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  • Springer  (485,438)
  • Nature Publishing Group
  • 2015-2019  (485,621)
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  • 1
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    Quorum sensing signal–response systems in Gram-negative bacteria (2016)
    Nature Publishing Group
    Details
    Publication Date: 2024-04-12
    Description: Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy.
    Type: Article , PeerReviewed
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  • 2
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    Advancing microbial sciences by individual-based modelling (2016)
    Nature Publishing Group
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    Publication Date: 2023-12-21
    Description: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage–CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).
    Type: Article , PeerReviewed
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  • 3
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    Identifying marginal supplying countries of wood products via trade network analysis (2017)
    Springer
    Details
    Publication Date: 2023-12-12
    Description: Purpose: The consequential inventory modeling approach for life cycle assessment implies that an increase in the demand for a specific product is met by the marginal suppliers within the market. The identification of marginal suppliers is however complicated by difficulties in defining appropriate geographical market delimitations. In this study, an advanced system thinking approach is proposed to address this challenge in the identification of marginal supplying countries of wood products. Methods: Groups of countries which represent geographical markets are identified from trade data by using a network analysis-based clustering technique. Within these markets, marginal supplying countries are selected based on positive historical increments. The analysis covers 12 different products and all countries in the world using trade data for the period 1998–2013. Results and discussion: Global indices allow differentiating how product-specific trade networks are separated into communities and how interconnected these networks are. Large differences between products and minor differences between trade years are observed. Communities identified for each product tend to overlap with existing geographical regions and seem thus realistic. By combining this information with product-specific production increment rankings, marginal supplying countries of wood products were identified. Conclusions: The identified geographical market delimitation is a key for proper consequential life cycle assessment (LCA) inventory modeling in areas such as timber-based construction and biomass-based energy production. The method can in principle be applied to any product for which trade network data are available and ideally should be accompanied by a detailed analysis of technological constrains within the identified supplying country.
    Type: Article , PeerReviewed
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  • 4
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    A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity (2015)
    Nature Publishing Group
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    Publication Date: 2023-11-29
    Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
    Type: Article , PeerReviewed
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  • 5
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    Seismological analyses of the seismic microzonation of 138 municipalities damaged by the 2016–2017 seismic sequence in Central Italy (2019)
    Springer
    Details
    Publication Date: 2023-11-21
    Description: This paper describes the seismological analyses performed within the framework of the seismic microzonation study for the reconstruction of 138 municipalities damaged by the 2016–2017 sequence in Central Italy. Many waveforms were recorded over approximately 15 years at approximately 180 instrumented sites equipped with permanent or temporary stations in an area that includes all the damaged localities. Site response was assessed using earthquake and noise recordings at the selected stations through different parameters, such as spectral amplification curves, fundamental resonance frequencies, site-specific response spectra, and average amplification factors. The present study was a collaboration of many different institutions under the coordination of the Italian Center for Seismic Microzonation and its applications. The results were homogenized and gathered into site-specific forms, which represent the main deliverable for the benefit of Italian Civil Protection. It is remarkable that the bulk of this study was performed in a very short period (approximately 2 months) to provide quantitative information for detailed microzonation and future reconstruction of the damaged municipalities.
    Description: Published
    Description: 5553–5593
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Site response analyses for complex geological and morphological conditions: relevant case-histories from 3rd level seismic microzonation in Central Italy (2019)
    Springer
    Details
    Publication Date: 2023-11-16
    Description: The paper presents the results of 5 case studies on complex site e ects selected within the project for the level 3 seismic microzonation of several municipalities of Central Italy dam- aged by the 2016 seismic sequence. The case studies are characterized by di erent geo- logical and morphological con gurations: Monte San Martino is located along a hill slope, Montedinove and Arquata del Tronto villages are located at ridge top whereas Capitignano and Norcia lie in correspondence of sediment- lled valleys. Peculiarities of the sites are constituted by the presence of weathered/jointed rock mass, fault zone, shear wave veloc- ity inversion, complex surface and buried morphologies. These factors make the de ni- tion of the subsoil model and the evaluation of the local response particularly complex and di cult to ascertain. For each site, after the discussion of the subsoil model, the results of site response numerical analyses are presented in terms of ampli cation factors and acceleration response spectra in selected points. The physical phenomena governing the site response have also been investigated at each site by comparing 1D and 2D numerical analyses. Implications are deduced for seismic microzonation studies in similar geological and morphological conditions.
    Description: Published
    Description: 5741–5777
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Seismic microzonation ; Ampli cation factors ; Response spectra ; Numerical analyses ; site response
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Loop Current variability - its relation to meridional overturning circulation and the impact of Mississippi discharge (2015)
    Springer
    Details
    Publication Date: 2023-11-08
    Description: The dynamics of the Loop Current (LC) in the Gulf of Mexico (GoM) during transient climates and interglacials, and its interaction with changes in sea level, atmospheric circulation, and Mississippi River (MR) discharge were studied. Geochemical proxy records and numerical modeling indicate that LC eddy shedding and its related heat transport into the GoM increased during the deglaciation. The model simulations imply decreased LC eddy shedding at lowered sea levels, while transports through Yucatan and Florida straits increased due to the southward migration of the Intertropical Convergence Zone (ITCZ) and increased wind-driven transport in the North Atlantic. Consistent with the model, (isotope) geochemical proxy records from the northern GoM show glacial/interglacial amplitudes significantly larger than in the Caribbean and extreme cooling during the Last Glacial Maximum (LGM) due to the vanishing LC eddy shedding. Prominent deglacial melt water releases observed south and west of the MR delta are neither present in the northeastern GoM, nor in sea-surface salinity-records in the subtropical North Atlantic. The freshwater signals were either a regionally restricted phenomenon or due to changes in the isotopic composition of the discharged water. Our results question the impact of MR megadischarges on the large-scale overturning circulation.
    Type: Book chapter , NonPeerReviewed
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  • 8
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    The use of a flow field correction technique for alleviating the North Atlantic cold bias with application to the Kiel Climate Model (2015)
    Springer
    Details
    Publication Date: 2023-11-08
    Description: The North Atlantic cold bias, associated with the misplacement of the North Atlantic Current (NAC) and typically extending from the surface to 1000 m depth, is a common problem in coupled models that compromises model fidelity. We investigate the use of a flow field correction (FFC) to adjust the path of the NAC and alleviate the cold bias. The FFC consists of three steps. First, climatological potential temperature (T) and salinity (S) fields for use with the model are produced using a three-dimensional restoring technique. Second, these T, S fields are used to modify the momentum equations of the ocean model. In the third stage, the correction term is diagnosed to construct a flow-independent correction. Results using the Kiel Climate Model show that the FFC allows the establishment of a northwest corner, substantially alleviating the subsurface cold bias. A cold bias remains at the surface but can be eliminated by additionally correcting the surface freshwater flux, without adjusting the surface heat flux seen by the ocean model. A model version in which only the surface fluxes of heat and freshwater are corrected continues to exhibit the incorrect path of the NAC and a strong subsurface bias. We also show that the bias in the atmospheric circulation is reduced in some corrected model versions. The FFC can be regarded as a way to correct for model error, e.g. associated with the deep water mass pathways and their impact on the large-scale ocean circulation, and unresolved processes such as eddy momentum flux convergence.
    Type: Article , PeerReviewed
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  • 9
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    Seamounts (2015)
    Springer
    Details
    Publication Date: 2023-11-08
    Description: Definition: Seamounts are literally mountains rising from the seafloor. More specifically, they are “any geographically isolated topographic feature on the seafloor taller than 100 m, including ones whose summit regions may temporarily emerge above sea level, but not including features that are located on continental shelves or that are part of other major landmasses” (Staudigel et al., 2010). The term “guyot” can be used for seamounts having a truncated cone shape with a flat summit produced by erosion at sea level (Hess, 1946), development of carbonate reefs (e.g., Flood, 1999), or partial collapse due to caldera formation (e.g., Batiza et al., 1984). Seamounts 〈1,000 m tall are sometimes referred to as “knolls” (e.g., Hirano et al., 2008). “Petit spots” are a newly discovered subset of sea knolls confined to the bulge of subducting oceanic plates of oceanic plates seaward of deep-sea trenches (Hirano et al., 2006).
    Type: Book chapter , NonPeerReviewed
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  • 10
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    The 12.4 ka Upper Apoyeque Tephra, Nicaragua: stratigraphy, dispersal, composition, magma reservoir conditions and trigger of the plinian eruption (2016)
    Springer
    Details
    Publication Date: 2023-11-08
    Description: Upper Apoyeque Tephra (UAq) was formed by a rhyodacitic plinian eruption in west-central Nicaragua at 12.4 ka BP. The fallout tephra was dispersed from a progressively rising plinian eruption column that became exposed to different wind speeds and directions at different heights in the stratosphere, leading to an asymmetric tephra fan with different facies in the western and southern sector. Tephra dispersal data integrated with geochemical compositions of lava flows in the area facilitate delimitation of the source vent to the south of Chiltepe Peninsula. UAq, Lower Apoyeque Tephra, Apoyeque Ignimbrite, and two lithic clasts in San Isidro Tephra together form a differentiation trend distinct from that of the younger tephras and lavas at Chiltepe Volcanic Complex in a TiO2 versus K2O diagram, compositionally precluding a genetic relationship of UAq with the present-day Apoyeque stratovolcano. Apoyeque Volcano in its present shape did not exist at the time of the UAq eruption. The surface expression of the UAq vent is now obscured by younger eruption products and lake water. Pressure-temperature constraints based on mineral-melt equilibria and fluid inclusions in plagioclase indicate at least two magma storage levels. Clinopyroxenes crystallised in a deep crustal reservoir at ~24 km depth as inferred from clinopyroxene-melt inclusion pairs. Chemical disequilibrium between clinopyroxenes and matrix glasses indicates rapid magma ascent to the shallower reservoir at ~5.4 km depth, where magnesiohornblendes and plagioclase fractionated at a temperature of ~830°C. Water concentrations were ~5.5 wt. % as derived from congruent results of amphibole and plagioclase-melt hygrometry. The eruption was triggered by injection of a hotter, more primitive melt into a water-supersaturated reservoir.
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