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  • Articles  (158,409)
  • American Chemical Society  (133,096)
  • Cell Press  (25,313)
  • 2020-2023  (17)
  • 2000-2004  (158,392)
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  • 1
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    Microplastics in the Weddell Sea (Antarctica): A Forensic Approach for Discrimination between Environmental and Vessel-Induced Microplastics (2021)
    American Chemical Society
    In:  EPIC3Environmental Science & Technology, American Chemical Society, ISSN: 0013-936X
    Details
    Publication Date: 2022-01-07
    Description: Microplastic (MP) pollution has been found in the Southern Ocean surrounding Antarctica, but many local regions within this vast area remain uninvestigated. The remote Weddell Sea contributes to the global thermohaline circulation, and one of the two Antarctic gyres is located in that region. In the present study, we evaluate MP (〉300 μm) concentration and composition in surface (n = 34) and subsurface water samples (n = 79, ∼11.2 m depth) of the Weddell Sea. All putative MP were analyzed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. MP was found in 65% of surface and 11.4% of subsurface samples, with mean (±standard deviation (SD)) concentrations of 0.01 (±0.01 SD) MP m–3 and 0.04 (±0.1 SD) MP m–3, respectively, being within the range of previously reported values for regions south of the Polar Front. Additionally, we aimed to determine whether identified paint fragments (n = 394) derive from the research vessel. Environmentally sampled fragments (n = 101) with similar ATR-FTIR spectra to reference paints from the research vessel and fresh paint references generated in the laboratory were further subjected to micro-X-ray fluorescence spectroscopy (μXRF) to compare their elemental composition. This revealed that 45.5% of all recovered MP derived from vessel-induced contamination. However, 11% of the measured fragments could be distinguished from the reference paints via their elemental composition. This study demonstrates that differentiation based purely on visual characteristics and FTIR spectroscopy might not be sufficient for accurately determining sample contamination sources.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 2
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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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  • 3
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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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  • 4
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    Plastic formulation is an emerging control of its photochemical fate in the ocean (2021)
    American Chemical Society
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walsh, A. N., Reddy, C. M., Niles, S. F., McKenna, A. M., Hansel, C. M., & Ward, C. P. Plastic formulation is an emerging control of its photochemical fate in the ocean. Environmental Science & Technology, 55(18), (2021): 12383–12392, https://doi.org/10.1021/acs.est.1c02272.
    Description: Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15–36% inorganic additives, primarily calcium carbonate (13–34%) and titanium dioxide (TiO2; 1–2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68–94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
    Description: Funding was provided by the Seaver Institute, the Gerstner Family Foundation, Woods Hole Oceanographic Institution, and the National Science Foundation Graduate Research Fellowship Program (A.N.W.). The Ion Cyclotron Resonance user facility at the National High Magnetic Field Laboratory is supported by the National Science Foundation Division of Chemistry and Division of Materials Research through DMR-1644779 and the State of Florida.
    Keywords: Plastic pollution ; Marine debris ; Additives ; Dissolved organic carbon ; Photochemical oxidation ; FT-ICR-MS ; Titanium dioxide
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum (2021)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Rapid degradation of cellulose diacetate by marine microbes (2022)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mazzotta, M. G., Reddy, C. M., & Ward, C. P. Rapid degradation of cellulose diacetate by marine microbes. Environmental Science & Technology Letters, 9(1), (2022): 37-41. https://doi.org/10.1021/acs.estlett.1c00843.
    Description: The persistence of cellulose diacetate (CDA), a biobased plastic used in textiles and single-use consumer products, in the ocean is currently unknown. Here, we probe the disintegration and degradation of CDA-based materials (25 μm films, 510 μm foam, and 97 g/m2 fabric) by marine microbes in a continuous flow seawater mesocosm. Photographic evidence and mass loss measurements demonstrate that CDA-based materials disintegrate in months. Disintegration is marked by the increasing esterase and cellulase activity of the biofilm community, suggesting that marine microbes degrade CDA. The natural abundance stable (13C) and radiocarbon (14C) isotopic signature of carbon dioxide respired during short-term bottle incubations confirms the rapid degradation of both acetyl and cellulosic components of CDA by seawater microbial communities. These findings challenge the paradigm set by governmental agencies and advocacy groups that CDA-based materials persist in the ocean for decades, and represent a positive step toward identifying high-utility, biobased plastics with low environmental persistence.
    Description: M.G.M., C.M.R., and C.P.W. thank Eastman Chemical Co. and Woods Hole Oceanographic Institution (WHOI) for scientific and financial support.
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Environmentally friendly and efficient hornet nest envelope-based photothermal absorbers (2022)
    American Chemical Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xie, L., Liu, X., Caratenuto, A., Tian, Y., Chen, F., DeGiorgis, J. A., Wan, Y., & Zheng, Y. Environmentally friendly and efficient hornet nest envelope-based photothermal absorbers. Acs Omega, 6(50), (2021): 34555–34562, https://doi.org/10.1021/acsomega.1c04851.
    Description: Water shortage is a critical global issue that threatens human health, environmental sustainability, and the preservation of Earth’s climate. Desalination from seawater and sewage is a promising avenue for alleviating this stress. In this work, we use the hornet nest envelope material to fabricate a biomass-based photothermal absorber as part of a desalination isolation system. This system realizes an evaporation rate of 3.98 kg m–2 h–1 under one-sun illumination, with prolonged evaporation rates all above 4 kg m–2 h–1. This system demonstrates a strong performance of 3.86 kg m–2 h–1 in 3.5 wt % saltwater, illustrating its effectiveness in evaporation seawater. Thus, with its excellent evaporation rate, great salt rejection ability, and easy fabrication approach, the hornet nest envelope constitutes a promising natural material for solar water treatment applications.
    Description: The authors acknowledge the support from the National Science Foundation, USA, through grant number CBET-1941743 and the National Science Foundation under EPSCoR Cooperation Agreement OIA-1655221.
    Repository Name: Woods Hole Open Access Server
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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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    AutoTuner: high fidelity and robust parameter selection for metabolomics data processing (2020)
    American Chemical Society
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLean, C., & Kujawinski, E. B. AutoTuner: high fidelity and robust parameter selection for metabolomics data processing. Analytical Chemistry, 92(8), (2020): 5724-5732, doi:10.1021/acs.analchem.9b04804.
    Description: Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters’ influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100–1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.
    Description: We thank Titus Brown and Ben Temperton for advice on the algorithm validation, Arthur Eschenlauer for constructive feedback on the software design, Krista Longnecker for continuous support and discussions, Gabriel Leventhal for mathematics advice, the users of AutoTuner for debugging help through Github, and David Angeles-Albores and two anonymous reviewers for critical feedback on the manuscript. Funding support included the National GEM Consortium and NSF graduate research program fellowships (C.M.) and grants from the MIT Microbiome Center (Award 6936800, E.B.K.) and the Simons Foundation (Award ID #509034, E.B.K.).
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Affinity purification of label-free tubulins from xenopus egg extracts (2021)
    Cell Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reusch, S., Biswas, A., Hirst, W. G., & Reber, S. Affinity purification of label-free tubulins from xenopus egg extracts. STAR Protocols, 1(3), (2020): 100151, doi:10.1016/j.xpro.2020.100151.
    Description: Cytoplasmic extracts from unfertilized Xenopus eggs have made important contributions to our understanding of microtubule dynamics, spindle assembly, and scaling. Until recently, these in vitro studies relied on the use of heterologous tubulin. This protocol allows for the purification of physiologically relevant Xenopus tubulins in milligram yield, which are a complex mixture of isoforms with various post-translational modifications. The protocol is applicable to any cell or tissue of interest. For complete details on the use and execution of this protocol, please refer to Hirst et al. (2020).
    Description: This article was prompted by our stay at the Marine Biological Laboratory (MBL), Woods Hole, MA, in the summer of 2016 funded by the Princeton-Humboldt Strategic Partnership Grant together with the lab of Sabine Petry (Princeton University). We are grateful to the National Xenopus Resource (NXR) for supplying frogs. For mass spectrometry, we would like to acknowledge the assistance of Benno Kuropka and Chris Weise from the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). We thank the Protein Expression Purification and Characterization (PEPC) facility at the MPI-CBG; in particular, we thank Aliona Bogdanova and Barbara Borgonovo. We thank all former and current members of the Reber lab for discussions and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding from the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University.
    Repository Name: Woods Hole Open Access Server
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