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  • Cell Press
  • Copernicus
  • 2020-2023  (16)
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  • 1
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    The genesis of Yedoma Ice Complex permafrost – grain-size endmember modeling analysis from Siberia and Alaska (2020)
    Copernicus
    In:  EPIC3E&G Quaternary Sci. J., Copernicus, 69, pp. 33-53, ISSN: 0424-7116
    Details
    Publication Date: 2022-04-19
    Description: The late Pleistocene Yedoma Ice Complex is an ice-rich and organic-bearing type of permafrost deposit widely distributed across Beringia and is assumed to be especially prone to deep degradation with warming temperature, which is a potential tipping point of the climate system. To better understand Yedoma formation, its local characteristics, and its regional sedimentological composition, we compiled the grain-size distributions (GSDs) of 771 samples from 23 Yedoma locations across the Arctic; samples from sites located close together were pooled to form 17 study sites. In addition, we studied 160 samples from three non-Yedoma ice-wedge polygon and floodplain sites for the comparison of Yedoma samples with Holocene depositional environments. The multimodal GSDs indicate that a variety of sediment production, transport, and depositional processes were involved in Yedoma formation. To disentangle these processes, a robust endmember modeling analysis (rEMMA) was performed. Nine robust grain-size endmembers (rEMs) characterize Yedoma deposits across Beringia. The study sites of Yedoma deposits were finally classified using cluster analysis. The resulting four clusters consisted of two to five sites that are distributed randomly across northeastern Siberia and Alaska, suggesting that the differences are associated with rather local conditions. In contrast to prior studies suggesting a largely aeolian contribution to Yedoma sedimentation, the wide range of rEMs indicates that aeolian sedimentation processes cannot explain the entire variability found in GSDs of Yedoma deposits. Instead, Yedoma sedimentation is controlled by local conditions such as source rocks and weathering processes, nearby paleotopography, and diverse sediment transport processes. Our findings support the hypothesis of a polygenetic Yedoma origin involving alluvial, fluvial, and niveo-aeolian transport; accumulation in ponding waters; and in situ frost weathering as well as postdepositional processes of solifluction, cryoturbation, and pedogenesis. The characteristic rEM composition of the Yedoma clusters will help to improve how grain-size-dependent parameters in permafrost models and soil carbon budgets are considered. Our results show the characteristic properties of ice-rich Yedoma deposits in the terrestrial Arctic. Characterizing and quantifying site-specific past depositional processes is crucial for elucidating and understanding the trajectories of this unique kind of ice-rich permafrost in a warmer future.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 2
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    Reduced El Niño variability in the mid-Pliocene according to the PlioMIP2 ensemble (2021)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 17(6), pp. 2427-2450, ISSN: 1814-9332
    Details
    Publication Date: 2022-01-10
    Description: The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Evaluating the large-scale hydrological cycle response within the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) ensemble (2021)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 17(6), pp. 2537-2558, ISSN: 1814-9332
    Details
    Publication Date: 2022-01-10
    Description: The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 4
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    INSTANCE – the Italian seismic dataset for machine learning (2021)
    Copernicus
    Details
    Publication Date: 2021-12-14
    Description: The Italian earthquake waveform data are collected here in a dataset suited for machine learning analysis (ML) applications. The dataset consists of nearly 1.2 million three-component (3C) waveform traces from about 50 000 earthquakes and more than 130 000 noise 3C waveform traces, for a total of about 43 000 h of data and an average of 21 3C traces provided per event. The earthquake list is based on the Italian Seismic Bulletin (http://terremoti.ingv.it/bsi, last access: 15 February 2020​​​​​​​) of the Istituto Nazionale di Geofisica e Vulcanologia between January 2005 and January 2020, and it includes events in the magnitude range between 0.0 and 6.5. The waveform data have been recorded primarily by the Italian National Seismic Network (network code IV) and include both weak- (HH, EH channels) and strong-motion (HN channels) recordings. All the waveform traces have a length of 120 s, are sampled at 100 Hz, and are provided both in counts and ground motion physical units after deconvolution of the instrument transfer functions. The waveform dataset is accompanied by metadata consisting of more than 100 parameters providing comprehensive information on the earthquake source, the recording stations, the trace features, and other derived quantities. This rich set of metadata allows the users to target the data selection for their own purposes. Much of these metadata can be used as labels in ML analysis or for other studies. The dataset, assembled in HDF5 format, is available at http://doi.org/10.13127/instance (Michelini et al., 2021).
    Description: Published
    Description: 5509–5544
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    A pushing mechanism for microtubule aster positioning in a large cell type (2020)
    Cell Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Meaders, J. L., de Matos, S. N., & Burgess, D. R. A pushing mechanism for microtubule aster positioning in a large cell type. Cell Reports, 33(1), (2020): 108213, doi:10.1016/j.celrep.2020.108213.
    Description: After fertilization, microtubule (MT) sperm asters undergo long-range migration to accurately position pronuclei. Due to the large sizes of zygotes, the forces driving aster migration are considered to be from pulling on the astral MTs by dynein, with no significant contribution from pushing forces. Here, we re-investigate the forces responsible for sperm aster centration in sea urchin zygotes. Our quantifications of aster geometry and MT density preclude a pulling mechanism. Manipulation of aster radial lengths and growth rates, combined with quantitative tracking of aster migration dynamics, indicates that aster migration is equal to the length of rear aster radii, supporting a pushing model for centration. We find that dynein inhibition causes an increase in aster migration rates. Finally, ablation of rear astral MTs halts migration, whereas front and side ablations do not. Collectively, our data indicate that a pushing mechanism can drive the migration of asters in a large cell type.
    Description: We would like to thank Dr. Jesse Gatlin for sending us the Tau-mCherry fusion protein for imaging live MTs. We would also like to thank Dr. Timothy Mitchison, Dr. Christine Field, and Dr. James Pelletier for supplying us with CA4, p150-CC1, and EB1-GFP peptides, as well as for fruitful discussions. Finally, we would like to thank Dr. Charles Shuster and Leslie Toledo-Jacobo for constructive feedback when preparing the manuscript. We thank Bret Judson and the Boston College Imaging Core for infrastructure and support. This material is based upon work supported by NSF grant no. 124425 to D.R.B.
    Keywords: Dynein ; Aster ; Microtubule ; Centrosome ; Pronucleus ; Fertilization ; Aster position
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization (2022)
    Cell Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stolp, Z. D., Kulkarni, M., Liu, Y., Zhu, C., Jalisi, A., Lin, S., Casadevall, A., Cunningham, K. W., Pineda, F. J., Teng, X., & Hardwick, J. M. Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Reports, 39(2), (2022): 110647, https://doi.org/10.1016/j.celrep.2022.110647.
    Description: Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans.
    Description: Funding sources: National Institutes of Health, United States grants AI144373 and NS127076 (J.M.H.), AI115016 and AI153414 (K.W.C.), and AI052733, AI152078, and HL059842 (A.C.); National Natural Science Foundation of China 31970550; and the Priority Academic Program Development of the Jiangsu Higher Education Institutes (X.T.).
    Keywords: Yeast ; Programmed cell death ; Vesicle trafficking ; AP-3 ; Vacuole ; Cryptococcus ; Yck3 ; Regulated cell death ; Lysosome ; Vacuolar membrane permeabilization
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Community comment on "Predicting trends in atmospheric CO2 across the Mid-Pleistocene Transition using existing climate archives" by Jordan R. W. Martin et al (2022)
    Copernicus
    In:  EPIC3Comment on egusphere-2022-574, EGUsphere, Copernicus
    Details
    Publication Date: 2022-10-24
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
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  • 8
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    Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production (2022)
    Cell Press
    In:  EPIC3Current Biology, Cell Press, ISSN: 09609822
    Details
    Publication Date: 2022-08-30
    Description: Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 9
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    AWI-CM3 coupled climate model: Description and evaluation experiments for a prototype post-CMIP6 model (2022)
    Copernicus
    In:  EPIC3EGUsphere, Copernicus
    Details
    Publication Date: 2022-06-29
    Description: We developed a new version of the Alfred Wegener Institute Climate Model (AWI-CM3), which has higher skills in representing the observed climatology and better computational efficiency than its predecessors. Its ocean component FESOM2 has the multi-resolution functionality typical for unstructured-mesh models while still featuring a scalability and efficiency similar to regular-grid models. The atmospheric component OpenIFS (CY43R3) enables the use of latest developments in the numerical weather prediction community in climate sciences. In this paper we describe the coupling of the model components and evaluate the model performance on a variable resolution (25–125 km) ocean mesh and a 61 km atmosphere grid, which serves as a reference and starting point for other on-going research activities with AWI-CM3. This includes the exploration of high and variable resolution, the development of a full Earth System Model as well as the creation of a new sea ice prediction system. At this early development stage and with the given coarse to medium resolutions, the model already features above CMIP6-average skills in representing the climatology and competitive model throughput. Finally we identify remaining biases and suggest further improvements to be made to the model.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 10
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    The influence of tides on the marine carbonate chemistry of a coastal polynya in the south-eastern Weddell Sea (2022)
    Copernicus
    In:  EPIC3Ocean Science, Copernicus, 18(5), pp. 1293-1320, ISSN: 1812-0792
    Details
    Publication Date: 2022-09-23
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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