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  • Wiley  (102)
  • American Institute of Physics
  • American Institute of Physics (AIP)
  • Cell Press
  • Oxford University Press
  • 2020-2023  (150)
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  • 1
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    Neogene and Quaternary reef terraces of Mangaia, Rarotonga and Aitutaki (southern Cook Islands, South Pacific) revisited: gauges of sea-level change and island uplift? (2022)
    Wiley
    Details
    Publication Date: 2022-12-19
    Description: New sedimentological data of facies and diagenesis as well as chronological data including strontium (87Sr/86Sr)-isotope ratios and uranium (U)-series dating, radiocarbon (14C) accelerator mass spectrometry (AMS) dating and biostratigraphy from elevated reef terraces (makatea) in the southern Cook Islands of Mangaia, Rarotonga and Aitutaki contribute to controversial discussions regarding age and sea-level relationships of these occurrences during the Neogene and Quaternary. The oldest limestones of the uplifted makatea island of Mangaia include reef-related facies which are mid-Miocene in age, based on new Sr-isotope and biostratigraphical data. In between these older deposits and the lowest coastal reef terrace of marine isotope stage (MIS) 5e, various older Pleistocene reef-related facies were identified. Based on Sr-isotope ratios, these were deposited during earlier Pleistocene highstands (as old as 2.28 Ma). Rare reef terraces on Rarotonga belong to the Plio-Pleistocene and the late Miocene, according to 87Sr/86Sr ratios. The late Miocene age is enigmatic as it exceeds the age of subaerially exposed volcanic rocks of Rarotonga island. The fossil reef could have formed on an older submarine volcanic high that was later displaced by younger volcanism to its present position, or the Sr-age could be too old due to diagenetic resetting. The Plio-Pleistocene Rarotonga reef terraces are overlain irregularly by Holocene reef deposits that are interpreted as storm rubble. Reef terraces on Aitutaki represent evidence of a higher-than-present (up to 1 m) sea-level during the late Holocene, based on 14C AMS age data. They are very similar to elevated late Holocene reefs of adjacent French Polynesia with regard to composition, elevation and age.
    Type: Book chapter , NonPeerReviewed
    Format: text
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  • 2
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    Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean (2022)
    Wiley
    Details
    Publication Date: 2022-12-12
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in . Journal of Phycology (2022), https://doi.org/10.1111/jpy.13230.
    Description: The marine green alga Brilliantia kiribatiensis gen. et sp. nov. is described from samples collected from the coral reefs of the Southern Line Islands, Republic of Kiribati, Pacific Ocean. Phylogenetic analysis of sequences of the large- and small-subunit rDNA and the rDNA internal transcribed spacer region revealed that Brilliantia is a member of the Boodleaceae (Cladophorales), containing the genera Apjohnia, Boodlea, Cladophoropsis, Chamaedoris, Phyllodictyon, and Struvea. Within this clade it formed a distinct lineage, sister to Struvea elegans, but more distantly related to the bona fide Struvea species (including the type S. plumosa). Brilliantia differs from the other genera by having a very simple architecture forming upright, unbranched, single-celled filaments attached to the substratum by a rhizoidal mat. Cell division occurs by segregative cell division only at the onset of reproduction. Based on current sample collection, B. kiribatiensis seems to be largely restricted to the Southern Line Islands, although it was also observed on neighboring islands, including Orona Atoll in the Phoenix Islands of Kiribati, and the Rangiroa and Takapoto Atolls in the Tuamotus of French Polynesia. This discovery highlights the likeliness that there is still much biodiversity yet to be discovered from these remote and pristine reefs of the central Pacific.
    Description: National Geographic Society
    Description: 2022-12-12
    Keywords: 18S nuclear ribosomal DNA ; Chlorophyta ; Cladophorales ; Molecular phylogeny ; Siphonocladales ; Ulvophyceae
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 3
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    Farm-waste-derived recyclable photothermal evaporator (2022)
    Cell Press
    Details
    Publication Date: 2022-11-18
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tian, Y., Liu, X., Li, J., Deng, Y., DeGiorgis, J. A., Zhou, S., Caratenuto, A., Minus, M. L., Wan, Y., Xiao, G., & Zheng, Y. Farm-waste-derived recyclable photothermal evaporator. Cell Reports Physical Science, 2(9), (2021): 100549, https://doi.org/10.1016./j.xcrp.2021.100549
    Description: Interfacial solar steam generation is emerging as a promising technique for efficient desalination. Although increasing efforts have been made, challenges exist for achieving a balance among a plethora of performance indicators—for example, rapid evaporation, durability, low-cost deployment, and salt rejection. Here, we demonstrate that carbonized manure can convert 98% of sunlight into heat, and the strong capillarity of porous carbon fibers networks pumps sufficient water to evaporation interfaces. Salt diffusion within microchannels enables quick salt drainage to the bulk seawater to prevent salt accumulation. With these advantages, this biomass-derived evaporator is demonstrated to feature a high evaporation rate of 2.81 kg m−2 h−1 under 1 sun with broad robustness to acidity and alkalinity. These advantages, together with facial deployment, offer an approach for converting farm waste to energy with high efficiency and easy implementation, which is particularly well suited for developing regions.
    Description: This project is supported by the National Science Foundation through grant no. CBET-1941743. This project is based upon work supported in part by the National Science Foundation under EPSCoR Cooperative Agreement no. OIA-1655221.
    Keywords: Biomass ; Recyclable ; Manure ; Farm waste ; Photothermal evaporation ; Desalination
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Mesopelagic-epipelagic fish nexus in viability and feasibility of commercial-scale mesopelagic fisheries (2022)
    Wiley
    Details
    Publication Date: 2022-11-07
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kourantidou, M., & Jin, D. Mesopelagic-epipelagic fish nexus in viability and feasibility of commercial-scale mesopelagic fisheries. Natural Resource Modeling, 35(4), (2022): e12350, https://doi.org/10.1111/nrm.12350.
    Description: While considerable scientific uncertainties persist for mesopelagic ecosystems, the fishing industry has developed a great interest in commercial exploitation with improved technologies as part of their search for new sources of feed for fishmeal and fish oil for aquaculture, which will intensify with the planet's growing population. The multiple uncertainties surrounding the ecosystem structure and particularly the size of biomass, hinder a good understanding of the risks associated with large-scale exploitation, which is needed for a management framework for sustainable ocean uses. Despite concerns regarding irreversible losses triggered by commercial fishing, work exploring the vulnerability of mesopelagic fish to harvesting is largely missing. This study investigates the economic feasibility of mesopelagic fishing which is the primary driver for any possible future expansion. Using very limited information currently available, we conduct a high-level assessment focusing on key ecological and economic interactions and develop an initial understanding of the economic feasibility of commercial harvesting for mesopelagic fish in the coming years. We conduct simulations using a classical bioeconomic model that captures two species groups, mesopelagic and epipelagic fish, using a wide range of price and cost parameters. We analyze different scenarios for the economic profitability of the fishery in a regional fishery management context. The results of our study highlight the importance of better understanding key biological and ecological mechanisms and parameters which can in turn help inform policies aimed at protecting the mesopelagic.
    Description: This study is supported by WHOI's Ocean Twilight Zone program which is part of the Audacious Project, a collaborative endeavor, housed at TED.
    Keywords: Bioeconomic analysis ; Commercial fisheries ; Ecological interactions ; Economic feasibility ; Mesopelagic fish ; Twilight zone
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Segment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii (2022)
    Wiley
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kuehn, E., Clausen, D. S., Null, R. W., Metzger, B. M., Willis, A. D., & Ozpolat, B. D. Segment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, (2021.): 1-16, https://doi.org/10.1002/jez.b.23100.
    Description: Development of sexual characters and generation of gametes are tightly coupled with growth. Platynereis dumerilii is a marine annelid that has been used to study germline development and gametogenesis. P. dumerilii has germ cell clusters found across the body in the juvenile worms, and the clusters eventually form the gametes. Like other segmented worms, P. dumerilii grows by adding new segments at its posterior end. The number of segments reflect the growth state of the worms and therefore is a useful and measurable growth state metric to study the growth-reproduction crosstalk. To understand how growth correlates with progression of gametogenesis, we investigated germline development across several developmental stages. We discovered a distinct transition period when worms increase the number of germline clusters at a particular segment number threshold. Additionally, we found that keeping worms short in segment number, by manipulating environmental conditions or via amputations, supported a segment number threshold requirement for germline development. Finally, we asked if these clusters in P. dumerilii play a role in regeneration (as similar free-roaming cells are observed in Hydra and planarian regeneration) and found that the clusters were not required for regeneration in P. dumerilii, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state of juvenile P. dumerilii leading to substantially increased germline expansion.
    Description: Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM138008 (to BDÖ) and R35GM133420 (to ADW) and Hibbitt Startup Funds (to BDÖ).
    Keywords: Annelida ; Critical size ; Developmental transition ; Gametogenesis ; Sexual reproduction
    Repository Name: Woods Hole Open Access Server
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  • 8
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    A pushing mechanism for microtubule aster positioning in a large cell type (2020)
    Cell Press
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    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
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  • 9
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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
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  • 10
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
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    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 da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
    Repository Name: Woods Hole Open Access Server
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