; 04. Solid Earth::04.02. Exploration geophysics::04.02.07. Instruments and techniques ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 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 ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 10
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    Comment on: ‘‘The dark nature of Somma-Vesuvius volcano:Evidence from the 3.5 ka BP Avellino eruption’’ by Milia A.Raspini A., Torrente M.M., (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We present here some criticism to the scientific content of the paper of Milia et al. [2007. The dark nature of Somma-Vesuvius volcano: evidence from the 3.5 ka B.P. Avellino eruption. Quaternary International, 173–174, 57–66] published in Quaternary International. Milia et al. (2007) interpreted seismic lines in the Gulf of Naples (southern Italy), and inferred the presence of deposits from a large debris avalanche which occurred just before the Avellino eruption of Somma-Vesuvius volcano. The authors supported their seismic profile interpretation with on-land stratigraphies and logs. However, we present here different on-land data that demonstrate the inconsistency of the occurrence of any debris avalanche before or after the Avellino eruption, and we provide also an alternative interpretation for the observed seismic facies offshore of Somma-Vesuvius.
    Description: Published
    Description: 102–109
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: open
    Keywords: Somma-Vesuvius volcano ; Avellino eruption ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 11
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    A new view of the He–Ar–CO2 degassing at mid-ocean ridges: Homogeneous composition of magmas from the upper mantle (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Deep-sea exploration is rapidly improving our understanding of volatiles geochemistry in mid-ocean-ridge igneous products. It is also placing greater constraints on degassing processes of the Earth’s mantle, with the result that degassing models based on vapour–melt equilibrium are no longer able to explain the increasing number of data. In fact, such models force to postulate an upper mantle strongly heterogeneous at any scale, and cannot account for the widespread carbon supersaturation of the recovered igneous products. Here we review the global He–Ar–CO2 dataset of fluid inclusions in mid-ocean-ridge glasses using the framework of advanced modelling of multicomponent bubble growth in magmas. We display that non-equilibrium fractionations among He, Ar and CO2, driven by their different diffusivities in silicate melts, are common in most of the natural conditions of magma decompression and their signature strongly depends on pressure of degassing. Due to the comparable Ar and CO2 diffusivity, magma degassing at low pressure fractionates both the He/Ar and He/CO2 ratio by a similar extent, while the slower CO2 diffusion at high pressure causes early kinetic effects on Ar/CO2 ratio and dramatically changes the degassing path. On this ground, the very different geochemical signatures among suites of data coming from different ridge segments mainly depend on the depth of the magma chamber where the melt was stored. Besides, the variations inside a single suite highlight variable ascent speed and cooling rate of the emplaced lava. The large variations in both the He/CO2 and Ar/CO2 ratios at almost constant He/Ar, displayed in glasses coming from the Mid-Atlantic Ridge 24–30 N segment and the Rodriguez Triple Junction, are therefore interpreted as a high-pressure signature. In contrast, the simultaneous increase in both He/CO2 and He/Ar of the East Pacific Rise, Pito Seamount and South-East Indian Ridge data sets suggests the dominance of low-pressure fractionation, implying that the shallow magma chambers are at a lower depth than those of the Mid- Atlantic Ridge 24–30 N and Rodriguez Triple Junction. Our conclusions support the presence of a relationship between spreading rate and depth of high-temperature zones below ridges, and are consistent with the depth of magma chambers as suggested from seismic studies. Non-equilibrium degassing explains the volatile systematics of mid-ocean-ridge basalts by starting from a single mantle-derived magma, dispensing with the supposed need for heterogeneities in abundance ratios of volatiles in the mantle below oceanic ridges.
    Description: Published
    Description: 1747–1763
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: nonequilibrium degassing ; MORB mantle ; geochemical modeling ; fluid inclusions ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 12
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    Looking into a volcanic area: An overview on the 350 m scientific drilling at Colli (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: A 350m deep boreholewas drilled in the Colli Albani volcanic district (Central Italy) in order to: understand the shallow crust structure beneath the volcanic complex; characterize the rock physical properties especially through in-situ measurements and, afterward, laboratory experiments; assess the local present-day stress field; install a broad-band seismometer at depth. The borehole is located adjacent to the western rim of the Tuscolano–Artemisio caldera, where several phenomena of unrest recently occurred. In 1989–90 a seismic swarm affected this area and a related uplift was recognized. In addition, high gas concentrations (mainly CO2 and H2S), in aquifers and soils, caused illnesses and casualties among inhabitants and animals in the past. We describe the investigations carried out at the drill site and the results achieved from data analysis.Wire-line drilling produced a complete stratigraphic record of the Quaternary volcanic units down to the Plio–Pleistocene sedimentary sequence and geophysical logs allowed a characterization of the rock physical properties. From a tectonic point of view, data provided by Dipmeter and Borehole Televiewer were used for investigations on the recent and present-day stress field and the results are compared to those available in the literature. In the volcanic units we recognized two main fracture systems, SW and NW dipping. Several faults intersecting the borehole showplaneswith oblique striae, indicating a prevalent strike–slip component of the movement. Finally, borehole breakout analysis defined an active stress field with a ∼E–Woriented minimum horizontal component. At the end of the drilling, a blow-out occurred, due to pressurized fluids trapped into the sandy unit drilled in the last fewmeters of the hole. Sampling these fluids gave an additional value to the borehole, providing information about the deep volcanic circulation and its possible connection to a deep-seated magma chamber. The main results show water with a Na–HCO3 chemistry and the highest salinity ever recognised in the area (Electrical Conductivity=10.12 mS/cm). Stable O and H isotopes reveal ameteoric origin ofwater and the absence of tritium points out a long residence time in the aquifer. Emitted gas is CO2-dominated, with N2 as second most important component. Helium isotopic composition of the gas allows us to estimate a magmatic component ranging in the interval 40–50%, one of the highest in the Colli Albani. Carbon isotopes of CO2 (−0.53‰ vs. PDB) suggest that it could derive partly froma magmatic source and partly by the thermal decarbonation of the carbonatic basement.
    Description: Published
    Description: 225-240
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: scientific drilling ; volcanic stratigraphy ; wireline logs ; fluid geochemistry ; Italy ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 13
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    Intrusion of eccentric dikes: The case of the 2001 eruption and its role in the dynamics of Mt. Etna volcano (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The 2001 eruption represents one of the most studied events both from volcanological and geophysical point of view on Mt. Etna. This eruption was a crucial event in the recent dynamic of the volcano, marking the passage from a period (March 1993 – June 2001) of moderate stability with slow, continuous flank sliding and contemporaneous summit eruptions, to a period (July 2001 to present) of dramatically increased flank deformations and flank eruptions. We show new GPS data and high precision relocation of seismicity in order to demonstrate the role of the 2001 intrusive phase in this change of the dynamic regime of the volcano. GPS data consist of two kinematic surveys carried out on 12 July, a few hours before the beginning of the seismic swarm, and on 17 July, just after the onset of eruptive activity. A picture of the spatial distribution of the sin-eruptive seismicity has been obtained using the HypoDD relocation algorithm based on the double-difference (DD) technique. Modeling of GPS measurements reveal a southward motion of the upper southern part of the volcano, driven by a NNW-SSE structure showing mainly left-lateral kinematics. Precise hypocenter location evidences an aseismic zone at about sea level, where the magma upraise was characterized by a much higher velocity and an abrupt westward shift, revealing the existence of a weakened or ductile zone. These results reveal how an intrusion of a dike can severely modify the shallow stress field, triggering significant flank failure. In 2001, the intrusion was driven by a weakened surface, which might correspond to a decollement plane of the portion of the volcano affected by flank instability, inducing an additional stress testified by GPS measurements and seismic data, which led to an acceleration of the sliding flanks.
    Description: In press
    Description: 1.1. TTC - Monitoraggio sismico del territorio nazionale
    Description: 1.3. TTC - Sorveglianza geodetica delle aree vulcaniche attive
    Description: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: 4.2. TTC - Scenari e mappe di pericolosità sismica
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: 4.4. Scenari e mitigazione del rischio ambientale
    Description: JCR Journal
    Description: reserved
    Keywords: Stress release ; Dike ; Volcano-tectonics ; Flank instability ; Mount Etna ; Instrumental monitoring ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes ; 04. Solid Earth::04.02. Exploration geophysics::04.02.99. General or miscellaneous ; 04. Solid Earth::04.03. Geodesy::04.03.99. General or miscellaneous ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring ; 04. Solid Earth::04.03. Geodesy::04.03.07. Satellite geodesy ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 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 ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 14
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    Structural features of the 2007 Stromboli eruption (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: On 27 February 2007, two NE–SW and NNW–SSE dike-fed effusive vents opened to the North (at 650 and 400 m above sea level, asl) of the summit craters at Stromboli, forming a fissure parallel to the inner walls of the Sciara del Fuoco (SdF) sector collapse depression. The formation of these vents was soon followed by rapid subsidence of the summit crater area. This partly obstructed the central conduit, temporarily choking the fissure and increasing the deformation of the upper part of SdF. The reactivation of the NNW–SSE vent and the opening of a new vent located at 500 m asl, fed by a second dike, released the internal pressure and surface deformation ceased. The eruption then continued again from the 400 m vent, after a summit explosion on 15 March, until ending in early April after a progressive decrease of magma output. Repeated NE–SW dike intrusions have occurred in recent years, close to the upper SE limit of the SdF. In that zone, named Bastimento, the eruptive fractures traced the discontinuities that borders the SdF, increasing the risk of triggering new sector collapse. Whereas the NE–SW trending structures lie along the regional volcanostructural trend of the Aeolian arc through Stromboli, the NNW–SSE vents are oblique to this trend and may be controlled by the anomalous stress field within the unstable flank of the SdF. Another fundamental aspect of the 2007 eruption is the collapse of the central conduit, due to the rapid and deep magma drainage linked to the opening of the 400 m vent. The intrusion of dikes and development of flank vents during the 2007 eruption could possibly have triggered catastrophic landslides and related tsunami or eruptive paroxysms, but the opening of new effusive vents released the internal pressures, diminishing the hazard.
    Description: In press
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: reserved
    Keywords: 2007 Stromboli eruption ; Dike-fed vent ; Volcano-Tectonics ; Conduit collapse ; Flank instability ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.08. Volcanic arcs ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.08. Risk::05.08.99. General or miscellaneous
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  • 15
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    Comparison between different methodologies for detecting Radon in soil along an active fault: the case of the Pernicana fault system, Mt. Etna (Italy) (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Three different methodologies were used to measure Radon (222Rn) in soil, based on both passive and active detection system. The first technique consisted of Solid State Nuclear Track Detectors (SSNTD), CR-39 type, and allowed integrated measurements. The second one consisted of a portable device for short time measurements. The last consisted of a continuous measurement device for extended monitoring, placed in selected sites. Soil 222Rn activity was measured together with soil Thoron (220Rn) and soil carbon dioxide (CO2) efflux, and it was compared with the content of radionuclides in the rocks. Two different soil gas horizontal transects were investigated across the Pernicana fault system (NE flank of Mount Etna), from November 2006 to April 2007. The results obtained with the three methodologies are in a general agreement with each other and reflect the tectonic settings of the investigated study area. The lowest 222Rn values were recorded just on the fault plane, and relatively higher values were recorded a few tens of meters from the fault axis on both of its sides. This pattern could be explained as a dilution effect resulting from high rates of soil CO2 efflux. Time variations of 222Rn activity were mostly linked to atmospheric influences, whereas no significant correlation with the volcanic activity was observed. In order to further investigate regional radon distributions, spot measurements were made to identify sites having high Rn emissions that could subsequently be monitored for temporal radon variations.. SSNTD measurements allow for extended-duration monitoring of a relatively large number of sites, although with some loss of temporal resolution due to their long integration time. Continuous monitoring probes are optimal for detailed time monitoring, but because of their expense, they can best be used to complement the information acquired with SSNTD in a network of monitored sites.
    Description: In press
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 4.4. Scenari e mitigazione del rischio ambientale
    Description: 4.5. Degassamento naturale
    Description: JCR Journal
    Description: reserved
    Keywords: Soil Radon and Thoron activity ; soil CO2 efflux ; Pernicana fault system ; Mount Etna ; volcano-tectonic monitoring ; 03. Hydrosphere::03.04. Chemical and biological::03.04.07. Radioactivity and isotopes ; 03. Hydrosphere::03.04. Chemical and biological::03.04.08. Instruments and techniques ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration ; 04. Solid Earth::04.02. Exploration geophysics::04.02.05. Downhole, radioactivity, remote sensing, and other methods ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.06. Rheology, friction, and structure of fault zones ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 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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  • 16
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    An exceptional case of endogenous lava dome growth (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: During an eruption at the Bocca Nuova, one of the summit craters of Mt. Etna, in October-November 1999 a part of the crater floor near its WNW rim was uplifted to form a dome-shaped feature that consisted of older lava and pyroclastics filling the crater. This endogenous dome grew rapidly over the crater rim, thus being perched precariously over the steep outer slope of the Bocca Nuova, and near-continuous collapse of its steep flanks generated swiftly moving pyroclastic avalanches over a period of several hours. These avalanches advanced at speeds of 10-20 m s-1 and extended up to 0.7 km from their source on top of lavas emplaced immediately before. Their deposits were subsequently covered by lava flows that issued from vents below the front of the dome and from the Bocca Nuova itself. Growth of the dome was caused by the vertical intrusion of magma in the marginal W part of the crater, which deformed and uplifted previously emplaced, still hot and plastically deformable eruptive products filling the crater. The resulting avalanches had all characteristics of pyroclastic flows spawned by collapse of unstable flanks of lava domes, but in this case the magma involved was of mafic (hawaiitic) composition and would have, under normal circumstances, produced fluid lava flows. The formation of the dome and the generation of the pyroclastic avalanches owe their occurrence to the rheological properties of the eruptive products filling the crater, which were transformed into the dome, and to the morphological configuration of the Bocca Nuova and its surroundings. The density contrast between successive erupted products may also have played a role. Although events of this type are to be considered exceptional at Etna, their recurrence might represent a serious hazard to visitors to the summit area.
    Description: Published
    Description: 115-128
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: JCR Journal
    Description: reserved
    Keywords: Mt. Etna ; Bocca Nuova ; endogenous lava dome ; pyroclastic avalanches ; magma ascent ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 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::05.02.03. Volcanic eruptions ; 05. General::05.08. Risk::05.08.99. General or miscellaneous
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  • 17
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    Magma dynamics during the 2007 Stromboli eruption (Aeolian Islands. Italy): mineralogical, geochemical and isotopic data (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: After the 6 month-long effusive event of 2002-2003, a new lava effusion occurred at Stromboli between 27 February and 2 April 2007. Despite the different durations, approximately the same volume of magma was emitted in both eruptions, in the order of 107 m3 . A paroxysmal eruption occurred at the summit craters in both the 2002–2003 and 2007 episodes, during which a significant amount of low porphyritic (LP), volatile- rich magma was erupted. In both cases, the paroxysm did not interrupt the lava emission. Here, we present compositional data, including texture, mineralogy, chemistry and Sr and Nd isotope ratios of bulk-rock, groundmass and separated minerals of lavas erupted in 2007, together with chemistry and Sr and Nd isotope composition of the pumices emitted during the 15 March paroxysm. As a whole, the lavas have the same texture and chemistry that characterize the highly porphyritic (HP) products usually erupted at Stromboli during normal Strombolian activity and effusive events. Compared to the previous HP products, the 2007 lavas show minor but systematic mineralogical and isotopic variations which are consistent with a modest increase of the magma supply rate of the volcano. Compositional variations during the entire duration of the event are very modest. Glass chemistry changes in lavas erupted in the second half of March can be explained by theminormixing between the volatile-rich LPmagma rising through the shallowmagmatic systemduring the 15 March paroxysm and the degassed residing HP magma. A first conclusion of this study is that there is no compositional evidence supporting major changes in the magma dynamics of the volcano accompanying the effusive activity, as also suggested for the 2002–2003 event. The activity of Stromboli is controlled by a steady state feeding system in which refilling, mixing, degassing and crystallization at shallow level continuously operate,withmodest oscillations in themagma supply rate. Switching between normal Strombolian and effusive activity is related to periods of relatively more vigorous refilling of the shallow system, leading to progressive pressure increase in the upper conduits associated with only minor compositional variations in the erupted products.
    Description: Published
    Description: 255–268
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli volcano ; petrological monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 18
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    Effects of wall-rock elasticity on magma flow in dykes during explosive eruptions (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Magma flow during explosive volcanic eruptions has been described assuming rigid conduits with simple cylindrical or planar geometries. Here we study the dynamics of explosive volcanic flows to take account of the role of elastic deformation of the conduit influenced by local magmatic pressure. Three cases are investigated: a dyke with elliptical cross-section, a cylindrical conduit and a deep dyke connected to a shallow cylinder. The model CPIUC (Macedonio et al., 2005) was used for simulations and generalized to account for elastic deformations of the conduit cross-section area due to magmatic overpressure. Fragmentation level is typically deeper in a dyke than in a cylinder. For flows in wide dykes pressure at the fragmentation depth can be lower than the surrounding lithostatic pressure by several tens of MPa, indicating that the wall-rocks of the dyke will be unstable, constraining the dyke width and eventually blocking the eruption. On the other hand, when the fragmentation level is shallow the corresponding lithostatic pressure is not large enough to close the dyke and eruptions from wide dykes are possible. The behaviour changes drastically when we assume the conduit is a dyke at depth that evolves to a cylinder near the surface. In this case even very wide dykes can be stable because the fragmentation level moves into the cylindrical region where deformation is negligible.
    Description: Published
    Description: 455–462
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: conduit geometry ; explosive eruption ; elastic effect ; dyke deformation ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.06. Rheology, friction, and structure of fault zones ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 19
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    Dike propagation in volcanic edifices: Overview and possible developments (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Eruptions are often fed by dikes; therefore, better knowledge of dike propagation is necessary to improve our understanding of how magma is transferred and extruded at volcanoes. This study presents an overview of dike patterns and the factors controlling dike propagation within volcanic edifices. Largely based on published data, three main types of dikes (regional, circumferential and radial) are illustrated and discussed. Dike pattern data from 25 volcanic edifices in different settings are compared to derive semi-quantitative relationships between the topography (relief, shape, height, and presence of sector collapses) of the volcano, tectonic setting (presence of a regional stress field), and mean composition (SiO2 content). The overview demonstrates how dike propagation in a volcano is not a random process; rather, it depends from the following factors (listed in order of importance): the presence of relief, the shape of the edifice and regional tectonic control. We find that taller volcanoes develop longer radial dikes, whose (mainly lateral) propagation is independent of the composition of magma or the aspect ratio of the edifice. Future research, starting from these preliminary evaluations, should be devoted to identifying dike propagation paths and likely locations of vent formation at specific volcanoes, to better aid hazards assessment.
    Description: In press
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: open
    Keywords: dikes ; volcanoes ; topography ; tectonic setting ; eruptions ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 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::05.02.03. Volcanic eruptions
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  • 20
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    Sub-surface dynamics and eruptive styles of maars in the Colli Albani Volcanic District, Central Italy (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Eruptive scenarios associated with the possible reactivation of maar-forming events in the Quaternary, ultrapotassic Colli Albani Volcanic District (CAVD) provides implications for volcanic hazard assessment in the densely populated area near Rome. Based on detailed stratigraphy, grain size, componentry, ash morphoscopy and petro-chemical analyses of maar eruption products, along with textural analysis of cored juvenile clasts, we attempt to reconstruct the eruptive dynamics of the Prata Porci and Albano maars, as related to pre- and syn-eruptive interactions between trachybasaltic to K-foiditic feeder magmas and carbonate–silicoclastic and subvolcanic country rocks. Magma volumes in the order of 0.5–3.1×108 m3 were erupted during the monogenetic Prata Porci maar activity and the three eruptive cycles of the Albano multiple maar, originating loose to strongly lithified, wet and dry pyroclastic surge deposits, Strombolian scoria fall horizons and lithic-rich explosion breccias. These deposits contain a wide range of accessory and accidental lithic clasts, with significant vertical stratigraphic variations in the lithic types and abundances. The two maar study cases hold a record of repeated transitions between magmatic (i.e, Strombolian fallout) and hydromagmatic (wet and dry pyroclastic surges) activity styles. Evidence of phreatic explosions, a common precursor of explosive volcanic activity, is only found at the base of the Prata Porci eruptive succession. The quantitative evaluation of the proportions of the different eruptive styles in the stratigraphic record of the two maars, based on magma vs. lithic volume estimates, reveals a prevailing magmatic character in terms of erupted magma volumes despite the hydromagmatic footprint. Different degrees of explosive magma–water interaction were apparently controlled by the different hydrogeological and geological–structural settings. In the Prata Porci case, shifts in the depth of magma fragmentation are proposed to have accompanied eruption style changes. In the Albano case, a deeply dissected geothermal aquifer in peri-caldera setting and variable mass eruption rates were the main controlling factors of repeated shifts in the eruptive style. Finally, textural evidence from cored juvenile clasts and analytical modeling of melt–solid heat transfer indicate that the interacting substrate in the Prata Porci case was at low, uniform temperature (~ 100 °C) as compared to the highly variable temperatures (up to 700–800 °C) inferred for the geothermal system beneath Albano.
    Description: In press
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: Maar ; Colli Albani ; eruptive styles ; explosive activity ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 21
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    Chronology of the 2007 eruption of Stromboli and the activity 1 of the Scientific Synthesis Group (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: On 27 February 2007, at 12.49 GMT, a new eruption of Stromboli took place with the effusion of a 15 lava flow from a fracture cutting the flank of the NE cone, which rapidly reached the sea. The eruption 16 had been heralded by an increase in the amplitude of tremor and flank movement since at least the 14th 17 of February. Short-term precursors were an increase in the rate of occurrence of small landslides within 18 the “Sciara del Fuoco” scar on the North-western flank of the volcano. A new effusive vent opened at 19 18.30 GMT on the Sciara del Fuoco at an height of 400 m asl. The new lava emission caused the 20 sudden termination of the summit flow and initiated a period of non-stationary lava outpouring which 21 ended on 2 April, 2007. The eruption has been characterized by a rapid decrease in the eruption rate after the first days and subsequently by episodic pulse increases. On the 15th 22 of March, the increase in 23 lava outpouring, monitored by a thermal camera, heralded by 9 minutes the occurrence of a violent 24 paroxysmal explosion with the formation of an impulsive eruption column and the emission of small 25 pumices mingled with black scoriae. The pumice had a bulk composition similar to that of the lava and 26 of the black scoriae, but with a distinct lower content of phenocrysts. A similar feature has been 27 repeateadly observed during the major explosive paroxysms of Stromboli. Short term precursors of the 28 paroxysm were recorded by strainmeter and tiltmeter stations. The volcano monitoring activity has 29 been made by a joint team of researchers from the INGV sections of Catania, Napoli, Palermo and 30 Rome, along with researchers from the University of Florence, Pisa, Roma Tre, and Palermo. The 31 scientific activity was coordinated by a Synthesis Group made up by the responsibles of the different 32 monitoring techniques of INGV and Universities and by the volcanic experts of Commissione Nazionale Grandi Rischi of the Prime Minister Office (Civil Protection Department). 33 The group made a 34 daily evaluation of the state of the volcano and transmitted its recommendations to the Civil Protection 35 Department (DPC). Several prevention measures were adopted by DPC, the main of which were the 36 evacuation of the coast zone when strong acceleration of the Sciara del Fuoco slope motion (occurred 37 twice) could led to a dangerous tsunami by flank collapse (as last occurred on 30 December 2002) and 38 four days before the 15 March paroxysm when access was prohibited to the part of the volcano above 39 290m asl
    Description: In press
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: open
    Keywords: Stromboli volcano ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 22
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    Dike propagation in volcanic edifices: Overview and possible developments (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Eruptions are fed by dikes; therefore, better knowledge of dike propagation is necessary to improve our understanding of how magma is transferred and extruded at volcanoes. This study presents an overview of dike patterns and the factors controlling dike propagation within volcanic edifices. Largely based on published data, three main types of dikes (regional, circumferential and radial) are illustrated and discussed. Dike pattern data from 25 volcanic edifices in different settings are compared to derive semi-quantitative relationships between the topography (relief, shape, height, and presence of sector collapses) of the volcano, tectonic setting (presence of a regional stress field), and mean composition (SiO2 content). The overview demonstrates how dike propagation in a volcano is not a random process; rather, it depends from the following factors (listed in order of importance): the presence of relief, the shape of the edifice and regional tectonic control. We find that taller volcanoes develop longer radial dikes, whose (mainly lateral) propagation is independent of the composition of magma or the aspect ratio of the edifice. Future research, starting from these preliminary evaluations, should be devoted to identifying dike propagation paths and likely locations of vent formation at specific volcanoes, to better aid hazards assessment.
    Description: Partly fundedwith DPC-INGVfunds (LAVAProject).
    Description: Published
    Description: 67–77
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: dikes ; volcanoes ; topography ; tectonic setting ; eruptions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 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::05.02.99. General or miscellaneous ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 05. General::05.08. Risk::05.08.99. General or miscellaneous
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  • 23
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    Intrusion of eccentric dikes: The case of the 2001 eruption and its role in the dynamics of Mt. Etna volcano (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The 2001 eruption represents one of the most studied events both from volcanological and geophysical point of view on Mt. Etna. This eruption was a crucial event in the recent dynamics of the volcano, marking the passage from a period (March 1993–June 2001) of moderate stability with slow, continuous flank sliding and contemporaneous summit eruptions, to a period (July 2001 to present) of dramatically increased flank deformations and flank eruptions. We show new GPS data and high precision relocation of seismicity in order to demonstrate the role of the 2001 intrusive phase in this change of the dynamic regime of the volcano. GPS data consist of two kinematic surveys carried out on 12 July, a few hours before the beginning of the seismic swarm, and on 17 July, just after the onset of eruptive activity. A picture of the spatial distribution of the sin-eruptive seismicity has been obtained using the HypoDD relocation algorithm based on the double-difference (DD) technique. Modeling of GPS measurements reveals a southward motion of the upper southern part of the volcano, driven by a NNW–SSE structure showing mainly left-lateral kinematics. Precise hypocenter location evidences an aseismic zone at about sea level, where the magma upraise was characterized by a much higher velocity and an abrupt westward shift, revealing the existence of a weakened or ductile zone. These results reveal how an intrusion of a dike can severely modify the shallow stress field, triggering significant flank failure. In 2001, the intrusion was driven by a weakened surface, which might correspond to a decollement plane of the portion of the volcano affected by flank instability, inducing an additional stress testified by GPS measurements and seismic data, which led to an acceleration of the sliding flanks.
    Description: This work was funded by the Istituto Nazionale di Geofisica e Vulcanologia and by the Dipartimento per la Protezione Civile (Italy).
    Description: Published
    Description: 78–86
    Description: 1.3. TTC - Sorveglianza geodetica delle aree vulcaniche attive
    Description: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.2. Tettonica attiva
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: reserved
    Keywords: stress release ; dike ; volcano-tectonics ; flank instability ; Mt. Etna ; instrumental monitoring ; 04. Solid Earth::04.01. Earth Interior::04.01.99. General or miscellaneous ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes ; 04. Solid Earth::04.02. Exploration geophysics::04.02.99. General or miscellaneous ; 04. Solid Earth::04.03. Geodesy::04.03.99. General or miscellaneous ; 04. Solid Earth::04.03. Geodesy::04.03.07. Satellite geodesy ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 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::05.02.99. General or miscellaneous ; 05. General::05.02. Data dissemination::05.02.02. Seismological data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 24
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    Paleo-environmental and volcano-tectonic evolution of the southeastern £ank of Mt. Etna during the last 225 ka inferred from the volcanic succession of the ‘Timpe’, Acireale, Sicily (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The tectonic escarpments locally known as ‘Timpe’ cut a large sector of the eastern flank of Etna, and allow an ancient volcanic succession dating back to 225 ka to be exposed. Geological and volcanological investigations carried out on this succession have allowed us to recognize relevant angular unconformities and volcanic features which are the remnants of eruptive fissures, as well as important changes in the nature, composition and magmatic affinity of the exposed volcanics. In particular, the recognition in the lower part of the succession of important and unequivocal evidence of ancient eruptive fissures led us to propose a local origin for these volcanics and to revise previous interpretations which attributed their westward-dipping to the progressive tectonic tilting of strata. These elements led us to reinterpret the main features of the volcanic activity occurring since 250 ka BP and their relationship with tectonic structures active in the eastern flank of Etna. We propose a complex paleo-environmental and volcanotectonic evolution of the southeastern flank of Mt. Etna, in which the Timpe fault system played the role of the crustal structure that allowed the rise and eruption of magmas in the above considered time span.
    Description: Published
    Description: 289-306
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: Mount Etna ; tectonics ; fisssure eruptions ; columnar basalt ; fault escarpment ; xenoliths ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.03. Geomorphology ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.04. Geology::04.04.06. Rheology, friction, and structure of fault zones ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.04. Geology::04.04.11. Instruments and techniques ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 04. Solid Earth::04.07. Tectonophysics::04.07.04. Plate boundaries, motion, and tectonics ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 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 ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 25
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    On the fractal dimension of the fallout deposits: A case study of the 79 A.D. Plinian eruption at Mt. Vesuvius (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We investigated the existence of a fractal law (power law) distribution of size pyroclastic fragments erupted during the fallout phase of the 79 A.D. Plinian eruption at Mt. Vesuvius. In particular, we performed a particle size distribution analysis on 18 white and grey pumice samples collected in six sites distributed in the SW sector of Mt. Vesuvius. Our measurements show that the fragmentation of samples in the investigated range (from 32 mm to 850 μm) follows a power law, guaranteeing the scale invariance of the process. The relationship frequency-size distribution of the fragments is verified independently from the nature (i.e., pumices and lithics) and stratigraphic height of the considered samples in the pyroclastic deposit. Therefore, the fractal fragmentation theory can be indicated for evaluating the relationship between the intensity of fragmentation (fractal dimension D) and eruption energy. In this way the apparent chaotic distribution of the particles in the fallout deposits hides a self-organized complexity revealed by the retrieved power law distribution. We further remark that a key aspect of our analysis is the founded evidence that the fractal dimension of the lithics is systematically greater than that of the pumices.
    Description: Published
    Description: 288–299
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: fragmentation ; power law distribution ; fractal dimension ; scale invariant ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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  • 26
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    The Afragola settlement near Vesuvius, Italy: The destruction and abandonment of a Bronze Age village revealed by archaeology, volcanology and rock-magnetism (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Public works in progress in the Campanian plain north of Somma- ^ Vesuvius recently encountered the remains 15 of a prehistoric settlement close to the town of Afragola. Rescue excavations brought to light a Bronze Age 16 village partially destroyed and buried by pyroclastic density currents (PDCs) of the Vesuvian Pomici di 17 Avellino eruption (3. ^ 8 14C ka BP) and subsequently sealed by alluvial deposits. Volcanological and rock- 18 ^ magnetic investigations supplemented the excavations. 19 Careful comparison between volcanological and archaeological stratigraphies led to an understanding of the 20 timing of the damage the buildings suffered when they were struck by a series of PDCs. The first engulfed the 21 village, located some 15 km to the north of the inferred vent, and penetrated into the dwellings without 22 causing major damage. The buildings were able to withstand the weak dynamic pressure of the currents and 23 deviate their path, as shown by the magnetic fabric analyses. Some later collapsed under the load of the 24 deposits piled up by successive currents. Stepwise demagnetization of the thermal remanent magnetization 25 (TRM) carried by potsherds embedded in the deposits yields deposition temperatures in the order of 260– 26 ^ 320 °C, fully consistent with those derived from pottery and lithic fragments from other distal and proximal 27 sites. The fairly uniform temperature of the deposits is here ascribed to the lack of pervasive air entrainment 28 into the currents. This, in turn, resulted from the lack of major topographical obstacles along the flat plain. 29 The coupling of structural damage and sedimentological analyses indicates that the currents were not 30 destructive in the Afragola area, but TRM data indicate they were still hot enough to cause death or severe 31 injury to humans and animals. The successful escape of the entire population is apparent from the lack of 32 human remains and from thousands of human footprints on the surface of the deposits left by the first PDCs. 33 People were thus able to walk barefoot across the already emplaced deposits and escape the subsequent 34 PDCs. The rapid cooling of the deposits was probably due to both their thinness and heat dissipation due to 35 condensation of water vapour released in the mixture by magma–water interaction
    Description: In press
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: pyroclastic density current ; Bronze Age ; magnetic fabric ; deposition temperature ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.05. Geomagnetism::04.05.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 27
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    First combined flux chamber survey of mercury and CO2 emissions from soil diffuse degassing at Solfatara of Pozzuoli crater, Campi Flegrei (Italy): Mapping and quantification of gas release (2015)
    Elsevier | Elsevier Science Limited
    Details
    Publication Date: 2017-04-04
    Description: There have been limited studies to date targeting gaseous elemental mercury (GEM) flux from soil emission in enriched volcanic substrates and its relation with CO2 release and tectonic structures. In order to evaluate and understand the processes of soil–air exchanges involved at Solfatara of Pozzuoli volcano, the most active zone of Campi Flegrei caldera (Italy), an intensive field measurement survey has been achieved in September 2013 by using high-time resolution techniques. Soil–air exchange fluxes of GEM and CO2 have been measured simultaneously at 116 points, widely distributed within the crater. Quantification of gas flux has been assessed by using field accumulation chamber method in conjunction with a Lumex®-RA 915 + portable mercury vapor analyzer and a LICOR for CO2 determination, respectively. The spatial distribution of GEM and CO2 emissions correlated quite closely with the hydrothermal and geological features of the studied area. The highest GEM fluxes (from 4.04 to 5.9 × 10− 5 g m− 2 d− 1) were encountered close to the southern part of the crater interested by an intense fumarolic activity and along the SE–SW tectonic fracture (1.26 × 10− 6–6.91 × 10− 5 g GEM m− 2 d− 1). Conversely, the lowest values have been detected all along the western rim of the crater, characterized by a weak gas flux and a lush vegetation on a very sealed clay soil, which likely inhibited mercury emission (range: 1.5 × 10− 7–7.18 × 10− 6 g GEM m− 2 d− 1). Results indicate that the GEM exchange between soil and air inside the Solfatara crater is about 2–3 orders of magnitude stronger than that in the background areas (10− 8–10− 7 g m− 2 d− 1). CO2 soil diffuse degassing exhibited an analogous spatial pattern to the GEM fluxes, with emission rates ranging from about 15 to ~ 20,000 g CO2 m− 2 d− 1, from the outermost western zones to the south-eastern sector of the crater. The observed significant correlation between GEM and CO2 suggested that in volcanic system GEM volatilizes from substrate in a similar manner to the release of CO2. The quantitative estimation of the total amount of CO2 and GEM released from the Solfatara crater gave values of about 304 ± 13 and 3.7 ± 0.2 × 10− 6 t d− 1, respectively. Finally, based on our dataset and previous work, we propose that an average GEM/CO2 molar ratio of ~ 2 × 10− 8 (n = 9) is best representative of hydrothermal degassing. Taking into account the uncertainty in global hydrothermal CO2 emissions from sub-aerial environments (~ 1012 Mol yr− 1), we infer a global volcanic GEM flux from hydrothermal environments of ~ about 8.5 t yr− 1. Although this value has to be considered as a lower limit for the global emission of GEM from these sources, we suggest that on a local scale hydrothermal activity can be regarded as a significant source of GEM than previously recognized to the atmospheric pool.
    Description: Published
    Description: 26-40
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: restricted
    Keywords: Flux Chamber Survey ; Mercury ; CO2 emissions ; Solfatara ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 28
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    "Explosive Energy" during volcanic eruptions from fractal analysis of pyroclasts (2006)
    Elsevier
    Details
    Publication Date: 2020-01-08
    Description: Despite recent advances by means of experiments and high-resolution surveys and the growing understanding of the physical processes before and during volcanic eruptions, duration and type of eruptive activity still remain highly unpredictable. This uncertainty hinders appropriate hazard and associated risk assessment tremendously. In an effort to counter this problem, experimentally generated pyroclasts have been studied by fractal statistics with the aim of evaluating possible relationships between eruption energy and fragmentation efficiency. Rapid decompression experiments have been performed on three differently porous sample sets of the 1990–1995 eruption of Unzen volcano (Japan) at 850 °C and at initial pressure values above the respective fragmentation threshold [U. Kueppers, B. Scheu, O. Spieler, D. B. Dingwell, Fragmentation efficiency of explosive volcanic eruptions: a study of experimentally generated pyroclasts. J. Volcanol. Geotherm. Res. 153 (2006) 125–135.,O. Spieler, B. Kennedy, U. Kueppers, D.B. Dingwell, B. Scheu, J. Taddeucci, The fragmentation threshold of pyroclastic rocks. EPSL 226 (2004) 139–148.]. The size distribution of generated pyroclasts has been studied by fractal fragmentation theory and the fractal dimension of fragmentation (Df), a value quantifying the intensity of fragmentation, has been measured for each sample. Results showthat size distribution of pyroclastic fragments follows a fractal law(i.e. power-law) in the investigated range of fragment sizes, indicating that fragmentation of experimental samples reflects a scale-invariant mechanism. In addition, Df is correlated positively with the potential energy for fragmentation (PEF) while showing a strong influence of the open porosity of the samples. Results obtained in this work indicate that fractal fragmentation theory may allow for quantifying fragmentation processes during explosive volcanic eruptions by calculating the fractal dimension of the size distribution of pyroclasts. It emerges fromthis study that fractal dimension may be utilised as a proxy for estimating the explosivity of volcanic eruptions by analysing their natural pyroclastic deposits.
    Description: Published
    Description: 800-807
    Description: open
    Keywords: volcanic fragmentation ; simulation of eruptions ; explosive energy ; pyroclasts ; fragment size distribution ; fractal fragmentation theory ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 29
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    8th Silicate Melt Workshop (2008)
    Elsevier
    Details
    Publication Date: 2020-02-24
    Description: Preface
    Description: Published
    Description: 77-79
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: Silicate Melt Workshop ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 30
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    FALL3D: A Computational Model for Trans-port and Deposition of Volcanic Ash (2008)
    Elsevier
    Details
    Publication Date: 2020-03-19
    Description: FALL3D is a 3-D time-dependent Eulerian model for the transport and deposition of 8 volcanic ash. The model solves the advection-diffusion-sedimentation (ADS) equa- 9 tion on a structured terrain-following grid using a second-order Finite Differences 10 (FD) explicit scheme. Different parameterizations for the eddy diffusivity tensor 11 and for the particle terminal settling velocities can be used. The code, written 12 in FORTRAN 90, is available in both serial and parallel versions for Windows and 13 Unix/Linux/Mac X Operating Systems (OS). A series of pre- and post-process util- 14 ity programs and OS-dependent scripts to launch them are also included in the 15 FALL3D distribution package. Although the model has been designed to forecast 16 volcanic ash concentration in the atmosphere and ash loading at ground, it can also 17 be used to model the transport of any kind of airborne solid particles. The model 18 inputs are meteorological data, topography, grain-size distribution, shape and den- 19 sity of particles, and mass rate of particle injected into the atmosphere. Optionally, 20 FALL3D can be coupled with the output of the meteorological processor CALMET, a 21 diagnostic model which generates 3-D time-dependent zero-divergence wind fields 22 from mesoscale forecasts incorporating local terrain effects. The FALL3D model can 23 be a tool for short-term ash deposition forecasting and for volcanic fallout hazard 24 assessment. As an example, an application to the 22 July 1998 Etna eruption is also 25 presented.
    Description: Published
    Description: 1334–1342
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: open
    Keywords: volcanic ash ; fallout ; computational model ; FORTRAN code ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.01. Computational geophysics::05.01.99. General or miscellaneous
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  • 31
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    Heterogeneities in magma chambers: Insights from the behavior of major and minor elements during mixing experiments with natural alkaline melts (2008)
    Elsevier
    Details
    Publication Date: 2020-01-08
    Description: We present new electron microprobe and Sr-isotope analytical results from mixing experiments using natural volcanic samples. In order to constrain the dynamics of such mixing events, we applied a Taylor– Couette flow, simulating forced convection under very low Reynolds numbers, in a time series ranging from 1 h up to 1 week. The end-member melts derive from samples of the Campanian Ignimbrite (CI), in Italy. The CI is thought to represent a layered reservoir formed in 3 stages: 1) a resident phono-trachytic magma reservoir (end-member A); replenished by 2) a less evolved trachybasaltic–trachytic magma (endmember B of trachytic composition); 3) short-term pre-eruptive mixing in the shallow chamber between a new trachytic and the phono-trachytic resident magmas. Our experiments are motivated by this hypothesis. The two end-members are stirred together, under constant low flow velocity (0.5 rotations per minute). This initially generates single convection cells, which cause progressive homogenization of some major components. This is the case after 1, 4 and 9 h. After 16 h the 87Sr/86Sr-isotopic system is homogenized and the starting compositions are fully mixed. Then separate convection cells and compositional layering for major and minor elements emerged. Based on microprobe measurements of quenched melts (glass) from the 16-hour, 25-hour and 1-week long experiments, we confirm the separation of layers having different densities. This phenomenon is locally complicated by the production of micro-volumes of unmixed melts. Our results support the effectiveness of the interplay between convection and diffusion, enhanced by a double-diffusive–convection-driven differentiation for moderately high-silica magmas under high (nearliquidus) temperatures, attesting that differentiation initiates in the liquidus before the onset of fractional crystallization.
    Description: Published
    Description: 131-145
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: reserved
    Keywords: Magma mixing ; Experiments ; Major and minor elements ; Advection/diffusion ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
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  • 32
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    Transient 3D numerical simulations of column collapse and pyroclastic density current scenarios at Vesuvius (2008)
    Elsevier
    Details
    Publication Date: 2021-09-20
    Description: Numerical simulations of column collapse and pyroclastic density current (PDC) scenarios at Vesuvius were carried out using a transient 3D flow model based on multiphase transport laws. The model describes the complex dynamics of the collapse as well as the effects of the 3D topography of the volcano on PDC propagation. Source conditions refer to a medium-scale sub-Plinian event and consider a pressure-balanced jet. Simulation results provide new insights into the complex dynamics of these phenomena. In particular: 1) column collapse can be characterized by different regimes, from incipient collapse to partial or nearly total collapse, thus confirming the possibility of a transitional field of behaviour of the column characterized by the contemporaneous and/or intermittent occurrence of ash fallout and PDCs; 2) the collapse regime can be characterized by its fraction of eruptive mass reaching the ground and generating PDCs; 3) within the range of the investigated source conditions, the propagation and hazard potential of PDCs appear to be directly correlated with the flow-rate of the mass collapsing to the ground, rather than to the collapse height of the column (this finding is in contrast with predictions based on the energy-line concept, which simply correlates the PDC runout and kinetic energy with the collapse height of the column); 4) first-order values of hazard variables associated with PDCs (i.e., dynamic pressure, temperature, airborne ash concentration) can be derived from simulation results, thereby providing initial estimates for the quantification of damage scenarios; 5) for scenarios assuming a location of the central vent coinciding with that of the present Gran Cono, Mount Somma significantly influences the propagation of PDCs, largely reducing their propagation in the northern sector, and diverting mass toward the west and southeast, accentuating runouts and hazard variables for these sectors; 6) the 2D modelling approximation can force an artificial radial propagation of the PDCs since it ignores azimuthal flows produced by real topographies that therefore need to be simulated in fully 3D conditions.
    Description: Published
    Description: 378-396
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: reserved
    Keywords: Vesuvius ; pyroclastic density current ; column collapse ; numerical simulation ; 3D modelling ; hazard assessment ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 33
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    Sub-surface dynamics and eruptive styles of maars in the Colli Albani Volcanic District, Central Italy (2009)
    Elsevier
    Details
    Publication Date: 2021-12-15
    Description: Eruptive scenarios associated with the possible reactivation of maar-forming events in the Quaternary, ultrapotassic Colli Albani Volcanic District (CAVD) provides implications for volcanic hazard assessment in the densely populated area near Rome. Based on detailed stratigraphy, grain size, componentry, ash morphoscopy and petro-chemical analyses of maar eruption products, along with textural analysis of cored juvenile clasts, we attempt to reconstruct the eruptive dynamics of the Prata Porci and Albano maars, as related to pre- and syn-eruptive interactions between trachybasaltic to K-foiditic feeder magmas and carbonate–silicoclastic and subvolcanic country rocks. Magma volumes in the order of 0.5–3.1×108 m3 were erupted during the monogenetic Prata Porci maar activity and the three eruptive cycles of the Albano multiple maar, originating loose to strongly lithified, wet and dry pyroclastic surge deposits, Strombolian scoria fall horizons and lithic-rich explosion breccias. These deposits contain a wide range of accessory and accidental lithic clasts, with significant vertical stratigraphic variations in the lithic types and abundances. The two maar study cases hold a record of repeated transitions between magmatic (i.e, Strombolian fallout) and hydromagmatic (wet and dry pyroclastic surges) activity styles. Evidence of phreatic explosions, a common precursor of explosive volcanic activity, is only found at the base of the Prata Porci eruptive succession. The quantitative evaluation of the proportions of the different eruptive styles in the stratigraphic record of the two maars, based on magma vs. lithic volume estimates, reveals a prevailing magmatic character in terms of erupted magma volumes despite the hydromagmatic footprint. Different degrees of explosive magma–water interaction were apparently controlled by the different hydrogeological and geological–structural settings. In the Prata Porci case, shifts in the depth of magma fragmentation are proposed to have accompanied eruption style changes. In the Albano case, a deeply dissected geothermal aquifer in peri-caldera setting and variable mass eruption rates were the main controlling factors of repeated shifts in the eruptive style. Finally, textural evidence from cored juvenile clasts and analytical modeling of melt–solid heat transfer indicate that the interacting substrate in the Prata Porci case was at low, uniform temperature (~ 100 °C) as compared to the highly variable temperatures (up to 700–800 °C) inferred for the geothermal system beneath Albano.
    Description: Protezione Civile, Italy 2004–2006 Agreement with Istituto Nazionale di Geofisica e Vulcanologia— INGV, project V3_1
    Description: Published
    Description: 189-202
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: maar ; hydromagmatic eruption ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Thinking beside the box: Should we care about the non-coding strand of the 16S rRNA gene? (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-31
    Description: The 16S rRNA gene (16S rDNA) codes for RNA that plays a fundamental role during translation in the ribosome and is used extensively as a marker gene to establish relationships among bacteria. However, the complementary non-coding 16S rDNA (nc16S rDNA) has been ignored. An idea emerged in the course of analyzing bacterial 16S rDNA sequences in search for nucleotide composition and substitution patterns: Does the nc16S rDNA code? If so, what does it code for? More importantly: Does 16S rDNA evolution reflect its own evolution or the evolution of its counterpart nc16S rDNA? The objective of this minireview is to discuss these thoughts. nc strands often encode small RNAs (sRNAs), ancient components of gene regulation. nc16S rDNA sequences from different bacterial groups were used to search for possible matches in the Bacterial Small Regulatory RNA Database. Intriguingly, the sequence of one published sRNA obtained from Legionella pneumophila (GenBank: AE017354.1) showed high non-random similarity with nc16S rDNA corresponding in part to the V5 region especially from Legionella and relatives. While the target(s) of this sRNA is unclear at the moment, its mere existence might open up a new chapter in the use of the 16S rDNA to study relationships among bacteria.
    Keywords: Physiology & Biochemistry
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    Morphological and enzymatic response of the thermotolerant fungus Fomes sp. EUM1 in solid state fermentation under thermal stress (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-05
    Description: Thermotolerance of the fungus Fomes sp. EUM1 was evaluated in solid state fermentation (SSF). This thermotolerant strain improved both hyphal invasiveness (38%) and length (17%) in adverse thermal conditions exceeding 30°C and to a maximum of 40°C. In contrast, hyphal branching decreased by 46% at 45°C. The production of cellulases over corn stover increased 1.6-fold in 30°C culture conditions, xylanases increased 2.8-fold at 40°C, while laccase production improved 2.7-fold at 35°C. Maximum production of lignocellulolytic enzymes was obtained at elevated temperatures in shorter fermentation times (8–6 days), although the proteases appeared as a thermal stress response associated with a drop in lignocellulolytic activities. Novel and multiple isoenzymes of xylanase (four bands) and cellulase (six bands) were secreted in the range of 20–150 kDa during growth in adverse temperature conditions. However, only a single laccase isoenzyme (46 kDa) was detected. This is the first report describing the advantages of a thermotolerant white-rot fungus in SSF. These results have important implications for large-scale SSF, where effects of metabolic heat are detrimental to growth and enzyme production, which are severely affected by the formation of high temperature gradients.
    Keywords: Physiology & Biochemistry
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    Analysis of a new cluster of genes involved in the synthesis of the unique volatile organic compound sodorifen of Serratia plymuthica 4Rx13 (2016)
    Oxford University Press
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    Publication Date: 2016-06-23
    Description: The rhizobacterium Serratia plymuthica 4Rx13 emits the novel and unique volatile sodorifen (C 16 H 26 ), which has a polymethylated bicyclic structure. Transcriptome analysis revealed that gene SOD_c20750 (annotated as terpene cyclase) is involved in the biosynthesis of sodorifen. Here we show that this gene is located in a small cluster of four genes ( SOD_c20750 – SOD_c20780 ), and the analysis of the knockout mutants demonstrated that SOD_c20760 (annotated as methyltransferase) and SOD_c20780 (annotated as isopentenyl pyrophosphate (IPP) isomerase) are needed for the biosynthesis of sodorifen, while a sodorifen-negative phenotype was not achieved with the SOD_c20770 (annotated as deoxy-xylulose-5-phosphate (DOXP) synthase) mutant. Altogether, the function of this new gene cluster was assigned to the biosynthesis of this structurally unusual volatile compound sodorifen.
    Keywords: Physiology & Biochemistry
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    D-serine transporter in Staphylococcus saprophyticus identified (2016)
    Oxford University Press
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    Publication Date: 2016-06-23
    Description: Among staphylococci Staphylococcus saprophyticus is the only species that is typically uropathogenic and an important cause of urinary tract infections in young women. The amino acid D-serine occurs in relatively high concentrations in human urine and has a bacteriostatic or toxic effect on many bacteria. In uropathogenic Escherichia coli and S. saprophyticus , the amino acid regulates the expression of virulence factors and can be used as a nutrient. The ability of uropathogens to respond to or to metabolize D-serine has been suggested as a factor that enables colonization of the urinary tract. Until now nothing is known about D-serine transport in S.   saprophyticus . We generated mutants of putative transporter genes in S.   saprophyticus 7108 that show homology to the D-serine transporter cyc A of E. coli and tested them in a D-serine depletion assay to analyze the D-serine uptake rate of the cells. The mutant of SPP1070 showed a strong decrease in D-serine uptake. Therefore, SSP1070 was identified as a major D-serine transporter in S. saprophyticus 7108 and was named D-serine transporter A (DstA). D-serine caused a prolonged lag phase of S. saprophyticus in a chemically defined medium. This negative effect was dependent on the presence of DstA.
    Keywords: Physiology & Biochemistry
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    Contribution of chloride channel permease to fluoride resistance in Streptococcus mutans (2016)
    Oxford University Press
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    Publication Date: 2016-05-12
    Description: Genes encoding fluoride transporters have been identified in bacterial and archaeal species. The genome sequence of the cariogenic  Streptococcus mutans  bacteria suggests the presence of a putative fluoride transporter, which is referred to as a chloride channel permease. Two homologues of this gene (GenBank locus tags SMU_1290c and SMU_1289c) reside in tandem in the genome of  S. mutans . The aim of this study was to determine whether the chloride channel permeases contribute to fluoride resistance. We constructed SMU_1290c- and SMU_1289c-knockout  S. mutans  UA159 strains. We also constructed a double-knockout strain lacking both genes. SMU_1290c or SMU_1289c was transformed into a fluoride transporter- disrupted  Escherichia coli strain. All bacterial strains were cultured under appropriate conditions with or without sodium fluoride, and fluoride resistance was evaluated. All three gene-knockout  S. mutans  strains showed lower resistance to sodium fluoride than did the wild-type strain. No significant changes in resistance to other sodium halides were recognized between the wild-type and double-knockout strains. Both SMU_1290c and SMU_1289c transformation rescued fluoride transporter-disrupted  E. coli  cell from fluoride toxicity. We conclude that the chloride channel permeases contribute to fluoride resistance in  S. mutans .
    Keywords: Physiology & Biochemistry
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    Nicotinamide cofactor ratios in engineered strains of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum (2016)
    Oxford University Press
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    Publication Date: 2016-05-12
    Description: Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are bacteria under investigation for production of biofuels from plant biomass. Thermoanaerobacterium saccharolyticum has been engineered to produce ethanol at high yield (〉90% of theoretical) and titer (〉70 g/l). Efforts to engineer C. thermocellum have not, to date, been as successful, and efforts are underway to transfer the ethanol production pathway from T. saccharolyticum to C. thermocellum . One potential challenge in transferring metabolic pathways is the possibility of incompatible levels of nicotinamide cofactors. These cofactors (NAD + , NADH, NADP + and NADPH) and their oxidation state are important in the context of microbial redox metabolism. In this study we directly measured the concentrations and reduced oxidized ratios of these cofactors in a number of strains of C. thermocellum and T. saccharolyticum by using acid/base extraction and enzymatic assays. We found that cofactor ratios are maintained in a fairly narrow range, regardless of the metabolic network modifications considered. We have found that the ratios are similar in both organisms, which is a relevant observation in the context of transferring the T. saccharolyticum ethanol production pathway to C. thermocellum .
    Keywords: Physiology & Biochemistry
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    Cadmium-induced cell killing in Sacharomyces cerevisiae involves increases in intracellular NO levels (2016)
    Oxford University Press
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    Publication Date: 2016-03-09
    Description: Cadmium is a widespread environmental pollutant and poses some potential risks to human health. However, the signaling events controlling cadmium toxicity are not fully understood. In this study, we examined the effect of cadmium chloride on cell viability and the intracellular nitric oxide (NO) level in yeast cells. The results showed that exposure of yeast cells to cadmium (0–100 μM) could induce cell killing with significantly increased intracellular NO levels. Morphological analysis of the nuclei with 4 ' ,6-diamidino-2-phenylindole staining and DNA strand breaks analysis showed that cadmium at 50 μM can induce cell apoptosis in yeast cells. Treatment of yeast cells with cadmium (50 μM) and the nitric oxide scavenger c-PTIO [2-(4-carboxyphenyl)-4,4,5,5-teramethylimidazoline-1-oxyl-3-oxide; 0.2 mM] showed that c-PTIO attenuated the cadmium-induced cell killing. Our findings indicated that cadmium-induced yeast cell killing is mediated by a directly increased intracellular NO level.
    Keywords: Physiology & Biochemistry
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    Identification of a glucose-mannose phosphotransferase system in Clostridium beijerinckii (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: Effective uptake of fermentable substrates is a fundamentally important aspect of any fermentation process. The solventogenic bacterium Clostridium beijerinckii is noted for its ability to ferment a wide range of carbohydrates, yet few of its sugar transport systems have been characterized. In common with other anaerobes, C. beijerinckii shows a marked dependence on the PEP-dependent phosphotransferase system (PTS) for sugar accumulation. In this study, the gene cbe0751 encoding the sugar-specific domains of a phosphotransferase belonging to the glucose family was cloned into an Escherichia coli strain lacking the ability to take up and phosphorylate glucose. Transformants gained ability to ferment glucose, and also mannose, and further analysis of a selected transformant demonstrated that it could take up and phosphorylate glucose, confirming that cbe0751 encodes a glucose PTS which also recognizes mannose as a substrate. RT-PCR analysis showed that cbe0751 was expressed in cultures grown on both substrates, but also to varying extents during growth on some other carbon sources. Although analogue inhibition studies suggested that Cbe0751 is not the only glucose PTS in C. beijerinckii , this system should nevertheless be regarded as a potential target for metabolic engineering to generate a strain showing improved sugar fermentation properties.
    Keywords: Physiology & Biochemistry
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    Heavy metal resistance in halophilic Bacteria and Archaea (2016)
    Oxford University Press
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    Publication Date: 2016-06-30
    Description: Heavy metals are dense chemicals with dual biological role as micronutrients and intoxicants. A few hypersaline environmental systems are naturally enriched with heavy metals, while most metal-contaminated sites are a consequence of human activities. Numerous halotolerant and moderately halophilic Bacteria possess metal tolerance, whereas a few archaeal counterparts share similar features. The main mechanisms underlying heavy metal resistance in halophilic Bacteria and Archaea include extracellular metal sequestration by biopolymers, metal efflux mediated by specific transporters and enzymatic detoxification. Biotransformation of metals by halophiles has implications both for trace metal turnover in natural saline ecosystems and for development of novel bioremediation strategies.
    Keywords: Physiology & Biochemistry
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    An ABC transporter involved in the control of streptomycin production in Streptomyces griseus (2016)
    Oxford University Press
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    Publication Date: 2016-06-30
    Description: We screened for a gene that inhibits streptomycin production in Streptomyces griseus when it is introduced on a high-copy-number plasmid pIJ702, and obtained a plasmid pKM545. The introduction of pKM545 abolished streptomycin production on all media tested including YMP-sugar and Nutrient broth. S1 protection analysis demonstrated that the introduction of this plasmid downregulated the transcriptional activity of the promoter preceding strR , the pathway-specific transcriptional regulator for streptomycin biosynthesis. The 2.8-kb Bam HI fragment cloned onto pKM545 contained two coding sequences SGR_5442 and 5443. These coding sequences and the two downstream ones (SGR_5444 and 5445) constituted a possible operon structure designated to be rspABCD (regulation of streptomycin production). RspB and RspC exhibited a marked similarity with an ATP-binding domain and a membrane-associating domain of an ABC-2 type transporter, respectively, suggesting that the Rsp proteins comprise a membrane exporter. The gene cluster consisting of the rsp operon and the upstream divergent small coding sequence (SGR_5441) was widely distributed to Streptomyces genome. An rspB mutant of S. griseus produced 3-fold streptomycin of the parental strain in YMP liquid medium. The evidence implies that the Rsp translocator is involved in the export of a substance that specifies the expression level of streptomycin biosynthesis genes in S. griseus .
    Keywords: Physiology & Biochemistry
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    Roles of two-component system AfsQ1/Q2 in regulating biosynthesis of the yellow-pigmented coelimycin P2 in Streptomyces coelicolor (2016)
    Oxford University Press
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    Publication Date: 2016-07-02
    Description: We previously demonstrated that in Streptomyces coelicolor two-component system AfsQ1/Q2 activates the production of the yellow-colored coelimycin P2 (also named as yCPK) on glutamate-supplemented minimal medium, and the response regulator AfsQ1 could specifically bind to the intergenic region between two structural genes, cpkA and cpkD . Here, a more in-depth investigation was performed to elucidate the mechanism underlying the role of AfsQ1/Q2 in regulating coelimycin P2 biosynthesis. Deletion of afsQ1/Q2 resulted in markedly decreased expression of the whole coelimycin P2 biosynthetic gene cluster. Electrophoretic mobility shift assays revealed that AfsQ1 bound only to the target site identified previously, but not to any other promoters in the gene cluster. Mutations of AfsQ1-binding motif only resulted in drastically reduced transcription of the cpkA/B/C operon (encoding three type I polyketide synthases) and intriguingly, led to enhanced expression of some coelimcyin P2 genes, particularly accA1 and scF . These results suggested the direct role of AfsQ1/Q2 in regulating coelimycin production, which is directly mediated by the structural genes, but not the cluster-situated regulatory genes, and also implied that other unknown mechanisms may be involved in AfsQ1/Q2-mediated regulation of coelimycin P2 biosynthesis.
    Keywords: Physiology & Biochemistry
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    Nitrate reduction in sulfate-reducing bacteria (2016)
    Oxford University Press
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    Publication Date: 2016-07-02
    Description: Sulfate-reducing bacteria (SRBs) gain their energy by coupling the oxidation of organic substrate to the reduction of sulfate to sulfide. Several SRBs are able to use alternative terminal electron acceptors to sulfate such as nitrate. Nitrate-reducing SRBs have been isolated from a diverse range of environments. In order to be able to understand the significance of nitrate reduction in SRBs, we need to examine the ecology and physiology of the nitrate-reducing SRB isolates.
    Keywords: Physiology & Biochemistry
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    The NarE protein of Neisseria gonorrhoeae catalyzes ADP-ribosylation of several ADP-ribose acceptors despite an N-terminal deletion (2016)
    Oxford University Press
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    Publication Date: 2016-08-18
    Description: The ADP-ribosylating enzymes are encoded in many pathogenic bacteria in order to affect essential functions of the host. In this study, we show that Neisseria gonorrhoeae possess a locus that corresponds to the ADP-ribosyltransferase NarE, a previously characterized enzyme in N. meningitidis . The 291 bp coding sequence of gonococcal narE shares 100% identity with part of the coding sequence of the meningococcal narE gene due to a frameshift previously described, thus leading to a 49-amino-acid deletion at the N-terminus of gonococcal NarE protein. However, we found a promoter region and a GTG start codon, which allowed expression of the protein as demonstrated by RT-PCR and western blot analyses. Using a gonococcal NarE–6xHis fusion protein, we demonstrated that the gonococcal enzyme underwent auto-ADP-ribosylation but to a lower extent than meningococcal NarE. We also observed that gonoccocal NarE exhibited ADP-ribosyltransferase activity using agmatine and cell-free host proteins as ADP-ribose acceptors, but its activity was inhibited by human β-defensins. Taken together, our results showed that NarE of Neisseria gonorrhoeae is a functional enzyme that possesses key features of bacterial ADP-ribosylating enzymes.
    Keywords: Physiology & Biochemistry
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    Inhibition by fructose 1,6-bisphosphate of transaldolase from Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-08-18
    Description: The effect of fructose 1,6-bisphosphate (Fru 1,6-P 2 ) on the regulatory enzymes of pentose phosphate pathway of Escherichia coli was examined. Fru 1,6-P 2 inhibited E. coli transaldolase (EC 2.2.1.2) competitively against fructose 6-phosphate and uncompetitively against erythrose 4-phosphate, whereas Fru 1,6-P 2 did not affect glucose 6-phosphate dehydrogenase (EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (EC 1.1.1.44). Kinetic results can be explained by assuming that transaldolase has two kinds of binding sites for Fru 1,6-P 2 : a competitive binding site for fructose 6-phosphate and a second binding site on the enzyme-erythrose 4-phosphate complex. Fru 1,6-P 2 increased resulting from the stimulation of glycolysis, can inhibit transaldolase and further participates in the elevation of the concentration of ribose 5-phosphate that can be preferentially utilized for anabolic reaction in exponential phase of E. coli .
    Keywords: Physiology & Biochemistry
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    Microbial oxidative sulfur metabolism: biochemical evidence of the membrane-bound heterodisulfide reductase-like complex of the bacterium Aquifex aeolicus (2016)
    Oxford University Press
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    Publication Date: 2016-07-03
    Description: The Hdr (heterodisulfide reductase)-like enzyme is predicted, from gene transcript profiling experiments previously published, to be essential in oxidative sulfur metabolism in a number of bacteria and archaea. Nevertheless, no biochemical and physicochemical data are available so far about this enzyme. Genes coding for it were identified in Aquifex aeolicus , a Gram-negative, hyperthermophilic, chemolithoautotrophic and microaerophilic bacterium that uses inorganic sulfur compounds as electron donor to grow. We provide biochemical evidence that this Hdr-like enzyme is present in this sulfur-oxidizing prokaryote (cultivated with thiosulfate or elemental sulfur). We demonstrate, by immunolocalization and cell fractionation, that Hdr-like enzyme is associated, presumably monotopically, with the membrane fraction. We show by co-immunoprecipitation assay or partial purification, that the Hdr proteins form a stable complex composed of at least five subunits, HdrA, HdrB1, HdrB2, HdrC1 and HdrC2, present in two forms of high molecular mass on native gel (~240 and 450 kDa). These studies allow us to propose a revised model for dissimilatory sulfur oxidation pathways in A. aeolicus , with Hdr predicted to generate sulfite.
    Keywords: Physiology & Biochemistry
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    Global transcriptional start site mapping in Geobacter sulfurreducens during growth with two different electron acceptors (2016)
    Oxford University Press
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    Publication Date: 2016-08-11
    Description: Geobacter sulfurreducens is an anaerobic soil bacterium that is involved in biogeochemical cycles of elements such as Fe and Mn. Although significant progress has been made in the understanding of the electron transfer processes in G. sulfurreducens , little is known about the regulatory mechanisms involved in their control. To expand the study of gene regulation in G. sulfurreducens , we carried out a genome-wide identification of transcription start sites (TSS) by 5'RACE and by deep RNA sequencing of primary mRNAs in two growth conditions. TSSs were identified along G. sulfurreducens genome and over 50% of them were located in the upstream region of the associated gene, and in some cases we detected genes with more than one TSS. Our global mapping of TSSs contributes with valuable information, which is needed for the study of transcript structure and transcription regulation signals and can ultimately contribute to the understanding of transcription initiation phenomena in G. sulfurreducens .
    Keywords: Physiology & Biochemistry
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    Membrane localization and topology of the DnpA protein control fluoroquinolone tolerance in Pseudomonas aeruginosa (2016)
    Oxford University Press
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    Publication Date: 2016-08-27
    Description: DnpA, a putative de- N -acetylase of the PIG-L superfamily, is required for antibiotic tolerance in Pseudomonas aeruginosa . Exactly how dnpA (gene locus PA5002) directs the formation of antibiotic-tolerant persister cells is currently unknown. Previous research provided evidence for a role in surface-associated process(es), possibly in lipopolysaccharide biosynthesis. In silico sequence analysis of DnpA predicts a single transmembrane domain and N in /C out orientation of DnpA. In contrast, we here show that DnpA is an integral inner membrane protein containing two transmembrane domains, with the major C-terminal part located at the cytoplasmic face. Correct insertion into the inner membrane is necessary for DnpA to promote fluoroquinolone tolerance. The membrane localization of DnpA further supports its role in cell envelope-associated process(es). In addition to shedding light on the biological role of DnpA, this study highlights the risks of overreliance on the predictive value of bioinformatics tools and the importance of rigorous experimental validation of in silico predictions.
    Keywords: Physiology & Biochemistry
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    Identification of a multidrug efflux pump in Mycobacterium smegmatis (2016)
    Oxford University Press
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    Publication Date: 2016-06-08
    Description: Cell wall impermeability and active efflux of drugs are among the primary reasons for drug resistance in mycobacteria. Efflux pumps are tripartite membrane localized transport proteins that expel drug molecules outside the cells. Several of such efflux pumps are annotated in mycobacteria, but few have been characterized, like MSMEG_2991, a putative efflux pump permease of Mycobacterium smegmatis . To substantiate this, we overexpressed MSMEG_2991 protein in Escherichia coli 2443. Expression of MSMEG_2991 elevated the resistance towards structurally unrelated groups of antibiotics. An active antibiotic efflux pump nature of MSMEG_2991 was revealed by assessing the acquisition of ciprofloxacin in the absence and presence of the efflux pump inhibitor, carbonyl cyanide m-chlorophenyl hydrazone, indicating the involvement of proton-motive force (pmf) during the efflux activity. MSMEG_2991 expression elevated biofilm formation in E. coli by 4-fold, keeping parity to some of the earlier reported efflux pumps. In silico analysis suggested the presence of 12 transmembrane helices in MSMEG_2991 resembling EmrD efflux pump of E. coli . Based on in vivo and in silico analyses, MSMEG_2991 may be designated as a pmf-mediated multidrug efflux pump protein that expels diverse groups of antibiotics and might as well be involved in the biofilm enhancement.
    Keywords: Physiology & Biochemistry
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    A new custom microarray for sRNA profiling in Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-06-08
    Description: Bacterial small RNAs (sRNAs) play essential roles in the post-transcriptional control of gene expression. To improve their detection by conventional microarrays, we designed a custom microarray containing a group of probes targeting known and some putative Escherichia coli sRNAs. To assess its potential in detection of sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells exponentially grown in rich (Luria–Bertani) and minimal (M9/glucose) media. We found that many sRNAs could yield reasonably strong and statistically significant signals corresponding to nearly all sRNAs annotated in the EcoCyc database. Besides differential expression of two sRNAs (GcvB and RydB), expression of other sRNAs was less affected by the composition of the growth media. Other examples of the differentially expressed sRNAs were revealed by comparing gene expression of the wild-type strain and its isogenic mutant lacking functional poly(A) polymerase I ( pcnB ). Further, northern blot analysis was employed to validate these data and to assess the existence of new putative sRNAs. Our results suggest that the use of custom microarrays with improved capacities for detection of sRNAs can offer an attractive opportunity for efficient gene expression profiling of sRNAs and their target mRNAs at the whole transcriptome level.
    Keywords: Physiology & Biochemistry
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    Identification of essential arginine residues of Escherichia coli DedA/Tvp38 family membrane proteins YqjA and YghB (2016)
    Oxford University Press
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    Publication Date: 2016-06-08
    Description: Escherichia coli DedA/Tvp38 family proteins YghB and YqjA are putative membrane transporters with 62% amino acid identity and overlapping functions. An E. coli strain (BC202) with nonpolar yghB and yqjA mutations displays cell-division defects and temperature sensitivity and is sensitive to antibiotics and alkaline pH. In this study, we performed site-directed mutagenesis on conserved, charged amino acids of YqjA and YghB. We discovered two conserved predicted membrane-embedded arginines (R130 and R136) that are critical for function in both proteins as defined by their ability to complement BC202 phenotypes, when expressed from a plasmid. Lysine can substitute for arginine at position R130 indicating a charge dependence at this position, but could not substitute at R136. In light of the established role that arginine plays in the translocation mechanism of numerous membrane transporters, we hypothesize that these amino acids play a role in the transport mechanism of these DedA/Tvp38 family proteins.
    Keywords: Physiology & Biochemistry
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    Boric acid-dependent decrease in regulatory histone H3 acetylation is not mutagenic in yeast (2016)
    Oxford University Press
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    Publication Date: 2016-06-02
    Description: Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations . The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.
    Keywords: Physiology & Biochemistry
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    The global regulator CodY is required for the fitness of Bacillus cereus in various laboratory media and certain beverages (2016)
    Oxford University Press
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    Publication Date: 2016-06-02
    Description: The impact of gene mutations on the growth of the cells can be studied using pure cultures. However, the importance of certain proteins and pathways can be also examined via co-culturing wild type and its mutant derivative. Here, the relative fitness of a mutant strain that lacks the global nitrogen regulator, CodY, was examined in Bacillus cereus , a food poisoning Gram-positive bacterium. Fitness measurements revealed that the codY strain was outcompeted when cocultured with the wild-type ATCC 14579 under various rich laboratory medium, and also when inoculated in certain beverages. In nutrient-poor minimal medium, the codY mutant had comparable fitness to the wild-type strain. Interestingly, the relative fitness of the codY strain was antagonistic when it was cultivated in apple or orange juices due to unknown properties of these beverages, highlighting the importance of chemical composition of the test medium during the bacterial fitness measurements.
    Keywords: Physiology & Biochemistry
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    Biofilm formation-defective mutants in Pseudomonas putida (2016)
    Oxford University Press
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    Publication Date: 2016-06-04
    Description: Out of 8000 candidates from a genetic screening for Pseudomonas putida KT2442 mutants showing defects in biofilm formation, 40 independent mutants with diminished levels of biofilm were analyzed. Most of these mutants carried insertions in genes of the lap cluster, whose products are responsible for synthesis, export and degradation of the adhesin LapA. All mutants in this class were strongly defective in biofilm formation. Mutants in the flagellar regulatory genes fleQ and flhF showed similar defects to that of the lap mutants . On the contrary, transposon insertions in the flagellar structural genes fliP and flgG , that also impair flagellar motility, had a modest defect in biofilm formation. A mutation in gacS , encoding the sensor element of the GacS/GacA two-component system, also had a moderate effect on biofilm formation. Additional insertions targeted genes involved in cell envelope function: PP3222, encoding the permease element of an ABC-type transporter and tolB , encoding the periplasmic component of the Tol-OprL system required for outer membrane stability. Our results underscore the central role of LapA, suggest cross-regulation between motility and adhesion functions and provide insights on the role of cell envelope trafficking and maintenance for biofilm development in P. putida .
    Keywords: Physiology & Biochemistry
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    Bioluminescence-based system for rapid detection of natural transformation (2016)
    Oxford University Press
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    Publication Date: 2016-06-04
    Description: Horizontal gene transfer plays a significant role in bacterial evolution and has major clinical importance. Thus, it is vital to understand the mechanisms and kinetics of genetic transformations. Natural transformation is the driving mechanism for horizontal gene transfer in diverse genera of bacteria. Our study introduces a simple and rapid method for the investigation of natural transformation. This highly sensitive system allows the detection of a transformation event directly from a bacterial population without any separation step or selection of cells. The system is based on the bacterial luciferase operon from Photorhabdus luminescens . The studied molecular tools consist of the functional modules luxCDE and luxAB , which involve a replicative plasmid and an integrative gene cassette. A well-established host for bacterial genetic investigations, Acinetobacter baylyi ADP1, is used as the model bacterium. We show that natural transformation followed by homologous recombination or plasmid recircularization can be readily detected in both actively growing and static biofilm-like cultures, including very rare transformation events. The system allows the detection of natural transformation within 1 h of introducing sample DNA into the culture. The introduced method provides a convenient means to study the kinetics of natural transformation under variable conditions and perturbations.
    Keywords: Physiology & Biochemistry
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    OxyR-regulated catalase activity is critical for oxidative stress resistance, nodulation and nitrogen fixation in Azorhizobium caulinodans (2016)
    Oxford University Press
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    Publication Date: 2016-06-04
    Description: The legume–rhizobial interaction results in the formation of symbiotic nodules in which rhizobia fix nitrogen. During the process of symbiosis, reactive oxygen species (ROS) are generated. Thus, the response of rhizobia to ROS is important for successful nodulation and nitrogen fixation. In this study, we investigated how Azorhizobium caulinodans , a rhizobium that forms both root and stem nodules on its host plant, regulates ROS resistance. We found that in-frame deletions of a gene encoding the putative catalase-peroxidase katG or a gene encoding a LysR-family regulatory protein, oxyR , exhibited increased sensitivity to H 2 O 2 . We then showed that OxyR positively regulated katG expression in an H 2 O 2 -independent fashion. Furthermore, we found that deletion of katG or oxyR led to significant reduction in the number of stem nodules and decrease of nitrogen fixation capacities in symbiosis. Our results revealed that KatG and OxyR are not only critical for antioxidant defense in vitro , but also important for nodule formation and nitrogen fixation during interaction with plant hosts.
    Keywords: Physiology & Biochemistry
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    Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-06-17
    Description: Peptidoglycan (also known as murein) is an important envelope component of bacteria, and its turnover usually takes place at considerable levels during normal growth. Amino sugars and murein tripeptide resulting from murein degradation are used for resynthesis of peptidoglycan or as self-generated nutrients or energy sources for cell growth. PgrR (regulator of peptide glycan recycling; formerly YcjZ) was recently identified as a repressor of several genes participating in uptake and degradation of murein tripeptide. In this study, we identified the ycjG gene involved in murein tripeptide degradation as a new direct target of PgrR. The expression of PgrR-regulated genes including ycjY , mppA , mpaA and ycjG was repressed in the presence of a good nitrogen source, but their expression increased under poor nitrogen conditions. Under nitrogen starvation, the pgrR mutant cells exhibited faster growth than wild-type cells, implying that derepression of genes under the control of PgrR may help cells overcome nitrogen limitation. Therefore, these results suggest that nitrogen starvation induces derepression of PgrR-controlled genes involved in uptake and degradation of murein tripeptide, and this may stimulate the utilization of murein tripeptide as a nitrogen source.
    Keywords: Physiology & Biochemistry
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    In vitro evidence that RNA Polymerase acetylation and acetyl phosphate-dependent CpxR phosphorylation affect cpxP transcription regulation (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: The central metabolite acetyl phosphate (acP) has long been proposed to influence transcription regulation by directly transferring its phosphoryl group to a number of response regulators in many bacterial species. Here, we provide in vitro evidence for this proposition and demonstrate, using an in vitro transcription system, that acP-dependent phosphorylation of aspartate 51 of CpxR induces transcription of one of its regulon members in E. coli , cpxP . We also used this in vitro transcription system to extend our previously reported in vivo data that hypothesized that acetylation of RNA polymerase (RNAP) influences acP-dependent cpxP transcription, using glutamine as a genetic mimic for acetylated arginine 291 of the carboxy-terminal domain of RNAP α subunit. The data we present here lend strong support to the hypothesis that acP has a direct effect on transcription regulation in E. coli via phosphorylation of CpxR, and that RNAP acetylation can modulate this response.
    Keywords: Physiology & Biochemistry
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    CrAgDb--a database of annotated chaperone repertoire in archaeal genomes (2016)
    Oxford University Press
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    Publication Date: 2016-03-02
    Description: Chaperones are a diverse class of ubiquitous proteins that assist other cellular proteins in folding correctly and maintaining their native structure. Many different chaperones cooperate to constitute the ‘proteostasis’ machinery in the cells. It has been proposed earlier that archaeal organisms could be ideal model systems for deciphering the basic functioning of the ‘protein folding machinery’ in higher eukaryotes. Several chaperone families have been characterized in archaea over the years but mostly one protein at a time, making it difficult to decipher the composition and mechanistics of the protein folding system as a whole. In order to deal with these lacunae, we have developed a database of all archaeal chaperone proteins, CrAgDb ( C haperone r epertoire in A rchaeal g enomes). The data have been presented in a systematic way with intuitive browse and search facilities for easy retrieval of information. Access to these curated datasets should expedite large-scale analysis of archaeal chaperone networks and significantly advance our understanding of operation and regulation of the protein folding machinery in archaea. Researchers could then translate this knowledge to comprehend the more complex protein folding pathways in eukaryotic systems. The database is freely available at http://14.139.227.92/mkumar/cragdb/ .
    Keywords: Physiology & Biochemistry
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    Cysteine biosynthesis in Lactobacillus casei: identification and characterization of a serine acetyltransferase (2016)
    Oxford University Press
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    Publication Date: 2016-02-07
    Description: In bacteria, cysteine can be synthesized from serine by two steps involving an L-serine O-acetyltransferase (SAT) and a cysteine synthase (CysK). While CysK is found in the publicly available annotated genome from Lactobacillus casei ATCC 334, a gene encoding SAT ( cysE ) is missing. In this study, we found that various strains of L. casei grew in a chemically defined medium containing sulfide as the sole sulfur source, indicating the presence of a serine O-acetyltransferase. The gene lying upstream of cysK is predicted to encode a homoserine trans-succinylase ( metA ). To study the function of this gene, it was cloned from L. casei FAM18110. The purified, recombinant protein did not acylate L-homoserine in vitro . Instead, it catalyzed the formation of O-acetyl serine from L-serine and acetyl-CoA. Furthermore, the plasmid expressing the L. casei gene complemented an Escherichia coli cysE mutant strain but not an E. coli metA mutant. This clearly demonstrated that the gene annotated as metA in fact encodes the SAT function and should be annotated as cysE .
    Keywords: Physiology & Biochemistry
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    Purification, characterization and physiological significance of a chitinase from the pilei of Coprinopsis cinerea fruiting bodies (2016)
    Oxford University Press
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    Publication Date: 2016-05-25
    Description: We purified a chitinase from pilei extractions of Coprinopsis cinerea fruiting bodies by ammonium sulfate precipitation and CM Sepharose cation exchange chromatography. MALDI-TOF/TOF MS analysis characterized this purified chitinase as a putative class V chitinase, ChiB1. ChiB1 hydrolyzed colloidal chitin and chitosan, whereas it did not hydrolyze chitin powder. ChiB1 cleaved only pNP-(GlcNAc) 2 , rather than pNP-GlcNAc or pNP-(Glc-NAc) 3 , to release nitrophenol. ChiB1 preferably and progressively released (GlcNAc)2 from (GlcNAc)6 and digested (GlcNAc)6 to two molecules of (GlcNAc)3 in a small proportion, but did not split (GlcNAc) 2 , so it is an exochitinase. ChiB1 has an optimum temperature range of 35°C to 40°C and an optimum pH of 5.0. ChiB1 exhibited Km and Vmax values of 2.63 mg ml –1 and 2.31 μmol min –1  mg protein –1 for colloidal chitin, respectively. The ChiB1 gene, along with another putative endochitinase (class III chitinase gene), was expressed dominantly among eight predicted chitinase genes in the genome, and its expression level increased with the maturation of fruiting bodies. ChiB1 incubation released a large amount of soluble β-glucan fractions from alkali-insoluble cell wall fractions of C. cinerea fruiting bodies, thereby it may promote the degradation of cell walls in synergy with the β-1,3-glucanases during pileus autolysis.
    Keywords: Physiology & Biochemistry
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    RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans (2016)
    Oxford University Press
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    Publication Date: 2016-03-24
    Description: Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase ( doxDA genes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase ( hdr genes) rather than sulfur oxygenase reductase ( sor ). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.
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    Watch out for your TRP1 marker: the effect of TRP1 gene on the growth at high and low temperatures in budding yeast (2016)
    Oxford University Press
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    Publication Date: 2016-04-24
    Description: TRP1 is a frequently used auxotrophic marker for genetic modifications and selections in trp – budding yeast strains, including the commonly used wild-type strain W303a. However, we found that introduction of the TRP1 gene into a trp – strain significantly affected vegetative growth at low and high temperatures. Therefore, caution should be needed when working in a trp – background strain and using the TRP1 marker to study stress response phenotypes, particularly when analyzing temperature sensitivities.
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    From CO2 to cell: energetic expense of creating biomass using the Calvin-Benson-Bassham and reductive citric acid cycles based on genome data (2016)
    Oxford University Press
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    Publication Date: 2016-03-18
    Description: The factors driving the dominance of the Calvin–Benson–Bassham cycle (CBB) or reductive citric acid cycle (rCAC) in autotrophic microorganisms in different habitats are debated. Based on costs for synthesizing a few metabolic intermediates, it has been suggested that the CBB poses a disadvantage due to higher metabolic cost. The purpose of this study was to extend this estimate of cost from metabolite synthesis to biomass synthesis. For 12 gammaproteobacteria (CBB) and five epsilonproteobacteria (rCAC), the amount of ATP to synthesize a gram of biomass from CO 2 was calculated from genome sequences via metabolic maps. The eleven central carbon metabolites needed to synthesize biomass were all less expensive to synthesize via the rCAC (66%–89% of the ATP needed to synthesize them via CBB). Differences in cell compositions did result in differing demands for metabolites among the organisms, but the differences in cost to synthesize biomass were small among organisms that used a particular pathway (e.g. rCAC), compared to the difference between pathways (rCAC versus CBB). The rCAC autotrophs averaged 0.195 moles ATP per g biomass, while their CBB counterparts averaged 0.238. This is the first in silico estimate of the relative expense of both pathways to generate biomass.
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    ydfD encodes a novel lytic protein in Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-03-05
    Description: Bacteria carry a number of genes that cause cell growth arrest or cell lysis upon expression. Notably, defective prophages retain many lysis proteins. Here, we identified a novel lytic gene, ydfD , on the Qin prophage segment of the Escherichia coli genome. YdfD lyses 99.9% of cells within 2 h of its induction. The co-expression of the upstream gene, dicB , encoding a cell division inhibitor, as well as sulA , encoding another cell division inhibitor, abolished YdfD-induced cell lysis. These results imply that YdfD-induced lysis is a cell division-dependent event. We further found that by deleting the hydrophobic 22-residue N-terminal domain, the resulting 42-residue C-terminal domain was still toxic to cause cell lysis. We propose that YdfD, associated with the cytoplasmic membrane, inhibits an essential cellular process(s).
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    Accumulation of PHA granules in Cupriavidus necator as seen by confocal fluorescence microscopy (2016)
    Oxford University Press
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    Publication Date: 2016-05-08
    Description: Many bacteria are capable of accumulating intracellular granules of polyhydroxyalkanoates (PHA). In this work, we developed confocal microscopy analysis of bacterial cells to study changes in the diameters of cells as well as PHA granules during growth and PHA accumulation in the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha ). The cell envelope was stained by DiD ® fluorescent probe and PHA granules by Nile Red. Signals from both probes were separated based on their spectral and fluorescence life-time properties. During growth and PHA accumulation, bacterial cells increased their length but the width of the cells remained constant. The volume fraction of PHA granules in cells increased during PHA accumulation, nevertheless, its value did not exceed 40 vol. % regardless of the PHA weight content. It seems that bacterial cultures lengthen the cells in order to control the PHA volume portion. However, since similar changes in cell length were also observed in a PHA non-accumulating mutant, it seems that there is no direct control mechanism, which regulates the prolongation of the cells with respect to PHA granules volume. It is more likely that PHA biosynthesis and the length of cells are influenced by the same external stimuli such as nutrient limitation.
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    Characterization of three positive regulators for tetramycin biosynthesis in Streptomyces ahygroscopicus (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Three putative regulatory genes, namely ttmRI, ttmRII and ttmRIII , which are present in the tetramycin ( ttm ) biosynthetic gene cluster, were found in Streptomyces ahygroscopicus . Disruption of ttmRI, ttmRII or ttmRIII reduced tetramycin production, and their complementation restored production to varying degrees. Gene expression analysis of the wild-type (WT) and mutant strains through reverse transcriptase–polymerase chain reaction (RT-PCR) of the ttm gene cluster showed that the expression levels of most of the biosynthetic genes were reduced in ttmRI , ttmRII and ttmRIII . Electrophoretic mobility shift assays demonstrated that TtmRI, TtmRII and TtmRIII bound the promoters of several genes in the ttm gene cluster. This study found that these three proteins are a group of positive regulators that activate the transcription of the ttm gene cluster in S. ahygroscopicus . In addition, ttmRII had a reduced degree of grey pigmentation. Thus, TtmRII has a pleiotropic regulatory function in the tetramycin biosynthetic pathway and in development.
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    A sulfide:quinone oxidoreductase from Chlorobaculum tepidum displays unusual kinetic properties (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Sulfide:quinone oxidoreductase (SQR) is the primary sulfide-oxidizing enzyme found in all three domains of life. Of the six phylogenetically distinct types of SQR, four have representatives that have been biochemically characterized. The genome of Chlorobaculum tepidum encodes three SQR homologs. One of these, encoded by CT1087, is a type VI SQR that has been previously shown to be required for growth at high sulfide concentrations and to be expressed in sulfide-dependent manner. Therefore, CT1087 was hypothesized to be a high sulfide adapted SQR. CT1087 was expressed in Escherichia coli with an N-terminal His-tag (CT1087NHis 6 ) and purified by Ni-NTA chromatography. CT1087NHis 6 was active and contained FAD as a strongly bound cofactor. The measured kinetic parameters for CT1087NHis 6 indicate a low affinity for sulfide and a high enzymatic turnover rate consistent with the hypothesis for its function inferred from genetic and expression data. These are the first kinetic data for a type VI SQR and have implications for structure-function analyses of all SQR's.
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    Gliding motility driven by individual cell-surface movements in a multicellular filamentous bacterium Chloroflexus aggregans (2016)
    Oxford University Press
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    Publication Date: 2016-04-08
    Description: Chloroflexus aggregans is an unbranched multicellular filamentous bacterium having the ability of gliding motility. The filament moves straightforward at a constant rate, ~3 μm sec –1 on solid surface and occasionally reverses the moving direction. In this study, we successfully detected movements of glass beads on the cell-surface along long axis of the filament indicating that the cell-surface movement was the direct force for gliding. Microscopic analyses found that the cell-surface movements were confined to a cell of the filament, and each cell independently moved and reversed the direction. To understand how the cellular movements determine the moving direction of the filament, we proposed a discrete-time stochastic model; sum of the directions of the cellular movements determines the moving direction of the filament only when the filament pauses, and after moving, the filament keeps the same directional movement until all the cells pause and/or move in the opposite direction. Monte Carlo simulation of this model showed that reversal frequency of longer filaments was relatively fixed to be low, but the frequency of shorter filaments varied widely. This simulation result appropriately explained the experimental observations. This study proposed the relevant mechanism adequately describing the motility of the multicellular filament in C. aggregans .
    Keywords: Physiology & Biochemistry
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    Identification and sequence analysis of pWcMBF8-1, a bacteriocin-encoding plasmid from the lactic acid bacterium Weissella confusa (2016)
    Oxford University Press
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    Publication Date: 2016-04-10
    Description: Members of the Gram-positive lactic acid bacteria (LAB) are well-known for their beneficial properties as starter cultures and probiotics. Many LAB species produce ribosomally synthesized proteinaceous antibiotics (bacteriocins). Weissella confusa MBF8-1 is a strain isolated from a fermented soybean product that not only produces useful exopolysaccharides but also exhibits bacteriocin activity, which we call weissellicin MBF. Here, we show that bacteriocin production by W. confusa MBF8-1 is specified by a large plasmid, pWcMBF8-1. Plasmid pWcMBF8-1 (GenBank accession number KR350502), which was identified from the W. confusa MBF8-1 draft genome sequence, is 17 643 bp in length with a G + C content of 34.8% and contains 25 open reading frames (ORFs). Six ORFs constitute the weissellicin MBF locus, encoding three putative double-glycine-motif peptides (Bac1, Bac2, Bac3), an ABC transporter complex (BacTE) and a putative immunity protein (BacI). Two ORFs encode plasmid partitioning and mobilization proteins, suggesting that pWcMBF8-1 is transferable to other hosts. To the best of our knowledge, plasmid pWcMBF8-1 not only represents the first large Weissella plasmid to be sequenced but also the first to be associated with bacteriocin production in W. confusa .
    Keywords: Physiology & Biochemistry
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    Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source (2016)
    Oxford University Press
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    Publication Date: 2016-04-20
    Description: Small non-coding regulatory RNAs (sRNAs) are key players in post-transcriptional regulation of gene expression. Hundreds of sRNAs have been identified in Sinorhizobium meliloti , but their biological function remains unknown for most of them. In this study, we characterized the expression pattern of the gene encoding the 77-nt sRNA MmgR in S. meliloti strain 2011. A chromosomal transcriptional reporter fusion (P mmgR - gfp ) showed that the mmgR promoter is active along different stages of the interaction with alfalfa roots. In pure cultures, P mmgR - gfp activity paralleled the sRNA abundance indicating that mmgR expression is primarily controlled at the level of transcriptional initiation. P mmgR - gfp activity was higher during growth in rhizobial defined medium (RDM) than in TY medium. Furthermore, P mmgR - gfp was induced at 60 min after shifting growing cells from TY to RDM medium, i.e. shorter than the cell doubling time. In defined RDM medium containing NO 3 – , both P mmgR - gfp and MmgR level were repressed by the addition of tryptone or single amino acids, suggesting that mmgR expression depends on the cellular nitrogen (N) status. In silico analysis failed to detect conserved motifs upstream the promoter RNA polymerase binding site, but revealed a strongly conserved motif centered at –28 that may be linked to the observed regulatory pattern by the N source.
    Keywords: Physiology & Biochemistry
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    Purification, characterization and function analysis of an extracellular {beta}-glucosidase from elongating stipe cell walls in Coprinopsis cinerea (2016)
    Oxford University Press
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    Publication Date: 2016-04-20
    Description: A β-glycoside hydrolase was isolated from cell walls material in Coprinopsis cinerea elongating stipes. By analysis of SDS-PAGE, MALDI-TOF/TOF MS and substrate specificity, this enzyme was characterized as an extracellular β-glucosidase which is a trimer consisting of three homosubunits. β-Glucosidase did not degrade β-glucans with modified ends, whereas it hydrolyzed various β-glucans with free ends and related oligosaccharides with β-1,3-, β-1,4- or β-1,6-linkages. Although this β-glucosidase possesses glycosyltransferase activity on laminarioligosaccharides, it did not transfer glucose residues from laminaritriose to β-glucan in stipe cell walls to produce larger β-glucan molecules; instead, it caused a decrease in the molecular size of stipe wall β-glucan by removing glucose. Relatively, the molecular size of wall β-glucans in the elongating apical stipe was less than that found in the non-elongating basal stipes, and this β-glucosidase was more highly expressed in the elongating apical stipe than in non-elongating basal regions. Therefore, we propose that β-glucosidase functions by trimming or cutting the β-glucan side chains on the β-1,3-glucan backbone to prevent them from forming longer branches, keeping the wall plastic to promote diffuse wall growth.
    Keywords: Physiology & Biochemistry
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    Molecular cloning and biochemical characterization of Xaa-Pro dipeptidyl-peptidase from Streptococcus mutans and its inhibition by anti-human DPP IV drugs (2016)
    Oxford University Press
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    Publication Date: 2016-04-21
    Description: Streptococcus mutans harbours an intracellular, human DPP IV-analogous enzyme Xaa-Pro dipeptidyl-peptidase (EC 3.4.14.11). According to previous reports, an extracellular isozyme in S. gordonii and S. suis has been associated with virulence. Speculating that even an intracellular form may aid in virulence of S. mutans , we have tried to purify, characterize and evaluate enzyme inhibition by specific inhibitors. The native enzyme was partially purified by ion-exchange and gel filtration chromatography. Owing to low yield, the enzyme was overexpressed in Lactococcus lactis and purified by affinity chromatography. The recombinant enzyme (rSm-XPDAP) had a specific activity of 1070 U mg –1 , while the V max and K m were 7 μM min –1 and 89 ± 7 μM ( n = 3), respectively. The serine protease inhibitor phenylmethylsulphonyl fluoride and a DPP IV-specific inhibitor diprotin A proved to be active against rSm-XPDAP. As a novel approach, the evaluation of the effect of anti-human DPP IV (AHD) drugs on rSm-XPDAP activity found saxagliptin to be effective to some extent ( K i = 129 ± 16 μM), which may lead to the synthesis and development of a new class of antimicrobial agents.
    Keywords: Physiology & Biochemistry
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    Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization (2016)
    Oxford University Press
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    Publication Date: 2016-10-22
    Description: The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.
    Keywords: Physiology & Biochemistry
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    Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression (2016)
    Oxford University Press
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    Publication Date: 2016-10-22
    Description: Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644 T , to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against 34 S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in 2 H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.
    Keywords: Physiology & Biochemistry
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    LnqR, a TetR-family transcriptional regulator, positively regulates lacticin Q production in Lactococcus lactis QU 5 (2016)
    Oxford University Press
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    Publication Date: 2016-09-17
    Description: Lacticin Q is an unmodified leaderless bacteriocin produced by Lactococcus lactis QU 5. It has been revealed that the production and self-immunity of lacticin Q are facilitated by a gene cluster lnqQBCDEF . The gene for a putative TetR-family transcriptional regulator, termed lnqR , was found nearby the lnqQBCDEF cluster, but its involvement in lacticin Q biosynthesis remained unknown. In this study, we created an LnqR-overexpressing QU 5 recombinant by using lactococcal constitutive promoter P 32 . The recombinant QU 5 showed enhanced production of and self-immunity to lacticin Q. RT-PCR analysis has revealed that an overexpression of LnqR increases the amounts of lnqQBCDEF transcripts, and these six genes are transcribed as an operon in a single transcriptional unit. Interestingly, LnqR expression and thus lacticin Q production by L. lactis QU 5 was found temperature dependent, while LnzR, an LnqR-homologue, in L. lactis QU 14 was expressed in a similar but not identical manner to LnqR, resulting in dissimilar bacteriocin productivities by these strains. This report demonstrates LnqR as the first TetR-family transcriptional regulator involved in LAB bacteriocin biosynthesis and that, as an exceptional case of TetR-family regulators, LnqR positively regulates the transcription of these biosynthetic genes.
    Keywords: Physiology & Biochemistry
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    Lipoprotein-like particles in a prokaryote: quinone droplets of Thermoplasma acidophilum (2016)
    Oxford University Press
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    Publication Date: 2016-09-09
    Description: Cytosolic, globular droplets with an average diameter of 50 nm were observed in vitrified Thermoplasma acidophilum cells by means of cryo-electron tomography. These droplets were isolated by column chromatography and immunoprecipitation protein purification methods. Subsequent chemical and biochemical analyses identified lipid and protein components, respectively. Two major lipid components, comigrating menaquinones at the solvent front and the slower migrating Thermoplasma polar lipid U4, were detected by TLC experiments. The major protein component was identified as the 153 amino acid long Ta0547 vitellogenin-N domain protein. This domain has been found so far exclusively in large lipid transport proteins of vertebrates and non-vertebrates. Blast protein database homology searches with Ta0547 did not return any eukaryal hits; homologous sequences were found only in thermo-acidophilic archaeons. However, a profile-sequence domain search performed with the vitellogenin-N domain (PF01347) hmm-profile against the T. acidophilum proteome returned Ta0547 as hit. Electron microscopy appearance of isolated droplets resembled to lipoprotein particles. However, no (tetraether) lipid layer could be detected on the droplets surface, rather hydrophobic compounds of the electron dense lumen were surrounded by a denser discontinuous protein boundary. Based on described features, these particles qualify for a novel lipoprotein particle category, what we nominated Thermoplasma Quinone Droplet.
    Keywords: Physiology & Biochemistry
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    Screening for Escherichia coli K-12 genes conferring glyoxal resistance or sensitivity by transposon insertions (2016)
    Oxford University Press
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    Publication Date: 2016-09-17
    Description: Glyoxal (GO) belongs to the reactive electrophilic species generated in vivo in all organisms. In order to identify targets of GO and their response mechanisms, we attempted to screen for GO-sensitive mutants by random insertions of Tn phoA -132. The genes responsible for GO susceptibility were functionally classified as the following: (i) tRNA modification; trmE , gidA and truA , (ii) DNA repair; recA and recC , (iii) toxin–antitoxin; mqsA and (iv) redox metabolism; yqhD and caiC . In addition, an insertion in the crp gene, encoding the cAMP responsive transcription factor, exhibits a GO-resistant phenotype, which is consistent with the phenotype of adenylate cyclase ( cya ) mutant showing GO resistance. This suggests that global regulation involving cAMP is operated in a stress response to GO. To further characterize the CRP-regulated genes directly associated with GO resistance, we created double mutants deficient in both crp and one of the candidate genes including yqhD , gloA and sodB . The results indicate that these genes are negatively regulated by CRP as confirmed by real-time RT-PCR. We propose that tRNA as well as DNA are the targets of GO and that toxin/antitoxin, antioxidant and cAMP are involved in cellular response to GO.
    Keywords: Physiology & Biochemistry
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    Low temperature-induced viable but not culturable state of Ralstonia eutropha and its relationship to accumulated polyhydroxybutyrate (2016)
    Oxford University Press
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    Publication Date: 2016-12-23
    Description: The culturability of Escherichia coli , Ralstonia eutropha and Bacillus subtilis after incubation in phosphate-buffered saline at either 5°C or 30°C was determined. The culturability of B. subtilis showed little dependence on temperature. The culturability of E. coli rapidly decreased at 30°C but remained almost constant at 5°C. In contrast, the culturability of R. eutropha decreased by three orders of magnitude at 5°C within 24 h but only moderately decreased (one order of magnitude) at 30°C. Remarkably, prolonged incubation of R. eutropha at 30°C resulted in a full recovery of colony forming units in contrast to only a partial recovery at 5°C. Ralstonia eutropha cells at 30°C remained culturable for 3 weeks while culturability at 5°C constantly decreased. The effect of temperature was significantly stronger in a polyhydroxybutyrate-negative mutant. Our data show that accumulated polyhydroxybutyrate has a cold-protective function and can prevent R. eutropha entering the viable but not culturable state.
    Keywords: Physiology & Biochemistry
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    Glutamine metabolism of Corynebacterium glutamicum: role of the glutaminase GlsK (2016)
    Oxford University Press
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    Publication Date: 2016-10-20
    Description: Corynebacterium glutamicum is able to metabolize different nitrogen and carbon sources. In standard minimal media, ammonium and urea typically serve as nitrogen source and glucose or sucrose as carbon and energy source; however, amino acids might also play a role as nitrogen, carbon and energy source. In this study, the function of the putative glutaminase GlsK was investigated. A glsK deletion strain showed impaired growth with L-glutamine as carbon and energy source, while growth was improved upon glsK overexpression. GlsK possesses a carboxy-terminal domain that seems to be restricted to Corynebacterium species . A truncated GlsK lacking this extension led to faster growth, indicating a regulatory function of this domain. In fact, GlsK activity is regulated in a pH-dependent manner depending on the carboxy-terminal extension, and is positively influenced by cAMP. Furthermore, the C-terminal extension seems to be important for oligomerization of GlsK.
    Keywords: Physiology & Biochemistry
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    ydjN encodes an S-sulfocysteine transporter required by Escherichia coli for growth on S-sulfocysteine as a sulfur source (2016)
    Oxford University Press
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    Publication Date: 2016-09-02
    Description: Sulfur is an essential element for growth and many physiological functions. As sulfur sources for Escherichia coli and related bacteria, specific transporters import various sulfur-containing compounds from the environment. In this study, we identified and characterized an alternative function of the cystine transporter YdjN in E. coli as a transporter of S -sulfocysteine, a sulfur-containing intermediate in the assimilatory cysteine biosynthesis that is used as a sulfur source for the growth of E. coli . We also demonstrated that the transport of S -sulfocysteine via YdjN depends on the transcriptional regulator CysB, a master regulator that controls most of the genes involved in sulfur assimilation and cysteine metabolism. We found that the use of S -sulfocysteine as a sulfur source depends on glutathione because mutations in glutathione biosynthetic genes abolish growth when S -sulfocysteine is used as a sole sulfur source, thereby supporting the previous findings that the conversion of S -sulfocysteine to cysteine is catalyzed by glutaredoxins. To the best of our knowledge, this is the first report of a functional S -sulfocysteine transporter across organisms, which strongly supports the hypothesis that S -sulfocysteine is not only a metabolic intermediate but also a physiologically significant substance in specific natural environments.
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    Temperature-regulated expression of type VI secretion systems in fish pathogen Pseudomonas plecoglossicida revealed by comparative secretome analysis (2016)
    Oxford University Press
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    Publication Date: 2016-12-16
    Description: Pseudomonas plecoglossicida is a facultative fish pathogen. Recent studies showed that P. plecoglossicida infection in fish was associated with temperature. The aim of this study was to compare the secretomes of P. plecoglossicida cultured in vitro at representative temperatures for pathogenic (20°C) and less pathogenic (30°C) phenotypes. Thirteen proteins in the culture supernatants of P. plecoglossicida showed significant difference in abundance at 20 vs. 30°C. Four proteins were strongly increased at 20°C, including two hemolysin co-regulated proteins (Hcp) that are part of the bacterial type VI secretion system (T6SS), flagellin and an unknown protein. Immunoblot analysis verified the induced secretion of Hcps at 20°C. Furthermore, the upregulation of Hcps at 20°C was confirmed at transcriptional level by RT-qPCR analysis, which also demonstrated the induction of expression of other T6SS-related genes at 20°C. Taken together, we demonstrate the presence of two functionally active T6SS proteins in fish pathogenic P. plecoglossicida strains, as evidenced by the secretion of the T6SS substrate Hcp, the production of which were found to be controlled by temperature. Our findings also support efforts to develop vaccines targeting secreted virulence factors as prophylactic strategies for diseases in fish caused by P. plecoglossicida .
    Keywords: Physiology & Biochemistry
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    Vitamin C targets (p)ppGpp synthesis leading to stalling of long-term survival and biofilm formation in Mycobacterium smegmatis (2017)
    Oxford University Press
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    Publication Date: 2017-01-13
    Description: Earlier, vitamin C was demonstrated to sterilize Mycobacterium tuberculosis culture via Fenton's reaction at high concentration. It alters the regulatory pathways associated with stress response and dormancy. Since (p)ppGpp is considered to be the master regulator of stress response and is responsible for bacterial survival under stress, we tested the effect of vitamin C on the formation of (p)ppGpp. In vivo estimation of (p)ppGpp showed a decrease in (p)ppGpp levels in vitamin C-treated M. smegmatis cells in comparison to the untreated cells. Furthermore, in vitro (p)ppGpp synthesis using Rel MSM enzyme was conducted in order to confirm the specificity of the inhibition in the presence of variable concentrations of vitamin C. We observed that vitamin C at high concentration can inhibit the synthesis of (p)ppGpp. We illustrated binding of vitamin C to Rel MSM by isothermal titration calorimetry. Enzyme kinetics was followed where K 0.5 was found to be increased with the concomitant reduction of V max value suggesting mixed inhibition. Both long-term survival and biofilm formation were inhibited by vitamin C. The experiments suggest that vitamin C has the potential to be developed as the inhibitor of (p)ppGpp synthesis and stress response, at least in the concentration range used here.
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    A role of nitrite reductase (NirBD) for NO homeostatic regulation in Streptomyces coelicolor A3(2) (2017)
    Oxford University Press
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    Publication Date: 2017-01-19
    Description: Although nitric oxide (NO) is an important signaling molecule in bacteria and higher organisms, excessive intracellular NO is highly reactive and dangerous. Therefore, living cells need strict regulation systems for cellular NO homeostasis. Recently, we discovered that Streptomyces coelicolor A3(2) retains the nitrogen oxide cycle (NO 3 – -〉NO 2 – -〉NO-〉NO 3 – ) and nitrite removal system. The nitrogen oxide cycle regulates cellular NO levels, thereby controlling secondary metabolism initiation (red-pigmented antibiotic, RED production) and morphological differentiation. Nitrite induces gene expression in neighboring cells, suggesting another role for this cycle as a producer of transmittable intercellular communication molecules. Here, we demonstrated that ammonium-producing nitrite reductase (NirBD) is involved in regulating NO homeostasis in S. coelicolor A3(2). NirBD was constitutively produced in culture independently of GlnR, a known transcriptional factor. NirBD cleared the accumulated nitrite from the medium. Nir deletion mutants showed increased NO-dependent gene expression at later culture stages, whereas the wild-type M145 showed decreased expression, suggesting that high NO concentration was maintained in the mutant. Moreover, the nir deletion mutant produced more RED than that produced by the wild-type M145. These results suggest that NO 2 – removal by NirBD is important to regulate NO homeostasis and to complete NO signaling in S. coelicolor .
    Keywords: Physiology & Biochemistry
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    Occurrence and biosynthesis of 3-mercaptopropionic acid in Methanocaldococcus jannaschii (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: In a non-targeted analysis of thiol-containing compounds in the hyperthermophilic methanogen Methanocaldococcus jannaschii , we discovered three unexpected metabolites: 3-mercaptopropionic acid (MPA), 2-hydroxy-4-mercaptobutyric acid (HMBA) and 4-mercapto-2-oxobutyric acid (MOB). HMBA and MOB have never been reported as natural products, while MPA is highly prevalent in aquatic environments as a result of biotic and abiotic processing of sulfur-containing compounds. This report provides evidence that HMBA and MOB are part of a biosynthetic pathway to generate MPA in M. jannaschii . We show that HMBA can be biosynthesized from malate semialdehyde and hydrogen sulfide, likely using a mechanism similar to that proposed for coenzyme M, coenzyme B and homocysteine biosynthesis in methanogens, where an aldehyde is converted to a thiol. The L-sulfolactate dehydrogenase, derived from the MJ1425 gene, is shown to catalyze the NAD-dependent oxidation of HMBA to MOB. Finally, we demonstrate that HMBA can be used as a biosynthetic precursor to MPA in M. jannaschii cell extracts. This proposed pathway may contribute to the wide occurrence of MPA in marine environments and indicates that MPA must serve some important function in M. jannaschii .
    Keywords: Physiology & Biochemistry
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    The main pigment of the dormant Mycobacterium smegmatis is porphyrin (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: Upon transition of Mycobacterium smegmatis into the dormant state, accumulation of a dark brown fluorescent pigment was observed. This pigment gave bright red fluorescence in both cells and the culture medium. Based on 1 H-NMR, MALDI and UV spectra, the fluorescent compounds, extracted from the culture medium as well as from the dormant cells, were concluded to be a mixture of free coproporphyrin III and uroporphyrin III and their corresponding methyl esters. A possible significance of porphyrin pigment accumulation in the dormant cells is discussed.
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    Identification of a gene involved in the regulation of hyphal growth of Epichloë festucae during symbiosis (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: Secreted proteins, those involved in cell wall biogenesis, are likely to play a role in communication in the symbiotic interaction between the fungal endophyte Epichloë festucae with perennial ryegrass ( Lolium perenne ), particularly given the close association between fungal hyphae and the plant cell wall. Our hypothesis was that secreted proteins are likely to be responsible for establishing and maintaining a normal symbiotic relationship. We analyzed an endophyte EST database for genes with predicted signal peptide sequences. Here, we report the identification and characterization of rhgA ; a gene involved in the regulation of hyphal growth in planta . In planta analysis of rhgA mutants showed that disruption of rhgA resulted in extensive unregulated hyphal growth. This phenotype was fully complemented by insertion of the rhgA gene and suggests that rhgA is important for maintaining normal hyphal growth during symbiosis.
    Keywords: Physiology & Biochemistry
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    Distension of the toga of Thermotoga maritima involves continued growth of the outer envelope as cells enter the stationary phase (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: Thermotoga maritima cells are distinguished by a sheath-like structure called the toga that loosely encloses single or multiple cells. During growth, and particularly at late phases of population growth, the toga distends from the poles of many cells. Little is known about this phenomenon so this study presents basic information about this process. We first provide quantitative data demonstrating that cells showing toga distensions increase in number during growth and that the phenomenon is not due to acidification of their growth medium. Comparisons of the area enclosed by these distended togas to the area of the cytoplasm show that the toga continues to grow as the growth of the cytoplasm ceases. Measuring the expression of many genes involved in toga composition and biosynthesis showed a 5.2-, 7.9- and 3-fold increase in the expression of toga structural protein genes ompB (porin), ompA1 and ompA2 (alpha helical, transperiplasm anchors), respectively. Additionally, expression of the putative pyruvyl transferase gene ( csaB ) was upregulated 4.4-fold in stationary phase, while the beta barrel assembly factor gene ( bamA ) showed only a 1.2-fold increase in expression. These findings demonstrate that toga distension is an active process and one that needs further investigation so we can understand the selective forces that operate in high-temperature environments.
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