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  • National Academy of Sciences  (4,351)
  • American Institute of Physics (AIP)
  • Cambridge University Press
  • Periodicals Archive Online (PAO)
  • 2020-2023  (20)
  • 2020-2022  (6,315)
  • 1975-1979
  • 1935-1939
  • 2020  (6,335)
  • 2020  (6,335)
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  • 2020-2023  (20)
  • 2020-2022  (6,315)
  • 1975-1979
  • 1935-1939
  • 2020-2024  (13)
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  • 1
    Publication Date: 2020-08-24
    Description: The effect of freshwater sources on wintertime sea-ice CO2 processes was studied from the glacier front to the outer Tempelfjorden, Svalbard, in sea ice, glacier ice, brine and snow. March–April 2012 was mild, and the fjord was mainly covered with drift ice, in contrast to the observed thicker fast ice in the colder April 2013. This resulted in different physical and chemical properties of the sea ice and under-ice water. Data from stable oxygen isotopic ratios and salinity showed that the sea ice at the glacier front in April 2012 contained on average 54% of frozen-in glacial meltwater. This was five times higher than in April 2013, where the ice was frozen seawater. In April 2012, the largest excess of sea-ice total alkalinity (AT), carbonate ion ([CO32−]) and bicarbonate ion concentrations ([HCO3−]) relative to salinity was mainly related to dissolved dolomite and calcite incorporated during freezing of mineral-enriched glacial water. In April 2013, the excess of these variables was mainly due to ikaite dissolution as a result of sea-ice processes. Dolomite dissolution increased sea-ice AT twice as much as ikaite and calcite dissolution, implying different buffering capacity and potential for ocean CO2 uptake in a changing climate.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
    Publication Date: 2020-09-24
    Description: Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Cambridge University Press
    In:  EPIC3Radiocarbon, Cambridge University Press, 62(4), pp. 865-871, ISSN: 0033-8222
    Publication Date: 2020-09-24
    Description: Beyond ~13.9 cal kBP, the IntCal20 radiocarbon (14C) calibration curve is based upon combining data across a range of different archives including corals and planktic foraminifera. In order to reliably incorporate such marine data into an atmospheric curve, we need to resolve these records into their constituent atmospheric signal and marine reservoir age. We present results of marine reservoir age simulations enabling this resolution, applying the LSG ocean general circulation model forced with various climatic background conditions and with atmospheric radiocarbon changes according to the Hulu Cave speleothem record. Simulating the spatiotemporal evolution of reservoir ages between 54,000 and 10,700 cal BP, we find reservoir ages between 500 and 1400 yr in the low- and mid-latitudes, but also more than 3000 yr in the polar seas. Our results are broadly in agreement with available marine radiocarbon reconstructions, with the caveat that continental margins, marginal seas, or tropical lagoons are not properly resolved in our coarse-resolution model.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2020-09-24
    Description: The concentration of radiocarbon (14C) differs between ocean and atmosphere. Radiocarbon determinations from samples which obtained their 14C in the marine environment therefore need a marine-specific calibration curve and cannot be calibrated directly against the atmospheric-based IntCal20 curve. This paper presents Marine20, an update to the internationally agreed marine radiocarbon age calibration curve that provides a non-polar global-average marine record of radiocarbon from 0–55 cal kBP and serves as a baseline for regional oceanic variation. Marine20 is intended for calibration of marine radiocarbon samples from non-polar regions; it is not suitable for calibration in polar regions where variability in sea ice extent, ocean upwelling and air-sea gas exchange may have caused larger changes to concentrations of marine radiocarbon. The Marine20 curve is based upon 500 simulations with an ocean/atmosphere/biosphere box-model of the global carbon cycle that has been forced by posterior realizations of our Northern Hemispheric atmospheric IntCal20 14C curve and reconstructed changes in CO2 obtained from ice core data. These forcings enable us to incorporate carbon cycle dynamics and temporal changes in the atmospheric 14C level. The box-model simulations of the global-average marine radiocarbon reservoir age are similar to those of a more complex three-dimensional ocean general circulation model. However, simplicity and speed of the box model allow us to use a Monte Carlo approach to rigorously propagate the uncertainty in both the historic concentration of atmospheric 14C and other key parameters of the carbon cycle through to our final Marine20 calibration curve. This robust propagation of uncertainty is fundamental to providing reliable precision for the radiocarbon age calibration of marine based samples. We make a first step towards deconvolving the contributions of different processes to the total uncertainty; discuss the main differences of Marine20 from the previous age calibration curve Marine13; and identify the limitations of our approach together with key areas for further work. The updated values for ΔR, the regional marine radiocarbon reservoir age corrections required to calibrate against Marine20, can be found at the data base http://calib.org/marine/.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2020-05-27
    Description: Volcanism and metamorphism are the principal geologic processes that drive carbon transfer from the interior of Earth to the surface reservoir.1–4 Input of carbon to the surface reservoir through volcanic degassing is balanced by removal through silicate weathering and the subduction of carbon-bearing marine deposits over million-year timescales. The magnitude of the volcanic carbon flux is thus of fundamental importance for stabilization of atmospheric CO2 and for long-term climate. It is likely that the “deep” carbon reservoir far exceeds the size of the surface reservoir in terms of mass;5,6 more than 99%of Earth’s carbon may reside in the core, mantle, and crust. The relatively high flux of volcanic carbon to the surface reservoir, combined with the reservoir’s small size, results in a short residence time for carbon in the ocean–atmosphere–biosphere system (~200 ka).7 The implication is that changes in the flux of volcanic carbon can affect the climate and ultimately the habitability of the planet on geologic timescales. In order to understand this delicate balance, we must first quantify the current volcanic flux of carbon to the atmosphere and understand the factors that control this flux.
    Description: Published
    Description: 188-236
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 6
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    Cambridge University Press
    In:  EPIC3The Species–Area Relationship, The Species–Area Relationship, Cambridge University Press, pp. 438-456
    Publication Date: 2020-11-04
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
    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 Peredo, E. L., & Cardon, Z. G. Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proceedings of the National Academy of Sciences of the United States of America, 117(29), 1(2020): 7438-17445, doi:10.1073/pnas.1906904117.
    Description: Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.
    Description: Dr. Louise Lewis (University of Connecticut) provided F. rotunda and A. deserticola. Suzanne Thomas and Jordan Stark provided expert technical assistance. This work was supported by the NSF, Division of Integrative Organismal Systems (1355085 to Z.G.C.), and an anonymous donor (to Z.G.C.).
    Keywords: Aquatic green algae ; Desert-evolved green algae ; Extremophiles ; Microbiotic ; Crusts ; Scenedesmaceae
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-10-31
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences of the United States of America, 116 (52) (2019): 26980-26990, doi: 10.1073/pnas.1911413116.
    Description: Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
    Description: We thank members of the D.J.S., H.A.H., and E.M. laboratories for helpful discussions. We thank the Genomic Sequencing and Analysis Facility (The University of Texas [UT] at Austin) for library preparation and sequencing and the bioinformatics consulting team at the UT Austin Center for Computational Biology and Bioinformatics for helpful advice. This work was supported by National Institutes of Health grant R01MH046742-29 (to E.M. and D.J.S.) and the National Institute of General Medical Sciences T32GM008396 (support for A.J.N.) and National Institute of Mental Health grant 5R25MH059472-18 and the Grass Foundation (support for Neural Systems and Behavior Course at the Marine Biological Laboratory).
    Keywords: qPCR ; RNA-seq ; Stomatogastric ; Expression profiling
    Repository Name: Woods Hole Open Access Server
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  • 9
    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 Lebrato, M., Garbe-Schönberg, D., Müller, M. N., Blanco-Ameijeiras, S., Feely, R. A., Lorenzoni, L., Molinero, J. C., Bremer, K., Jones, D. O. B., Iglesias-Rodriguez, D., Greeley, D., Lamare, M. D., Paulmier, A., Graco, M., Cartes, J., Barcelos E Ramos, J., de Lara, A., Sanchez-Leal, R., Jimenez, P., Paparazzo, F. E., Hartman, S. E., Westernströer, U., Küter, M., Benavides, R., da Silva, A. F., Bell, S., Payne, C., Olafsdottir, S., Robinson, K., Jantunen, L. M., Korablev, A., Webster, R. J., Jones, E. M., Gilg, O., Bailly du Bois, P., Beldowski, J., Ashjian, C., Yahia, N. D., Twining, B., Chen, X. G., Tseng, L. C., Hwang, J. S., Dahms, H. U., & Oschlies, A. Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean. Proceedings of the National Academy of Sciences of the United States of America, 117(36), (2020): 22281-22292, doi:10.1073/pnas.1918943117.
    Description: Seawater Mg:Ca and Sr:Ca ratios are biogeochemical parameters reflecting the Earth–ocean–atmosphere dynamic exchange of elements. The ratios’ dependence on the environment and organisms' biology facilitates their application in marine sciences. Here, we present a measured single-laboratory dataset, combined with previous data, to test the assumption of limited seawater Mg:Ca and Sr:Ca variability across marine environments globally. High variability was found in open-ocean upwelling and polar regions, shelves/neritic and river-influenced areas, where seawater Mg:Ca and Sr:Ca ratios range from ∼4.40 to 6.40 mmol:mol and ∼6.95 to 9.80 mmol:mol, respectively. Open-ocean seawater Mg:Ca is semiconservative (∼4.90 to 5.30 mol:mol), while Sr:Ca is more variable and nonconservative (∼7.70 to 8.80 mmol:mol); both ratios are nonconservative in coastal seas. Further, the Ca, Mg, and Sr elemental fluxes are connected to large total alkalinity deviations from International Association for the Physical Sciences of the Oceans (IAPSO) standard values. Because there is significant modern seawater Mg:Ca and Sr:Ca ratios variability across marine environments we cannot absolutely assume that fossil archives using taxa-specific proxies reflect true global seawater chemistry but rather taxa- and process-specific ecosystem variations, reflecting regional conditions. This variability could reconcile secular seawater Mg:Ca and Sr:Ca ratio reconstructions using different taxa and techniques by assuming an error of 1 to 1.50 mol:mol, and 1 to 1.90 mmol:mol, respectively. The modern ratios’ variability is similar to the reconstructed rise over 20 Ma (Neogene Period), nurturing the question of seminonconservative behavior of Ca, Mg, and Sr over modern Earth geological history with an overlooked environmental effect.
    Description: We thank the researchers, staff, students, and volunteers in all the expeditions around the world for their contributions. One anonymous referee and Bernhard Peucker-Ehenbrink, Woods Hole Oceanographic Institution, contributed significantly to the final version of the manuscript. This study was developed under a grant from the Federal Ministry of Education and Research to D.G.-S. under contract 03F0722A, by the Kiel Cluster of Excellence “The Future Ocean” (D1067/87) to A.O. and M.L., and by the “European project on Ocean Acidification” (European Community’s Seventh Framework Programme FP7/2007-2013, grant agreement 211384) to A.O. and M.L. Additional funding was provided from project DOSMARES CTM2010-21810-C03-02, by the UK Natural Environment Research Council, to the National Oceanography Centre. This is Pacific Marine Environmental Laboratory contribution number 5046.
    Keywords: global ; seawater ; Mg:Ca ; Sr:Ca ; biogeochemistry
    Repository Name: Woods Hole Open Access Server
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  • 10
    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 Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.
    Description: Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
    Description: We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H.
    Keywords: Deep biosphere ; Microbiome ; Dispersal
    Repository Name: Woods Hole Open Access Server
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  • 11
    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 MBL Hernandez, C. M., van Daalen, S. F., Caswell, H., Neubert, M. G., & Gribble, K. E. A demographic and evolutionary analysis of maternal effect senescence. Proceedings of the National Academy of Sciences of the United States of America, 17(28), (2020):16431-16437, doi: 10.1073/pnas.1919988117.
    Description: Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate, Brachionus manjavacas (Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness for B. manjavacas and that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.
    Description: K.E.G. was supported by Grant 5K01AG049049 from the National Institute on Aging and by the Bay and Paul Foundations. H.C. and S.F.v.D. were supported by the European Research Council through Advanced Grants 322829 and 788195 and by the Dutch Research Council through Grant ALWOP.2015.100. C.M.H. was supported by a National Science Foundation Graduate Research Fellowship. M.G.N. received funding from The Paul MacDonald Fye Chair for Excellence in Oceanography at the Woods Hole Oceanographic Institution.
    Keywords: Aging ; Demography ; Fitness ; Maternal effects ; Selection gradients
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  • 12
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 117(22), (2020): 12215-12221, doi: 10.1073/pnas.1918439117.
    Description: Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteria Synechococcus at the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundant Synechococcus and are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared with Synechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region’s primary productivity than their standing stocks suggest.
    Description: We thank E. T. Crockford, E. E. Peacock, J. Fredericks, Z. Sandwith, the MVCO Operations Team, and divers of the Woods Hole Oceanographic Institution diving program. This work was supported by NSF Grants OCE-0119915 (to R.J.O. and H.M.S.) and OCE-1655686 (to M.G.N., R.J.O., A.R.S., and H.M.O.); NASA Grants NNX11AF07G (to H.M.S.) and NNX13AC98G (to H.M.S.); Gordon and Betty Moore Foundation Grant GGA#934 (to H.M.S.); and Simons Foundation Grant 561126 (to H.M.S.).
    Description: 2020-11-15
    Keywords: Picoeukaryotes ; Flow cytometry ; Matrix model ; Primary productivity
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  • 13
    Publication Date: 2022-10-26
    Description: © The Author(s), 202. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Sylva, S. P., Ono, S., German, C. R., & Seewald, J. S. Abiotic redox reactions in hydrothermal mixing zones: decreased energy availability for the subsurface biosphere. Proceedings of the National Academy of Sciences of the United States of America, 117(34), (2020): 20453-20461, doi:10.1073/pnas.2003108117.
    Description: Subseafloor mixing of high-temperature hot-spring fluids with cold seawater creates intermediate-temperature diffuse fluids that are replete with potential chemical energy. This energy can be harnessed by a chemosynthetic biosphere that permeates hydrothermal regions on Earth. Shifts in the abundance of redox-reactive species in diffuse fluids are often interpreted to reflect the direct influence of subseafloor microbial activity on fluid geochemical budgets. Here, we examine hydrothermal fluids venting at 44 to 149 °C at the Piccard hydrothermal field that span the canonical 122 °C limit to life, and thus provide a rare opportunity to study the transition between habitable and uninhabitable environments. In contrast with previous studies, we show that hydrocarbons are contributed by biomass pyrolysis, while abiotic sulfate (SO42−) reduction produces large depletions in H2. The latter process consumes energy that could otherwise support key metabolic strategies employed by the subseafloor biosphere. Available Gibbs free energy is reduced by 71 to 86% across the habitable temperature range for both hydrogenotrophic SO42− reduction to hydrogen sulfide (H2S) and carbon dioxide (CO2) reduction to methane (CH4). The abiotic H2 sink we identify has implications for the productivity of subseafloor microbial ecosystems and is an important process to consider within models of H2 production and consumption in young oceanic crust.
    Description: Financial support was provided by the National Aeronautics and Space Administration (NASA) Astrobiology program (Awards NNX09AB75G and 80NSSC19K1427 to C.R.G. and J.S.S.) and the NSF (Award OCE-1061863 to C.R.G. and J.S.S.). Ship and vehicle time for cruise FK008 was provided by the Schmidt Ocean Institute. We thank the ROV Jason II and HROV Nereus groups, and the captain, officers, and crew of R/V Atlantis (AT18-16) and R/V Falkor (FK008) for their dedication to skillful operations at sea. We thank our scientific colleagues from both cruises, as well as Meg Tivey, Frieder Klein, and Scott Wankel for insightful discussions. We are grateful to the editor and two anonymous reviewers for providing helpful comments and suggestions.
    Keywords: Hydrothermal vent ; Subsurface biosphere ; Bioenergetics ; Biogeochemistry
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  • 14
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hughen, K. A., & Heaton, T. J. Updated Cariaco Basin C-14 calibration dataset from 0-60 cal kyr BP. Radiocarbon, 62(4), (2020): 1001-1043, doi:10.1017/RDC.2020.53.
    Description: We present new updates to the calendar and radiocarbon (14C) chronologies for the Cariaco Basin, Venezuela. Calendar ages were generated by tuning abrupt climate shifts in Cariaco Basin sediments to those in speleothems from Hulu Cave. After the original Cariaco-Hulu calendar age model was published, Hulu Cave δ18O records have been augmented with increased temporal resolution and a greater number of U/Th dates. These updated Hulu Cave records provide increased accuracy as well as precision in the final Cariaco calendar age model. The depth scale for the Ocean Drilling Program Site 1002D sediment core, the primary source of samples for 14C dating, has been corrected to account for missing sediment from a core break, eliminating age-depth anomalies that afflicted the earlier calendar age models. Individual 14C dates for the Cariaco Basin remain unchanged from previous papers, although detailed comparisons of the Cariaco calibration dataset to those from Hulu Cave and Lake Suigetsu suggest that the Cariaco marine reservoir age may have shifted systematically during the past. We describe these recent changes to the Cariaco datasets and provide the data in a comprehensive format that will facilitate use by the community.
    Description: K.A. Hughen was supported by funds from U.S. NSF grant #OCE-1657191, and by the Investment in Science Fund at WHOI. T.J. Heaton is supported by a Leverhulme Trust Fellowship RF-2019-140\9, “Improving the Measurement of Time Using Radiocarbon”.
    Keywords: Calibration ; Climate ; Radiocarbon
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  • 15
    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ackley, S. F., Perovich, D. K., Maksym, T., Weissling, B., & Xie, H. Surface flooding of Antarctic summer sea ice. Annals of Glaciology, 61(82), (2020): 117-126, doi:10.1017/aog.2020.22.
    Description: The surface flooding of Antarctic sea ice in summer covers 50% or more of the sea-ice area in the major summer ice packs, the western Weddell and the Bellingshausen-Amundsen Seas. Two CRREL ice mass-balance buoys were deployed on the Amundsen Sea pack in late December 2010 from the icebreaker Oden, bridging the summer period (January–February 2011). Temperature records from thermistors embedded vertically in the snow and ice showed progressive increases in the depth of the flooded layer (up to 0.3–0.35 m) on the ice cover during January and February. While the snow depth was relatively unchanged from accumulation (〈10 cm), ice thickness decreased by up to a meter from bottom melting during this period. Contemporaneous with the high bottom melting, under-ice water temperatures up to 1°C above the freezing point were found. The high temperature arises from solar heating of the upper mixed layer which can occur when ice concentration in the local area falls and lower albedo ocean water is exposed to radiative heating. The higher proportion of snow ice found in the Amundsen Sea pack ice therefore results from both winter snowfall and summer ice bottom melt found here that can lead to extensive surface flooding.
    Description: This work was supported by the National Science Foundation grant to UTSA, ANT-0839053-Sea Ice System in Antarctic Summer (S.F. Ackley, H. Xie and B. Weissling), and to WHOI, ANT-1341513 (T. Maksym), and by the NASA Center for Advanced Measurements in Extreme Environments or NASA-CAMEE at UTSA, NASA #80NSSC19M0194 (S.F. Ackley, H. Xie, B.Weissling).
    Keywords: Ice/ocean interactions ; Sea ice ; Sea-ice growth and decay ; Snow/ice surface processes
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  • 16
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences (2020): 201913625, doi: 10.1073/pnas.1913625117.
    Description: Oceanic transform faults display a unique combination of seismic and aseismic slip behavior, including a large globally averaged seismic deficit, and the local occurrence of repeating magnitude (M) ∼6 earthquakes with abundant foreshocks and seismic swarms, as on the Gofar transform of the East Pacific Rise and the Blanco Ridge in the northeast Pacific Ocean. However, the underlying mechanisms that govern the partitioning between seismic and aseismic slip and their interaction remain unclear. Here we present a numerical modeling study of earthquake sequences and aseismic transient slip on oceanic transform faults. In the model, strong dilatancy strengthening, supported by seismic imaging that indicates enhanced fluid-filled porosity and possible hydrothermal circulation down to the brittle–ductile transition, effectively stabilizes along-strike seismic rupture propagation and results in rupture barriers where aseismic transients arise episodically. The modeled slow slip migrates along the barrier zones at speeds ∼10 to 600 m/h, spatiotemporally correlated with the observed migration of seismic swarms on the Gofar transform. Our model thus suggests the possible prevalence of episodic aseismic transients in M ∼6 rupture barrier zones that host active swarms on oceanic transform faults and provides candidates for future seafloor geodesy experiments to verify the relation between aseismic fault slip, earthquake swarms, and fault zone hydromechanical properties.
    Description: We thank Joan Gomberg, Ruth Harris, Steve Hickman, Shane Detweiler, Mike Diggles, and two anonymous external reviewers for their thoughtful comments that helped to improve the manuscript. This study was supported by Natural Sciences and Engineering Research Council of Canada Discovery Grants RGPIN/418338-2012 and RGPIN-2018-05389; and NSF Grants OCE-10-61203 and OCE-18-33279.
    Description: 2020-10-28
    Keywords: Oceanic transform faults ; Earthquake rupture segmentation ; Aseismic transients ; Seismic swarms
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  • 17
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reimer, P. J., Austin, W. E. N., Bard, E., Bayliss, A., Blackwell, P. G., Ramsey, C. B., Butzin, M., Cheng, H., Edwards, R. L., Friedrich, M., Grootes, P. M., Guilderson, T. P., Hajdas, I., Heaton, T. J., Hogg, A. G., Hughen, K. A., Kromer, B., Manning, S. W., Muscheler, R., Palmer, J. G., Pearson, C., van der Plicht, J., Reimer, R. W., Richards, D. A., Scott, E. M., Southon, J. R., Turney, C. S. M., Wacker, L., Adolphi, F., Buentgen, U., Capano, M., Fahrni, S. M., Fogtmann-Schulz, A., Friedrich, R., Koehler, P., Kudsk, S., Miyake, F., Olsen, J., Reinig, F., Sakamoto, M., Sookdeo, A., & Talamo, S. The Intcal20 Northern Hemisphere radiocarbon age calibration curve (0-55 cal kBP). Radiocarbon, 62(4), (2020): 725-757, doi:10.1017/RDC.2020.41.
    Description: Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
    Description: We would like to thank the National Natural Science Foundation of China grants NSFC 41888101 and NSFC 41731174, the 111 program of China (D19002), U.S. NSF Grant 1702816, and the Malcolm H. Wiener Foundation for support for research that contributed to the IntCal20 curve. The work on the Swiss and German YD trees was funded by the German Science foundation and the Swiss National Foundation (grant number: 200021L_157187). The operation in Aix-en-Provence is funded by the EQUIPEX ASTER-CEREGE, the Collège de France and the ANR project CARBOTRYDH (to EB). The work on the correlation of tree ring 14C with ice core 10Be was partially supported by the Swedish Research Council and the Knut and Alice Wallenberg foundation. M. Butzin was supported by the German Federal Ministry of Education and Research (BMBF) as Research for Sustainable Development (FONA; http://www.fona.de) through the PalMod project (grant number: 01LP1505B). S. Talamo and M. Friedrich are funded by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No. 803147-RESOLUTION, awarded to ST). CA. Turney would like to acknowledge support of the Australian Research Council (FL100100195 and DP170104665). P. Reimer and W. Austin acknowledge the support of the UKRI Natural Environment Research Council (Grant NE/M004619/1). T.J. Heaton is supported by a Leverhulme Trust Fellowship RF-2019-140\9. Other datasets and the IntCal20 database were created without external support through internal funding by the respective laboratories. We also would like to thank various institutions that provided funding or facilities for meetings.
    Keywords: Calibration curve ; Radiocarbon ; IntCal20
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  • 18
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Buesseler, K. O., Boyd, P. W., Black, E. E., & Siegel, D. A. Metrics that matter for assessing the ocean biological carbon pump. Proceedings of the National Academy of Sciences of the United States of America, (2020): 201918114, doi: 10.1073/pnas.1918114117.
    Description: The biological carbon pump (BCP) comprises wide-ranging processes that set carbon supply, consumption, and storage in the oceans’ interior. It is becoming increasingly evident that small changes in the efficiency of the BCP can significantly alter ocean carbon sequestration and, thus, atmospheric CO2 and climate, as well as the functioning of midwater ecosystems. Earth system models, including those used by the United Nation’s Intergovernmental Panel on Climate Change, most often assess POC (particulate organic carbon) flux into the ocean interior at a fixed reference depth. The extrapolation of these fluxes to other depths, which defines the BCP efficiencies, is often executed using an idealized and empirically based flux-vs.-depth relationship, often referred to as the “Martin curve.” We use a new compilation of POC fluxes in the upper ocean to reveal very different patterns in BCP efficiencies depending upon whether the fluxes are assessed at a fixed reference depth or relative to the depth of the sunlit euphotic zone (Ez). We find that the fixed-depth approach underestimates BCP efficiencies when the Ez is shallow, and vice versa. This adjustment alters regional assessments of BCP efficiencies as well as global carbon budgets and the interpretation of prior BCP studies. With several international studies recently underway to study the ocean BCP, there are new and unique opportunities to improve our understanding of the mechanistic controls on BCP efficiencies. However, we will only be able to compare results between studies if we use a common set of Ez-based metrics.
    Description: We thank the many scientists whose ideas and contributions over the years are the foundation of this paper. This includes A. Martin, who led the organization of the BIARRITZ group (now JETZON) workshop in July 2019, discussions at which helped to motivate this article. We thank D. Karl for pointing us in the right direction for this paper format at PNAS and two thoughtful reviewers who through their comments helped to improve this manuscript. Support for writing this piece is acknowledged from several sources, including the Woods Hole Oceanographic Institution’s Ocean Twilight Zone project (K.O.B.); NASA as part of the EXport Processes in the global Ocean from RemoTe Sensing (EXPORTS) program (K.O.B. and D.A.S.). E.E.B. was supported by a postdoctoral fellowship through the Ocean Frontier Institute at Dalhousie University. P.W.B. was supported by the Australian Research Council through a Laureate (FL160100131).
    Keywords: Biological carbon pump ; Twilight zone ; Particle flux
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  • 19
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 117(26), (2020): 14618-14621, doi:10.1073/pnas.2008009117.
    Description: Plastic pollution is one of the most visible and complex environmental issues today. Interested and concerned parties include researchers, governmental agencies, nongovernmental organizations, industry, media, and the general public. One key assumption behind the issue and the public outcry is that plastics last indefinitely in the environment, resulting in chronic exposure that harms animals and humans. But the data supporting this assumption are scant.
    Description: We thank Briana Prado, Cassia Armstrong, and Anna Walsh for their help with the review, Kenneth Kostel, Katie Linehan, Daniel Ward, and Rose Cory for feedback on an earlier version of this piece, John Furfey for assistance with tracking down the original sources of the environmental lifetime estimates, and Natalie Reiner for help with Fig. 1. We acknowledge financial support from Woods Hole Oceanographic Institution (Woods Hole, MA) and the Seaver Institute (Los Angeles, CA).
    Description: 2020-12-10
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  • 20
    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 Heaton, T. J., Koehler, P., Butzin, M., Bard, E., Reimer, R. W., Austin, W. E. N., Ramsey, C. B., Grootes, P. M., Hughen, K. A., Kromer, B., Reimer, P. J., Adkins, J., Burke, A., Cook, M. S., Olsen, J., & Skinner, L. C. Marine20-the marine radiocarbon age calibration curve (0-55,000 cal BP). Radiocarbon, 62(4), (2020): 779-820, doi:10.1017/RDC.2020.68.
    Description: The concentration of radiocarbon (14C) differs between ocean and atmosphere. Radiocarbon determinations from samples which obtained their 14C in the marine environment therefore need a marine-specific calibration curve and cannot be calibrated directly against the atmospheric-based IntCal20 curve. This paper presents Marine20, an update to the internationally agreed marine radiocarbon age calibration curve that provides a non-polar global-average marine record of radiocarbon from 0–55 cal kBP and serves as a baseline for regional oceanic variation. Marine20 is intended for calibration of marine radiocarbon samples from non-polar regions; it is not suitable for calibration in polar regions where variability in sea ice extent, ocean upwelling and air-sea gas exchange may have caused larger changes to concentrations of marine radiocarbon. The Marine20 curve is based upon 500 simulations with an ocean/atmosphere/biosphere box-model of the global carbon cycle that has been forced by posterior realizations of our Northern Hemispheric atmospheric IntCal20 14C curve and reconstructed changes in CO2 obtained from ice core data. These forcings enable us to incorporate carbon cycle dynamics and temporal changes in the atmospheric 14C level. The box-model simulations of the global-average marine radiocarbon reservoir age are similar to those of a more complex three-dimensional ocean general circulation model. However, simplicity and speed of the box model allow us to use a Monte Carlo approach to rigorously propagate the uncertainty in both the historic concentration of atmospheric 14C and other key parameters of the carbon cycle through to our final Marine20 calibration curve. This robust propagation of uncertainty is fundamental to providing reliable precision for the radiocarbon age calibration of marine based samples. We make a first step towards deconvolving the contributions of different processes to the total uncertainty; discuss the main differences of Marine20 from the previous age calibration curve Marine13; and identify the limitations of our approach together with key areas for further work. The updated values for ΔR, the regional marine radiocarbon reservoir age corrections required to calibrate against Marine20, can be found at the data base http://calib.org/marine/.
    Description: We would like to thank Jeremy Oakley and Richard Bintanja for informative discussions during the development of this work. T.J. Heaton is supported by a Leverhulme Trust Fellowship RF-2019-140\9, “Improving the Measurement of Time Using Radiocarbon”. M Butzin is supported by the German Federal Ministry of Education and Research (BMBF), as Research for Sustainability initiative (FONA); www.fona.de through the PalMod project (grant numbers: 01LP1505B, 01LP1919A). E. Bard is supported by EQUIPEX ASTER-CEREGE and ANR CARBOTRYDH. Meetings of the IntCal Marine Focus group have been supported by Collège de France. Data are available on the PANGAEA database at doi:10.159/ANGAEA.914500.
    Keywords: Bayesian modeling ; calibration ; carbon cycle ; computer model ; marine environment
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  • 21
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 117(25), (2020): 13983-13990, doi: 10.1073/pnas.1922190117.
    Description: The two dominant drivers of the global mean sea level (GMSL) variability at interannual timescales are steric changes due to changes in ocean heat content and barystatic changes due to the exchange of water mass between land and ocean. With Gravity Recovery and Climate Experiment (GRACE) satellites and Argo profiling floats, it has been possible to measure the relative steric and barystatic contributions to GMSL since 2004. While efforts to “close the GMSL budget” with satellite altimetry and other observing systems have been largely successful with regards to trends, the short time period covered by these records prohibits a full understanding of the drivers of interannual to decadal variability in GMSL. One particular area of focus is the link between variations in the El Niño−Southern Oscillation (ENSO) and GMSL. Recent literature disagrees on the relative importance of steric and barystatic contributions to interannual to decadal variability in GMSL. Here, we use a multivariate data analysis technique to estimate variability in barystatic and steric contributions to GMSL back to 1982. These independent estimates explain most of the observed interannual variability in satellite altimeter-measured GMSL. Both processes, which are highly correlated with ENSO variations, contribute about equally to observed interannual GMSL variability. A theoretical scaling analysis corroborates the observational results. The improved understanding of the origins of interannual variability in GMSL has important implications for our understanding of long-term trends in sea level, the hydrological cycle, and the planet’s radiation imbalance.
    Description: The research was carried out at JPL, California Institute of Technology, under a contract with NASA. This study was funded by NASA Grants NNX17AH35G (Ocean Surface Topography Science Team), 80NSSC17K0564, and 80NSSC17K0565 (NASA Sea Level Change Team). The efforts of J.T.F. in this work were also supported by NSF Award AGS-1419571, and by the Regional and Global Model Analysis component of the Earth and Environmental System Modeling Program of the US Department of Energy's Office of Biological & Environmental Research via National Science Foundation Grant IA 1844590. C.G.P. was supported by the J. Lamar Worzel Assistant Scientist Fund and the Penzance Endowed Fund in Support of Assistant Scientists at the Woods Hole Oceanographic Institution.
    Description: 2020-12-08
    Keywords: Sea level ; Climate variability ; Global mean sea level ; Satellite altimetry
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  • 22
    Publication Date: 2022-10-26
    Description: © The Author(s), [year]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Broadley, M. W., Barry, P. H., Bekaert, D. V., Byrne, D. J., Caracausi, A., Ballentine, C. J., & Marty, B. Identification of chondritic krypton and xenon in Yellowstone gases and the timing of terrestrial volatile accretion. Proceedings of the National Academy of Sciences of the United States of America, 117 (25), (2020): 13997-14004, doi: 10.1073/pnas.2003907117.
    Description: Identifying the origin of noble gases in Earth’s mantle can provide crucial constraints on the source and timing of volatile (C, N, H2O, noble gases, etc.) delivery to Earth. It remains unclear whether the early Earth was able to directly capture and retain volatiles throughout accretion or whether it accreted anhydrously and subsequently acquired volatiles through later additions of chondritic material. Here, we report high-precision noble gas isotopic data from volcanic gases emanating from, in and around, the Yellowstone caldera (Wyoming, United States). We show that the He and Ne isotopic and elemental signatures of the Yellowstone gas requires an input from an undegassed mantle plume. Coupled with the distinct ratio of 129Xe to primordial Xe isotopes in Yellowstone compared with mid-ocean ridge basalt (MORB) samples, this confirms that the deep plume and shallow MORB mantles have remained distinct from one another for the majority of Earth’s history. Krypton and xenon isotopes in the Yellowstone mantle plume are found to be chondritic in origin, similar to the MORB source mantle. This is in contrast with the origin of neon in the mantle, which exhibits an isotopic dichotomy between solar plume and chondritic MORB mantle sources. The co-occurrence of solar and chondritic noble gases in the deep mantle is thought to reflect the heterogeneous nature of Earth’s volatile accretion during the lifetime of the protosolar nebula. It notably implies that the Earth was able to retain its chondritic volatiles since its earliest stages of accretion, and not only through late additions.
    Description: Samples were collected as part of Study YELL-08056: Xenon Anomalies in the Yellowstone Hotspot. We thank Annie Carlson and all of the rangers at the Yellowstone National Park for providing invaluable advice and help when collecting the samples. M.W.B., D.V.B., D.J.B., and B.M. were supported by the European Research Council (PHOTONIS Project Grant 695618). This work was partially supported by Grants G-2016-7206 and G-2017-9696 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory (to P.H.B.) and UK National Environment Research Council Deep Volatile Grant NE/M000427/1 (to C.J.B.). We also thank Laurent Zimmerman for providing help with the analysis. Finally, we thank the editor for efficient handling of our manuscript and the two anonymous reviewers for their insightful comments. This is CRPG contribution 2998.
    Keywords: Origin of Earth’s volatiles ; Accretion ; Mantle plume ; Noble gases ; Yellowstone
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  • 23
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Roberts, Mark L., Elder, Kathryn L., Jenkins, William J., Gagnon, Alan R., Xu, Li, Hlavenka, Joshua D., & Longworth, Brett E. C-14 Blank Corrections for 25-100 mu G samples at the National Ocean Sciences AMS Laboratory. Radiocarbon, 61(5), (2019): 1403-1411, Doi: 10.1017/RDC.2019.74.
    Description: Replicate radiocarbon (14C) measurements of organic and inorganic control samples, with known Fraction Modern values in the range Fm = 0–1.5 and mass range 6 μg–2 mg carbon, are used to determine both the mass and radiocarbon content of the blank carbon introduced during sample processing and measurement in our laboratory. These data are used to model, separately for organic and inorganic samples, the blank contribution and subsequently “blank correct” measured unknowns in the mass range 25–100 μg. Data, formulas, and an assessment of the precision and accuracy of the blank correction are presented.
    Description: This work is supported by a Cooperative Agreement (OCE-1755125) with the U.S. National Science Foundation.
    Keywords: AMS ; AMS dating ; Blank corrections
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  • 24
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Wankel, S. D., & Hansel, C. M. Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen. Proceedings of the National Academy of Sciences of the United States of America, 117(7), (2020): 3433-3439, doi:10.1073/pnas.1912313117.
    Description: The balance between sources and sinks of molecular oxygen in the oceans has greatly impacted the composition of Earth’s atmosphere since the evolution of oxygenic photosynthesis, thereby exerting key influence on Earth’s climate and the redox state of (sub)surface Earth. The canonical source and sink terms of the marine oxygen budget include photosynthesis, respiration, photorespiration, the Mehler reaction, and other smaller terms. However, recent advances in understanding cryptic oxygen cycling, namely the ubiquitous one-electron reduction of O2 to superoxide by microorganisms outside the cell, remains unexplored as a potential player in global oxygen dynamics. Here we show that dark extracellular superoxide production by marine microbes represents a previously unconsidered global oxygen flux and sink comparable in magnitude to other key terms. We estimate that extracellular superoxide production represents a gross oxygen sink comprising about a third of marine gross oxygen production, and a net oxygen sink amounting to 15 to 50% of that. We further demonstrate that this total marine dark extracellular superoxide flux is consistent with concentrations of superoxide in marine environments. These findings underscore prolific marine sources of reactive oxygen species and a complex and dynamic oxygen cycle in which oxygen consumption and corresponding carbon oxidation are not necessarily confined to cell membranes or exclusively related to respiration. This revised model of the marine oxygen cycle will ultimately allow for greater reconciliation among estimates of primary production and respiration and a greater mechanistic understanding of redox cycling in the ocean.
    Description: This work was supported by NASA Earth and Space Science Fellowship NNX15AR62H to K.M.S., NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., and NSF Division of Ocean Sciences grant 1355720 to C.M.H. This research was further supported in part by Hanse-Wissenschaftskolleg Institute of Advanced Study fellowships to C.M.H. and S.D.W. We thank Danielle Hicks for assistance with figures and Community Earth Systems Model (CESM) Large Ensemble Project for the availability and use of its data product. The CESM project is primarily supported by the NSF.
    Keywords: Microbial superoxide ; Reactive oxygen species ; Marine dissolved oxygen
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  • 25
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baker, M. G., Aster, R. C., Anthony, R. E., Chaput, J., Wiens, D. A., Nyblade, A., Bromirski, P. D., Gerstoft, P., & Stephen, R. A. Seasonal and spatial variations in the ocean-coupled ambient wavefield of the Ross Ice Shelf. Journal of Glaciology, 65(254), (2019): 912-925, doi:10.1017/jog.2019.64.
    Description: The Ross Ice Shelf (RIS) is host to a broadband, multimode seismic wavefield that is excited in response to atmospheric, oceanic and solid Earth source processes. A 34-station broadband seismographic network installed on the RIS from late 2014 through early 2017 produced continuous vibrational observations of Earth's largest ice shelf at both floating and grounded locations. We characterize temporal and spatial variations in broadband ambient wavefield power, with a focus on period bands associated with primary (10–20 s) and secondary (5–10 s) microseism signals, and an oceanic source process near the ice front (0.4–4.0 s). Horizontal component signals on floating stations overwhelmingly reflect oceanic excitations year-round due to near-complete isolation from solid Earth shear waves. The spectrum at all periods is shown to be strongly modulated by the concentration of sea ice near the ice shelf front. Contiguous and extensive sea ice damps ocean wave coupling sufficiently so that wintertime background levels can approach or surpass those of land-sited stations in Antarctica.
    Description: This research was supported by NSF grants PLR-1142518, 1141916, 1142126, 1246151 and 1246416. JC was additionally supported by Yates funds in the Colorado State University Department of Mathematics. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107. We thank Reinhard Flick and Patrick Shore for their support during field work, Tom Bolmer in locating stations and preparing maps, and the US Antarctic Program for logistical support. The seismic instruments were provided by the Incorporated Research Institutions for Seismology (IRIS) through the PASSCAL Instrument Center at New Mexico Tech. Data collected are available through the IRIS Data Management Center under RIS and DRIS network code XH. The PSD-PDFs presented in this study were processed with the IRIS Noise Tool Kit (Bahavar and others, 2013). The facilities of the IRIS Consortium are supported by the National Science Foundation under Cooperative Agreement EAR-1261681 and the DOE National Nuclear Security Administration. The authors appreciate the support of the University of Wisconsin-Madison Automatic Weather Station Program for the data set, data display and information; funded under NSF grant number ANT-1543305. The Ross Ice Shelf profiles were generated using the Antarctic Mapping Tools (Greene and others, 2017). Regional maps were generated with the Generic Mapping Tools (Wessel and Smith, 1998). Topography and bathymetry data for all maps in this study were sourced from the National Geophysical Data Center ETOPO1 Global Relief Model (doi:10.7289/V5C8276M). We thank two anonymous reviewers for suggestions on the scope and organization of this paper.
    Keywords: Antarctic glaciology ; Ice shelves ; Seismology
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  • 26
    Publication Date: 2022-10-21
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ackley, S. F., Stammerjohn, S., Maksym, T., Smith, M., Cassano, J., Guest, P., Tison, J., Delille, B., Loose, B., Sedwick, P., DePace, L., Roach, L., & Parno, J. Sea-ice production and air/ice/ocean/biogeochemistry interactions in the Ross Sea during the PIPERS 2017 autumn field campaign. Annals of Glaciology, 61(82), (2020): 181-195, doi:10.1017/aog.2020.31.
    Description: The Ross Sea is known for showing the greatest sea-ice increase, as observed globally, particularly from 1979 to 2015. However, corresponding changes in sea-ice thickness and production in the Ross Sea are not known, nor how these changes have impacted water masses, carbon fluxes, biogeochemical processes and availability of micronutrients. The PIPERS project sought to address these questions during an autumn ship campaign in 2017 and two spring airborne campaigns in 2016 and 2017. PIPERS used a multidisciplinary approach of manned and autonomous platforms to study the coupled air/ice/ocean/biogeochemical interactions during autumn and related those to spring conditions. Unexpectedly, the Ross Sea experienced record low sea ice in spring 2016 and autumn 2017. The delayed ice advance in 2017 contributed to (1) increased ice production and export in coastal polynyas, (2) thinner snow and ice cover in the central pack, (3) lower sea-ice Chl-a burdens and differences in sympagic communities, (4) sustained ocean heat flux delaying ice thickening and (5) a melting, anomalously southward ice edge persisting into winter. Despite these impacts, airborne observations in spring 2017 suggest that winter ice production over the continental shelf was likely not anomalous.
    Description: NSF supported PIPERS award numbers: ANT-1341717 (S.F. Ackley, UTSA); ANT-1341513 (E. Maksym, WHOI); ANT-1341606 (S. Stammerjohn and J. Cassano, U Colorado); ANT-1341725 (P. Guest, NPS). P. Sedwick was supported by NSF ANT-1543483. S.F. Ackley was also supported by NASA Grant 80NSSC19M0194 to the Center for Advanced Measurements in Extreme Environments at UTSA. S. Stammerjohn was also supported by the LTER Program under NFS award number ANT-0823101 (H. Ducklow, LDEO/Columbia University). Additional support was by the Belgian F.R.S-FNRS (project ISOGGAP and IODIne, contract T.0268.16 and J.0262.17, respectively). Bruno Delille is a research associate of the F.R.S.-FNRS. Terra-Sar-X quicklook imagery was coordinated by Kathrin Hoeppner at DLR, and Andy Archer (with the Antarctic Support Contractor) provided selected (cloud-free) MODIS scenes and daily maps of AMSR2 sea-ice concentration.
    Keywords: Atmosphere/ice/ocean interactions ; Ice/ocean interactions ; Sea ice ; Sea-ice growth and decay
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  • 27
    Publication Date: 2020-05-15
    Description: Amyloidoses (misfolded polypeptide accumulation) are among the most debilitating diseases our aging societies face. Amyloidogenesis can be catalyzed by hydrophobic–hydrophilic interfaces (e.g., air–water interface in vitro [AWI]). We recently demonstrated hydrogelation of the amyloidogenic type II diabetes-associated islet amyloid polypeptide (IAPP), a hydrophobic–hydrophilic interface-dependent process with complex kinetics. We demonstrate that human IAPP undergoes AWI-catalyzed liquid–liquid phase separation (LLPS), which initiates hydrogelation and aggregation. Insulin modulates these processes but does not prevent them. Using nonamyloidogenic rat IAPP, we show that, whereas LLPS does not require the amyloidogenic sequence, hydrogelation and aggregation do. Interestingly, both insulin and rat sequence delayed IAPP LLPS, which may reflect physiology. By developing an experimental setup and analysis tools, we show that, within the whole system (beyond the droplet stage), macroscopic interconnected aggregate clusters form, grow, fuse, and evolve via internal rearrangement, leading to overall hydrogelation. As the AWI-adsorbed gelled layer matures, its microviscosity increases. LLPS-driven aggregation may be a common amyloid feature and integral to pathology.
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  • 28
    Publication Date: 2020-06-15
    Description: Human speech production requires the ability to couple motor actions with their auditory consequences. Nonhuman primates might not have speech because they lack this ability. To address this question, we trained macaques to perform an auditory–motor task producing sound sequences via hand presses on a newly designed device (“monkey piano”). Catch trials were interspersed to ascertain the monkeys were listening to the sounds they produced. Functional MRI was then used to map brain activity while the animals listened attentively to the sound sequences they had learned to produce and to two control sequences, which were either completely unfamiliar or familiar through passive exposure only. All sounds activated auditory midbrain and cortex, but listening to the sequences that were learned by self-production additionally activated the putamen and the hand and arm regions of motor cortex. These results indicate that, in principle, monkeys are capable of forming internal models linking sound perception and production in motor regions of the brain, so this ability is not special to speech in humans. However, the coupling of sounds and actions in nonhuman primates (and the availability of an internal model supporting it) seems not to extend to the upper vocal tract, that is, the supralaryngeal articulators, which are key for the production of speech sounds in humans. The origin of speech may have required the evolution of a “command apparatus” similar to the control of the hand, which was crucial for the evolution of tool use.
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  • 29
    Publication Date: 2020-02-28
    Description: Induction of longstanding immunologic tolerance is essential for survival of transplanted organs and tissues. Despite recent advances in immunosuppression protocols, allograft damage inflicted by antibody specific for donor organs continues to represent a major obstacle to graft survival. Here we report that activation of regulatory CD8 T cells (CD8 Treg) that recognize the Qa-1 class Ib major histocompatibility complex (MHC), a mouse homolog of human leukocyte antigen-E (HLA-E), inhibits antibody-mediated immune rejection of heart allografts. We analyzed this response using a mouse model that harbors a point mutation in the class Ib MHC molecule Qa-1, which disrupts Qa-1 binding to the T cell receptor (TCR)–CD8 complex and impairs the CD8 Treg response. Despite administration of cytotoxic T lymphocyte antigen 4 (CTLA-4) immunoglobulin (Ig), Qa-1 mutant mice developed robust donor-specific antibody responses and accelerated heart graft rejection. We show that these allo-antibody responses reflect diminished Qa-1–restricted CD8 Treg-mediated suppression of host follicular helper T cell-dependent antibody production. These findings underscore the critical contribution of this Qa-1/HLA-E-dependent regulatory pathway to maintenance of transplanted organs and suggest therapeutic approaches to ameliorate allograft rejection.
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  • 30
    Publication Date: 2020-06-29
    Description: Under steady-state conditions, the immune system is poised to sense and respond to the microbiota. As such, immunity to the microbiota, including T cell responses, is expected to precede any inflammatory trigger. How this pool of preformed microbiota-specific T cells contributes to tissue pathologies remains unclear. Here, using an experimental model of psoriasis, we show that recall responses to commensal skin fungi can significantly aggravate tissue inflammation. Enhanced pathology caused by fungi preexposure depends on Th17 responses and neutrophil extracellular traps and recapitulates features of the transcriptional landscape of human lesional psoriatic skin. Together, our results propose that recall responses directed to skin fungi can directly promote skin inflammation and that exploration of tissue inflammation should be assessed in the context of recall responses to the microbiota.
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  • 31
  • 32
    Publication Date: 2020-06-25
    Description: Low availability of nitrogen (N) is often a major limiting factor to crop yield in most nutrient-poor soils. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most land plants that enhance plant nutrient uptake, particularly of phosphate. A growing number of reports point to the substantially increased N accumulation in many mycorrhizal plants; however, the contribution of AM symbiosis to plant N nutrition and the mechanisms underlying the AM-mediated N acquisition are still in the early stages of being understood. Here, we report that inoculation with AM fungusRhizophagus irregularisremarkably promoted rice (Oryza sativa) growth and N acquisition, and about 42% of the overall N acquired by rice roots could be delivered via the symbiotic route under N-NO3−supply condition. Mycorrhizal colonization strongly induced expression of the putative nitrate transporter geneOsNPF4.5in rice roots, and its orthologsZmNPF4.5inZea maysandSbNPF4.5inSorghum bicolor. OsNPF4.5 is exclusively expressed in the cells containing arbuscules and displayed a low-affinity NO3−transport activity when expressed inXenopus laevisoocytes. Moreover, knockout ofOsNPF4.5resulted in a 45% decrease in symbiotic N uptake and a significant reduction in arbuscule incidence when NO3−was supplied as an N source. Based on our results, we propose that the NPF4.5 plays a key role in mycorrhizal NO3−acquisition, a symbiotic N uptake route that might be highly conserved in gramineous species.
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  • 33
    Publication Date: 2020-06-29
    Description: Folate deprivation drives the instability of a group of rare fragile sites (RFSs) characterized by CGG trinucleotide repeat (TNR) sequences. Pathological expansion of the TNR within theFRAXAlocus perturbs DNA replication and is the major causative factor for fragile X syndrome, a sex-linked disorder associated with cognitive impairment. Although folate-sensitive RFSs share many features with common fragile sites (CFSs; which are found in all individuals), they are induced by different stresses and share no sequence similarity. It is known that a pathway (termed MiDAS) is employed to complete the replication of CFSs in early mitosis. This process requires RAD52 and is implicated in generating translocations and copy number changes at CFSs in cancers. However, it is unclear whether RFSs also utilize MiDAS and to what extent the fragility of CFSs and RFSs arises by shared or distinct mechanisms. Here, we demonstrate that MiDAS does occur atFRAXAfollowing folate deprivation but proceeds via a pathway that shows some mechanistic differences from that at CFSs, being dependent on RAD51, SLX1, and POLD3. A failure to complete MiDAS atFRAXAleads to severe locus instability and missegregation in mitosis. We propose that break-induced DNA replication is required for the replication ofFRAXAunder folate stress and define a cellular function for human SLX1. These findings provide insights into how folate deprivation drives instability in the human genome.
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  • 34
    Publication Date: 2020-01-28
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  • 35
    Publication Date: 2020-03-10
    Description: Necroptosis is a regulated necrotic cell death pathway involved in development and disease. Its signaling cascade results in the formation of disulfide bond-dependent amyloid-like polymers of mixed lineage kinase domain-like protein (MLKL), which mediate proinflammatory cell membrane disruption. We screened compound libraries provided by the National Cancer Institute and identified a small-molecule inhibitor of necroptosis named necroptosis-blocking compound 1 (NBC1). Biotin-labeled NBC1 specifically conjugates to heat shock protein Hsp70. NBC1 and PES-Cl, a known Hsp70 substrate-binding inhibitor, block the formation of MLKL polymers, but not MLKL tetramers in necroptosis-induced cells. In vitro,recombinant Hsp70 interacts with the N-terminal domain (NTD) of MLKL and promotes NTD polymerization, which has been shown to mediate the cell killing activity. Furthermore, the substrate-binding domain (SBD) of Hsp70 is sufficient to promote MLKL polymerization. NBC1 covalently conjugates cysteine 574 and cysteine 603 of the SBD to block its function. In addition, an SBD mutant with both cysteines mutated to serines loses its ability to promote MLKL polymerization. Interestingly, knockdown of Hsp70 in cells leads to MLKL destabilization, suggesting that MLKL might also be a client protein of Hsp70. In summary, using NBC1, an inhibitor of necroptosis, we identified Hsp70 as a molecular chaperone performing dual functions in necroptosis. It stabilizes MLKL protein under normal condition and promotes MLKL polymerization through its substrate-binding domain during necroptosis.
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  • 36
    Publication Date: 2020-02-04
    Description: Developing B cells can be positively or negatively selected by self-antigens, but the mechanisms that determine these outcomes are incompletely understood. Here, we show that a B cell intrinsic switch between positive and negative selection during ontogeny is determined by a change from Lin28b to let-7 gene expression. Ectopic expression of a Lin28b transgene in murine B cells restored the positive selection of autoreactive B-1 B cells by self-antigen in adult bone marrow. Analysis of antigen-specific immature B cells in early and late ontogeny identified Lin28b-dependent genes associated with B-1 B cell development, including Arid3a and Bhleh41, and Lin28b-independent effects are associated with the presence or absence of self-antigen. These findings identify cell intrinsic and extrinsic determinants of B cell fate during ontogeny and reconcile lineage and selection theories of B cell development. They explain how changes in the balance of positive and negative selection may be able to adapt to meet the immunological needs of an individual during its lifetime.
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  • 37
    Publication Date: 2020-06-29
    Description: Nature has inspired the design of robots in which soft actuators enable tasks such as handling of fragile objects and adapting to unstructured environments. Those tasks are difficult for traditional robots, which predominantly consist of hard components. Electrohydraulic soft actuators are liquid-filled shells that deform upon the application of electric fields; they excel among soft actuators with muscle-like force outputs and actuation strains, and with actuation frequencies above 100 Hz. However, the fundamental physics that governs the dynamics of electrohydraulic soft actuators is unexplored. Here, we study the dynamics of electrohydraulic soft actuators using the Peano-HASEL (hydraulically amplified self-healing electrostatic) actuator as a model system. Using experiments and a scaling analysis, we discover two dynamic regimes: a regime in which viscous dissipation reduces the actuation speed and a regime governed by inertial effects in which high-speed actuation is possible. For each regime, we derive a timescale that describes the influence of geometry, materials system, and applied external loads on the actuation speed. We also derive a model to study the dynamic behavior of Peano-HASEL actuators in both regimes. Although this analysis focuses on the Peano-HASEL actuator, the presented results may readily be generalized to other electrohydraulic actuators. When designed to operate in the inertial regime, electrohydraulic actuators will enable bio-inspired robots with unprecedented speeds of motion.
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  • 38
    Publication Date: 2020-06-29
    Description: Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate,Brachionus manjavacas(Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness forB. manjavacasand that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.
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  • 39
    Publication Date: 2020-06-29
    Description: Autism spectrum disorder (ASD) is characterized by impaired social interactions and communication. The pathogenesis of ASD is not known, but it involves activation of microglia. We had shown that the peptide neurotensin (NT) is increased in the serum of children with ASD and stimulates cultured adult human microglia to secrete the proinflammatory molecules IL-1β and CXCL8. This process is inhibited by the cytokine IL-37. Another cytokine, IL-38, has been reported to have antiinflammatory actions. In this report, we show that pretreatment of cultured adult human microglia with recombinant IL-38 (aa3-152, 1–100 ng/mL) inhibits (P〈 0.0001) NT-stimulated (10 nM) secretion of IL-1β (at 1 ng/mL) and CXCL8 (at 100 ng/mL). In fact, IL-38 (aa3-152, 1 ng/mL) is more potent than IL-37 (100 ng/mL). Here, we report that pretreatment with IL-38 (100 ng/mL) of embryonic microglia (HMC3), in which secretion of IL-1β was undetectable, inhibits secretion of CXCL8 (P= 0.004). Gene expression of IL-38 and its receptor IL-36R are decreased (P= 0.001 andP= 0.04, respectively) in amygdala from patients with ASD (n= 8) compared to non-ASD controls (n= 8), obtained from the University of Maryland NeuroBioBank. IL-38 is increased (P= 0.03) in the serum of children with ASD. These findings indicate an important role for IL-38 in the inhibition of activation of human microglia, thus supporting its development as a treatment approach for ASD.
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  • 40
    Publication Date: 2020-06-29
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  • 41
    Publication Date: 2020-06-29
    Description: Biomolecules can undergo liquid–liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA “nanostar” particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this “active dissolution” process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution (“boiling”) temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation (“bubbling”) events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.
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  • 42
    Publication Date: 2020-06-29
    Description: Chemosensory communication is essential to insect biology, playing indispensable roles during mate-finding, foraging, and oviposition behaviors. These traits are particularly important during speciation, where chemical perception may serve to establish species barriers. However, identifying genes associated with such complex behavioral traits remains a significant challenge. Through a combination of transcriptomic and genomic approaches, we characterize the genetic architecture of chemoperception and the role of chemosensing during speciation for a young species pair ofHeliconiusbutterflies,Heliconius melpomeneandHeliconius cydno. We provide a detailed description of chemosensory gene-expression profiles as they relate to sensory tissue (antennae, legs, and mouthparts), sex (male and female), and life stage (unmated and mated female butterflies). Our results untangle the potential role of chemical communication in establishing barriers during speciation and identify strong candidate genes for mate and host plant choice behaviors. Of the 252 chemosensory genes,HmOBP20(involved in volatile detection) andHmGr56(a putative synephrine-related receptor) emerge as strong candidates for divergence in pheromone detection and host plant discrimination, respectively. These two genes are not physically linked to wing-color pattern loci or other genomic regions associated with visual mate preference. Altogether, our results provide evidence for chemosensory divergence betweenH. melpomeneandH. cydno, two rarely hybridizing butterflies with distinct mate and host plant preferences, a finding that supports a polygenic architecture of species boundaries.
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  • 43
    Publication Date: 2020-06-01
    Description: Encoding activity in the medial temporal lobe, presumably evoked by the presentation of stimuli (postonset activity), is known to predict subsequent memory. However, several independent lines of research suggest that preonset activity also affects subsequent memory. We investigated the role of preonset and postonset single-unit and multiunit activity recorded from epilepsy patients as they completed a continuous recognition task. In this task, words were presented in a continuous series and eventually began to repeat. For each word, the patient’s task was to decide whether it was novel or repeated. We found that preonset spiking activity in the hippocampus (when the word was novel) predicted subsequent memory (when the word was later repeated). Postonset activity during encoding also predicted subsequent memory, but was simply a continuation of preonset activity. The predictive effect of preonset spiking activity was much stronger in the hippocampus than in three other brain regions (amygdala, anterior cingulate, and prefrontal cortex). In addition, preonset and postonset activity around the encoding of novel words did not predict memory performance for novel words (i.e., correctly classifying the word as novel), and preonset and postonset activity around the time of retrieval did not predict memory performance for repeated words (i.e., correctly classifying the word as repeated). Thus, the only predictive effect was between preonset activity (along with its postonset continuation) at the time of encoding and subsequent memory. Taken together, these findings indicate that preonset hippocampal activity does not reflect general arousal/attention but instead reflects what we term “attention to encoding.”
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  • 44
    Publication Date: 2020-06-01
    Description: The Q fever agentCoxiella burnetiiuses a defect in organelle trafficking/intracellular multiplication (Dot/Icm) type 4b secretion system (T4SS) to silence the host innate immune response during infection. By investigatingC. burnetiieffector proteins containing eukaryotic-like domains, here we identify NopA (nucleolar protein A), which displays four regulator of chromosome condensation (RCC) repeats, homologous to those found in the eukaryotic Ras-related nuclear protein (Ran) guanine nucleotide exchange factor (GEF) RCC1. Accordingly, NopA is found associated with the chromatin nuclear fraction of cells and uses the RCC-like domain to interact with Ran. Interestingly, NopA triggers an accumulation of Ran-GTP, which accumulates at nucleoli of transfected or infected cells, thus perturbing the nuclear import of transcription factors of the innate immune signaling pathway. Accordingly, qRT-PCR analysis on a panel of cytokines shows that cells exposed to theC. burnetii nopA::Tn or a Dot/Icm-defectivedotA::Tn mutant strain present a functional innate immune response, as opposed to cells exposed to wild-typeC. burnetiior the correspondingnopAcomplemented strain. Thus, NopA is an important regulator of the innate immune response allowingCoxiellato behave as a stealth pathogen.
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  • 45
    Publication Date: 2020-06-01
    Description: The protooncogene MYC regulates a variety of cellular processes, including proliferation and metabolism. Maintaining MYC at homeostatic levels is critical to normal cell function; overexpression drives many cancers. MYC stability is regulated through phosphorylation: phosphorylation at Thr58 signals degradation while Ser62 phosphorylation leads to its stabilization and functional activation. The bromodomain protein 4 (BRD4) is a transcriptional and epigenetic regulator with intrinsic kinase and histone acetyltransferase (HAT) activities that activates transcription of key protooncogenes, includingMYC. We report that BRD4 phosphorylates MYC at Thr58, leading to MYC ubiquitination and degradation, thereby regulating MYC target genes. Importantly, BRD4 degradation, but not inhibition, results in increased levels of MYC protein. Conversely, MYC inhibits BRD4’s HAT activity, suggesting that MYC regulates its own transcription by limiting BRD4-mediated chromatin remodeling of its locus. The MYC stabilizing kinase, ERK1, regulates MYC levels directly and indirectly by inhibiting BRD4 kinase activity. These findings demonstrate that BRD4 negatively regulates MYC levels, which is counteracted by ERK1 activation.
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  • 46
    Publication Date: 2020-06-01
    Description: We report national scale estimates of CO2emissions from fossil-fuel combustion and cement production in the United States based directly on atmospheric observations, using a dual-tracer inverse modeling framework and CO2andΔ14CO2measurements obtained primarily from the North American portion of the National Oceanic and Atmospheric Administration’s Global Greenhouse Gas Reference Network. The derived US national total for 2010 is 1,653 ± 30 TgC yr−1with an uncertainty (1σ) that takes into account random errors associated with atmospheric transport, atmospheric measurements, and specified prior CO2and14C fluxes. The atmosphere-derived estimate is significantly larger (〉3σ) than US national emissions for 2010 from three global inventories widely used for CO2accounting, even after adjustments for emissions that might be sensed by the atmospheric network, but which are not included in inventory totals. It is also larger (〉2σ) than a similarly adjusted total from the US Environmental Protection Agency (EPA), but overlaps EPA’s reported upper 95% confidence limit. In contrast, the atmosphere-derived estimate is within1σof the adjusted 2010 annual total and nine of 12 adjusted monthly totals aggregated from the latest version of the high-resolution, US-specific “Vulcan” emission data product. Derived emissions appear to be robust to a range of assumed prior emissions and other parameters of the inversion framework. While we cannot rule out a possible bias from assumed prior Net Ecosystem Exchange over North America, we show that this can be overcome with additionalΔ14CO2measurements. These results indicate the strong potential for quantification of US emissions and their multiyear trends from atmospheric observations.
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  • 47
    Publication Date: 2020-06-01
    Description: T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCRα and -β chains, which govern interactions with peptide–MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of naïve T cells. We established two mouse strains carrying distinct allelic variants ofH2-Aand analyzed thymic and peripheral production and TCR repertoires of naïve conventional CD4+T (Tconv) and naïve regulatory CD4+T (Treg) cells. Compared with tuberculosis-resistant C57BL/6 (H2-Ab) mice, the tuberculosis-susceptible H2-Ajmice had fewer CD4+T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for Tconvand was compensated for by peripheral reconstitution for Treg. We show that H2-Ajfavors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3α and CDR3β, suggesting more stringent selection against a narrower peptide–MHC-II context. H2-Ajand H2-Abmice have prominent reciprocal differences in CDR3α and CDR3β features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the naïve CD4+T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.
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  • 48
    Publication Date: 2020-06-01
    Description: Merkel cell carcinoma (MCC) is a lethal skin cancer that metastasizes rapidly. Few effective treatments are available for patients with metastatic MCC. Poor intratumoral T cell infiltration and activation are major barriers that prevent MCC eradication by the immune system. However, the mechanisms that drive the immunologically restrictive tumor microenvironment remain poorly understood. In this study, we discovered that the innate immune regulator stimulator of IFN genes (STING) is completely silenced in MCCs. To reactivate STING in MCC, we developed an application of a human STING mutant, STINGS162A/G230I/Q266I, which we found to be readily stimulated by a mouse STING agonist, DMXAA. This STING molecule was efficiently delivered to MCC cells via an AAV vector. Introducing STINGS162A/G230I/Q266Iexpression and stimulating its activity by DMXAA in MCC cells reactivates their antitumor inflammatory cytokine/chemokine production. In response to MCC cells with restored STING, cocultured T cells expressing MCPyV-specific T cell receptors (TCRs) show increased cytokine production, migration toward tumor cells, and tumor cell killing. Our study therefore suggests that STING deficiency contributes to the immune suppressive nature of MCCs. More importantly, DMXAA stimulation of STINGS162A/G230I/Q266Icauses robust cell death in MCCs as well as several other STING-silenced cancers. Because tumor antigens and DNA released by dying cancer cells have the potential to amplify innate immune response and activate antitumor adaptive responses, our finding indicates that targeted delivery and activation of STINGS162A/G230I/Q266Iin tumor cells holds great therapeutic promise for the treatment of MCC and many other STING-deficient cancers.
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  • 49
    Publication Date: 2020-05-19
    Description: With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 (“DRC66”)—a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.
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  • 50
    Publication Date: 2020-05-19
    Description: Genetic factors and socioeconomic status (SES) inequalities play a large role in educational attainment, and both have been associated with variations in brain structure and cognition. However, genetics and SES are correlated, and no prior study has assessed their neural associations independently. Here we used a polygenic score for educational attainment (EduYears-PGS), as well as SES, in a longitudinal study of 551 adolescents to tease apart genetic and environmental associations with brain development and cognition. Subjects received a structural MRI scan at ages 14 and 19. At both time points, they performed three working memory (WM) tasks. SES and EduYears-PGS were correlated (r= 0.27) and had both common and independent associations with brain structure and cognition. Specifically, lower SES was related to less total cortical surface area and lower WM. EduYears-PGS was also related to total cortical surface area, but in addition had a regional association with surface area in the right parietal lobe, a region related to nonverbal cognitive functions, including mathematics, spatial cognition, and WM. SES, but not EduYears-PGS, was related to a change in total cortical surface area from age 14 to 19. This study demonstrates a regional association of EduYears-PGS and the independent prediction of SES with cognitive function and brain development. It suggests that the SES inequalities, in particular parental education, are related to global aspects of cortical development, and exert a persistent influence on brain development during adolescence.
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  • 51
    Publication Date: 2020-06-08
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  • 52
    Publication Date: 2020-05-18
    Description: Life emerged on Earth within the first quintile of its habitable window, but a technological civilization did not blossom until its last. Efforts to infer the rate of abiogenesis, based on its early emergence, are frustrated by the selection effect that if the evolution of intelligence is a slow process, then life’s early start may simply be a prerequisite to our existence, rather than useful evidence for optimism. In this work, we interpret the chronology of these two events in a Bayesian framework, extending upon previous work by considering that the evolutionary timescale is itself an unknown that needs to be jointly inferred, rather than fiducially set. We further adopt an objective Bayesian approach, such that our results would be agreed upon even by those using wildly different priors for the rates of abiogenesis and evolution—common points of contention for this problem. It is then shown that the earliest microfossil evidence for life indicates that the rate of abiogenesis is at least 2.8 times more likely to be a typically rapid process, rather than a slow one. This modest limiting Bayes factor rises to 8.7 if we accept the more disputed evidence of13C-depleted zircon deposits [E. A. Bell, P. Boehnke, T. M. Harrison, W. L. Mao,Proc. Natl. Acad. Sci. U.S.A.112, 14518–14521 (2015)]. For intelligence evolution, it is found that a rare-intelligence scenario is slightly favored at 3:2 betting odds. Thus, if we reran Earth’s clock, one should statistically favor life to frequently reemerge, but intelligence may not be as inevitable.
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  • 53
    Publication Date: 2020-05-27
    Description: Networks of branched actin filaments formed by Arp2/3 complex generate and experience mechanical forces during essential cellular functions, including cell motility and endocytosis. External forces regulate the assembly and architecture of branched actin networks both in vitro and in cells. Considerably less is known about how mechanical forces influence the disassembly of actin filament networks, specifically, the dissociation of branches. We used microfluidics to apply force to branches formed from purified muscle actin and fission yeast Arp2/3 complex and observed debranching events in real time with total internal reflection fluorescence microscopy. Low forces in the range of 0 pN to 2 pN on branches accelerated their dissociation from mother filaments more than two orders of magnitude, from hours to
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  • 54
    Publication Date: 2020-05-28
    Description: Exploiting bacteriophage-derived homologous recombination processes has enabled precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we introduce a high-throughput method for SSAP discovery that we call “serial enrichment for efficient recombineering” (SEER). By performing SEER inEscherichia colito screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold inE. coli, while PapRecT enables efficient recombineering inPseudomonas aeruginosa, a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.
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  • 55
    Publication Date: 2020-05-15
    Description: A catalytic prior distribution is designed to stabilize a high-dimensional “working model” by shrinking it toward a “simplified model.” The shrinkage is achieved by supplementing the observed data with a small amount of “synthetic data” generated from a predictive distribution under the simpler model. We apply this framework to generalized linear models, where we propose various strategies for the specification of a tuning parameter governing the degree of shrinkage and study resultant theoretical properties. In simulations, the resulting posterior estimation using such a catalytic prior outperforms maximum likelihood estimation from the working model and is generally comparable with or superior to existing competitive methods in terms of frequentist prediction accuracy of point estimation and coverage accuracy of interval estimation. The catalytic priors have simple interpretations and are easy to formulate.
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  • 56
    Publication Date: 2020-05-14
    Description: Apicomplexan parasites use a specialized cilium structure called the apical complex to organize their secretory organelles and invasion machinery. The apical complex is integrally associated with both the parasite plasma membrane and an intermediate filament cytoskeleton called the inner-membrane complex (IMC). While the apical complex is essential to the parasitic lifestyle, little is known about the regulation of apical complex biogenesis. Here, we identify AC9 (apical cap protein 9), a largely intrinsically disordered component of theToxoplasma gondiiIMC, as essential for apical complex development, and therefore for host cell invasion and egress. Parasites lacking AC9 fail to successfully assemble the tubulin-rich core of their apical complex, called the conoid. We use proximity biotinylation to identify the AC9 interaction network, which includes the kinase extracellular signal-regulated kinase 7 (ERK7). Like AC9, ERK7 is required for apical complex biogenesis. We demonstrate that AC9 directly binds ERK7 through a conserved C-terminal motif and that this interaction is essential for ERK7 localization and function at the apical cap. The crystal structure of the ERK7–AC9 complex reveals that AC9 is not only a scaffold but also inhibits ERK7 through an unusual set of contacts that displaces nucleotide from the kinase active site. ERK7 is an ancient and autoactivating member of the mitogen-activated kinase (MAPK) family and its regulation is poorly understood in all organisms. We propose that AC9 dually regulates ERK7 by scaffolding and concentrating it at its site of action while maintaining it in an “off” state until the specific binding of a true substrate.
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  • 57
    Publication Date: 2020-05-15
    Description: Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by17O NMR spectroscopy at 35.2 T (or 1,500 MHz for1H) and computational studies. While backbone15N spectra clearly indicate structural symmetry between the two subunits, single site17O labels of the pore-lining carbonyls report two resonances, implying a break in dimer symmetry caused by the selective interactions with the water wire. The17O shifts document selective water hydrogen bonding with carbonyl oxygens that are stable on the millisecond timescale. Such interactions are supported by density functional theory calculations on snapshots taken from molecular dynamics simulations. Water hydrogen bonding in the pore is restricted to just three simultaneous interactions, unlike bulk water environs. The stability of the water wire orientation and its electric dipole leads to opposite charge-dipole interactions for K+ions bound at the two ends of the pore, thereby providing a simple explanation for an ∼20-fold difference in K+affinity between two binding sites that are ∼24 Å apart. The17O NMR spectroscopy reported here represents a breakthrough in high field NMR technology that will have applications throughout molecular biophysics, because of the acute sensitivity of the17O nucleus to its chemical environment.
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  • 58
    Publication Date: 2020-05-28
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  • 59
    Publication Date: 2020-05-18
    Description: HRAS, NRAS, and KRAS4A/KRAS4B comprise the RAS family of small GTPases that regulate signaling pathways controlling cell proliferation, differentiation, and survival. RAS pathway abnormalities cause developmental disorders and cancers. We found that KRAS4B colocalizes on the cell membrane with other RAS isoforms and a subset of prenylated small GTPase family members using a live-cell quantitative split luciferase complementation assay. RAS protein coclustering is mainly mediated by membrane association-facilitated interactions (MAFIs). Using the RAS–RBD (CRAF RAS binding domain) interaction as a model system, we showed that MAFI alone is not sufficient to induce RBD-mediated RAS inhibition. Surprisingly, we discovered that high-affinity membrane-targeted RAS binding proteins inhibit RAS activity and deplete RAS proteins through an autophagosome–lysosome-mediated degradation pathway. Our results provide a mechanism for regulating RAS activity and protein levels, a more detailed understanding of which should lead to therapeutic strategies for inhibiting and depleting oncogenic RAS proteins.
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  • 60
    Publication Date: 2020-06-01
    Description: The ability to modulate cellular electrophysiology is fundamental to the investigation of development, function, and disease. Currently, there is a need for remote, nongenetic, light-induced control of cellular activity in two-dimensional (2D) and three-dimensional (3D) platforms. Here, we report a breakthrough hybrid nanomaterial for remote, nongenetic, photothermal stimulation of 2D and 3D neural cellular systems. We combine one-dimensional (1D) nanowires (NWs) and 2D graphene flakes grown out-of-plane for highly controlled photothermal stimulation at subcellular precision without the need for genetic modification, with laser energies lower than a hundred nanojoules, one to two orders of magnitude lower than Au-, C-, and Si-based nanomaterials. Photothermal stimulation using NW-templated 3D fuzzy graphene (NT-3DFG) is flexible due to its broadband absorption and does not generate cellular stress. Therefore, it serves as a powerful toolset for studies of cell signaling within and between tissues and can enable therapeutic interventions.
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  • 61
    Publication Date: 2020-06-02
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  • 62
    Publication Date: 2020-05-18
    Description: The androgen receptor (AR) antagonist enzalutamide is one of the principal treatments for men with castration-resistant prostate cancer (CRPC). However, not all patients respond, and resistance mechanisms are largely unknown. We hypothesized that genomic and transcriptional features from metastatic CRPC biopsies prior to treatment would be predictive of de novo treatment resistance. To this end, we conducted a phase II trial of enzalutamide treatment (160 mg/d) in 36 men with metastatic CRPC. Thirty-four patients were evaluable for the primary end point of a prostate-specific antigen (PSA)50 response (PSA decline ≥50% at 12 wk vs. baseline). Nine patients were classified as nonresponders (PSA decline
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  • 63
    Publication Date: 2020-05-18
    Description: Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. A weighted gene coexpression network (WGCN) analysis suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during the regulation of cuticular wax deposition. Genetic analyses reveal thatphyB1 phyB2double mutants of maize exhibit abnormal cuticle composition, supporting the predictions of our coexpression analysis. Reverse genetic analyses also show thatphymutants of the mossPhyscomitrella patensexhibit abnormal cuticle composition, suggesting an ancestral role for PHYTOCHROME-mediated, light-stimulated regulation of cuticle development during plant evolution.
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  • 64
    Publication Date: 2020-05-14
    Description: In multiple sclerosis (MS), Th17 cells are critical drivers of autoimmune central nervous system (CNS) inflammation and demyelination. Th17 cells exhibit functional heterogeneity fostering both pathogenic and nonpathogenic, tissue-protective functions. Still, the factors that control Th17 pathogenicity remain incompletely defined. Here, using experimental autoimmune encephalomyelitis, an established mouse MS model, we report that therapeutic administration of activin-A ameliorates disease severity and alleviates CNS immunopathology and demyelination, associated with decreased activation of Th17 cells. In fact, activin-A signaling through activin-like kinase-4 receptor represses pathogenic transcriptional programs in Th17-polarized cells, while it enhances antiinflammatory gene modules. Whole-genome profiling and in vivo functional studies revealed that activation of the ATP-depleting CD39 and CD73 ectonucleotidases is essential for activin-A–induced suppression of the pathogenic signature and the encephalitogenic functions of Th17 cells. Mechanistically, the aryl hydrocarbon receptor, along with STAT3 and c-Maf, are recruited to promoter elements onEntpd1andNt5e(encoding CD39 and CD73, respectively) and other antiinflammatory genes, and control their expression in Th17 cells in response to activin-A. Notably, we show that activin-A negatively regulates the metabolic sensor, hypoxia-inducible factor-1α, and key inflammatory proteins linked to pathogenic Th17 cell states. Of translational relevance, we demonstrate that activin-A is induced in the CNS of individuals with MS and restrains human Th17 cell responses. These findings uncover activin-A as a critical controller of Th17 cell pathogenicity that can be targeted for the suppression of autoimmune CNS inflammation.
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  • 65
    Publication Date: 2020-06-01
    Description: The Hippo pathway plays a pivotal role in tissue homeostasis and tumor suppression. YAP and TAZ are downstream effectors of the Hippo pathway, and their activities are tightly suppressed by phosphorylation-dependent cytoplasmic retention. However, the molecular mechanisms governing YAP/TAZ nuclear localization have not been fully elucidated. Here, we report that Mastermind-like 1 and 2 (MAML1/2) are indispensable for YAP/TAZ nuclear localization and transcriptional activities. Ectopic expression or depletion of MAML1/2 induces nuclear translocation or cytoplasmic retention of YAP/TAZ, respectively. Additionally, mutation of the MAML nuclear localization signal, as well as its YAP/TAZ interacting region, both abolish nuclear localization and transcriptional activity of YAP/TAZ. Importantly, we demonstrate that the level ofMAML1messenger RNA (mRNA) is regulated by microRNA-30c (miR-30c) in a cell-density-dependent manner. In vivo and clinical results suggest that MAML potentiates YAP/TAZ oncogenic function and positively correlates with YAP/TAZ activation in human cancer patients, suggesting pathological relevance in the context of cancer development. Overall, our study not only provides mechanistic insight into the regulation of YAP/TAZ subcellular localization, but it also strongly suggests that the miR30c–MAML–YAP/TAZ axis is a potential therapeutic target for developing novel cancer treatments.
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  • 66
    Publication Date: 2020-05-27
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  • 67
    Publication Date: 2020-05-29
    Description: The Pioneer 100 Wellness Project involved quantitatively profiling 108 participants’ molecular physiology over time, including genomes, gut microbiomes, blood metabolomes, blood proteomes, clinical chemistries, and data from wearable devices. Here, we present a longitudinal analysis focused specifically around the Pioneer 100 gut microbiomes. We distinguished a subpopulation of individuals with reduced gut diversity, elevated relative abundance of the genusPrevotella, and reduced levels of the genusBacteroides. We found that the relative abundances ofBacteroidesandPrevotellawere significantly correlated with certain serum metabolites, including omega-6 fatty acids. Primary dimensions in distance-based redundancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed aBacteroides/Prevotelladichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions betweenBacteroides-dominated andPrevotella-dominated communities were rare, suggesting the presence of a barrier between these states. One implication is that interventions seeking to transition betweenBacteroides- andPrevotella-dominated communities will need to identify permissible paths through ecological state-space that circumvent this apparent barrier.
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  • 68
    Publication Date: 2020-05-19
    Description: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a dismal prognosis. Currently, there is no effective therapy for PDAC, and a detailed molecular and functional evaluation of PDACs is needed to identify and develop better therapeutic strategies. Here we show that the transcription factor Krüppel-like factor 7 (KLF7) is overexpressed in PDACs, and that inhibition of KLF7 blocks PDAC tumor growth and metastasis in cell culture and in mice. KLF7 expression in PDACs can be up-regulated due to activation of a MAP kinase pathway or inactivation of the tumor suppressor p53, two alterations that occur in a large majority of PDACs. ShRNA-mediated knockdown of KLF7 inhibits the expression of IFN-stimulated genes (ISGs), which are necessary for KLF7-mediated PDAC tumor growth and metastasis. KLF7 knockdown also results in the down-regulation of Discs Large MAGUK Scaffold Protein 3 (DLG3), resulting in Golgi complex fragmentation, and reduced protein glycosylation, leading to reduced secretion of cancer-promoting growth factors, such as chemokines. Genetic or pharmacologic activation of Golgi complex fragmentation blocks PDAC growth and metastasis similar to KLF7 inhibition. Our results demonstrate a therapeutically amenable, KLF7-driven pathway that promotes PDAC growth and metastasis by activating ISGs and maintaining Golgi complex integrity.
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  • 69
    Publication Date: 2020-05-27
    Description: Two-dimensional (2D) molybdenum disulfide (MoS2) nanomaterials are an emerging class of biomaterials that are photoresponsive at near-infrared wavelengths (NIR). Here, we demonstrate the ability of 2D MoS2to modulate cellular functions of human stem cells through photothermal mechanisms. The interaction of MoS2and NIR stimulation of MoS2with human stem cells is investigated using whole-transcriptome sequencing (RNA-seq). Global gene expression profile of stem cells reveals significant influence of MoS2and NIR stimulation of MoS2on integrins, cellular migration, and wound healing. The combination of MoS2and NIR light may provide new approaches to regulate and direct these cellular functions for the purposes of regenerative medicine as well as cancer therapy.
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  • 70
    Publication Date: 2020-05-18
    Description: Spin Hall effect (SHE), a mechanism by which materials convert achargecurrent into aspincurrent, invokes interesting physics and promises to empower transformative, energy-efficient memory technology. However, fundamental questions remain about the essential factors that determine SHE. Here, we solve this open problem, presenting a comprehensive theory of five rational design principles for achievinggiantintrinsic SHE in transition metal oxides. Arising from our key insight regarding the inherently geometric nature of SHE, we demonstrate that two of these design principles are weak crystal fields and the presence of structural distortions. Moreover, we discover that antiperovskites are a highly promising class of materials for achieving giant SHE, reaching SHE values anorder of magnitudelarger than that reported for any oxide. Additionally, we derive three other design principles for enhancing SHE. Our findings bring deeper insight into the physics driving SHE and could help enhance and externally control SHE values.
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  • 71
    Publication Date: 2020-05-18
    Description: Split inteins are privileged molecular scaffolds for the chemical modification of proteins. Though efficient for in vitro applications, these polypeptide ligases have not been utilized for the semisynthesis of proteins in live cells. Here, we biochemically and structurally characterize the naturally split intein VidaL. We show that this split intein, which features the shortest known N-terminal fragment, supports rapid and efficient proteintrans-splicing under a range of conditions, enabling semisynthesis of modified proteins both in vitro and in mammalian cells. The utility of this protein engineering system is illustrated through the traceless assembly of multidomain proteins whose biophysical properties render them incompatible with a single expression system, as well as by the semisynthesis of dual posttranslationally modified histone proteins in live cells. We also exploit the domain swapping function of VidaL to effect simultaneous modification and translocation of the nuclear protein HP1α in live cells. Collectively, our studies highlight the VidaL system as a tool for the precise chemical modification of cellular proteins with spatial and temporal control.
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  • 72
    Publication Date: 2020-05-19
    Description: Lesch-Nyhan disease (LND), caused by a deficient salvage purine pathway, is characterized by severe neurological manifestations and uric acid overproduction. However, uric acid is not responsible for brain dysfunction, and it has been suggested that purine nucleotide depletion, or accumulation of other toxic purine intermediates, could be more relevant. Here we show that purine alterations in LND fibroblasts depend on the level of folic acid in the culture media. Thus, physiological levels of folic acid induce accumulation of 5-aminoimidazole-4-carboxamide riboside 5′-monophosphate (ZMP), an intermediary of de novo purine biosynthetic pathway, and depletion of ATP. Additionally, Z-nucleotide derivatives (AICAr, AICA) are detected at high levels in the urine of patients with LND and its variants (hypoxanthine-guanine phosphoribosyltransferase [HGprt]-related neurological dysfunction and HGprt-related hyperuricemia), and the ratio of AICAr/AICA is significantly increased in patients with neurological problems (LND and HGprt-related neurological dysfunction). Moreover, AICAr is present in the cerebrospinal fluid of patients with LND, but not in control individuals. We hypothesize that purine alterations detected in LND fibroblasts may also occur in the brain of patients with LND.
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  • 73
    Publication Date: 2020-05-19
    Description: PD-1 and PD-L1 act to restrict T cell responses in cancer and contribute to self-tolerance. Consistent with this role, PD-1 checkpoint inhibitors have been associated with immune-related adverse events (irAEs), immune toxicities thought to be autoimmune in origin. Analyses of dermatological irAEs have identified an association with improved overall survival (OS) following anti–PD-(L)1 therapy, but the factors that contribute to this relationship are poorly understood. We collected germline whole-genome sequencing data from IMvigor211, a recent phase 3 randomized controlled trial comparing atezolizumab (anti–PD-L1) monotherapy to chemotherapy in bladder cancer. We found that high vitiligo, high psoriasis, and low atopic dermatitis polygenic risk scores (PRSs) were associated with longer OS under anti–PD-L1 monotherapy as compared to chemotherapy, reflecting the Th17 polarization of these diseases. PRSs were not correlated with tumor mutation burden, PD-L1 immunohistochemistry, nor T-effector gene signatures. Shared genetic factors impact risk for dermatological autoimmunity and anti–PD-L1 monotherapy in bladder cancer.
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  • 74
    Publication Date: 2020-05-19
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  • 75
    Publication Date: 2020-05-19
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  • 76
    Publication Date: 2020-05-20
    Description: Synthetic chemical elicitors, so called plant strengtheners, can protect plants from pests and pathogens. Most plant strengtheners act by modifying defense signaling pathways, and little is known about other mechanisms by which they may increase plant resistance. Moreover, whether plant strengtheners that enhance insect resistance actually enhance crop yields is often unclear. Here, we uncover how a mechanism by which 4-fluorophenoxyacetic acid (4-FPA) protects cereals from piercing-sucking insects and thereby increases rice yield in the field. Four-FPA does not stimulate hormonal signaling, but modulates the production of peroxidases, H2O2, and flavonoids and directly triggers the formation of flavonoid polymers. The increased deposition of phenolic polymers in rice parenchyma cells of 4-FPA-treated plants is associated with a decreased capacity of the white-backed planthopper (WBPH)Sogatella furciferato reach the plant phloem. We demonstrate that application of 4-PFA in the field enhances rice yield by reducing the abundance of, and damage caused by, insect pests. We demonstrate that 4-FPA also increases the resistance of other major cereals such as wheat and barley to piercing-sucking insect pests. This study unravels a mode of action by which plant strengtheners can suppress herbivores and increase crop yield. We postulate that this represents a conserved defense mechanism of plants against piercing-sucking insect pests, at least in cereals.
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  • 77
    Publication Date: 2020-05-18
    Description: The mechanisms that regulate germinal center (GC) B cell responses in the spleen are not fully understood. Here we use a combination of pharmacologic and genetic approaches to delete SIGN-R1+marginal zone (MZ) macrophages and reveal their specific contribution to the regulation of humoral immunity in the spleen. We find that while SIGN-R1+macrophages were not essential for initial activation of B cells, they were required for maturation of the response and development of GC B cells. These defects could be corrected when follicular helper T (Tfh) cells were induced before macrophage ablation or when Tfh responses were enhanced. Moreover, we show that in the absence of SIGN-R1+macrophages, DCIR2+dendritic cells (DCs), which play a key role in priming Tfh responses, were unable to cluster to the interfollicular regions of the spleen and were instead displaced to the MZ. Restoring SIGN-R1+macrophages to the spleen corrected positioning of DCIR2+DCs and rescued the GC B cell response. Our study reveals a previously unappreciated role for SIGN-R1+macrophages in regulation of the GC reaction and highlights the functional specification of macrophage subsets in the MZ compartment.
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  • 78
    Publication Date: 2020-05-11
    Description: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein which forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, altered neuronal dendritic morphology is a common theme among several neurological disorders and is thought to precede neurodegeneration. We previously found that both TDP-43 overexpression (OE) and knockdown (KD) result in reduced dendritic branching of cortical neurons. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as an approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 RNA targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescues defects in dendritic branching. Finally, we demonstrate, using RNA sequencing, that TDP-43 OE and KD cause similar changes in the abundance of specific messenger RNAs, consistent with their ability to produce similar morphological defects. Our data therefore provide a mechanism by which TDP-43 dysfunction interferes with dendritic branching, and may define pathways for therapeutic intervention in neurodegenerative diseases.
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  • 79
    Publication Date: 2020-02-03
    Description: Exposure to loud sound damages the postsynaptic terminals of spiral ganglion neurons (SGNs) on cochlear inner hair cells (IHCs), resulting in loss of synapses, a process termed synaptopathy. Glutamatergic neurotransmission via α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)-type receptors is required for synaptopathy, and here we identify a possible involvement of GluA2-lacking Ca2+-permeable AMPA receptors (CP-AMPARs) using IEM-1460, which has been shown to block GluA2-lacking AMPARs. In CBA/CaJ mice, a 2-h exposure to 100-dB sound pressure level octave band (8 to 16 kHz) noise results in no permanent threshold shift but does cause significant synaptopathy and a reduction in auditory brainstem response (ABR) wave-I amplitude. Chronic intracochlear perfusion of IEM-1460 in artificial perilymph (AP) into adult CBA/CaJ mice prevented the decrease in ABR wave-I amplitude and the synaptopathy relative to intracochlear perfusion of AP alone. Interestingly, IEM-1460 itself did not affect the ABR threshold, presumably because GluA2-containing AMPARs can sustain sufficient synaptic transmission to evoke low-threshold responses during blockade of GluA2-lacking AMPARs. On individual postsynaptic densities, we observed GluA2-lacking nanodomains alongside regions with robust GluA2 expression, consistent with the idea that individual synapses have both CP-AMPARs and Ca2+-impermeable AMPARs. SGNs innervating the same IHC differ in their relative vulnerability to noise. We found local heterogeneity among synapses in the relative abundance of GluA2 subunits that may underlie such differences in vulnerability. We propose a role for GluA2-lacking CP-AMPARs in noise-induced cochlear synaptopathy whereby differences among synapses account for differences in excitotoxic susceptibility. These data suggest a means of maintaining normal hearing thresholds while protecting against noise-induced synaptopathy, via selective blockade of CP-AMPARs.
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  • 80
    Publication Date: 2020-01-24
    Description: Obesity is associated with a chronic state of low-grade inflammation and progressive tissue infiltration by immune cells and increased expression of inflammatory cytokines. It is established that interleukin 6 (IL6) regulates multiple aspects of metabolism, including glucose disposal, lipolysis, oxidative metabolism, and energy expenditure. IL6 is secreted by many tissues, but the role of individual cell types is unclear. We tested the role of specific cells using a mouse model with conditional expression of the Il6 gene. We found that IL6 derived from adipocytes increased, while IL6 derived from myeloid cells and muscle suppressed, macrophage infiltration of adipose tissue. These opposite actions were associated with a switch of IL6 signaling from a canonical mode (myeloid cells) to a noncanonical trans-signaling mode (adipocytes and muscle) with increased expression of the ADAM10/17 metalloprotease that promotes trans-signaling by the soluble IL6 receptor α. Collectively, these data demonstrate that the source of IL6 production plays a major role in the physiological regulation of metabolism.
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  • 81
    Publication Date: 2020-02-10
    Description: Lung cancer is the leading cause of cancer-related deaths worldwide and non-small cell lung cancer (NSCLC) accounts for over 80% of lung cancer cases. The RNA binding protein, QKI, belongs to the STAR family and plays tumor-suppressive functions in NSCLC. QKI-5 is a major isoform of QKIs and is predominantly expressed in NSCLC. However, the underlying mechanisms of QKI-5 in NSCLC progression remain unclear. We found that QKI-5 regulated microRNA (miRNA), miR-196b-5p, and its expression was significantly up-regulated in NSCLC tissues. Up-regulated miR-196b-5p promotes lung cancer cell migration, proliferation, and cell cycle through directly targeting the tumor suppressors, GATA6 and TSPAN12. Both GATA6 and TSPAN12 expressions were down-regulated in NSCLC patient tissue samples and were negatively correlated with miR-196b-5p expression. Mouse xenograft models demonstrated that miR-196b-5p functions as a potent onco-miRNA, whereas TSPAN12 functions as a tumor suppressor in NSCLC in vivo. QKI-5 bound to miR-196b-5p and influenced its stability, resulting in up-regulated miR-196b-5p expression in NSCLC. Further analysis showed that hypomethylation in the promoter region enhanced miR-196b-5p expression in NSCLC. Our findings indicate that QKI-5 may exhibit novel anticancer mechanisms by regulating miRNA in NSCLC, and targeting the QKI5∼miR-196b-5p∼GATA6/TSPAN12 pathway may enable effectively treating some NSCLCs.
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  • 82
    Publication Date: 2020-05-11
    Description: The neonicotinoid nitenpyram (NPM) is a multifunctional nitroenamine [(R1N)(R2N)C=CHNO2] pesticide. As a nitroalkene, it is structurally similar to other emerging contaminants such as the pharmaceuticals ranitidine and nizatidine. Because ozone is a common atmospheric oxidant, such compounds may be oxidized on contact with air to form new products that have different toxicity compared to the parent compounds. Here we show that oxidation of thin solid films of NPM by gas-phase ozone produces unexpected products, the majority of which do not contain oxygen, despite the highly oxidizing reactant. A further surprising finding is the formation of gas-phase nitrous acid (HONO), a species known to be a major photolytic source of the highly reactive hydroxyl radical in air. The results of application of a kinetic multilayer model show that reaction was not restricted to the surface layers but, at sufficiently high ozone concentrations, occurred throughout the film. The rate constant derived for the O3−NPM reaction is 1 × 10−18cm3⋅s−1, and the diffusion coefficient of ozone in the thin film is 9 × 10−10cm2⋅s−1. These findings highlight the unique chemistry of multifunctional nitroenamines and demonstrate that known chemical mechanisms for individual moieties in such compounds cannot be extrapolated from simple alkenes. This is critical for guiding assessments of the environmental fates and impacts of pesticides and pharmaceuticals, and for providing guidance in designing better future alternatives.
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  • 83
    Publication Date: 2020-05-11
    Description: Human T cell leukemia virus 1 (HTLV-1) causes the functionally debilitating disease HTLV-1–associated myelopathy/tropical spastic paraparesis (HAM/TSP) as well as adult T cell leukemia lymphoma (ATLL). Although there were concerns that the mortality of HAM/TSP could be affected by the development of ATLL, prospective evidence was lacking in this area. In this 5-y prospective cohort study, we determined the mortality, prevalence, and incidence of ATLL in 527 HAM/TSP patients. The standard mortality ratio of HAM/TSP patients was 2.25, and ATLL was one of the major causes of death (5/33 deaths). ATLL prevalence and incidence in these patients were 3.0% and 3.81 per 1,000 person-y, respectively. To identify patients at a high risk of developing ATLL, flow cytometry, Southern blotting, and targeted sequencing data were analyzed in a separate cohort of 218 HAM/TSP patients. In 17% of the HAM/TSP patients, we identified an increase in T cells positive for cell adhesion molecule 1 (CADM1), a marker for ATLL and HTLV-1–infected cells. Genomic analysis revealed that somatic mutations of HTLV-1–infected cells were seen in 90% of these cases and 11% of them had dominant clone and developed ATLL in the longitudinal observation. In this study, we were able to demonstrate the increased mortality in patients with HAM/TSP and a significant effect of ATLL on their prognosis. Having dominant clonal expansion of HTLV-1–infected cells with ATLL-associated somatic mutations may be important characteristics of patients with HAM/TSP who are at an increased risk of developing ATLL.
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  • 84
    Publication Date: 2020-05-15
    Description: Three-dimensional (3D) shape perception is one of the most important functions of vision. It is crucial for many tasks, from object recognition to tool use, and yet how the brain represents shape remains poorly understood. Most theories focus on purely geometrical computations (e.g., estimating depths, curvatures, symmetries). Here, however, we find that shape perception also involves sophisticated inferences that parse shapes into features with distinct causal origins. Inspired by marble sculptures such as Strazza’sThe Veiled Virgin(1850), which vividly depict figures swathed in cloth, we created composite shapes by wrapping unfamiliar forms in textile, so that the observable surface relief was the result of complex interactions between the underlying object and overlying fabric. Making sense of such structures requires segmenting the shape based on their causes, to distinguish whether lumps and ridges are due to the shrouded object or to the ripples and folds of the overlying cloth. Three-dimensional scans of the objects with and without the textile provided ground-truth measures of the true physical surface reliefs, against which observers’ judgments could be compared. In a virtual painting task, participants indicated which surface ridges appeared to be caused by the hidden object and which were due to the drapery. In another experiment, participants indicated the perceived depth profile of both surface layers. Their responses reveal that they can robustly distinguish features belonging to the textile from those due to the underlying object. Together, these findings reveal the operation of visual shape-segmentation processes that parse shapes based on their causal origin.
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  • 85
    Publication Date: 2020-05-11
    Description: The ability to detect sparse signals from noisy, high-dimensional data is a top priority in modern science and engineering. It is well known that a sparse solution of the linear systemAρ=b0can be found efficiently with anℓ1-norm minimization approach if the data are noiseless. However, detection of the signal from data corrupted by noise is still a challenging problem as the solution depends, in general, on a regularization parameter with optimal value that is not easy to choose. We propose an efficient approach that does not require any parameter estimation. We introduce a no-phantom weight τ and the Noise Collector matrix C and solve an augmented systemAρ+Cη=b0+e, where e is the noise. We show that theℓ1-norm minimal solution of this system has zero false discovery rate for any level of noise, with probability that tends to one as the dimension ofb0increases to infinity. We obtain exact support recovery if the noise is not too large and develop a fast Noise Collector algorithm, which makes the computational cost of solving the augmented system comparable with that of the original one. We demonstrate the effectiveness of the method in applications to passive array imaging.
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  • 86
    Publication Date: 2020-05-11
    Description: Understanding the timing and mechanisms of amino acid synthesis and racemization on asteroidal parent bodies is key to demonstrating how amino acids evolved to be mostly left-handed in living organisms on Earth. It has been postulated that racemization can occur rapidly dependent on several factors, including the pH of the aqueous solution. Here, we conduct nanoscale geochemical analysis of a framboidal magnetite grain within the Tagish Lake carbonaceous chondrite to demonstrate that the interlocking crystal arrangement formed within a sodium-rich, alkaline fluid environment. Notably, we report on the discovery of Na-enriched subgrain boundaries and nanometer-scale Ca and Mg layers surrounding individual framboids. These interstitial coatings would yield a surface charge state of zero in more-alkaline fluids and prevent assimilation of the individual framboids into a single grain. This basic solution would support rapid synthesis and racemization rates on the order of years, suggesting that the low abundances of amino acids in Tagish Lake cannot be ascribed to fluid chemistry.
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  • 87
    Publication Date: 2020-05-13
    Description: Endothelial cell nitric oxide (NO) synthase (eNOS), the enzyme responsible for synthesis of NO in endothelial cells, is regulated by complex posttranslational mechanisms. Sinusoidal portal hypertension, a disorder characterized by liver sinusoidal endothelial cell (SEC) injury with resultant reduced eNOS activity and NO production within the liver, has been associated with defects in eNOS protein–protein interactions and posttranslational modifications. We and others have previously identified novel eNOS interactors, including G protein-coupled receptor (GPCR) kinase interactor 1 (GIT1), which we found to play an unexpected stimulatory role in GPCR-mediated eNOS signaling. Here we report that β-arrestin 2 (β-Arr2), a canonical GPCR signaling partner, localizes in SECs with eNOS in a GIT1/eNOS/NO signaling module. Most importantly, we show that β-Arr2 stimulates eNOS activity, and that β-Arr2 expression is reduced and formation of the GIT1/eNOS/NO signaling module is interrupted during liver injury. In β-Arr2–deficient mice, bile duct ligation injury (BDL) led to significantly reduced eNOS activity and to a dramatic increase in portal hypertension compared to BDL in wild-type mice. Overexpression of β-Arr2 in injured or β-Arr2–deficient SECs rescued eNOS function by increasing eNOS complex formation and NO production. We also found that β-Arr2–mediated GIT1/eNOS complex formation is dependent on Erk1/2 and Src, two kinases known to interact with and be activated by β-Arr2 in response to GCPR activation. Our data emphasize that β-Arr2 is an integral component of the GIT1/eNOS/NO signaling pathway and have implications for the pathogenesis of sinusoidal portal hypertension.
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  • 88
    Publication Date: 2020-05-11
    Description: Alcohol-related liver disease (ALD) accounts for the majority of cirrhosis and liver-related deaths worldwide. Activation of IFN-regulatory factor (IRF3) initiates alcohol-induced hepatocyte apoptosis, which fuels a robust secondary inflammatory response that drives ALD. The dominant molecular mechanism by which alcohol activates IRF3 and the pathways that amplify inflammatory signals in ALD remains unknown. Here we show that cytoplasmic sensor cyclic guanosine monophosphate-adenosine monophosphate (AMP) synthase (cGAS) drives IRF3 activation in both alcohol-injured hepatocytes and the neighboring parenchyma via a gap junction intercellular communication pathway. Hepatic RNA-seq analysis of patients with a wide spectrum of ALD revealed that expression of the cGAS-IRF3 pathway correlated positively with disease severity. Alcohol-fed mice demonstrated increased hepatic expression of the cGAS-IRF3 pathway. Mice genetically deficient in cGAS and IRF3 were protected against ALD. Ablation of cGAS in hepatocytes only phenocopied this hepatoprotection, highlighting the critical role of hepatocytes in fueling the cGAS-IRF3 response to alcohol. We identified connexin 32 (Cx32), the predominant hepatic gap junction, as a critical regulator of spreading cGAS-driven IRF3 activation through the liver parenchyma. Disruption of Cx32 in ALD impaired IRF3-stimulated gene expression, resulting in decreased hepatic injury despite an increase in hepatic steatosis. Taken together, these results identify cGAS and Cx32 as key factors in ALD pathogenesis and as potential therapeutic targets for hepatoprotection.
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  • 89
    Publication Date: 2020-05-12
    Description: Spiders are one of the most successful venomous animals, with more than 48,000 described species. Most spider venoms are dominated by cysteine-rich peptides with a diverse range of pharmacological activities. Some spider venoms contain thousands of unique peptides, but little is known about the mechanisms used to generate such complex chemical arsenals. We used an integrated transcriptomic, proteomic, and structural biology approach to demonstrate that the lethal Australian funnel-web spider produces 33 superfamilies of venom peptides and proteins. Twenty-six of the 33 superfamilies are disulfide-rich peptides, and we show that 15 of these are knottins that contribute 〉90% of the venom proteome. NMR analyses revealed that most of these disulfide-rich peptides are structurally related and range in complexity from simple to highly elaborated knottin domains, as well as double-knot toxins, that likely evolved from a single ancestral toxin gene.
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  • 90
    Publication Date: 2020-02-10
    Description: Small molecules can affect many cellular processes. The disambiguation of these effects to identify the causative mechanisms of cell death is extremely challenging. This challenge impacts both clinical development and the interpretation of chemical genetic experiments. CX-5461 was developed as a selective RNA polymerase I inhibitor, but recent evidence suggests that it may cause DNA damage and induce G-quadraplex formation. Here we use three complimentary data mining modalities alongside biochemical and cell biological assays to show that CX-5461 exerts its primary cytotoxic activity through topoisomerase II poisoning. We then show that acquired resistance to CX-5461 in previously sensitive lymphoma cells confers collateral resistance to the topoisomerase II poison doxorubicin. Doxorubicin is already a frontline chemotherapy in a variety of hematopoietic malignancies, and CX-5461 is being tested in relapse/refractory hematopoietic tumors. Our data suggest that the mechanism of cell death induced by CX-5461 is critical for rational clinical development in these patients. Moreover, CX-5461 usage as a specific chemical genetic probe of RNA polymerase I function is challenging to interpret. Our multimodal data-driven approach is a useful way to detangle the intended and unintended mechanisms of drug action across diverse essential cellular processes.
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  • 91
    Publication Date: 2020-04-22
    Description: Isoprene has the highest emission into Earth’s atmosphere of any nonmethane hydrocarbon. Atmospheric processing of alkenes, including isoprene, via ozonolysis leads to the formation of zwitterionic reactive intermediates, known as Criegee intermediates (CIs). Direct studies have revealed that reactions involving simple CIs can significantly impact the tropospheric oxidizing capacity, enhance particulate formation, and degrade local air quality. Methyl vinyl ketone oxide (MVK-oxide) is a four-carbon, asymmetric, resonance-stabilized CI, produced with 21 to 23% yield from isoprene ozonolysis, yet its reactivity has not been directly studied. We present direct kinetic measurements of MVK-oxide reactions with key atmospheric species using absorption spectroscopy. Direct UV-Vis absorption spectra from two independent flow cell experiments overlap with the molecular beam UV-Vis-depletion spectra reported recently [M. F. Vansco, B. Marchetti, M. I. Lester, J. Chem. Phys. 149, 44309 (2018)] but suggest different conformer distributions under jet-cooled and thermal conditions. Comparison of the experimental lifetime herein with theory indicates only the syn-conformers are observed; anti-conformers are calculated to be removed much more rapidly via unimolecular decay. We observe experimentally and predict theoretically fast reaction of syn-MVK-oxide with SO2 and formic acid, similar to smaller alkyl-substituted CIs, and by contrast, slow removal in the presence of water. We determine products through complementary multiplexed photoionization mass spectrometry, observing SO3 and identifying organic hydroperoxide formation from reaction with SO2 and formic acid, respectively. The tropospheric implications of these reactions are evaluated using a global chemistry and transport model.
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  • 92
    Publication Date: 2020-06-15
    Description: The total amount of rainfall associated with tropical cyclones (TCs) over a given region is proportional to rainfall intensity and the inverse of TC translation speed. Although the contributions of increase in rainfall intensity to larger total rainfall amounts have been extensively examined, observational evidence on impacts of the recently reported but still debated long-term slowdown of TCs on local total rainfall amounts is limited. Here, we find that both observations and the multimodel ensemble of Global Climate Model simulations show a significant slowdown of TCs (11% in observations and 10% in simulations, respectively) from 1961 to 2017 over the coast of China. Our analyses of long-term observations find a significant increase in the 90th percentile of TC-induced local rainfall totals and significant inverse relationships between TC translation speeds and local rainfall totals over the study period. The study also shows that TCs with lower translation speed and higher rainfall totals occurred more frequently after 1990 in the Pearl River Delta in southern China. Our probability analysis indicates that slow-moving TCs are more likely to generate heavy rainfall of higher total amounts than fast-moving TCs. Our findings suggest that slowdown of TCs tends to elevate local rainfall totals and thus impose greater flood risks at the regional scale.
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  • 93
    Publication Date: 2020-01-21
    Description: A 194-cm-long total-body positron emission tomography/computed tomography (PET/CT) scanner (uEXPLORER), has been constructed to offer a transformative platform for human radiotracer imaging in clinical research and healthcare. Its total-body coverage and exceptional sensitivity provide opportunities for innovative studies of physiology, biochemistry, and pharmacology. The objective of this study is to develop a method to perform ultrahigh (100 ms) temporal resolution dynamic PET imaging by combining advanced dynamic image reconstruction paradigms with the uEXPLORER scanner. We aim to capture the fast dynamics of initial radiotracer distribution, as well as cardiac motion, in the human body. The results show that we can visualize radiotracer transport in the body on timescales of 100 ms and obtain motion-frozen images with superior image quality compared to conventional methods. The proposed method has applications in studying fast tracer dynamics, such as blood flow and the dynamic response to neural modulation, as well as performing real-time motion tracking (e.g., cardiac and respiratory motion, and gross body motion) without any external monitoring device (e.g., electrocardiogram, breathing belt, or optical trackers).
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  • 94
    Publication Date: 2020-01-13
    Description: The use of bacteriophages (phages) for antibacterial therapy is under increasing consideration to treat antimicrobial-resistant infections. Phages have evolved multiple mechanisms to target their bacterial hosts, such as high-affinity, environmentally hardy receptor-binding proteins. However, traditional phage therapy suffers from multiple challenges stemming from the use of an exponentially replicating, evolving entity whose biology is not fully characterized (e.g., potential gene transduction). To address this problem, we conjugate the phages to gold nanorods, creating a reagent that can be destroyed upon use (termed “phanorods”). Chimeric phages were engineered to attach specifically to several Gram-negative organisms, including the human pathogens Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae, and the plant pathogen Xanthomonas campestris. The bioconjugated phanorods could selectively target and kill specific bacterial cells using photothermal ablation. Following excitation by near-infrared light, gold nanorods release energy through nonradiative decay pathways, locally generating heat that efficiently kills targeted bacterial cells. Specificity was highlighted in the context of a P. aeruginosa biofilm, in which phanorod irradiation killed bacterial cells while causing minimal damage to epithelial cells. Local temperature and viscosity measurements revealed highly localized and selective ablation of the bacteria. Irradiation of the phanorods also destroyed the phages, preventing replication and reducing potential risks of traditional phage therapy while enabling control over dosing. The phanorod strategy integrates the highly evolved targeting strategies of phages with the photothermal properties of gold nanorods, creating a well-controlled platform for systematic killing of bacterial cells.
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  • 95
    Publication Date: 2020-05-01
    Description: While the concept of intercellular mechanical communication has been revealed, the mechanistic insights have been poorly evidenced in the context of myofibroblast–fibroblast interaction during fibrosis expansion. Here we report and systematically investigate the mechanical force-mediated myofibroblast–fibroblast cross talk via the fibrous matrix, which we termed paratensile signaling. Paratensile signaling enables instantaneous and long-range mechanotransduction via collagen fibers (less than 1 s over 70 μm) to activate a single fibroblast, which is intracellularly mediated by DDR2 and integrin signaling pathways in a calcium-dependent manner through the mechanosensitive Piezo1 ion channel. By correlating in vitro fibroblast foci growth models with mathematical modeling, we demonstrate that the single-cell-level spatiotemporal feature of paratensile signaling can be applied to elucidate the tissue-level fibrosis expansion and that blocking paratensile signaling can effectively attenuate the fibroblast to myofibroblast transition at the border of fibrotic and normal tissue. Our comprehensive investigation of paratensile signaling in fibrosis expansion broadens the understanding of cellular dynamics during fibrogenesis and inspires antifibrotic intervention strategies targeting paratensile signaling.
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  • 96
    Publication Date: 2020-02-18
    Description: The opportunistic pathogenPseudomonas aeruginosais a major cause of antibiotic-tolerant infections in humans.P. aeruginosaevades antibiotics in bacterial biofilms by up-regulating expression of a symbiotic filamentous inoviral prophage, Pf4. We investigated the mechanism of phage-mediated antibiotic tolerance using biochemical reconstitution combined with structural biology and high-resolution cellular imaging. We resolved electron cryomicroscopy atomic structures of Pf4 with and without its linear single-stranded DNA genome, and studied Pf4 assembly into liquid crystalline droplets using optical microscopy and electron cryotomography. By biochemically replicating conditions necessary for antibiotic protection, we found that phage liquid crystalline droplets form phase-separated occlusive compartments around rod-shaped bacteria leading to increased bacterial survival. Encapsulation by these compartments was observed even when inanimate colloidal rods were used to mimic rod-shaped bacteria, suggesting that shape and size complementarity profoundly influences the process. Filamentous inoviruses are pervasive across prokaryotes, and in particular, several Gram-negative bacterial pathogens includingNeisseria meningitidis,Vibrio cholerae,andSalmonella entericaharbor these prophages. We propose that biophysical occlusion mediated by secreted filamentous molecules such as Pf4 may be a general strategy of bacterial survival in harsh environments.
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  • 97
    Publication Date: 2020-03-03
    Description: Human profilin I reduces aggregation and concomitant toxicity of the polyglutamine-containing N-terminal region of the huntingtin protein encoded by exon 1 (httex1) and responsible for Huntington’s disease. Here, we investigate the interaction of profilin with httex1using NMR techniques designed to quantitatively analyze the kinetics and equilibria of chemical exchange at atomic resolution, including relaxation dispersion, exchange-induced shifts, and lifetime line broadening. We first show that the presence of two polyproline tracts in httex1, absent from a shorter huntingtin variant studied previously, modulates the kinetics of the transient branched oligomerization pathway that precedes nucleation, resulting in an increase in the populations of the on-pathway helical coiled-coil dimeric and tetrameric species (τex≤ 50 to 70 μs), while leaving the population of the off-pathway (nonproductive) dimeric species largely unaffected (τex∼750 μs). Next, we show that the affinity of a single molecule of profilin to the polyproline tracts is in the micromolar range (Kdiss∼ 17 and ∼ 31 μM), but binding of a second molecule of profilin is negatively cooperative, with the affinity reduced ∼11-fold. The lifetime of a 1:1 complex of httex1with profilin, determined using a shorter huntingtin variant containing only a single polyproline tract, is shown to be on the submillisecond timescale (τex∼ 600 μs andKdiss∼ 50 μM). Finally, we demonstrate that, in stable profilin–httex1complexes, the productive oligomerization pathway, leading to the formation of helical coiled-coil httex1tetramers, is completely abolished, and only the pathway resulting in “nonproductive” dimers remains active, thereby providing a mechanistic basis for how profilin reduces aggregation and toxicity of httex1.
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  • 98
    Publication Date: 2020-05-26
    Description: The mechano-bactericidal activity of nanostructured surfaces has become the focus of intensive research toward the development of a new generation of antibacterial surfaces, particularly in the current era of emerging antibiotic resistance. This work demonstrates the effects of an incremental increase of nanopillar height on nanostructure-induced bacterial cell death. We propose that the mechanical lysis of bacterial cells can be influenced by the degree of elasticity and clustering of highly ordered silicon nanopillar arrays. Herein, silicon nanopillar arrays with diameter 35 nm, periodicity 90 nm and increasing heights of 220, 360, and 420 nm were fabricated using deep UV immersion lithography. Nanoarrays of 360-nm-height pillars exhibited the highest degree of bactericidal activity toward both Gram stain-negativePseudomonas aeruginosaand Gram stain-positiveStaphylococcus aureusbacteria, inducing 95 ± 5% and 83 ± 12% cell death, respectively. At heights of 360 nm, increased nanopillar elasticity contributes to the onset of pillar deformation in response to bacterial adhesion to the surface. Theoretical analyses of pillar elasticity confirm that deflection, deformation force, and mechanical energies are more significant for the substrata possessing more flexible pillars. Increased storage and release of mechanical energy may explain the enhanced bactericidal action of these nanopillar arrays toward bacterial cells contacting the surface; however, with further increase of nanopillar height (420 nm), the forces (and tensions) can be partially compensated by irreversible interpillar adhesion that reduces their bactericidal effect. These findings can be used to inform the design of next-generation mechano-responsive surfaces with tuneable bactericidal characteristics for antimicrobial surface technologies.
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  • 99
    Publication Date: 2020-03-02
    Description: Posttranslational modifications (PTMs) are important physiological means to regulate the activities and structures of central regulatory proteins in health and disease. Small GTPases have been recognized as important molecules that are targeted by PTMs during infections of mammalian cells by bacterial pathogens. The enzymes DrrA/SidM and AnkX fromLegionella pneumophilaAMPylate and phosphocholinate Rab1b during infection, respectively. Cdc42 is AMPylated by IbpA fromHistophilus somniat tyrosine 32 or by VopS fromVibrio parahaemolyticusat threonine 35. These modifications take place in the important regulatory switch I or switch II regions of the GTPases. Since Rab1b and Cdc42 are central regulators of intracellular vesicular trafficking and of the actin cytoskeleton, their modifications by bacterial pathogens have a profound impact on the course of infection. Here, we addressed the biochemical and structural consequences of GTPase AMPylation and phosphocholination. By combining biochemical experiments and NMR analysis, we demonstrate that AMPylation can overrule the activity state of Rab1b that is commonly dictated by binding to guanosine diphosphate or guanosine triphosphate. Thus, PTMs may exert conformational control over small GTPases and may add another previously unrecognized layer of activity control to this important regulatory protein family.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 100
    Publication Date: 2020-05-04
    Description: Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis of premature infants and an orphan disease with no specific treatment. Most patients with confirmed NEC develop moderate-severe thrombocytopenia requiring one or more platelet transfusions. Here we used our neonatal murine model of NEC-related thrombocytopenia to investigate mechanisms of platelet depletion associated with this disease [K. Namachivayam, K. MohanKumar, L. Garg, B. A. Torres, A. Maheshwari, Pediatr. Res. 81, 817–824 (2017)]. In this model, enteral administration of immunogen trinitrobenzene sulfonate (TNBS) in 10-d-old mouse pups produces an acute necrotizing ileocolitis resembling human NEC within 24 h, and these mice developed thrombocytopenia at 12 to 15 h. We hypothesized that platelet activation and depletion occur during intestinal injury following exposure to bacterial products translocated across the damaged mucosa. Surprisingly, platelet activation began in our model 3 h after TNBS administration, antedating mucosal injury or endotoxinemia. Platelet activation was triggered by thrombin, which, in turn, was activated by tissue factor released from intestinal macrophages. Compared to adults, neonatal platelets showed enhanced sensitivity to thrombin due to higher expression of several downstream signaling mediators and the deficiency of endogenous thrombin antagonists. The expression of tissue factor in intestinal macrophages was also unique to the neonate. Targeted inhibition of thrombin by a nanomedicine-based approach was protective without increasing interstitial hemorrhages in the inflamed bowel or other organs. In support of these data, we detected increased circulating tissue factor and thrombin-antithrombin complexes in patients with NEC. Our findings show that platelet activation is an important pathophysiological event and a potential therapeutic target in NEC.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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