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  • Physiology & Biochemistry  (57)
  • 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring  (22)
  • Oxford University Press  (57)
  • American Geophysical Union  (20)
  • INGV  (1)
  • Molecular Diversity Preservation International  (1)
  • 2015-2019  (79)
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  • 1945-1949
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  • 1
    Publication Date: 2020-12-14
    Description: Explosive volcanic eruptions are defined as the violent ejection of gas and hot fragments from a vent in the Earth's crust. Knowledge of ejection velocity is crucial for understanding and modeling relevant physical processes of an eruption, and yet direct measurements are still a difficult task with largely variable results. Here we apply pioneering high-speed imaging to measure the ejection velocity of pyroclasts from Strombolian explosive eruptions with an unparalleled temporal resolution. Measured supersonic velocities, up to 405 m/s, are twice higher than previously reported for such eruptions. Individual Strombolian explosions include multiple, sub-second-lasting ejection pulses characterized by an exponential decay of velocity. When fitted with an empirical model from shock-tube experiments literature, this decay allows constraining the length of the pressurized gas pockets responsible for the ejection pulses. These results directly impact eruption modeling and related hazard assessment, as well as the interpretation of geophysical signals from monitoring networks.
    Description: INGV-DPC “V2” and “Paroxysm”, FIRB-MIUR “Research and Development of New Technologies for Protection and Defense of Territory from Natural Risks”, and FP7-PEOPLE-IEF-2008 – 235328 Projects
    Description: Published
    Description: L02301
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: strombolian ; ejection velocity ; explosive eruption ; 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::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-02-10
    Description: Continuous gravity data collected near the summit eruptive vent at Kīlauea Volcano, Hawaiʻi, during 2011–2015 show a strong correlation with summit-area surface deformation and the level of the lava lake within the vent over periods of days to weeks, suggesting that changes in gravity reflect variations in volcanic activity. Joint analysis of gravity and lava level time series data indicates that over the entire time period studied, the average density of the lava within the upper tens to hundreds of meters of the summit eruptive vent remained low—approximately 1000–1500 kg/m^3. The ratio of gravity change (adjusted for Earth tides and instrumental drift) to lava level change measured over 15 day windows rose gradually over the course of 2011–2015, probably reflecting either (1) a small increase in the density of lava within the eruptive vent or (2) an increase in the volume of lava within the vent due to gradual vent enlargement. Superimposed on the overall time series were transient spikes of mass change associated with inflation and deflation of Kīlauea’s summit and coincident changes in lava level. The unexpectedly strong mass variations during these episodes suggest magma flux to and from the shallow magmatic system without commensurate deformation, perhaps indicating magma accumulation within, and withdrawal from, void space—a process that might not otherwise be apparent from lava level and deformation data alone. Continuous gravity data thus provide unique insights into magmatic processes, arguing for continued application of the method at other frequently active volcanoes.
    Description: Published
    Description: 5477–5492
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Kīlauea Volcano; gravity changes; lava lake; volcano monitoring ; 04. Solid Earth::04.02. Exploration geophysics::04.02.02. Gravity methods ; 04. Solid Earth::04.03. Geodesy::04.03.05. Gravity variations ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
    Publication Date: 2021-03-01
    Description: A new period of eruptive activity started at Turrialba volcano, Costa Rica, in 2010 after almost 150 years of quiescence. This activity has been characterized by sporadic explosions whose frequency clearly increased since October 2014. This study aimed to identify the mechanisms that triggered the resumption of this eruptive activity and characterize the evolution of the phenomena over the past 2 years. We integrate 3He/4He data available on fumarole gases collected in the summit area of Turrialba between 1999 and 2011 with new measurements made on samples collected between September 2014 and February 2016. The results of a petrological investigation of the products that erupted between October 2014 and May 2015 are also presented. We infer that the resumption of eruptive activity in 2010 was triggered by a replenishment of the plumbing system of Turrialba by a new batch of magma. This is supported by the increase in 3He/4He values observed since 2005 at the crater fumaroles and by comparable high values in September 2014, just before the onset of the new eruptive phase. The presence of a number of fresh and juvenile glassy shards in the erupted products increased between October 2014 and May 2015, suggesting the involvement of new magma with a composition similar to that erupted in 1864–1866. We conclude that the increase in 3He/4He at the summit fumaroles since October 2015 represents strong evidence of a new phase of magma replenishment, which implies that the level of activity remains high at the volcano.
    Description: Published
    Description: 3V. Proprietà dei magmi e dei prodotti vulcanici
    Description: 4V. Dinamica dei processi pre-eruttivi
    Description: 5V. Dinamica dei processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: Turrialba volcano ; eruptive activity ; 3He/4He ; fumarole gases ; glassy shards ; juvenile component ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.08. Volcanic arcs ; 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::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 4
    Publication Date: 2020-12-15
    Description: We have analyzed a focal mechanism data set for Mount Vesuvius, consisting of 197 focal mechanisms of events recorded from 1999 to 2012. Using different approaches and a comparison between observations and numerical models, we have determined the spatial variations in the stress field beneath the volcano. The main results highlight the presence of two seismogenic volumes characterized by markedly different stress patterns. The two volumes are separated by a layer where the seismic strain release shows a significant decrease. Previous studies postulated the existence, at about the same depth, of a ductile layer allowing the spreading of the Mount Vesuvius edifice. We interpreted the difference in the stress pattern within the two volumes as the effect of a mechanical decoupling caused by the aforementioned ductile layer. The stress pattern in the top volume is dominated by a reverse faulting style, which agrees with the hypothesis of a seismicity driven by the spreading process. This agrees also with the persistent character of the seismicity located within this volume. Conversely, the stress field determined for the deep volume is consistent with a background regional field locally perturbed by the effects of the topography and of heterogeneities in the volcanic structure. Since the seismicity of the deep volume shows an intermittent behavior and has shown to be linked to geochemical variations in the fumaroles of the volcano, we hypothesize that it results from the effect of fluid injection episodes, possibly of magmatic origin, perturbing the pore pressure within the hydrothermal system.
    Description: Published
    Description: 1181–1199
    Description: 4T. Fisica dei terremoti e scenari cosismici
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: vesuvius ; stress inversion ; focal mechanisms ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 5
    Publication Date: 2021-04-07
    Description: Integrating geodetic, seismic, and petrological data for a recent eruptive episode at Mount Etna has enabled us to define the history of magma storage and transfer within the multilevel structure of the volcano, providing spatial and temporal constraints for magma movements before the eruption. Geodetic data related to the July–August 2014 activity provide evidence of a magma reservoir at ~4 km below sea level. This reservoir pressurized from late March 2014 and fed magmas that were then erupted from vents on the lower eastern flank of North-East Crater (NEC) and at New South-East Crater (NSEC) summit crater during the July eruptive activity. Magma drainage caused its depressurization since mid-July. Textural and microanalytical data obtained from plagioclase crystals indicate similar disequilibrium textures and compositions at the cores in lavas erupted at the base of NEC and NSEC, suggesting comparable deep histories of evolution and ascent. Conversely, the compositional differences observed at the crystal rims have been associated to distinct degassing styles during storage in a shallow magma reservoir. Seismic data have constrained depth for a shallow part of the plumbing system at 1–2 km above sea level. Timescales of magma storage and transfer have also been calculated through diffusion modeling of zoning in olivine crystals of the two systems. Our data reveal a common deep history of magmas from the two systems, which is consistent with a recharging phase by more mafic magma between late March and early June 2014. Later, the magma continued its crystallization under distinct chemical and physical conditions at shallower levels.
    Description: The petrological part of this study was supported by the FIR 2014 research grant to Marco Viccaro from the University of Catania (Italy), grant number 2F119B, title of the project “Dynamics of evolution, ascent and emplacement of basic magmas: case-studies from eruptive manifestations of Eastern Sicily”.
    Description: Published
    Description: 5659–5678
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Petrology ; eruption ; GPS ; volcano seismology ; Etna ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.03. Geodesy::04.03.07. Satellite geodesy ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 6
    Publication Date: 2017-04-04
    Description: A new eruption started at Stromboli on August 6, 2014, which had been preceded by 2 months of increased Strombolian activity and several lava overflows from the craters. The eruption was characterized by a lava effusion in Sciara del Fuoco from a fracture at 650 m a.s.l. that lasted until November 13–17. Here we present the first geochemical observations of this eruption, based on the soil CO2 flux in the summit area, and on 3He/4He ratios in the thermal waters near Stromboli village. We infer that this eruption was triggered by the gradual replenishment of the feeding system by a CO2- and 3He-rich magma at the end of 2013 and after June 2014, suggested by the increase in 3He/4He ratio before eruption, which reached its highest value since 2007. We thus infer that this eruption was unusual and we finally speculate on the evolutionary scenario of post eruption.
    Description: Published
    Description: 2235–2243
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: Stromboli ; eruption ; soil CO2 flux ; 3He/4He ratio ; thermal waters ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 7
    Publication Date: 2017-04-04
    Description: The marine sector of the Campi Flegrei caldera has started to be monitored over the long-term with a seafloor equipment deployed in the Gulf of Pozzuoli from 2008. The equipment includes a set of geophysical, oceanographic and environmental sensors integrated in a marine platform that was specifically designed for real-time monitoring. This platform, named CUMAS (Cabled Underwater Multidisciplinary Acquisition System), was installed in the center of the Gulf at about 2.5 km south of Pozzuoli where the sea depth is about 100 m [Iannaccone et al., 2010]. The CUMAS system consists of a seafloor module connected by cable to a buoy (elastic beacon type) equipped with autonomous power supply systems, real-time data- transmission devices and a weather station. The core of CUMAS is the seafloor module that contains geophysical and oceanographic sensors, in particular, a three-component broadband seismometer, a best in class three axis MEMS accelerometer, a low-frequency hydrophone and a high-resolution sea bottom pressure recorder. A single-point acoustic, three-component, water-current meter and a water-temperature sensor were also installed to monitor some water local physical parameters. A set of status sensors, which also included a digital compass and a two-component digital tilt-meter, were added to track the attitude of the module over the course of the experiment. The marine monitoring system transmits the data in real-time and is integrated into the Monitoring Center in Naples managed by INGV-Osservatorio Vesuviano. A continuous GPS station has been installed since the end of 2011 on the top of the buoy. The elastic beacon buoy forms a structure which is rigidly connected by a mechanical cable to the ballast on the sea bottom, a submerged float at the base of the buoy maintains tension on the cable and ensure the overall buoyancy of the system. In this way, any vertical movement of the seafloor propagates rigidly to the emerged part of the buoy itself, allowing measurement of the vertical movement of the sea floor by the GPS station. The analysis of about 17 months of continuous GPS data, from January 2012 to May 2013, revealed an overall uplift of about 3-4 cm allowing a first measurement of vertical seafloor displacement in the Campi Flegrei caldera [De Martino et al., 2014]. A new opportunity to enhance the deployed system was given by a national project, EMSO-MedIT, which is providing the necessary resources to expand the data acquisition to other areas of the Gulf of Pozzuoli. New improved systems similar to CUMAS are going to be deployed in three additional marine sites of the Gulf of Pozzuoli and the existing tide gauges network will be renewed with state-of-art sensors. The overall new monitoring infrastructure will allow to extensively map the seafloor vertical displacement and to improve the interpretative models of the bradyseism phenomenon including a more accurate location of earthquakes in the marine areas and extending to lower magnitude values the detection of the seismic activity.
    Description: INGV, Comune di Nicolosi, Parco dell'Etna, Funivia dell'Etna
    Description: Published
    Description: Nicolosi (Catania) -I TALY
    Description: 1IT. Reti di monitoraggio e Osservazioni
    Description: open
    Keywords: Monitoring System in Marine Sector ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 8
    Publication Date: 2020-02-24
    Description: This work arises from the field observations made during the civil protection emergency period connected to the 2007 Stromboli eruption. We observed changes in the shallow feeding system of the volcano to which we give a volcanological interpretation and the relative implications. Here we describe the processes that occurred in the upper feeding system from the end of the 2007 effusive eruption on 3 April to the renewal of the strombolian explosive activity at the summit craters (30 June), interpreted using multidisciplinary data. We used thermal camera data collected both from helicopter and from a fixed station at 400 m to retrieve the evolving summit crater activity. These data, compared with seismic signals and published geochemical records, allowed us to detail the shifting of the degassing activity within the crater terrace from NE to SW, occurred between 15 and 25 April 2007 prior to the resumption of the strombolian activity. In particular, from mid-April, a gradual SW displacement in the maximum apparent temperatures was recorded at the vents within the summit craters, together with a change in the very long period location and confirmed by variations in geochemical indicators (CO2∕SO2 plume ratios and CO2 fluxes) from literature. The shallow feeding system experienced a major readjustment after the end of the effusive activity, determining variations in the pressure leakage of the source, slowly deepening and shifting toward SW. All these data, together with the framework supplied by previous structural surveys, allowed us to propose that the compaction of debris accumulated in the uppermost conduit by inward crater collapses, occurred in early March, produced the observed anomalies. At Stromboli, major morphology changes, taking place in the following years, were anticipated by these small and apparently minor processes occurred in the upper feeding system. Other studies are relating similar changes to modifications of the eruptive activity also at other open-conduit volcanoes, so we believe that it may be important to have a constant monitoring of these phenomena in order to better understand their shallow feeding systems.
    Description: This paper was partially supported by a grant to S.C. (Project INGV-DPC Paroxysm V2/03, 2008–2010) funded by the Istituto Nazionale di Geofisica e Vulcanologia and by the Italian Civil Protection.
    Description: Published
    Description: 7376–7395
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Stromboli volcano ; thermal imaging ; multidisciplinary study ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 9
    Publication Date: 2017-04-04
    Description: An array of nine three-component broadband seismometers was deployed in two different configurations on Stromboli volcano. The analysis of the seismic wavefield related to volcanic explosions revealed some observations which offer a completely new insight into the internal dynamics of a volcano. These new observations are restricted to the low-frequency range below 1 Hz and underline, therefore, the superiority of broadband recordings over conventional short-period observations. Surprisingly simple wavelets indicate an initially contracting source mechanism. Gas-jets that could not be seen in a short-period seismic record at all, generate a clear dilatational wavelet in a broadband recording suggesting the same contracting source mechanism. The analysis of particle motion and seismic array techniques permits a location of the seismic source. We find low-frequency signals of 3s and 6s period that are not related to eruptions and do not share a common source with the eruption-related events. A video recording of visible volcanic activity at the crater region allows one to correlate precisely eruptive features with seismic signals.
    Description: Published
    Description: 749-752
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: N/A or not JCR
    Description: restricted
    Keywords: Stromboli ; volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-04
    Description: High-speed imaging of explosive eruptions at Stromboli (Italy), Fuego (Guatemala), and Yasur (Vanuatu) volcanoes allowed visualization of pressure waves from seconds-long explosions. From the explosion jets, waves radiate with variable geometry, timing, and apparent direction and velocity. Both the explosion jets and their wave fields are replicated well by numerical simulations of supersonic jets impulsively released from a pressurized vessel. The scaled acoustic signal from one explosion at Stromboli displays a frequency pattern with an excellent match to those from the simulated jets. We conclude that both the observed waves and the audible sound from the explosions are jet noise, i.e., the typical acoustic field radiating from high-velocity jets. Volcanic jet noise was previously quantified only in the infrasonic emissions from large, sub-Plinian to Plinian eruptions. Our combined approach allows us to define the spatial and temporal evolution of audible jet noise from supersonic jets in small-scale volcanic eruptions.
    Description: INGV-DPC “V2” and “Paroxysm,” FIRB-MIUR “Research and Development of New Technologies for Protection and Defense of Territory from Natural Risks,” and FP7-PEOPLE-IEF-2008–235328 “NEMOH” ITN projects
    Description: Published
    Description: 3096–3102
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: jet noise ; volcano acoustics ; Stromboli ; Yasur ; Fuego ; strombolian eruption ; 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 ; 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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  • 11
    Publication Date: 2017-04-04
    Description: The fumarolic gas output has not been quantified for any of the currently deforming calderas worldwide, due to the lack of suitable gas flux sensing techniques. In view of resumption of ground uplift (since 2005) and the associated variations in gas chemistry, Campi Flegrei, in southern Italy, is one of the restless calderas where gas flux observations are especially necessary. Here we report the first ever obtained estimate of the Campi Flegrei fumarolic gas output, based on a set of MultiGAS surveys (performed in 2012 and 2013) with an ad-hoc-designed measurement setup. We estimate that the current Campi Flegrei fumarolic sulphur (S) flux is low, on the order of 1.5–2.2 tons/day, suggesting substantial scrubbing of magmatic S by the hydrothermal system. However, the fumarolic carbon dioxide (CO2) output is ∼460±160 tons/day (mean±SD), which is surprisingly high for a dormant volcano in the hydrothermal stage of activity, and results in a combined (fumaroles + soil) CO2 output of ∼1560 tons/day. Assuming magma to be the predominant source, we propose that the current CO2 output can be supplied by either (i) a large (0.6–4.6 km3), deeply stored (〉7 km) magmatic source with low CO2 contents (0.05–0.1 wt%) or (ii) by a small to medium-sized (∼0.01–0.1 km3) but CO2-rich (2 wt%) magma, possibly stored at pressures of ∼100 to 120 MPa. Independent geophysical evidence (e.g., inferred from geodetic and gravity data) is needed to distinguish between these two possibilities.
    Description: Published
    Description: 4153–4169
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Campi Flegrei ; calderas ; gas output ; 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::04.08.06. 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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2017-04-04
    Description: The interpretation of dynamic processes that occur in volcanic calderas is not simple. The ground deformations and the local seismicity, which in other volcanic contexts are usually regarded as precursors to eruption, in caldera environment in many cases are not followed by any eruption. We formulate a general hypothesis that can explain these behaviors. Our hypothesis is that the intrusion of a sill can be responsible for the dynamics observed during unrest at calderas. In order to investigate the reliability of this hypothesis, we developed a dynamic model of sill intrusion in a shallow volcanic environment. In our model, the sill, fed by a deeper magma reservoir, intrudes below a horizontal elastic plate, representing the overlying rocks, and expands with axisymmetric geometry. The model is based on the numerical solution of the equation for the elastic plate, coupled with a Navier-Stokes equation for simulating the dynamics of the sill intrusion. We performed a number of simulations, with the objective of showing the main features of the model. In the experiments, when the feeding process stops, the vertical movement reverses its trend and the area of maximum uplift undergoes subsidence. Under certain conditions the subsidence can occur even during the intrusion of the sill. The stress field produced by the intrusion is mainly concentrated in a circular zone that follows the sill intrusion front. The features predicted by the model are consistent with many observations carried out on different calderas as reported in the scientific literature.
    Description: Published
    Description: 3986–4000
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: sill intrusion ; caldera ; volcano geodesy ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.05. Mathematical geophysics::05.05.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 13
    Publication Date: 2017-04-04
    Description: Mt Etna volcano (Italy) typically generates lava fountains and Strombolian eruptions from the summit craters, producing significant emissions of tephra which may cause moderate to high impact both in the atmosphere and on the ground. However, we have also witnessed a number of minor ash emissions that, although far less powerful, may pose considerable volcanic hazards. In this paper, we deal with three ash emissions occurring in 2010 (8 April at Southeast Crater, 25 August at Bocca Nuova, and 14–15 November at Northeast Crater), correlating their volcanological features with the associated seismoacoustic signals. We provide details regarding the chronology, eruption column, dispersal of the deposit, and texture (grain size, componentry and morphology) of the emitted ash. Each eruptive episode has also been characterized by means of seismo-acoustic analyses evaluating the volcanic acoustic-seismic ratio (VASR). Furthermore, the source of volcanic tremor recorded from March to December 2010 was localized. The joint volcanological and seismo-acoustic analyses allowed distinguishing two main kinds of ash emissions: types a (8 April and 25 August) and b (14–15 November). Regarding the former, the accumulation of gas below a dense cap rock obstructing the conduit vent, giving rise, with the uncorking, to impulsive explosivity, was hypothesized. The latter type instead is characterized by a longer-lasting and less explosivity, likely due to the existence of open conduit conditions. Therefore, type b ash emissions are less hazardous than type a. This simple model, regarding minor explosive activity, may constitute a starting point to assess the volcanic risk from unexpected explosions.
    Description: Published
    Description: 51-70
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: reserved
    Keywords: Mt Etna ; seismo-acoustic signals ; ash emissions ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2017-04-04
    Description: Between January 2011 and April 2013, Mt. Etna's eruptive activity consisted of episodic intra-crater strombolian explosions and paroxysms from Bocca Nuova, Voragine, and the New South-East (NSEC) summit craters, respectively. Eruptions from NSEC consisted of initial increasing strombolian activity and lava flow output, passing to short-lasting lava fountaining. In this study we present seismic, infrasound, radiometric, plume SO2 and HCl fluxes and geodetic data collected by the INGV monitoring system between May 2012 and April 2013. The multi-parametric approach enabled characterization of NSEC eruptive activity at both daily and monthly time scales and tracking of magma movement within Mt. Etna's plumbing system. While seismic, infrasound and radiometric signals give insight on the energy and features of the 13 paroxysms fed by NSEC, SO2 and halogen fluxes shed light on the likely mechanisms triggering the eruptive phenomena. GPS data provided clear evidence of pressurization of Mt. Etna's plumbing system from May 2012 to middle February 2013 and depressurization during the February-April 2013 eruptive activity. Taking into account geochemical data, we propose that the paroxysms' sequence represented the climax of a waxing-waning phase of degassing that had started as early as December 2012, and eventually ended in April 2013. Integration of the multidisciplinary observations suggests that the February-April 2013 eruptive activity reflects a phase of release of a volatile-rich batch of magma that had been stored in the shallow volcano plumbing system at least four months before, and with the majority of gas released between February and March 2013. This article is protected by copyright. All rights reserved.
    Description: European FP7 MED-SUV (MEditerranean SUpersite Volcanoes). Grant Number: 308665 European Research Council European FP7 (FP/2007-2013)/ERC. Grant Number: 279802 SIGMA (Sistema Integrato di sensori in ambiente cloud per la Gestione Multirischio Avanzata)
    Description: Published
    Description: 1932–1949
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Mt. Etna ; paroxysmal activity ; SO2 and HCl fluxes ; infrasound and seismic signals ; radiometry ; ground deformation ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    Publication Date: 2017-04-04
    Description: We present the results of laboratory experiments on the aggregation and disaggregation of colliding volcanic ash particles. Ash particles of different composition and size 〈90 µm were held in turbulent suspension and filmed in high speed while colliding, aggregating, and disaggregating, forming a growing layer of electrostatically bound particles along a vertical plate. At room conditions and regardless of composition, 60–80% of the colliding particles smaller than 32 µm remained aggregated. In contrast, aggregation of particles larger than 63 µm was negligible, and, when a layer formed, periods when disaggregation (mainly by collisions or drag) exceeded aggregation occurred twice as frequently than for smaller particles. An empirical relationship linking the aggregation index, i.e., the effective fraction of aggregated particles surviving disaggregation, to the mean particle collision kinetic energy is provided. Our results have potential implications on the dynamics of volcanic plumes and ash mobility in the environment.
    Description: INGV-DPC project V1 “Probabilistic evaluation of volcanic hazard”; EU Seventh Programme FP7 “MED-SUV” grant agreement 308665
    Description: Published
    Description: 1068–1075
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 2IT. Laboratori sperimentali e analitici
    Description: JCR Journal
    Description: restricted
    Keywords: volcanic ash ; disaggregation ; experimental modeling ; volcanic plumes ; aggregation processes ; colliding particles ; sticking rate ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
    Publication Date: 2017-04-04
    Description: Piton de la Fournaise (PdF) is recognised as one of the world’s most active volcanoes in terms of eruptive frequency and the substantial quantity of lava produced. Yet, with the sole exception of rather modest intracrateric fumarole activity, this seems to be in contrast with an apparent absence of any type of natural fluid emission during periods of quiescence. Measurement campaigns were undertaken during a long-lasting quiescent period (2012-2014) and just after a short lived summit eruption (June 2014) in order to identify potential degassing areas in relation to the main structural features of the volcano (ex. rift zones) with the aim of developing a broader understanding of the geometry of the plumbing and degassing system. In order to assess the possible existence of anomalous soil CO2 flux, 513 measurements were taken along transects roughly orthogonal to the known tectonic lineaments crossing PdF edifice. In addition, 53 samples of gas for C isotope analysis were taken at measurement points that showed a relatively high CO2 concentration in the soil. CO2 flux values range from 10 to 1300 g m-2 d-1 while 13C are between -26.6 to -8‰. The results of our investigation clearly indicate that there is a strong spatial correlation between the anomalous high values of diffusive soil emissions and the main rift zones cutting the PdF massif and, moreover, that generally high soil CO2 fluxes show a d13C signature clearly related to a magmatic origin.
    Description: INSU (CNRS) and La Réunion Préfecture (Projet pour la quantification de l’aléa volcanique à La Réunion)
    Description: Published
    Description: 4388–4404
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: CO2 soil degassing anomalies at Piton de la Fournaise ; d13C magmatic signature ; Close link between anomalous CO2 degassing and the main seismotectonic structures ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 17
    Publication Date: 2017-04-04
    Description: This paper focuses on the chemical composition changes in soil gases through both a theoretical model and laboratory experiments. The model describes the one-dimensional mass transfer process, which is triggered by changes in the flux parameters of the system, and the time-dependent evolution of the composition of the soil gases as a function of i) the pristine gas mixture, ii) the diffusivity of the chemicals, and iii) the thickness of the transited medium. Carbon dioxide (CO2), hydrogen (H2), and helium (He) were used in a laboratory-scale flux simulator to investigate the evolution of the gas composition profile in an artificial soil of constant thickness. The agreement between the theoretical calculations and the experimental results supports the validity of the model. Our results indicate a good reproducibility of the transient changes in the concentrations of CO2, He, and H2 in CO2-rich gas mixtures that contain He and H2 as trace gases. Finally, the theoretical results were used to analyze the H2 and CO2 continuous monitoring data collected at Etna volcano in 2010
    Description: Published
    Description: 1565–1583
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: 1IT. Reti di monitoraggio e Osservazioni
    Description: JCR Journal
    Description: open
    Keywords: Soil gases ; Volcanic gas composition ; Hydrogen ; Carbon dioxide ; CO2 ; Helium ; 03. Hydrosphere::03.04. Chemical and biological::03.04.05. Gases ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 18
    Publication Date: 2017-04-04
    Description: On 28 December 2014, eruptive activity resumed at Mount Etna with fire fountain activity feeding two lava flows on the eastern and southwestern upper flanks of the volcano. Unlike all previous summit activity, this eruption produced clear deformation at the summit of the volcano. GPS displacements and Sentinel-1A ascending interferogramswere calculated in order to image the ground deformation pattern accompanying the eruption. The displacements observed by GPS depict a local ground deformation pattern, affecting only the upperpart of the volcano.Despite snowcover onthe summit, differential interferometry synthetic aperture radar (DInSAR) data allowed obtainingmore detail onthe grounddeformation pattern on the upper eastern side of the volcano. Three-dimensional GPS displacements inversion located a very shallow NE-SW intrusion just beneath the New Southeast Crater. However, this model cannot justify all the deformation observed by DInSAR thus revealing a gravitational failure of the lava flow field
    Description: Published
    Description: 2727–2733
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: Sentinel-1A interferogram details the ground deformation field ; GPS data are analyzed for modeling the dyke intrusion ; Data comparison highlights an incipient slope failure ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 19
    Publication Date: 2017-04-04
    Description: During volcanic eruptions, measurements of the rate at which magma is erupted underpin hazard assessments. For eruptions dominated by the effusion of lava, estimates are often made using satellite data; here, in a case study at Mount Etna (Sicily), we make the first measurements based on terrestrial laser scanning (TLS), and we also include explosive products. During the study period (17–21 July 2012), regular Strombolian explosions were occurring within the Bocca Nuova crater, producing a ~50 m-high scoria cone and a small lava flow field. TLS surveys over multi-day intervals determined a mean cone growth rate (effusive and explosive products) of ~0.24 m3·s−1. Differences between 0.3-m resolution DEMs acquired at 10-minute intervals captured the evolution of a breakout lava flow lobe advancing at 0.01–0.03 m3·s−1. Partial occlusion within the crater prevented similar measurement of the main flow, but integrating TLS data with time-lapse imagery enabled lava viscosity (7.4 × 105 Pa·s) to be derived from surface velocities and, hence, a flux of 0.11 m3·s−1 to be calculated. Total dense rock equivalent magma discharge estimates are ~0.1–0.2 m3·s−1 over the measurement period and suggest that simultaneous estimates from satellite data are somewhat overestimated. Our results support the use of integrated TLS and time-lapse photography for ground-truthing space-based measurements and highlight the value of interactive image analysis when automated approaches, such as particle image velocimetry (PIV), fail.
    Description: Published
    Description: 14967 - 14987
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: lava flow; scoria cone; effusion rate; terrestrial laser scanning; time-lapse photography; Mt. Etna ; 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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 20
    Publication Date: 2017-04-04
    Description: To evaluate the volcanic processes leading to the 25–26 October 2013 lava fountain at Mount Etna, we jointly investigated gravity, GPS, and DInSARmeasurements covering the late-June to early-November time interval. We used finite element modeling to infer a shallow magmatic reservoir which (i) inflated since July 2013, (ii) fed the volcanic activity at the summit craters during 25–26 October, and (iii) deflated due to magma drainage related to this volcanic activity. We suggested that this reservoir belongs to a shallow volume, which is located beneath the summit area and is replenished by magma rising from deep reservoirs and fed the short-term volcanic activity, representing a persistent shallow magmatic plumbing system of Etna. In addition, the model results show that there is a large discrepancy between the erupted and shallow reservoir deflation volumes, which could be reasonably attributable to a highly compressible volatile-rich magma.
    Description: Published
    Description: 3246–3253
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: open
    Keywords: Gravity and deformation signatures of the 26 October 2013 Mount Etna lava fountain ; Integrated finite element-based inversion of gravity and GPS data ; Inference on a highly compressible volatile-rich magma in the magmatic reservoir ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 21
    Publication Date: 2021-12-15
    Description: Relationships between frequency and intensity of volcanic eruptions are actively sought by geophysicists for both monitoring and research purposes. By analyzing surveillance videos of persistent volcanic activity at Stromboli (Italy), we derived the frequency and jet height of 〉4000 explosions that occurred in 72 h-long time windows sampled yearly from 2005 to 2009. We found a positive relationship linking explosion frequency and jet height (linked to eruption intensity) when averaging the two parameters over time intervals from hours to days, with a stronger correlation for longer intervals. We interpret this behavior as the response of the magmatic system to variable influx of magma and gas at depth, increased flux at depth causing more frequent and stronger explosions at the surface. This relationship entails concurrent control of source processes over explosion frequency and intensity, directly impacting modeling of explosion sources at persistently active volcanoes in general and hazard assessment at Stromboli in particular.
    Description: DPC-INGV Project V2 “Paroxysm”
    Description: Published
    Description: 1–5
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; Strombolian frequency ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 22
    Publication Date: 2023-01-19
    Description: In situ measurements have been the basis for monitoring volcanic gas emissions for many years and—being complemented by remote sensing techniques—still play an important role to date. Concerning in situ techniques for sampling a dilute plume, an increase in accuracy and a reduction of detection limits are still necessary for most gases (e.g., CO2, SO2, HCl, HF, HBr, HI). In this work, the Raschig-Tube technique (RT) is modified and utilized for application on volcanic plumes. The theoretical and experimental absorption properties of the RT and the Drechsel bottle (DB) setups are characterized and both are applied simultaneously to the well-established Filter packs technique (FP) in the field (on Stromboli Island and Mount Etna). The comparison points out that FPs are the most practical to apply but the results are errorprone compared to RT and DB, whereas the RT results in up to 13 times higher analyte concentrations than the DB in the same sampling time. An optimization of the analytical procedure, including sample pretreatment and analysis by titration, Ion Chromatography, and Inductively Coupled Plasma Mass Spectrometry, led to a comprehensive data set covering a wide range of compounds. In particular, less abundant species were quantified more accurately and iodine was detected for the first time in Stromboli’s plume. Simultaneously applying Multiaxis Differential Optical Absorption Spectroscopy (MAX-DOAS) the chemical transformation of emitted bromide into bromine monoxide (BrO) from Stromboli and Etna was determined to 3–6% and 7%, respectively, within less than 5 min after the gas release from the active vents.
    Description: Published
    Description: 2797–2820
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: plume ; volcano ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 23
    Publication Date: 2016-07-31
    Description: The 16S rRNA gene (16S rDNA) codes for RNA that plays a fundamental role during translation in the ribosome and is used extensively as a marker gene to establish relationships among bacteria. However, the complementary non-coding 16S rDNA (nc16S rDNA) has been ignored. An idea emerged in the course of analyzing bacterial 16S rDNA sequences in search for nucleotide composition and substitution patterns: Does the nc16S rDNA code? If so, what does it code for? More importantly: Does 16S rDNA evolution reflect its own evolution or the evolution of its counterpart nc16S rDNA? The objective of this minireview is to discuss these thoughts. nc strands often encode small RNAs (sRNAs), ancient components of gene regulation. nc16S rDNA sequences from different bacterial groups were used to search for possible matches in the Bacterial Small Regulatory RNA Database. Intriguingly, the sequence of one published sRNA obtained from Legionella pneumophila (GenBank: AE017354.1) showed high non-random similarity with nc16S rDNA corresponding in part to the V5 region especially from Legionella and relatives. While the target(s) of this sRNA is unclear at the moment, its mere existence might open up a new chapter in the use of the 16S rDNA to study relationships among bacteria.
    Keywords: Physiology & Biochemistry
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  • 24
    Publication Date: 2016-08-05
    Description: Thermotolerance of the fungus Fomes sp. EUM1 was evaluated in solid state fermentation (SSF). This thermotolerant strain improved both hyphal invasiveness (38%) and length (17%) in adverse thermal conditions exceeding 30°C and to a maximum of 40°C. In contrast, hyphal branching decreased by 46% at 45°C. The production of cellulases over corn stover increased 1.6-fold in 30°C culture conditions, xylanases increased 2.8-fold at 40°C, while laccase production improved 2.7-fold at 35°C. Maximum production of lignocellulolytic enzymes was obtained at elevated temperatures in shorter fermentation times (8–6 days), although the proteases appeared as a thermal stress response associated with a drop in lignocellulolytic activities. Novel and multiple isoenzymes of xylanase (four bands) and cellulase (six bands) were secreted in the range of 20–150 kDa during growth in adverse temperature conditions. However, only a single laccase isoenzyme (46 kDa) was detected. This is the first report describing the advantages of a thermotolerant white-rot fungus in SSF. These results have important implications for large-scale SSF, where effects of metabolic heat are detrimental to growth and enzyme production, which are severely affected by the formation of high temperature gradients.
    Keywords: Physiology & Biochemistry
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  • 25
    Publication Date: 2016-06-23
    Description: The rhizobacterium Serratia plymuthica 4Rx13 emits the novel and unique volatile sodorifen (C 16 H 26 ), which has a polymethylated bicyclic structure. Transcriptome analysis revealed that gene SOD_c20750 (annotated as terpene cyclase) is involved in the biosynthesis of sodorifen. Here we show that this gene is located in a small cluster of four genes ( SOD_c20750 – SOD_c20780 ), and the analysis of the knockout mutants demonstrated that SOD_c20760 (annotated as methyltransferase) and SOD_c20780 (annotated as isopentenyl pyrophosphate (IPP) isomerase) are needed for the biosynthesis of sodorifen, while a sodorifen-negative phenotype was not achieved with the SOD_c20770 (annotated as deoxy-xylulose-5-phosphate (DOXP) synthase) mutant. Altogether, the function of this new gene cluster was assigned to the biosynthesis of this structurally unusual volatile compound sodorifen.
    Keywords: Physiology & Biochemistry
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  • 26
    Publication Date: 2016-06-23
    Description: Among staphylococci Staphylococcus saprophyticus is the only species that is typically uropathogenic and an important cause of urinary tract infections in young women. The amino acid D-serine occurs in relatively high concentrations in human urine and has a bacteriostatic or toxic effect on many bacteria. In uropathogenic Escherichia coli and S. saprophyticus , the amino acid regulates the expression of virulence factors and can be used as a nutrient. The ability of uropathogens to respond to or to metabolize D-serine has been suggested as a factor that enables colonization of the urinary tract. Until now nothing is known about D-serine transport in S.   saprophyticus . We generated mutants of putative transporter genes in S.   saprophyticus 7108 that show homology to the D-serine transporter cyc A of E. coli and tested them in a D-serine depletion assay to analyze the D-serine uptake rate of the cells. The mutant of SPP1070 showed a strong decrease in D-serine uptake. Therefore, SSP1070 was identified as a major D-serine transporter in S. saprophyticus 7108 and was named D-serine transporter A (DstA). D-serine caused a prolonged lag phase of S. saprophyticus in a chemically defined medium. This negative effect was dependent on the presence of DstA.
    Keywords: Physiology & Biochemistry
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  • 27
    Publication Date: 2016-05-12
    Description: Genes encoding fluoride transporters have been identified in bacterial and archaeal species. The genome sequence of the cariogenic  Streptococcus mutans  bacteria suggests the presence of a putative fluoride transporter, which is referred to as a chloride channel permease. Two homologues of this gene (GenBank locus tags SMU_1290c and SMU_1289c) reside in tandem in the genome of  S. mutans . The aim of this study was to determine whether the chloride channel permeases contribute to fluoride resistance. We constructed SMU_1290c- and SMU_1289c-knockout  S. mutans  UA159 strains. We also constructed a double-knockout strain lacking both genes. SMU_1290c or SMU_1289c was transformed into a fluoride transporter- disrupted  Escherichia coli strain. All bacterial strains were cultured under appropriate conditions with or without sodium fluoride, and fluoride resistance was evaluated. All three gene-knockout  S. mutans  strains showed lower resistance to sodium fluoride than did the wild-type strain. No significant changes in resistance to other sodium halides were recognized between the wild-type and double-knockout strains. Both SMU_1290c and SMU_1289c transformation rescued fluoride transporter-disrupted  E. coli  cell from fluoride toxicity. We conclude that the chloride channel permeases contribute to fluoride resistance in  S. mutans .
    Keywords: Physiology & Biochemistry
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  • 28
    Publication Date: 2016-05-12
    Description: Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are bacteria under investigation for production of biofuels from plant biomass. Thermoanaerobacterium saccharolyticum has been engineered to produce ethanol at high yield (〉90% of theoretical) and titer (〉70 g/l). Efforts to engineer C. thermocellum have not, to date, been as successful, and efforts are underway to transfer the ethanol production pathway from T. saccharolyticum to C. thermocellum . One potential challenge in transferring metabolic pathways is the possibility of incompatible levels of nicotinamide cofactors. These cofactors (NAD + , NADH, NADP + and NADPH) and their oxidation state are important in the context of microbial redox metabolism. In this study we directly measured the concentrations and reduced oxidized ratios of these cofactors in a number of strains of C. thermocellum and T. saccharolyticum by using acid/base extraction and enzymatic assays. We found that cofactor ratios are maintained in a fairly narrow range, regardless of the metabolic network modifications considered. We have found that the ratios are similar in both organisms, which is a relevant observation in the context of transferring the T. saccharolyticum ethanol production pathway to C. thermocellum .
    Keywords: Physiology & Biochemistry
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  • 29
    Publication Date: 2016-03-09
    Description: Cadmium is a widespread environmental pollutant and poses some potential risks to human health. However, the signaling events controlling cadmium toxicity are not fully understood. In this study, we examined the effect of cadmium chloride on cell viability and the intracellular nitric oxide (NO) level in yeast cells. The results showed that exposure of yeast cells to cadmium (0–100 μM) could induce cell killing with significantly increased intracellular NO levels. Morphological analysis of the nuclei with 4 ' ,6-diamidino-2-phenylindole staining and DNA strand breaks analysis showed that cadmium at 50 μM can induce cell apoptosis in yeast cells. Treatment of yeast cells with cadmium (50 μM) and the nitric oxide scavenger c-PTIO [2-(4-carboxyphenyl)-4,4,5,5-teramethylimidazoline-1-oxyl-3-oxide; 0.2 mM] showed that c-PTIO attenuated the cadmium-induced cell killing. Our findings indicated that cadmium-induced yeast cell killing is mediated by a directly increased intracellular NO level.
    Keywords: Physiology & Biochemistry
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  • 30
    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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  • 31
    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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  • 32
    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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  • 33
    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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  • 34
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    Oxford University Press
    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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  • 35
    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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  • 36
    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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  • 37
    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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  • 38
    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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  • 39
    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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  • 40
    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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  • 41
    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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  • 42
    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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  • 43
    Publication Date: 2016-06-02
    Description: Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations . The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.
    Keywords: Physiology & Biochemistry
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  • 44
    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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  • 45
    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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  • 46
    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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  • 47
    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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  • 48
    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.
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  • 49
    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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  • 50
    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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  • 51
    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 .
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  • 52
    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.
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  • 53
    Publication Date: 2016-03-24
    Description: Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase ( doxDA genes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase ( hdr genes) rather than sulfur oxygenase reductase ( sor ). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.
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  • 54
    Publication Date: 2016-04-24
    Description: TRP1 is a frequently used auxotrophic marker for genetic modifications and selections in trp – budding yeast strains, including the commonly used wild-type strain W303a. However, we found that introduction of the TRP1 gene into a trp – strain significantly affected vegetative growth at low and high temperatures. Therefore, caution should be needed when working in a trp – background strain and using the TRP1 marker to study stress response phenotypes, particularly when analyzing temperature sensitivities.
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  • 55
    Publication Date: 2016-03-18
    Description: The factors driving the dominance of the Calvin–Benson–Bassham cycle (CBB) or reductive citric acid cycle (rCAC) in autotrophic microorganisms in different habitats are debated. Based on costs for synthesizing a few metabolic intermediates, it has been suggested that the CBB poses a disadvantage due to higher metabolic cost. The purpose of this study was to extend this estimate of cost from metabolite synthesis to biomass synthesis. For 12 gammaproteobacteria (CBB) and five epsilonproteobacteria (rCAC), the amount of ATP to synthesize a gram of biomass from CO 2 was calculated from genome sequences via metabolic maps. The eleven central carbon metabolites needed to synthesize biomass were all less expensive to synthesize via the rCAC (66%–89% of the ATP needed to synthesize them via CBB). Differences in cell compositions did result in differing demands for metabolites among the organisms, but the differences in cost to synthesize biomass were small among organisms that used a particular pathway (e.g. rCAC), compared to the difference between pathways (rCAC versus CBB). The rCAC autotrophs averaged 0.195 moles ATP per g biomass, while their CBB counterparts averaged 0.238. This is the first in silico estimate of the relative expense of both pathways to generate biomass.
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  • 56
    Publication Date: 2016-03-05
    Description: Bacteria carry a number of genes that cause cell growth arrest or cell lysis upon expression. Notably, defective prophages retain many lysis proteins. Here, we identified a novel lytic gene, ydfD , on the Qin prophage segment of the Escherichia coli genome. YdfD lyses 99.9% of cells within 2 h of its induction. The co-expression of the upstream gene, dicB , encoding a cell division inhibitor, as well as sulA , encoding another cell division inhibitor, abolished YdfD-induced cell lysis. These results imply that YdfD-induced lysis is a cell division-dependent event. We further found that by deleting the hydrophobic 22-residue N-terminal domain, the resulting 42-residue C-terminal domain was still toxic to cause cell lysis. We propose that YdfD, associated with the cytoplasmic membrane, inhibits an essential cellular process(s).
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  • 57
    Publication Date: 2016-05-08
    Description: Many bacteria are capable of accumulating intracellular granules of polyhydroxyalkanoates (PHA). In this work, we developed confocal microscopy analysis of bacterial cells to study changes in the diameters of cells as well as PHA granules during growth and PHA accumulation in the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha ). The cell envelope was stained by DiD ® fluorescent probe and PHA granules by Nile Red. Signals from both probes were separated based on their spectral and fluorescence life-time properties. During growth and PHA accumulation, bacterial cells increased their length but the width of the cells remained constant. The volume fraction of PHA granules in cells increased during PHA accumulation, nevertheless, its value did not exceed 40 vol. % regardless of the PHA weight content. It seems that bacterial cultures lengthen the cells in order to control the PHA volume portion. However, since similar changes in cell length were also observed in a PHA non-accumulating mutant, it seems that there is no direct control mechanism, which regulates the prolongation of the cells with respect to PHA granules volume. It is more likely that PHA biosynthesis and the length of cells are influenced by the same external stimuli such as nutrient limitation.
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  • 58
    Publication Date: 2016-05-20
    Description: Three putative regulatory genes, namely ttmRI, ttmRII and ttmRIII , which are present in the tetramycin ( ttm ) biosynthetic gene cluster, were found in Streptomyces ahygroscopicus . Disruption of ttmRI, ttmRII or ttmRIII reduced tetramycin production, and their complementation restored production to varying degrees. Gene expression analysis of the wild-type (WT) and mutant strains through reverse transcriptase–polymerase chain reaction (RT-PCR) of the ttm gene cluster showed that the expression levels of most of the biosynthetic genes were reduced in ttmRI , ttmRII and ttmRIII . Electrophoretic mobility shift assays demonstrated that TtmRI, TtmRII and TtmRIII bound the promoters of several genes in the ttm gene cluster. This study found that these three proteins are a group of positive regulators that activate the transcription of the ttm gene cluster in S. ahygroscopicus . In addition, ttmRII had a reduced degree of grey pigmentation. Thus, TtmRII has a pleiotropic regulatory function in the tetramycin biosynthetic pathway and in development.
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  • 59
    Publication Date: 2016-05-20
    Description: Sulfide:quinone oxidoreductase (SQR) is the primary sulfide-oxidizing enzyme found in all three domains of life. Of the six phylogenetically distinct types of SQR, four have representatives that have been biochemically characterized. The genome of Chlorobaculum tepidum encodes three SQR homologs. One of these, encoded by CT1087, is a type VI SQR that has been previously shown to be required for growth at high sulfide concentrations and to be expressed in sulfide-dependent manner. Therefore, CT1087 was hypothesized to be a high sulfide adapted SQR. CT1087 was expressed in Escherichia coli with an N-terminal His-tag (CT1087NHis 6 ) and purified by Ni-NTA chromatography. CT1087NHis 6 was active and contained FAD as a strongly bound cofactor. The measured kinetic parameters for CT1087NHis 6 indicate a low affinity for sulfide and a high enzymatic turnover rate consistent with the hypothesis for its function inferred from genetic and expression data. These are the first kinetic data for a type VI SQR and have implications for structure-function analyses of all SQR's.
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  • 60
    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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  • 61
    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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  • 62
    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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  • 63
    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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  • 64
    Publication Date: 2016-04-21
    Description: Streptococcus mutans harbours an intracellular, human DPP IV-analogous enzyme Xaa-Pro dipeptidyl-peptidase (EC 3.4.14.11). According to previous reports, an extracellular isozyme in S. gordonii and S. suis has been associated with virulence. Speculating that even an intracellular form may aid in virulence of S. mutans , we have tried to purify, characterize and evaluate enzyme inhibition by specific inhibitors. The native enzyme was partially purified by ion-exchange and gel filtration chromatography. Owing to low yield, the enzyme was overexpressed in Lactococcus lactis and purified by affinity chromatography. The recombinant enzyme (rSm-XPDAP) had a specific activity of 1070 U mg –1 , while the V max and K m were 7 μM min –1 and 89 ± 7 μM ( n = 3), respectively. The serine protease inhibitor phenylmethylsulphonyl fluoride and a DPP IV-specific inhibitor diprotin A proved to be active against rSm-XPDAP. As a novel approach, the evaluation of the effect of anti-human DPP IV (AHD) drugs on rSm-XPDAP activity found saxagliptin to be effective to some extent ( K i = 129 ± 16 μM), which may lead to the synthesis and development of a new class of antimicrobial agents.
    Keywords: Physiology & Biochemistry
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  • 65
    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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  • 66
    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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  • 67
    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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  • 68
    Publication Date: 2016-09-09
    Description: Cytosolic, globular droplets with an average diameter of 50 nm were observed in vitrified Thermoplasma acidophilum cells by means of cryo-electron tomography. These droplets were isolated by column chromatography and immunoprecipitation protein purification methods. Subsequent chemical and biochemical analyses identified lipid and protein components, respectively. Two major lipid components, comigrating menaquinones at the solvent front and the slower migrating Thermoplasma polar lipid U4, were detected by TLC experiments. The major protein component was identified as the 153 amino acid long Ta0547 vitellogenin-N domain protein. This domain has been found so far exclusively in large lipid transport proteins of vertebrates and non-vertebrates. Blast protein database homology searches with Ta0547 did not return any eukaryal hits; homologous sequences were found only in thermo-acidophilic archaeons. However, a profile-sequence domain search performed with the vitellogenin-N domain (PF01347) hmm-profile against the T. acidophilum proteome returned Ta0547 as hit. Electron microscopy appearance of isolated droplets resembled to lipoprotein particles. However, no (tetraether) lipid layer could be detected on the droplets surface, rather hydrophobic compounds of the electron dense lumen were surrounded by a denser discontinuous protein boundary. Based on described features, these particles qualify for a novel lipoprotein particle category, what we nominated Thermoplasma Quinone Droplet.
    Keywords: Physiology & Biochemistry
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  • 69
    Publication Date: 2016-09-17
    Description: Glyoxal (GO) belongs to the reactive electrophilic species generated in vivo in all organisms. In order to identify targets of GO and their response mechanisms, we attempted to screen for GO-sensitive mutants by random insertions of Tn phoA -132. The genes responsible for GO susceptibility were functionally classified as the following: (i) tRNA modification; trmE , gidA and truA , (ii) DNA repair; recA and recC , (iii) toxin–antitoxin; mqsA and (iv) redox metabolism; yqhD and caiC . In addition, an insertion in the crp gene, encoding the cAMP responsive transcription factor, exhibits a GO-resistant phenotype, which is consistent with the phenotype of adenylate cyclase ( cya ) mutant showing GO resistance. This suggests that global regulation involving cAMP is operated in a stress response to GO. To further characterize the CRP-regulated genes directly associated with GO resistance, we created double mutants deficient in both crp and one of the candidate genes including yqhD , gloA and sodB . The results indicate that these genes are negatively regulated by CRP as confirmed by real-time RT-PCR. We propose that tRNA as well as DNA are the targets of GO and that toxin/antitoxin, antioxidant and cAMP are involved in cellular response to GO.
    Keywords: Physiology & Biochemistry
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  • 70
    Publication Date: 2016-12-23
    Description: The culturability of Escherichia coli , Ralstonia eutropha and Bacillus subtilis after incubation in phosphate-buffered saline at either 5°C or 30°C was determined. The culturability of B. subtilis showed little dependence on temperature. The culturability of E. coli rapidly decreased at 30°C but remained almost constant at 5°C. In contrast, the culturability of R. eutropha decreased by three orders of magnitude at 5°C within 24 h but only moderately decreased (one order of magnitude) at 30°C. Remarkably, prolonged incubation of R. eutropha at 30°C resulted in a full recovery of colony forming units in contrast to only a partial recovery at 5°C. Ralstonia eutropha cells at 30°C remained culturable for 3 weeks while culturability at 5°C constantly decreased. The effect of temperature was significantly stronger in a polyhydroxybutyrate-negative mutant. Our data show that accumulated polyhydroxybutyrate has a cold-protective function and can prevent R. eutropha entering the viable but not culturable state.
    Keywords: Physiology & Biochemistry
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  • 71
    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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  • 72
    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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  • 73
    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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  • 74
    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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  • 75
    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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  • 76
    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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  • 77
    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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  • 78
    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.
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  • 79
    Publication Date: 2016-10-08
    Description: Thermotoga maritima cells are distinguished by a sheath-like structure called the toga that loosely encloses single or multiple cells. During growth, and particularly at late phases of population growth, the toga distends from the poles of many cells. Little is known about this phenomenon so this study presents basic information about this process. We first provide quantitative data demonstrating that cells showing toga distensions increase in number during growth and that the phenomenon is not due to acidification of their growth medium. Comparisons of the area enclosed by these distended togas to the area of the cytoplasm show that the toga continues to grow as the growth of the cytoplasm ceases. Measuring the expression of many genes involved in toga composition and biosynthesis showed a 5.2-, 7.9- and 3-fold increase in the expression of toga structural protein genes ompB (porin), ompA1 and ompA2 (alpha helical, transperiplasm anchors), respectively. Additionally, expression of the putative pyruvyl transferase gene ( csaB ) was upregulated 4.4-fold in stationary phase, while the beta barrel assembly factor gene ( bamA ) showed only a 1.2-fold increase in expression. These findings demonstrate that toga distension is an active process and one that needs further investigation so we can understand the selective forces that operate in high-temperature environments.
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