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  • Frontiers Media  (145)
  • American Association for the Advancement of Science (AAAS)
  • Wiley-Blackwell
  • Springer Nature
  • 2020-2023  (181)
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  • 1
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    Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation (2020)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yoshii, A., & Green, W. N. Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation. Frontiers in Synaptic Neuroscience, 12(27), (2020), doi:10.3389/fnsyn.2020.00027.
    Description: Protein palmitoylation, the reversible addition of palmitate to proteins, is a dynamic post-translational modification. Both membrane (e.g., channels, transporters, and receptors) and cytoplasmic proteins (e.g., cell adhesion, scaffolding, cytoskeletal, and signaling molecules) are substrates. In mammals, palmitoylation is mediated by 23-24 palmitoyl acyltransferases (PATs), also called ZDHHCs for their catalytic aspartate-histidine-histidine-cysteine (DHCC) domain. PATs are integral membrane proteins found in cellular membranes. In the palmitoylation cycle, palmitate is removed by the depalmitoylation enzymes, acyl palmitoyl transferases (APT1 and 2), and α/β Hydrolase domain-containing protein 17 (ABHD17A-C). These are cytoplasmic proteins that are targeted to membranes where they are substrates for PATs. The second class of depalmitoylating enzymes are palmitoyl thioesterases, PPT1 and 2, discovered through their association with infantile neuronal ceroid lipofuscinosis. These are secreted proteins found in the lumen of intracellular organelles, primarily lysosomes, where their function as depalmitoylating enzymes is unclear.
    Description: This work was supported by University of Illinois start-up fund (to AY) and NIH/NIDA (grant DA044760 to WG).
    Keywords: palmitoylation and depalmitoylation ; synaptic plasticity ; axonal growth ; lysosome ; neurodegenerative disease ; neuronal ceroid lipofuscinoses (NCL) ; Huntington disease
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Ancestral absence of electron transport chains in Patescibacteria and DPANN (2020)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.
    Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
    Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.
    Keywords: Bacteria ; Archaea ; evolution ; genomics fermentation ; respiration ; oxidoreductases
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ferrer-González, F. X., Widner, B., Holderman, N. R., Glushka, J., Edison, A. S., Kujawinski, E. B., & Moran, M. A. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME Journal, (2020), doi:10.1038/s41396-020-00811-y.
    Description: The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation (5503) and the National Science Foundation (IOS-1656311) to MAM, ASE, and EBK, and by the Simons Foundation grant 542391 to MAM within the Principles of Microbial Ecosystems (PriME) Collaborative.
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Exploring Employee Perceptions towards Smart Working during the COVID-19 Pandemic: a Comparative Analysis of Two Italian Public Research Organizations (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Of all the socio-economic changes caused by the Covid-19 pandemic, the disruption to workforce organizations will probably leave the largest indelible mark. The way work will be organized in the future will be closely linked to the experience of work-ing under the same institution’s response to the pandemic. This paper aims to fill the gap in knowledge about smart working (SW) in public organizations, with a focus on the experience of the employees of two Italian research organizations, CNR and INGV. Analysing primary data, it explored and assessed how SW had been experi-enced following the implementation of governmental measures aimed at limiting the spread of COVID-19
    Description: Published
    Description: 815–833
    Description: 2TM. Divulgazione Scientifica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Combining audio and visual displays to highlight temporal and spatial seismic patterns (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Data visualization, and to a lesser extent data sonification, are classic tools to the scientific community. However, these two approaches are very rarely combined, although they are highly complementary: our visual system is good at recognizing spatial patterns, whereas our auditory system is better tuned for temporal patterns. In this article, data representation methods are proposed that combine visualization, sonification, and spatial audio techniques, in order to optimize the user’s perception of spatial and temporal patterns in a single display, to increase the feeling of immersion, and to take advantage of multimodal integration mechanisms. Three seismic data sets are used to illustrate the methods, covering different physical phenomena, time scales, spatial distributions, and spatio-temporal dynamics. The methods are adapted to the specificities of each data set, and to the amount of information that the designer wants to display. This leads to further developments, namely the use of audification with two time scales, the switch from pure audification to time-modulated noise, and the switch from pure audification to sonic icons. First user feedback from live demonstrations indicates that the methods presented in this article seem to enhance the perception of spatio-temporal patterns, which is a key parameter to the understanding of seismically active systems, and a step towards apprehending the processes that drive this activity.
    Description: Published
    Description: 125–142
    Description: 7T. Variazioni delle caratteristiche crostali e "precursori"
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Deep water inflow slowed offshore expansion of the West Antarctic Ice Sheet at the Eocene-Oligocene transition (2022)
    Springer Nature
    In:  EPIC3Nature Communications Earth & Environment, Springer Nature, 3(1)
    Details
    Publication Date: 2022-02-21
    Description: The stability of the West Antarctic Ice Sheet is threatened by the incursion of warm Circumpolar Deepwater which flows southwards via cross-shelf troughs towards the coast there melting ice shelves. However, the onset of this oceanic forcing on the development and evolution of the West Antarctic Ice Sheet remains poorly understood. Here, we use single- and multichannel seismic reflection profiles to investigate the architecture of a sediment body on the shelf of the Amundsen Sea Embayment. We estimate the formation age of this sediment body to be around the Eocene-Oligocene Transition and find that it possesses the geometry and depositional pattern of a plastered sediment drift. We suggest this indicates a southward inflow of deep water which probably supplied heat and, thus, prevented West Antarctic Ice Sheet advance beyond the coast at this time. We conclude that the West Antarctic Ice Sheet has likely experienced a strong oceanic influence on its dynamics since its initial formation.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 7
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    Short-term clustering modeling of seismicity in Eastern Aegean Sea (Greece): a retrospective forecast test of the 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos earthquake sequences (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-03
    Description: Short-term earthquake clustering properties in the Eastern Aegean Sea (Greece) area investigated through the application of an epidemic type stochastic model (Epidemic Type Earthquake Sequence; ETES). The computations are performed in an earthquake catalog covering the period 2008 to 2020 and including 2332 events with a completeness threshold of Mc = 3.1 and separated into two subcatalogs. The first subcatalog is employed for the learning period, which is between 2008/01/01 and 2016/12/31 (N = 1197 earthquakes), and used for the model’s parameters estimation. The second subcatalog from 2017/01/01 to 2020/11/10 (1135 earthquakes), in which the sequences of 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos main shocks are included, and used for a retrospective forecast testing based on the constructed model. The estimated model parameters imply a swarm like behavior, indicating the ability of earthquakes of small to moderate magnitude above Mc to produce their own offsprings, along with the stronger earthquakes. The retrospective evaluation of the model is examined in the three aftershock sequences, where lack of foreshocks resulted in low predictability of the mainshocks, with estimated daily probabilities around 10– 5. Immediately after the mainshocks occurrence the model adjusts with notable resemblance between the expected and observed aftershock rates, particularly for earthquakes with M ≥ 3.5.
    Description: Published
    Description: 1085–1099
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Simulation of non-stationary stochastic ground motions based on recent Italian earthquakes (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: This work presents an up-to-date model for the simulation of non-stationary ground motions, including several novelties compared to the original study of Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996). The selection of the input motion in the framework of earthquake engineering has become progressively more important with the growing use of nonlinear dynamic analyses. Regardless of the increasing availability of large strong motion databases, ground motion records are not always available for a given earthquake scenario and site condition, requiring the adoption of simulated time series. Among the different techniques for the generation of ground motion records, we focused on the methods based on stochastic simulations, considering the time- frequency decomposition of the seismic ground motion. We updated the non-stationary stochastic model initially developed in Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996) and later modified by Pousse et al. (Bull Seism Soc Am 96:2103–2117, 2006) and Laurendeau et al. (Nonstationary stochastic simulation of strong ground-motion time histories: application to the Japanese database. 15 WCEE Lisbon, 2012). The model is based on the S-transform that implicitly considers both the amplitude and frequency modulation. The four model parameters required for the simulation are: Arias intensity, significant duration, central frequency, and frequency bandwidth. They were obtained from an empirical ground motion model calibrated using the accelerometric records included in the updated Italian strong-motion database ITACA. The simulated accelerograms show a good match with the ground motion model prediction of several amplitude and frequency measures, such as Arias intensity, peak acceleration, peak velocity, Fourier spectra, and response spectra.
    Description: Published
    Description: 3287–3315
    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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  • 9
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    Insights on the Italian Seismic Network from location uncertainties (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-01
    Description: Probabilistic earthquake locations provide confidence intervals for the hypocentre solutions such as errors encountered in the position, the origin time, and in magnitude. If the relationship of the parameters relative to the local arrangement of the seismic network is considered, such as the node distance, the number of stations, the seismic gap, and the quality of phase readings), the uncertainties can then provide insights on the location capability of the network. In this paper, we collect the earthquake data recorded from the Italian Seismic Network for a time span of 5 years. The data pertain to three different catalogues according to the progressive refinement phases of the location procedure: automatic location, revised location, and published location. By means of spatial analysis,we assess the distribution of the location-related and network-related estimators across the study area. These estimators are subsequently combined to assess the existence of spatial correlations at a local scale. The results indicate that the Italian network is generally able to provide robust locations at the national scale and for smaller earthquakes, and the elongated shape of Italy (and of its network) does not cause systematic bias in the locations. However, we highlight the existence of subregions in which the performance of the network is weaker. At present, a unique 2D, 3-layer velocity model is used for the earthquake location procedure, and this could represent the main limitation for the improvement of the locations. Therefore, the assessment of locally optimized velocity models is the priority for the homogenization and the improvement of the Italian Seismic Network performance.
    Description: Published
    Description: 1061–1076
    Description: 1IT. Reti di monitoraggio e sorveglianza
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    New trenching results along the İznik segment of the central strand of the North Anatolian Fault (Turkey): an integration with preexisting data (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-06
    Description: This paper provides a new contribution to the construction of the complex and fragmentary mosaic of the Late Holocene earthquakes history of the İznik segment of the central strand of the North Anatolian Fault (CNAF) in Turkey. The CNAF clearly displays lower dextral slip rates with respect to the northern strand however, surface rupturing and large damaging earthquakes (M 〉 7) occurred in the past, leaving clear signatures in the built and natural environments. The association of these historical events to specific earthquake sources (e.g., Gemlik, İznik, or Geyve fault segments) is still a matter of debate. We excavated two trenches across the İznik fault trace near Mustafali, a village about 10 km WSW of İznik where the morphological fault scarp was visible although modified by agricultural activities. Radiocarbon and TL dating on samples collected from the trenches show that the displaced deposits are very recent and span the past 2 millennia at most. Evidence for four surface faulting events was found in the Mustafali trenches. The integration of these results with historical data and previous paleoseismological data yields an updated Late Holocene history of surface-rupturing earthquakes along the İznik Fault in 1855, 740 (715), 362, and 121 CE. Evidence for the large M7 + historical earthquake dated 1419 CE generally attributed to this fault, was not found at any trench site along the İznik fault nor in the subaqueous record. This unfit between paleoseismological, stratigraphic, and historical data highlights one more time the urge for extensive paleoseismological trenching and offshore campaigns because of the high potential to solve the uncertainties on the seismogenic history (age, earthquake location, extent of the rupture and size) of this portion of NAFZ and especially on the attribution of historical earthquakes to the causative fault.
    Description: Published
    Description: 115–128
    Description: 2T. Deformazione crostale attiva
    Description: N/A or not JCR
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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