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  • Physiology & Biochemistry  (57)
  • 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions  (30)
  • Oxford University Press  (57)
  • Elsevier  (30)
  • 2015-2019  (58)
  • 2005-2009  (29)
  • 1945-1949
Collection
Keywords
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  • 2015-2019  (58)
  • 2005-2009  (29)
  • 1945-1949
  • 2010-2014  (7)
Year
  • 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)
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  • 2
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    Dynamics of magma ascent and fragmentation in trachytic versus rhyolitic eruptions (2005)
    Elsevier
    Details
    Publication Date: 2020-10-29
    Description: We have performed a parametric study on the dynamics of trachytic (alkaline) versus rhyolitic (calc-alkaline) eruptions by employing a steady, isothermal, multiphase non-equilibrium model of conduit flow and fragmentation. The employed compositions correspond to a typical rhyolite and to trachytic liquids from Phlegrean Fields eruptions, for which detailed viscosity measurements have been performed. The investigated conditions include conduit diameters in the range 30–90 m and total water contents from 2 to 6 wt%, corresponding to mass flow rates in the range 106–108 kg/s. The numerical results show that rhyolites fragment deep in the conduit and at a gas volume fraction ranging from 0.64 to 0.76, while for trachytes fragmentation is found to occur at much shallower levels and higher vesicularities (0.81–0.85). An unexpected result is that low-viscosity trachytes can be associated with lower mass flow rates with respect to more viscous rhyolites. This is due to the non-linear combined effects of viscosity and water solubility affecting the whole eruption dynamics. The lower viscosity of trachytes, together with higher water solubility, results in delayed fragmentation, or in a longer bubbly flow region within the conduit where viscous forces are dominant. Therefore, the total dissipation due to viscous forces can be higher for the less viscous trachytic magma, depending on the specific conditions and trachytic composition employed. The fragmentation conditions determined through the simulations agree with measured vesicularities in natural pumice clasts of both magma compositions. In fact, vesicularities average 0.80 in pumice from alkaline eruptions at Phlegrean Fields, while they tend to be lower in most calc-alkaline pumices. The results of numerical simulations suggest that higher vesicularities in alkaline products are related to delayed fragmentation of magmas with this composition. Despite large differences in the distribution of flow variables which occur in the deep conduit region and at fragmentation, the flow dynamics of rhyolites and trachytes in the upper conduit and at the vent can be very similar, at equal conduit size and total water content. This is consistent with similar phenomenologies of eruptions associated with the two magma types.
    Description: Published
    Description: 93-108
    Description: partially_open
    Keywords: trachytic magma ; conduit flow ; eruption dynamics and numerical simulations ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 3
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    The age of the Neapolitan Yellow Tu caldera-forming eruption (Campi Flegrei caldera-Italy) assessed by 40Ar/39Ar dating method (2005)
    Elsevier
    Details
    Publication Date: 2020-12-17
    Description: The Neapolitan Yellow Tuff (NYT) is the product of the largest known trachytic phreatoplinian eruption. It covered an area larger than 1000 km2 with an estimated volume of about 40 km3 of erupted magma. During the course of the eruption a caldera collapsed within the previously formed Campanian Ignimbrite caldera. The resulting nested structure strongly influenced the following volcanic activity in the Campi Flegrei caldera. As previous dating of the NYT does not converge toward a unique result, a new set of 40Ar/39Ar age determinations has been carried out to better constrain the age of the eruption. Two variants of the 40Ar/39Ar dating method were applied to determine the age of the NYT eruption: (1) single-crystal total fusion (SCTF), on an individual phenocryst of feldspar, and (2) laser incremental heating (LIH), on bulk aliquots of feldspar phenocrysts. The results of the SCTF analyses show that the overall sample weighted mean age, derived from the conventional age calculation, is 15.6 ;0.8 ka. A weighted mean of the isochron age is 15.3 ;1.2 ka (2c), and has been assumed as the best indicator of age to be derived from the SCTF analyses. The LIH analyses results show that plateau ages vary from 15.4; 0.5 to 14.5; 0.5 ka. The overall weighted mean age of the isochron results is 14.9;0.4 ka (2c). This result has been assumed as the reference age for the NYT eruption, and agrees with the SCTF age. The new age obtained for the NYT deposits is of great relevance for the understanding of the evolution and the present state of the Campi Flegrei caldera and collocates the NYT in a crucial stratigraphical position to date the climatic oscillations that occurred between the Late Glacial and the Holocene.
    Description: Published
    Description: 157-170
    Description: partially_open
    Keywords: Neapolitan Yellow Tuff ; Campi Flegrei caldera ; 40Ar/39Ar dating method ; Geochronology ; Late Glacial ; Holocene ; 04. Solid Earth::04.04. Geology::04.04.02. Geochronology ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Chemical evolution of thermal waters and changes in the hydrothermal system of Papandayan volcano (West Java, Indonesia) after the November 2002 eruption (2008)
    Elsevier
    Details
    Publication Date: 2021-05-17
    Description: Papandayan is a stratovolcano situated in West Java, Indonesia. Since the last magmatic eruption in 1772,only few hydrothermal explosions have occurred. An explosive eruption occurred in November 2002 and ejected ash and altered rocks. The altered rocks show that an advanced argillic alteration took place in the hydrothermal system by interaction between acid fluids and rocks. Four zones of alteration have been defined and are limited in extension and shape along faults or across permeable structures at different levels beneath the active crater of the volcano. At the present time, the activity is centered in the northeast crater with discharge of low temperature fumaroles and acid hot springs. Two types of acid fluids are emitted in the crater of Papandayan volcano: (1) acid sulfate-chloride waters with pH between 1.6 and 4.6 and (2) acid sulfate waters with pH between 1.2 and 2.5. The water samples collected after the eruption on January 2003 reveal an increase in the SO4/Cl and Mg/Cl ratios. This evolution is likely explained by an increase in the neutralization of acid fluids and tends to show that water–rock interactions were more significant after the eruption. The evolution in the chemistry observed since 2003 is the consequence of the opening of new fractures at depth where unaltered (or less altered) volcanic rocks were in contact with the ascending acid waters. The high δ34S values (9–17‰) observed in acid sulfatechloride waters before the November 2002 eruption suggest that a significant fraction of dissolved sulfates was formed by the disproportionation of magmatic SO2. On the other hand, the low δ34S (−0.3–7‰) observed in hot spring waters sampled after the eruption suggest that the hydrothermal contribution (i.e. the surficial oxidation of hydrogen sulfide) has increased.
    Description: Published
    Description: 276-286
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Papandayan volcano ; Indonesia ; phreatic eruption ; hydrothermal system ; fluid geochemistry ; advanced argillic alteration ; gas geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 5
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    Mid-distal occurrences of the Albano Maar pyroclastic deposits and their relevance for reassessing the eruptive scenarios of the most recent activity at the Colli Albani Volcanic District, Central Italy (2007)
    Elsevier
    Details
    Publication Date: 2021-01-25
    Description: The Late Pleistocene Albano Maar hosted the most recent volcanic activity of the Colli Albani Volcanic District, represented at nearvent sections by a thick pyroclastic succession of seven units clustered in two main eruptive cycles dated at around 70–68 and 41–36 ka B.P., respectively. Recent stratigraphic investigations allowed us to recognise a pyroclastic succession comprising four eruptive units widely spread in the northeastern sectors of the Colli Albani volcano, up to 15km eastward from the Albano Maar. Integrated tephrostratigraphic, morpho-pedostratigraphic, archaeological, petrological and geochemical analyses enable us to recognise them as distal deposits of the first, third, fifth and seventh Albano Maar eruptions, enlarging significantly their previously supposed dispersion area. Further tephrostratigraphic studies in central Apennine area, allowed us to identify the Albano Maar products in Late Pleistocene deposits of several intermountain basins, extending still further the dispersion area of distal ash fallout as far as 100–120km from the vent. On the basis of the identification and the study of these previously unrecognised mid-distal Albano Maar deposits, a reappraisal of the eruptive scenarios and related energetic parameters is proposed.
    Description: Published
    Description: 160–178
    Description: 1.5. TTC - Sorveglianza dell'attività eruttiva dei vulcani
    Description: JCR Journal
    Description: reserved
    Keywords: Colli Albani ; Albano ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 6
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    Numerical simulation of pyroclastic density currents on Campi Flegrei topography: a tool for statistical hazard estimation. (2006)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We describe a numerical simulation of both concentrated and dilute gravity-driven pyroclastic flows on a digital topographic model of the Campi Flegrei volcanic field. Families of numerical flows are generated by sampling a multi-dimensional matrix of vent coordinates, flow properties and dynamical parameters within a wide range of values. Hazard maps are constructed from the data base of simulated flows, using a mixed deterministic^statistical approach. The set of probable vents covers the area of recent eruptions. Results show the key role of topography in controlling the flow dispersion. The maximum hazard appears to be the NE sector of the caldera. Flows in the eastern sector, including the city of Naples, are shown to be efficiently hindered by the Posillipo and Camaldoli hills at the caldera borders, thus reducing the hazard. The results represent the first physically based estimate of hazard from pyroclastic flows in this densely populated area, and can be used for civil defence purposes.
    Description: Published
    Description: 1-14
    Description: partially_open
    Keywords: Campi flegrei ; calderas ; pyroclastic flows ; hazard maps ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 7
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    An advanced video-based system for monitoring active volcanoes (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Video surveillance systems are consolidated techniques for monitoring eruptive phenomena in volcanic areas. Along with these systems, which use standard video cameras, people working in this field sometimes make use of infrared cameras providing useful information about the thermal evolution of eruptions. Real-time analysis of the acquired frames is required, along with image storing, to analyze and classify the activity of volcanoes. Human effort and large storing capabilities are hence required to perform monitoring tasks. In this paper we present a new strategy aimed at improving the performance of video surveillance systems in terms of human-independent image processing and storing optimization. The proposed methodology is based on real-time thermo-graphic analysis of the area considered. The analysis is performed by processing images acquired with an IR camera and extracting information about meaningful volcanic events. Two software tools were developed. The first provides information about the activity being monitored and automatically adapts the image storing rate. The second tool automatically produces useful information about the eruptive activity encompassed by a selected frame sequence. The software developed includes a suitable user interface allowing for convenient management of the acquired images and easy access to information about the volcanic activity monitored.
    Description: Published
    Description: 85-91
    Description: reserved
    Keywords: Volcano monitoring ; Image processing ; Smart storing rate ; Eruption data ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 8
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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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  • 9
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    Insight on recent Stromboli eruption inferred from terrestrial and satellite ground deformation measurements (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The multi-parametric permanent system (tilt and GPS networks, robotized geodetic station) for monitoring ground deformation at Stromboli volcano was set up in the 1990s and later greatly improved during the effusive event of 2002–2003. Unlike other volcanoes, e.g. Mt. Etna, the magnitude of ground deformation signals of Stromboli is very small and through the entire period of operation of the monitoring system, only two major episodes of deformation, in 1994–1995 and 2000, which did not lead to an eruption but rather pure intrusion, were measured. Similarly to the 2002–2003 eruption, no important deformations were detected in the months before the 2007 eruption. However, unlike the 2002–2003 eruption, GPS and tilt stations recorded a continuous deflation during the entire 2007 eruption, which allowed us to infer a vertical elongated prolate ellipsoidal source, centered below the summit craters at depth of about 2.8 km b.s.l. Due to its geometry and position, this source simulates an elongated plumbing system connecting the deeper LP magma storage (depth from 5 to 10 km) with the HP shallower storage (0.8–3 km), both previously identified by petrologic and geochemical studies. This result represents the first contribution of geophysics to the definition of the plumbing system of Stromboli at intermediate depth. Finally, no deformation due to the plumbing system was measured for a long time after the end of the eruption. Meanwhile, the new terrestrial geodetic monitoring system installed within the Sciara del Fuoco, on the lava fan formed during the eruption, indicated that during the first months after the end of the eruption the ground velocity progressively decreased in time, suggesting that part of the deformation was due to the thermal contraction of the lava flow.
    Description: Published
    Description: 172-181
    Description: 1.3. TTC - Sorveglianza geodetica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; Ground Deformation ; source modelling ; flank instability ; 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::04.03. Geodesy::04.03.09. Instruments and techniques ; 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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    Rapid morphological changes at the summit of an active volcano: reappraisal of the poorly documented 1964 eruption of Mount Etna (Italy) (2005)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: While the eruptive record of Mount Etna is reasonably complete for the past 400 years, the activity of the early and late 1960s, which took place at the summit, is poorly documented in the scientific literature. From 1955 to 1971, the Central and Northeast Craters were the sites of long-lived mild Strombolian and effusive activity, and numerous brief episodes of vigorous eruptive activity, which led to repeated overflows of lava onto the external flanks of the volcano. A reconstruction of the sequence of the more important of these events based on research in largely obscure and nearly inaccessible sources permits a better understanding of the eruption dynamics and rough estimates of erupted volumes and of the changes to the morphology of the summit area. During the first half of 1964, the activity culminated in a series of highly dynamic events at the Central Crater including the opening of a fissure on the E flank of the central summit cone, lava fountains, voluminous tephra emission, prolonged strong activity with continuous lava overflows, and growth of large pyroclastic intracrater cones. Among the most notable processes during this eruption was the breaching of a section of the crater wall, which was caused by lateral pressure of lava ponding within the crater. Comparison with the apparently similar summit activity of 1999 allows us to state that (a) lava overflows from large pit craters at the summit are often accompanied by breaching of the crater walls, which represents a significant hazard to nearby observers, and that (b) eruptive activity in 1999 was much more complex and voluminous than in 1964. For 1960s standards however, the 1964 activity was the most important summit eruption in terms of intensity and output rates for about 100 years, causing profound changes to the summit morphology and obliterating definitively the former Central Crater.
    Description: Published
    Description: 203-218
    Description: partially_open
    Keywords: Mount Etna ; Summit eruption ; Crater morphology and Lava overflows ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 11
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    New integrated geodetic monitoring system at Stromboli volcano (Italy) (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Stromboli is a composite volcano, rising about 2.5 km above the sea floor, whose top lies about 1 km above the sea level forming the northernmost island of the Aeolian Archipelago volcanic arc (Tyrrhenian Sea). On December 28th, 2002, lava flows outpoured from the northern wall of NE crater and come down in the Sciara del Fuoco (SdF), a deep depression that marks the NW flank of the volcano edifice. On December 30th, 2002, two landslides occurred on the northern part of the SdF; it moved a mass in the order of tens of millions of cubic meters both above and below the sea level. The landslide produced a tsunami that causes significant damage on the eastern cost of the island, reaching the others Aeolian Islands and the Sicilian and south Italian coasts. This event lead to the upgrade of the ground deformation monitoring system, already existing on the island; the new requirement was the real-time detection of the deformations related to potential slope failures of the SdF. To this aim, a remotely controlled monitoring system, based both on GPS and topographic techniques was planned and set up in few months. The new monitoring system allowed to continuously measure the ground deformations occurring on the SdF, by integrating both terrestrial topographic and satellite geodetic techniques. Despite this system was severely damaged during the 7-months lasting eruption, it allowed to monitor important eruptive phases. For the first time, an accurate data set about the actual mass movements of the SdF and the crater area was available. It provided data that significantly supported the Civil Protection Authorities in making decisions and constrain the hypothesis about the landslide movements and volcanic activity. After the end of the eruption, the system was reinstated in order to optimize the instruments and to set up a monitoring system aimed at measuring deformations forecasting other flank collapses.
    Description: Dipartimento Nazionale della Protezione Civile
    Description: Published
    Description: 13–31
    Description: 1.3. TTC - Sorveglianza geodetica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; Ground deformation ; Real-time monitoring ; Eruption forecasting ; Landslide forecasting ; 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::04.03. Geodesy::04.03.09. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 12
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    Tephra fallout of 2001 Etna flank eruption: Analysis of the deposit and plume dispersion (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Tephra fallout represented a major source of hazard for eastern Sicily during the 2001 eruption of Mt. Etna (Italy) between 19 July and 6 August. Long-lasting explosive activity was generated from the 2570 m vent, producing a volcanic plume up to 5 km high above sea level. The eruption caused copious lapilli and ash fallout over the volcano flanks for several days. Flight operations were cancelled at the Catania and Reggio Calabria airports; health risk and economic damage put communities living close to this active volcano on the alert. The explosive activity at the 2570 m vent had three main phases characterized by phreatomagmatic, magmatic and vulcanian explosions. In this paper, we analyze the first explosive phase between 19 and 24 July that formed a tephra deposit on the volcano's south-east flanks. Immediately after the first phase of the eruption, numerous tephra samples were collected in order to draw an isomass map, calculate physical parameters for the eruption and analyze the plume dispersion on the basis of deposit geometry. The tephra deposit shows a bilobate shape due to the change with time of both the vigour of the eruption and the wind direction and velocity that caused a higher rate of particle accumulation along two dispersal axes (SE and SSE). The total mass of tephra erupted was calculated with two different fitting methods: exponential line segments and a power law fit on the semi-logarithmic plot of mass per unit area versus , resulting in values of 1.02 109 kg and 2.31 109 kg, respectively. The whole deposit grain-size was calculated applying the Voronoi tessellation method, it shows a mode of 2 and thus indicates a high degree of magma fragmentation during the first phase of the eruption. Plume dispersal was investigated by an advection–diffusion model to reconstruct the tephra deposit. In the modelling, we took into account the variations of wind direction and velocity, and eruption intensity by dividing the explosive phase into sixteen sub-eruptions and considering the final deposit as the sum of the mass computed for each sub-eruption. Using best fit procedures, we find that the optimal agreement between computed values and field data is obtained by using the total mass calculated with the power law fit and a terminal settling velocity distribution with a particle aggregation model. The computed tephra dispersal was able to reproduce the bilobate shape of the real deposit. This work proves that advection–diffusion models can describe sedimentation processes of weak, i.e., bent-over, long-lasting plumes if the variations of wind direction and velocity, and eruptive intensity are included.
    Description: Published
    Description: 147-164
    Description: 3.6. Fisica del vulcanismo
    Description: JCR Journal
    Description: reserved
    Keywords: Mt. Etna ; basaltic explosive activity ; violent strombolian eruption ; tephra deposit ; dispersal modelling ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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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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    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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  • 15
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    Vesuvius: A historical approach to the 1631 eruption "cold data" from the analysis of three contemporary treatises (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The 1631 Vesuvius eruption is one of its best known and most studied of its type. However, the historical approach performed within the framework of the Exploris project highlighted new evidence from previously unused or unknown historical sources. These consist of three treatises that were contemporary to the event; although written in Latin, they have been fully translated and analysed. To guarantee systematic use and open access to the large amount of information they contain, they have been provided as a small database. These treatises have provided new information on phenomena that preceded and accompanied the eruption of 1631, making possible the formation of a complex chronological profile, starting from around 6 months before the eruption. The anthropic impact is also outlined. The method applied has produced a chronology of “cold data”, which are not interpreted from the volcanological standpoint, but only derived directly from the analysed history and sequence of the texts. The analysis of the three treatises has not, however, solved all of the problems connected with the detailed knowledge of the event in 1631. Indeed, problems of two kinds persist: a) linguistic correspondence between the volcanological terms of today and those used in the texts; b) the lack of precision of the measures indicated. Here, the main results obtained from this analysis method are presented, along with a discussion of their limitations and some new perspectives.
    Description: Published
    Description: 347-358
    Description: 3.10. Sismologia storica e archeosismologia
    Description: JCR Journal
    Description: reserved
    Keywords: historical volcanology ; Vesuvius ; 1631 eruption chronology ; precursors ; treatises ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 16
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    The influence of conduit processes on changes in style of basaltic Plinian eruptions: Tarawera 1886 and Etna 122 BC (2005)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Basaltic volcanism is most typically thought to produce effusion of lava, with the most explosive manifestations ranging from mild Strombolian activity to more energetic fire fountain eruptions. However, some basaltic eruptions are now recognized as extremely violent, i.e., generating widespread phreatomagmatic, subplinian and Plinian fall deposits. We focus here on the influence of conduit processes, especially partial open-system degassing, in triggering abrupt changes in style and intensity that occurred during two examples of basaltic Plinian volcanism. We use the 1886 eruption of Tarawera, New Zealand, the youngest known basaltic Plinian eruption and the only one for which there are detailed written eyewitness accounts, and the well-documented 122 BC eruption of Mount Etna, Italy, and present new grain size and vesicularity data from the proximal deposits. These data show that even during extremely powerful basaltic eruptions, conduit processes play a critical role in modifying the form of the eruptions. Even with very high discharge, and presumably ascent, rates, partial open-system behaviour of basaltic melts becomes a critical factor that leads to development of domains of largely stagnant and outgassed melt that restricts the effective radius of the conduit. The exact path taken in the waning stages of the eruptions varied, in response to factors which included conduit geometry, efficiency and extent of outgassing and availability of ground water, but a relatively abrupt cessation to sustained high-intensity discharge was an inevitable consequence of the degassing processes.
    Description: Published
    Description: 1-14
    Description: partially_open
    Keywords: basaltic Plinian eruption ; Etna ; Tarawera and explosive volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 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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  • 17
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    Contrasting triggering mechanisms of the 2001 and 2002–2003 eruptions of Mount Etna (Italy) (2005)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Mount Etna produced two significant eruptions in 2001 and 2002–2003, which we have analysed using geological, seismic and deformation data. These eruptions showed some similarities, such as the activating of two magmatic plumbing systems (central–lateral and eccentric), but they differed in their triggering mechanisms. While the 2001 eruption was largely the result of the emplacement of a N–S eccentric dike (independent from the central conduits) consistent with E–W regional extension, the 2002–2003 eruption occurred in response to a major flank slip on the eastern and southeastern sides of the volcano. This is demonstrated by the spatial and temporal distribution of seismicity and deformation preceding and accompanying the two eruptions. During the months prior to the 2001 eruption, most epicenters were concentrated on the southern flank, at depths of 5–15 km below sea level. During the 4 days before the eruption, earthquake hypocenters migrated to shallower levels (from 5 km bsl. upward) indicating the emplacement of the eccentric dike. This is confirmed by the patterns of ground fracturing observed in the field and deformation documented by electronic distance measurements (EDM). In contrast, the months before the 2002–2003 eruption were characterised by shallower seismicity, mainly concentrated along the active faults bordering the slipping flank sector. Flank slip accelerated in September 2002 and a second, more vigorous acceleration of flank slip occurred on 26–27 October 2002, accompanying the opening of eruptive vents. The very short (2 h) seismic crisis preceding the onset of eruptive activity stands in neat contrast with the 4 days of intense seismicity before the 2001 eruption. Subsequently, flank slip-deformation extended all over the eastern and southeastern flanks of the volcano, causing serious damage in this sector. The events of 2001–2003 can be seen as a continuous chain of intimately interacting processes including regional tectonics, magma accumulation and eruption, and flank instability. In this scenario the 2001 eruption led to increased flank instability that subsequently accelerated and culminated with the massive flank slip, which in turn facilitated the 2002–2003 eruption. This sequence of events points to a long-term feedback mechanism between magmatism and flank instability at Etna.
    Description: Published
    Description: 235-255
    Description: partially_open
    Keywords: eruption triggering ; central–lateral vs. eccentric eruptions ; flank instability and slip ; volcano-tectonics ; Mt. Etna ; instrumental monitoring ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 18
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    Explosive activity at mt. etna summit craters and source modeling by using high precision continuous tilt (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: We investigated the relationships between modelled strain produced by explosive activity through a volcanic conduit, observed paroxystic episodes on Mt. Etna, and high-precision continuous tilt signals recorded during such events from the tilt monitoring network. The tilt changes detected during two different explosive episodes were compared with those calculated from analytical models of ground deformation in order to constrain source properties. The July 22, 1998 subplinian explosion from Voragine crater produced small tilt changes (order of 0.5–1.5 μrad) recorded over the entire volcano edifice, implying a small storage at nearly 2.5 km below sea level. The 1998–2000 period was characterized by tens of spectacular lava fountains from the South-East crater. Very small tilt change (∼ 0.1 μrad) was recorded by a single station on the high north-eastern flank of Mt. Etna and indicated the action of a limited and shallow conduit with 1.5–1.9 km depth. These results provide a contribution to better infer the shallow plumbing system beneath Mt. Etna.
    Description: Published
    Description: 221–234
    Description: reserved
    Keywords: explosive activity ; tilt data ; volcano source modeling ; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 19
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    Volcanic aerosol optical characteristics of Mt. Etna tropospheric (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: Tropospheric volcanic plume features have been derived from airborne multispectral images collected during field measurement campaigns at the Mt. Etna volcano in June 1997, during a quiescent period, and in July 2001 during an eruptive period. Results have been obtained in terms of mapping the volcanic aerosol optical thickness (AOT), the A ˚ ngstro¨ m parameters and the water vapor content using different bands from visible to infrared. The AOT values show average values of 0.1 and 1, for quiescent and eruptive plumes, respectively, demonstrating that this geophysical parameter well indicates a major contribution of particulates in the explosive plume with respect to the quiescent one. The mapping of A ˚ ngstro¨ m parameters, in the explosive case, indicates the presence of larger particles and their distribution along the plume, while in the quiescent case indicates the particle size is dominated by small particles with an effective radius about 1 mm. Further in the quiescent case, the map of water vapor shows low values indicating that water vapor emitted condenses mainly in aerosols.
    Description: Published
    Description: 981-994
    Description: 1.10. TTC - Telerilevamento
    Description: JCR Journal
    Description: reserved
    Keywords: Mt. Etna; Volcanic aerosol; Mivis; Radiative transfer model ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 20
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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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  • 21
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    First historical evidence of a significant Mt.Etna eruption in 1224 (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The 1224 Mt. Etna eruption is a significant event both in terms of the mass of erupted materials and because it involved the lower eastern slope of the volcano, reaching down to the sea. Nevertheless, it is unknown to current historical catalogues. According to the historical sources, only two other lava flows actually reached as far as the sea: in 396 BC, just north of the present-day inhabited area of Acireale, according to the geological data alone, and in 1669, when the lava covered the south-eastern flank of Mt. Etna and damaged Catania. We present and discuss the two medieval sources that attest to the eruption of 1224 and make available the original texts. Furthermore, through the close analysis of the historical and topographic context of the Etna area, taking account of the roads and ports in the early 13th century, we have tried to single out the possible area of the lava's outlet into the sea in 1224 on historical grounds. A repeat of an eruption similar to that of 1224 would have a serious impact to day as the coast is densely populated.
    Description: Published
    Description: 693-700
    Description: 3.10. Sismologia storica e archeosismologia
    Description: JCR Journal
    Description: open
    Keywords: historical volcanology ; Etna ; medieval eruptions ; historical catalogues ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 22
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    Explosive volcanism in the central Mediterranean area during the late Quaternary-linking sources and distal archives (2008)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: no abstract
    Description: Published
    Description: V–VII
    Description: 3.5. Geologia e storia dei sistemi vulcanici
    Description: JCR Journal
    Description: reserved
    Keywords: Explosive volcanism ; distal archives ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 23
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    Geochemical evaluation of observed changes in volcanic activity during the 2007 eruption at Stromboli (Italy) (2009)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: On February 27, 2007 a new eruption started at Stromboli that lasted until April 2 and included a paroxysmal explosion on March 15. Geochemical monitoring carried out over several years revealed some appreciable variations that preceded both the eruption onset and the explosion. The carbon dioxide (CO2) flux from the soil at Pizzo Sopra La Fossa markedly increased a few days before the eruption onset, and continued during lava effusion to reach its maximum value (at 90,000 g m−2 d−1) a few days before the paroxysm. Almost contemporarily, the δ13CCO2 of the SC5 fumarole located in the summit area increased markedly, peaking just before the explosion (δ13CCO2~−1.8‰). Following the paroxysm, helium (He) isotopes measured in the gases dissolved in the basal thermal aquifer sharply increased. Almost contemporarily, the automatic station of CO2 flux recorded an anomalous degassing rate. Also temperatures and the vertical thermal gradient, which had been measured since November 2006 in the soil at Pizzo Sopra La Fossa, showed appreciable variabilities that lasted until the end of the eruption. The geochemical variations indicated the degassing of a new batch of volatile-rich magma that preceded and probably fed the paroxysm. The anomalous 3He/4He ratio suggested that the ascent of a second batch of volatile-rich magma toward the surface was probably responsible of the resumption of the ordinary activity. A comparison with the geochemical variations observed during the 2002–2003 eruption indicated that the 2007 eruption was less energetic.
    Description: Published
    Description: 246-254
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: geochemistry ; eruption ; dissolved gases ; Stromboli ; volcanic activity ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 24
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 25
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 26
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    Scaling characteristics of local geomagnetic field and seismicity at Etna volcano and their dynamics in relation to the eruptive activity (2005)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The evolution of scaling characteristics of the local geomagnetic field and of the seismicity at Etna volcano is studied in relation to the strong eruptive activity occurred here from 2000 to 2002. Scaling laws are found in the hourly time variability of magnetic data and in the seismicity pattern. The scaling exponents suggest the presence of persistent temporal fluctuations. Clear links between the dynamics of the measured data and the eruptive volcanic episodes are revealed. Fractal dimensions of seismicity seem to be always correlated to the beginning of main eruptive events, while strong alterations of the dynamics of the local magnetic field take place only when the eruptive fractures opened very close to the magnetic sites.
    Description: Published
    Description: 96-106
    Description: partially_open
    Keywords: scaling characteristics ; volcanic eruptions ; geomagnetic field ; seismic activity ; Mt. Etna ; 04. Solid Earth::04.05. Geomagnetism::04.05.02. Geomagnetic field variations and reversals ; 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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  • 27
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 28
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    Open-path FTIR spectroscopy of magma degassing processes during eight lava fountains on Mount Etna (2015)
    Elsevier
    Details
    Publication Date: 2020-02-24
    Description: In June–July 2001 a series of 16 discrete lava fountain paroxysms occurred at the Southeast summit crater (SEC) of Mount Etna, preceding a 28-day long violent flank eruption. Each paroxysm was preceded by lava effusion, growing seismic tremor and a crescendo of Strombolian explosive activity culminating into powerful lava fountaining up to 500m in height. During 8 of these 16 events we could measure the chemical composition of the magmatic gas phase (H2O, CO2, SO2, HCl, HF and CO), using open-path Fourier transform infrared (OP-FTIR) spectrometry at ∼1–2km distance from SEC and absorption spectra of the radiation emitted by hot lava fragments. We show that each fountaining episode was characterized by increasingly CO2-rich gas release, with CO2/SO2and CO2/HCl ratios peaking in coincidence with maxima in seismic tremor and fountain height, whilst the SO2/HCl ratio showed a weak inverse relationship with respect to eruption intensity. Moreover, peak values in both CO2/SO2ratio and seismic tremor amplitude for each paroxysm were found to increase linearly in proportion with the repose interval (2–6 days) between lava fountains. These observations, together with a model of volatile degassing at Etna, support the following driving process. Prior to and during the June–July 2001 lava fountain sequence, the shallow (∼2km) magma reservoir feeding SEC received an increasing influx of deeply derived carbon dioxide, likely promoted by the deep ascent of volatile-rich primitive basalt that produced the subsequent flank eruption. This CO2-rich gas supply led to gas accumulation and overpressure in SEC reservoir, generating a bubble foam layer whose periodical collapse powered the successive fountaining events. The anti-correlation between SO2/HCl and eruption intensity is best explained by enhanced syn-eruptive degassing of chlorine from finer particles produced during more intense magma fragmentation.
    Description: Published
    Description: 123-134
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: FTIR remote sensing ; lava fountains ; gas composition ; magma degassing ; separate CO2transfer ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
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  • 29
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    The Campanian Ignimbrite and Codola tephra layers: Two temporal/stratigraphic markers for the Early Upper Palaeolithic in southern Italy and eastern Europe (2008)
    Elsevier
    Details
    Publication Date: 2020-02-24
    Description: Tephra layers from archaeological sites in southern Italy and eastern Europe stratigraphically associated with cultural levels containing Early Upper Palaeolithic industry were analysed. The results confirm the occurrence of the Campanian Ignimbrite tephra (CI; ca. 40 cal ka BP) at Castelcivita Cave (southern Italy), Temnata Cave (Bulgaria) and in the Kostenki–Borshchevo area of the Russian Plain. This tephra, originated from the largest eruption of the Phlegrean Field caldera, represents the widest volcanic deposit and one of the most important temporal/stratigraphic markers of western Eurasia. At Paglicci Cave and lesser sites in the Apulia region we recognise a chemically and texturally different tephra, which lithologically, chronologically and chemically matches the physical and chemical characteristics of the Plinian eruption of Codola; a poorly known Late Pleistocene explosive event from the Neapolitan volcanoes, likely Somma–Vesuvius. For this latter, we propose a preliminary age estimate of ca. 33 cal ka BP and a correlation to the widespread C-10 marine tephra of the central Mediterranean. The stratigraphic position of both CI and Codola tephra layers at Castelcivita and Paglicci help date the first and the last documented appearance of Early Upper Palaeolithic industries of southern Italy to ca. 41–40 and 33 cal ka BP, respectively, or between two interstadial oscillations of the Monticchio pollen record – to which the CI and Codola tephras are physically correlated – corresponding to the Greenland interstadials 10–9 and 5. In eastern Europe, the stratigraphic and chronometric data seem to indicate an earlier appearance of the Early Upper Palaeolithic industries, which would predate of two millennia at least the overlying CI tephra. The tephrostratigraphic correlation indicates that in both regions the innovations connected with the so-called Early Upper Palaeolithic – encompassing subsistence strategy and stone tool technology – appeared and evolved during one of the most unstable climatic phases of the Last Glacial period. On this basis, the marked environmental unpredictability characterising this time-span is seen as a potential ecological factor involved in the cultural changes observed.
    Description: Published
    Description: 208–226
    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: Campanian Ignimbrite ; Early Upper Palaeolithic ; Codola Plinian eruption ; south-eastern Europe ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 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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  • 30
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    A case history of paroxysmal explosion at Stromboli: Timing and dynamics of the April 5, 2003 event (2007)
    Elsevier
    Details
    Publication Date: 2023-01-16
    Description: On April 5, 2003, Stromboli volcano (Italy) produced the most violent explosion of the past 50 years. The event was exceptionally well documented thanks to the presence on the island of several scientists and a large number of instruments deployed over the preceding months to monitor the effusive eruption that began in December 2002. Integration of visual documentation, deposit features and geophysical data allowed an accurate reconstruction of the explosive event and its dynamics. The eruption consisted of a 8-min long explosive event which evolved through four phases whose timing was precisely recorded by an infrared thermometer located about 450 m from the summit crater. Phases 2 and 3 lasted 39 and 42 s, respectively. Both had an impulsive character, were responsible for ejecting almost the entire mass of the pyroclastic products. Phases 1 and 4 represented, respectively, a short-lived precursory event and a waning tale. During Phase 2, meter-sized ballistic blocks were launched with velocities of 170 m/s to altitudes of up to 1400 m above the craters. These fell on the volcano flanks and on the village of Ginostra, about 2 km distant from the vent. A vertical jet rose above the craters which developed to feed a convective plume that reached a height of up to 4 km. The calculated mass of the Phase 2 fallout deposit and mass discharge rate were 1.1–1.4×108 kg and 2.8– 3.6×106 kg/s, respectively. During Phase 3 a scoria flow deposit, with an estimated volume of 0.9–1.1×104 m3, was erupted from the same vent that fed the ongoing sustained lava flow. The average mass discharge rate for this phase was 2.5–3.1×105 kg/s. Products emitted during Phases 2 and 3 consisted of lithic and fresh magmatic material in similar proportions. The juvenile fraction consisted of a deep-originated, almost aphyric, highly vesicular pumice mingled with a shallow-derived, crystal-rich, moderately vesicular scoria. Similarities with the eruption dynamics of other historical paroxysms at Stromboli makes the April 5, 2003 explosion representative of these highly energetic events that constitute the most hazardous volcanic phenomena at Stromboli volcano.
    Description: Published
    Description: 594-606
    Description: JCR Journal
    Description: reserved
    Keywords: stromboli ; Thermal monitoring; paroxysm ; explosive dynamics ; ballistic ejecta ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 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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  • 31
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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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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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
    Details
    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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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    D-serine transporter in Staphylococcus saprophyticus identified (2016)
    Oxford University Press
    Details
    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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 35
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    Contribution of chloride channel permease to fluoride resistance in Streptococcus mutans (2016)
    Oxford University Press
    Details
    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
    Print ISSN: 0378-1097
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  • 36
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    Nicotinamide cofactor ratios in engineered strains of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum (2016)
    Oxford University Press
    Details
    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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 37
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    Cadmium-induced cell killing in Sacharomyces cerevisiae involves increases in intracellular NO levels (2016)
    Oxford University Press
    Details
    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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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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.
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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.
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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.
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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.
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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.
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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/ .
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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).
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
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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.
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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.
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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
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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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.
    Keywords: Physiology & Biochemistry
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