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  • MDPI Publishing  (52,519)
  • American Meteorological Society
  • Leipzig : Akad. Verlagsges.
  • National Academy of Sciences
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  • 1950-1954  (1,806)
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  • 1
    Publication Date: 2019-03-27
    Description: The first in situ measurements of seawater density that referred to a geographical position at sea and time of the year were carried out by Count Luigi Ferdinando Marsili between 1679 and 1680 in the Adriatic Sea, Aegean Sea, Marmara Sea, and the Bosporus. Not only was this the first investigation with documented oceanographic measurements carried out at stations, but themeasurements were described in such an accurateway that the authorswere able to reconstruct the observations in modern units. These first measurements concern the ‘‘specific gravity’’ of seawaters (i.e., the ratio between fluid densities). The data reported in the historical oceanographic treatise Osservazioni intorno al Bosforo Tracio (Marsili) allowed the reconstruction of the seawater density at different geographic locations between 1679 and 1680. Marsili’s experimental methodology included the collection of surface and deep water samples, the analysis of the samples with a hydrostatic ampoule, and the use of a reference water to standardize the measurements.Acomparison of reconstructed densities with present-day values shows an agreement within 10%–20% uncertainty, owing to various aspects of the measurement methodology that are difficult to reconstruct from the documentary evidence. Marsili also measured the current speed and the depth of the current inversion in the Bosporus, which are consistent with the present-day knowledge. The experimental data collected in the Bosporus enabledMarsili to enunciate a theory on the cause of the two-layer flow at the strait, demonstrated by his laboratory experiment and later confirmed by many analytical and numerical studies.
    Description: American Meteorological Society.
    Description: Published
    Description: 845 - 860
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Keywords: Ocean ; Density currents ; Measurements ; Ship observations
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in he balance of salinity variance in a partially stratified estuary: Implications for exchange flow, mixing, and stratification. Journal of Physical Oceanography, 48(12), (2018) 2887-2899., doi: 10.1175/JPO-D-18-0032.1.
    Description: Salinity variance dissipation is related to exchange flow through the salinity variance balance equation, and meanwhile its magnitude is also proportional to the turbulence production and stratification inside the estuary. As river flow increases, estuarine volume-integrated salinity variance dissipation increases owing to more variance input from the open boundaries driven by exchange flow and river flow. This corresponds to the increased efficient conversion of turbulence production to salinity variance dissipation due to the intensified stratification with higher river flow. Through the spring–neap cycle, the temporal variation of salinity variance dissipation is more dependent on stratification than turbulence production, so it reaches its maximum during the transition from neap to spring tides. During most of the transition time from spring to neap tides, the advective input of salinity variance from the open boundaries is larger than dissipation, resulting in the net increase of variance, which is mainly expressed as vertical variance, that is, stratification. The intensified stratification in turn increases salinity variance dissipation. During neap tides, a large amount of enhanced salinity variance dissipation is induced by the internal shear stress near the halocline. During most of the transition time from neap to spring tides, dissipation becomes larger than the advective input, so salinity variance decreases and the stratification is destroyed.
    Description: TW was supported by the National Key R&D Program of China (Grant 2017YFA0604104), National Natural Science Foundation of China (Grant 41706002), Natural Science Foundation of Jiangsu Province (Grant BK20170864), and MEL Visiting Fellowship (MELRS1617). WRG was supported by NSF Grant OCE 1736539. Part of this work is finished during TW’s visit in MEL and WHOI. We would like to acknowledge John Warner for providing the codes of the Hudson estuary model, and Parker MacCready, the editor, and two reviewers for their insightful suggestions on improving the manuscript.
    Description: 2019-06-06
    Keywords: Estuaries ; Dynamics ; Mixing ; Density Currents
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It 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 115(52), (2018): E12275-E12284. doi: 10.1073/pnas.1805243115.
    Description: Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.
    Description: We thank the captain and crew of the R/V Melville and the CCGS J. P. Tully as well as the participants of the IRNBRU (MV1405) cruise for the California-based data, particularly K. Ellis [University of North Carolina (UNC)], T. Coale (University of California, San Diego), F. Kuzminov (Rutgers), H. McNair [University of California, Santa Barbara (UCSB)], and J. Jones (UCSB). W. Burns (UNC), S. Haines (UNC), and S. Bargu (Louisiana State University) assisted with sample processing and analysis. This work was funded by the National Science Foundation Grants OCE-1334935 (to A.M.), OCE-1334632 (to B.S.T.), OCE-1333929 (to K.T.), OCE-1334387 (to M.A.B.), OCE-1259776 (to K.W.B), and DGE-1650116 (Graduate Research Fellowship to R.H.L).
    Description: 2019-06-11
    Keywords: phytoplankton ; iron limitation ; Pseudo-nitzschia ; ferritin ; metatranscriptomics
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Monthly Weather Review 147(1), (2019): 389-406. doi: 10.1175/MWR-D-18-0158.1.
    Description: The quasi-biennial oscillation (QBO) is stratified by stratospheric zonal wind direction and height into four phase pairs [easterly midstratospheric winds (QBOEM), easterly lower-stratospheric winds, westerly midstratospheric winds (QBOWM), and westerly lower-stratospheric winds] using an empirical orthogonal function analysis of daily stratospheric (100–10 hPa) zonal wind data during 1980–2017. Madden–Julian oscillation (MJO) events in which the MJO convective envelope moved eastward across the Maritime Continent (MC) during 1980–2017 are identified using the Real-time Multivariate MJO (RMM) index and the outgoing longwave radiation (OLR) MJO index (OMI). Comparison of RMM amplitudes by the QBO phase pair over the MC (RMM phases 4 and 5) reveals that boreal winter MJO events have the strongest amplitudes during QBOEM and the weakest amplitudes during QBOWM, which is consistent with QBO-driven differences in upper-tropospheric lower-stratospheric (UTLS) static stability. Additionally, boreal winter RMM events over the MC strengthen during QBOEM and weaken during QBOWM. In the OMI, those amplitude changes generally shift eastward to the eastern MC and western Pacific Ocean, which may result from differences in RMM and OMI index methodologies. During boreal summer, as the northeastward-propagating boreal summer intraseasonal oscillation (BSISO) becomes the dominant mode of intraseasonal variability, these relationships are reversed. Zonal differences in UTLS stability anomalies are consistent with amplitude changes of eastward-propagating MJO events across the MC during boreal winter, and meridional stability differences are consistent with amplitude changes of northeastward-propagating BSISO events during boreal summer. Results remain consistent when stratifying by neutral ENSO phase.
    Description: The authors are grateful for the funding provided by the Office of Naval Research Propagation of Intra-Seasonal Tropical Oscillations (ONR PISTON) Award N0001416WX01752 and the USNA Trident Scholar program. The authors also appreciate the helpful comments of the two external reviewers.
    Description: 2019-07-07
    Keywords: Maritime Continent ; Madden-Julian oscillation ; Quasibiennial oscillation
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2019-10-29
    Description: The ozonesonde is a small balloon-borne instrument that is attached to a standard radiosonde to measure profiles of ozone from the surface to 35 km with ∼100-m vertical resolution. Ozonesonde data constitute a mainstay of satellite calibration and are used for climatologies and analysis of trends, especially in the lower stratosphere where satellites are most uncertain. The electrochemical concentration cell (ECC) ozonesonde has been deployed at ∼100 stations worldwide since the 1960s, with changes over time in manufacture and procedures, including details of the cell chemical solution and data processing. As a consequence, there are biases among different stations and discontinuities in profile time series from individual site records. For 22 years the Jülich (Germany) Ozonesonde Intercomparison Experiment (JOSIE) has periodically tested ozonesondes in a simulation chamber designated the World Calibration Centre for Ozonesondes (WCCOS) by WMO. During October–November 2017 a JOSIE campaign evaluated the sondes and procedures used in Southern Hemisphere Additional Ozonesondes (SHADOZ), a 14-station sonde network operating in the tropics and subtropics. A distinctive feature of the 2017 JOSIE was that the tests were conducted by operators from eight SHADOZ stations. Experimental protocols for the SHADOZ sonde configurations, which represent most of those in use today, are described, along with preliminary results. SHADOZ stations that follow WMO-recommended protocols record total ozone within 3% of the JOSIE reference instrument. These results and prior JOSIEs demonstrate that regular testing is essential to maintain best practices in ozonesonde operations and to ensure high-quality data for the satellite and ozone assessment communities.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17934-17942, doi:10.1073/pnas.1910121116.
    Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
    Description: We are grateful to Martin Kolisko and Fabien Burki for helpful discussion about and comments on the phylogenetic analysis; and Filip Husnik and Vittorio Boscaro for valuable comments on the manuscript. This work was supported by a grant from the National Science Foundation to R.J.G. and P.J.K. (PLR-1341362) and from the Natural Sciences and Engineering Research Council of Canada to P.J.K. (RGPIN-2014-03994).
    Description: 2020-02-19
    Keywords: plastid endosymbiosis ; kleptoplasty ; dinoflagellates ; plastid integration
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(7), (2019): 1889-1904, doi:10.1175/JPO-D-19-0053.1.
    Description: A high-resolution numerical model, together with in situ and satellite observations, is used to explore the nature and dynamics of the dominant high-frequency (from one day to one week) variability in Denmark Strait. Mooring measurements in the center of the strait reveal that warm water “flooding events” occur, whereby the North Icelandic Irminger Current (NIIC) propagates offshore and advects subtropical-origin water northward through the deepest part of the sill. Two other types of mesoscale processes in Denmark Strait have been described previously in the literature, known as “boluses” and “pulses,” associated with a raising and lowering of the overflow water interface. Our measurements reveal that flooding events occur in conjunction with especially pronounced pulses. The model indicates that the NIIC hydrographic front is maintained by a balance between frontogenesis by the large-scale flow and frontolysis by baroclinic instability. Specifically, the temperature and salinity tendency equations demonstrate that the eddies act to relax the front, while the mean flow acts to sharpen it. Furthermore, the model reveals that the two dense water processes—boluses and pulses (and hence flooding events)—are dynamically related to each other and tied to the meandering of the hydrographic front in the strait. Our study thus provides a general framework for interpreting the short-time-scale variability of Denmark Strait Overflow Water entering the Irminger Sea.
    Description: MAS was supported by the National Science Foundation (NSF) under Grants OCE-1558742 and OCE-1534618. RSP, PL, and DM were supported by NSF under Grants OCE-1558742 and OCE-1259618. WJvA was supported by the Helmholtz Infrastructure Initiative FRAM. TWNH and MA were supported by NSF under Grants OCE-1633124 and OCE-118123.
    Description: 2020-07-01
    Keywords: Baroclinic flows ; Frontogenesis/frontolysis ; Meridional overturning circulation ; Ocean dynamics ; Topographic effects
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-10-27
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Marine Science and Engineering 6(4), (2018): 144. doi:10.3390/jmse6040144.
    Description: Geochronologies derived from sediment cores in coastal locations are often used to infer event bed characteristics such as deposit thicknesses and accumulation rates. Such studies commonly use naturally occurring, short-lived radioisotopes, such as Beryllium-7 (7Be) and Thorium-234 (234Th), to study depositional and post-depositional processes. These radioisotope activities, however, are not generally represented in sediment transport models that characterize coastal flood and storm deposition with grain size patterns and deposit thicknesses. We modified the Community Sediment Transport Modeling System (CSTMS) to account for reactive tracers and used this capability to represent the behavior of these short-lived radioisotopes on the sediment bed. This paper describes the model and presents results from a set of idealized, one-dimensional (vertical) test cases. The model configuration represented fluvial deposition followed by periods of episodic storm resuspension. Sensitivity tests explored the influence on seabed radioisotope profiles by the intensities of bioturbation and wave resuspension and the thickness of fluvial deposits. The intensity of biodiffusion affected the persistence of fluvial event beds as evidenced by 7Be. Both resuspension and biodiffusion increased the modeled seabed inventory of 234Th. A thick fluvial deposit increased the seabed inventory of 7Be and 234Th but mixing over time greatly reduced the difference in inventory of 234Th in fluvial deposits of different thicknesses.
    Description: The Bureau of Ocean Energy Management (BOEM) provided funding for Birchler, Harris, and Kniskern. During his M.S. program Birchler received additional funds from VIMS’ Office of Academic Studies. This work was partially supported by the U.S. Geological Survey, Coastal and Marine Geology Program.
    Keywords: Numerical model ; Sediment transport ; Marine ; Short-lived radioisotopes
    Repository Name: Woods Hole Open Access Server
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  • 9
    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 Diaz, J. M., Plummer, S., Hansel, C. M., Andeer, P. F., Saito, M. A., & McIlvin, M. R. NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica. Proceedings of the National Academy of Sciences of the United States of America, 116 (33), (2019): 16448-16453, doi: 10.1073/pnas.1821233116.
    Description: Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.
    Description: This work was supported by a postdoctoral fellowship from the Ford Foundation (to J.M.D.), the National Science Foundation (NSF) under grants OCE 1225801 (to J.M.D.) and OCE 1246174 (to C.M.H.), a Junior Faculty Seed Grant from the University of Georgia Research Foundation (to J.M.D.), and a National Science Foundation Graduate Research Fellowship (to S.P.). The FIRe was purchased through a NSF equipment improvement grant (1624593).The authors thank Melissa Soule for assistance with LC/MS/MS analysis of peptide samples.
    Keywords: Reactive oxygen species ; Photosynthesis ; Oxidative stress ; Biogeochemistry
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  • 10
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. 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 116(27), (2019): 13233-13238, doi: 10.1073/pnas.1904087116.
    Description: The overturning circulation of the global ocean is critically shaped by deep-ocean mixing, which transforms cold waters sinking at high latitudes into warmer, shallower waters. The effectiveness of mixing in driving this transformation is jointly set by two factors: the intensity of turbulence near topography and the rate at which well-mixed boundary waters are exchanged with the stratified ocean interior. Here, we use innovative observations of a major branch of the overturning circulation—an abyssal boundary current in the Southern Ocean—to identify a previously undocumented mixing mechanism, by which deep-ocean waters are efficiently laundered through intensified near-boundary turbulence and boundary–interior exchange. The linchpin of the mechanism is the generation of submesoscale dynamical instabilities by the flow of deep-ocean waters along a steep topographic boundary. As the conditions conducive to this mode of mixing are common to many abyssal boundary currents, our findings highlight an imperative for its representation in models of oceanic overturning.
    Description: The DynOPO project is supported by the UK Natural Environment Research Council (grants NE/K013181/1 and NE/K012843/1) and the US National Science Foundation (grants OCE-1536453 and OCE-1536779). A.C.N.G. acknowledges the support of the Royal Society and the Wolfson Foundation. S.L. acknowledges the support of award NA14OAR4320106 from the National Oceanic and Atmospheric Administration, US Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the US Department of Commerce. We are grateful to the scientific party, crew, and technicians on the RRS James Clark Ross for their hard work during data collection.
    Description: 2019-12-18
    Keywords: Ocean mixing ; Overturning circulation ; Submesoscale instabilities ; Turbulence
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  • 11
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 32(2), (2019): 549-573. doi: 10.1175/JCLI-D-18-0413.1.
    Description: Time series of surface meteorology and air–sea fluxes from the northern Bay of Bengal are analyzed, quantifying annual and seasonal means, variability, and the potential for surface fluxes to contribute significantly to variability in surface temperature and salinity. Strong signals were associated with solar insolation and its modulation by cloud cover, and, in the 5- to 50-day range, with intraseasonal oscillations (ISOs). The northeast (NE) monsoon (DJF) was typically cloud free, with strong latent heat loss and several moderate wind events, and had the only seasonal mean ocean heat loss. The spring intermonsoon (MAM) was cloud free and had light winds and the strongest ocean heating. Strong ISOs and Tropical Cyclone Komen were seen in the southwest (SW) monsoon (JJA), when 65% of the 2.2-m total rain fell, and oceanic mean heating was small. The fall intermonsoon (SON) initially had moderate convective systems and mean ocean heating, with a transition to drier winds and mean ocean heat loss in the last month. Observed surface freshwater flux applied to a layer of the observed thickness produced drops in salinity with timing and magnitude similar to the initial drops in salinity in the summer monsoon, but did not reproduce the salinity variability of the fall intermonsoon. Observed surface heat flux has the potential to cause the temperature trends of the different seasons, but uncertainty in how shortwave radiation is absorbed in the upper ocean limits quantifying the role of surface forcing in the evolution of mixed layer temperature.
    Description: The deployment of the Woods Hole Oceanographic Institution (WHOI) mooring and RW and JTF were supported by the U.S. Office of Naval Research, Grant N00014-13-1-0453. DS acknowledges support from the Ministry of Earth Sciences under India’s National Monsoon Mission. HS acknowledges support from the Office of Naval Research Grants N00014-13-1-0453 and N00014-17-12398. The deployment of the WHOI mooring was done by RV Sagar Nidhi and the recovery by RV Sagar Kanya; the help of the crew and science parties is gratefully acknowledged as is the ongoing support at NIOT in Chennai and by other colleagues in India of this mooring work. The work of the staff of the WHOI Upper Ocean Process Group in the design, building, deployment, and recovery of the mooring and in processing the data is gratefully acknowledged. The software for the wavelet analysis was provided by Torrence and Compo (1998). Feedback on the paper by Dr. Amit Tandon and two anonymous reviewers is gratefully acknowledged. This paper is dedicated to Dr. Frank Bradley.
    Description: 2019-06-28
    Keywords: Atmosphere-ocean interaction ; Monsoons ; Air-sea interaction ; Surface fluxes
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  • 12
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    American Meteorological Society
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography, 49 (2), (2019): 607-630, doi:10.1175/JPO-D-18-0166.1.
    Description: The Lagrangian motion in the eddy field produced from an unstable retrograde jet along the shelf break is studied from idealized numerical experiments with a primitive equation model. The jet is initially in thermal wind balance with a cross-isobath density gradient and is not subjected to any atmospheric forcing. Over the course of the model integration, the jet becomes unstable and produces a quasi-stationary eddy field over a 2-month period. During this period, the cross-slope flow at the shelf break is characterized by along-slope correlation scales of O(10) km and temporal correlation scales of a few days. The relative dispersion of parcels across isobaths is found to increase with time as tb, where 1 〈 b 〈 2. This mixed diffusive–ballistic regime appears to reflect the combined effects of (i) the short length scales of velocity correlation at the shelf break and (ii) the seaward excursion of monopolar and dipolar vortices. Cross-slope dispersion is greater offshore of the front than inshore of the front, as offshore parcels are both subducted onshore below density surfaces and translated offshore with eddies. Nonetheless, the exchange of parcels across the jet remains very limited on the monthly time scale. Particles originating from the bottom experience upward displacements of a few tens of meters and seaward displacements of O(100) km, suggesting that the eddy activity engendered by an unstable along-slope jet provides another mechanism for bottom boundary layer detachment near the shelf edge.
    Description: The author expresses his gratitude to the researchers who contributed to the development and public dissemination of POM [for a list of contributors, see Mellor (2002) and comments in the source code]. Discussions with Kenneth Brink, Hyodae Seo, and Weifeng Zhang have been helpful. Comments provided by Kenneth Brink on a draft are gratefully acknowledged. The criticism from two anonymous reviewers allowed us to better focus the manuscript and to significantly improve its clarity. This work has been supported by Grant OCE-1556400 from the U.S. National Science Foundation.
    Description: 2020-02-18
    Keywords: Dispersion ; Eddies ; Frontogenesis/frontolysis ; Instability ; Lagrangian circulation/transport ; Jets
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  • 13
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(6), (2019): 1577-1592, doi:10.1175/JPO-D-18-0124.1.
    Description: The main source feeding the abyssal circulation of the North Pacific is the deep, northward flow of 5–6 Sverdrups (Sv; 1 Sv ≡ 106 m3 s−1) through the Samoan Passage. A recent field campaign has shown that this flow is hydraulically controlled and that it experiences hydraulic jumps accompanied by strong mixing and dissipation concentrated near several deep sills. By our estimates, the diapycnal density flux associated with this mixing is considerably larger than the diapycnal flux across a typical isopycnal surface extending over the abyssal North Pacific. According to historical hydrographic observations, a second source of abyssal water for the North Pacific is 2.3–2.8 Sv of the dense flow that is diverted around the Manihiki Plateau to the east, bypassing the Samoan Passage. This bypass flow is not confined to a channel and is therefore less likely to experience the strong mixing that is associated with hydraulic transitions. The partitioning of flux between the two branches of the deep flow could therefore be relevant to the distribution of Pacific abyssal mixing. To gain insight into the factors that control the partitioning between these two branches, we develop an abyssal and equator-proximal extension of the “island rule.” Novel features include provisions for the presence of hydraulic jumps as well as identification of an appropriate integration circuit for an abyssal layer to the east of the island. Evaluation of the corresponding circulation integral leads to a prediction of 0.4–2.4 Sv of bypass flow. The circulation integral clearly identifies dissipation and frictional drag effects within the Samoan Passage as crucial elements in partitioning the flow.
    Description: This work was supported by the National Science Foundation under Grants OCE-1029268, OCE-1029483, OCE-1657264, OCE-1657870, OCE-1658027, and OCE-1657795. We thank the captain, crew, and engineers at APL/UW for their hard work and skill.
    Description: 2020-06-11
    Keywords: Abyssal circulation ; Bottom currents ; Boundary currents ; Channel flows ; Mixing ; Transport
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  • 14
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(9), (2019): 2337-2343, doi:10.1175/JPO-D-19-0097.1.
    Description: The weakly unstable, two-layer model of baroclinic instability is studied in a configuration in which the flow is perturbed at the inflow section of a channel by a slow and periodic perturbation. In a parameter regime where the governing equation would be the Lorenz equations for chaos if the development occurs only in time, the solution behavior becomes considerably more complex as a function of time and downstream coordinate. In the absence of the beta effect it has earlier been shown that the chaotic behavior along characteristics renders the solution nearly discontinuous in the slow downstream coordinate of the asymptotic model. The additional presence of the beta effect, although expunging the chaos for large enough values of the beta parameter, also provides an additional mechanism for abrupt spatial change.
    Description: 2020-02-28
    Keywords: Cyclogenesis/cyclolysis ; Eddies ; Microscale processes/variability ; Stability
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  • 15
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric Sciences 76(10), (2019): 3013-3027, doi:10.1175/JAS-D-19-0095.1.
    Description: Recently Nakamura and Huang proposed a semiempirical, one-dimensional model of atmospheric blocking based on the observed budget of local wave activity in the boreal winter. The model dynamics is akin to that of traffic flow, wherein blocking manifests as traffic jams when the streamwise flux of local wave activity reaches capacity. Stationary waves modulate the jet stream’s capacity to transmit transient waves and thereby localize block formation. Since the model is inexpensive to run numerically, it is suited for computing blocking statistics as a function of climate variables from large-ensemble, parameter sweep experiments. We explore sensitivity of blocking statistics to (i) stationary wave amplitude, (ii) background jet speed, and (iii) transient eddy forcing, using frequency, persistence, and prevalence as metrics. For each combination of parameters we perform 240 runs of 180-day simulations with aperiodic transient eddy forcing, each time randomizing the phase relations in forcing. The model climate shifts rapidly from a block-free state to a block-dominant state as the stationary wave amplitude is increased and/or the jet speed is decreased. When eddy forcing is increased, prevalence increases similarly but frequency decreases as blocks merge and become more persistent. It is argued that the present-day climate lies close to the boundary of the two states and hence its blocking statistics are sensitive to climate perturbations. The result underscores the low confidence in GCM-based assessment of the future trend of blocking under a changing climate, while it also provides a theoretical basis for evaluating model biases and understanding trends in reanalysis data.
    Description: The main results of this paper emerged from a group project during Rossbypalooza, a student-led summer school at the University of Chicago in June 2018, with the theme of “Understanding climate through simple models.” The authors thank the participants of the summer school for their valuable feedback. Constructive criticisms of the two anonymous reviewers greatly improved the quality of the manuscript. The work is supported by NSF Grants AGS1563307 and AGS1810964
    Keywords: Blocking ; Nonlinear dynamics ; Planetary waves ; Potential vorticity ; Wave breaking ; Climate variability
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  • 16
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(7), (2019): 1973-1994, doi: 10.1175/JPO-D-18-0194.1.
    Description: Using 18 days of field observations, we investigate the diurnal (D1) frequency wave dynamics on the Tasmanian eastern continental shelf. At this latitude, the D1 frequency is subinertial and separable from the highly energetic near-inertial motion. We use a linear coastal-trapped wave (CTW) solution with the observed background current, stratification, and shelf bathymetry to determine the modal structure of the first three resonant CTWs. We associate the observed D1 velocity with a superimposed mode-zero and mode-one CTW, with mode one dominating mode zero. Both the observed and mode-one D1 velocity was intensified near the thermocline, with stronger velocities occurring when the thermocline stratification was stronger and/or the thermocline was deeper (up to the shelfbreak depth). The CTW modal structure and amplitude varied with the background stratification and alongshore current, with no spring–neap relationship evident for the observed 18 days. Within the surface and bottom Ekman layers on the shelf, the observed velocity phase changed in the cross-shelf and/or vertical directions, inconsistent with an alongshore propagating CTW. In the near-surface and near-bottom regions, the linear CTW solution also did not match the observed velocity, particularly within the bottom Ekman layer. Boundary layer processes were likely causing this observed inconsistency with linear CTW theory. As linear CTW solutions have an idealized representation of boundary dynamics, they should be cautiously applied on the shelf.
    Description: An Australian Research Council Discovery Project (DP 140101322), and a UWA Research Collaboration Award funded this work. T. L. Schlosser acknowledges the support of an Australian Government Research Training Program (RTP) Scholarship. We thank the crew, volunteers and scientists who aided in the field data collection aboard the R/V Revelle, which was funded by the National Science Foundation (OCE-1129763). The continental slope moorings, T4 (M32) and T3 (M44), were also funded by the National Science Foundation (OCE-1129763) and were conceived, planned, and executed by Matthew Alford, Jennifer Mackinnon, Jonathan Nash, Harper Simmons, and Gunnar Voet. We also thank Harper Simmons for the combined R/V Revelle multibeam and Geoscience Australia bathymetry used in this study. We thank the two anonymous reviewers whose comments improved this work.
    Description: 2020-01-16
    Keywords: Australia ; Continental shelf/slope ; Boundary currents ; Dynamics ; Waves, oceanic
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  • 17
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Semper, S., Vage, K., Pickart, R. S., Valdimarsson, H., Torres, D. J., & Jonsson, S. The emergence of the North Icelandic Jet and its evolution from northeast Iceland to Denmark Strait. Journal of Physical Oceanography, 49(10), (2019): 2499-2521, doi:10.1175/JPO-D-19-0088.1.
    Description: The North Icelandic Jet (NIJ) is an important source of dense water to the overflow plume passing through Denmark Strait. The properties, structure, and transport of the NIJ are investigated for the first time along its entire pathway following the continental slope north of Iceland, using 13 hydrographic/velocity surveys of high spatial resolution conducted between 2004 and 2018. The comprehensive dataset reveals that the current originates northeast of Iceland and increases in volume transport by roughly 0.4 Sv (1 Sv ≡ 106 m3 s−1) per 100 km until 300 km upstream of Denmark Strait, at which point the highest transport is reached. The bulk of the NIJ transport is confined to a small area in Θ–S space centered near −0.29° ± 0.16°C in Conservative Temperature and 35.075 ± 0.006 g kg−1 in Absolute Salinity. While the hydrographic properties of this transport mode are not significantly modified along the NIJ’s pathway, the transport estimates vary considerably between and within the surveys. Neither a clear seasonal signal nor a consistent link to atmospheric forcing was found, but barotropic and/or baroclinic instability is likely active in the current. The NIJ displays a double-core structure in roughly 50% of the occupations, with the two cores centered at the 600- and 800-m isobaths, respectively. The transport of overflow water 300 km upstream of Denmark Strait exceeds 1.8 ± 0.3 Sv, which is substantially larger than estimates from a year-long mooring array and hydrographic/velocity surveys closer to the strait, where the NIJ merges with the separated East Greenland Current. This implies a more substantial contribution of the NIJ to the Denmark Strait overflow plume than previously envisaged.
    Description: Six different research vessels were involved in the collection of the data used in this study: RRS James Clark Ross, R/V Knorr, R/V Bjarni Sæmundsson, R/V Håkon Mosby, NRV Alliance, and R/V Kristine Bonnevie. We thank the captain and crew of each of these vessels for their hard work as well as the many watch standers who have sailed on the cruises and helped collect the measurements. We also thank Frank Bahr for processing the VMADCP data collected on NRV Alliance and Magnús Danielsen for the processing of the hydrographic data collected on R/V Bjarni Sæmundsson. We acknowledge Leah Trafford McRaven for assistance with Fig. 1 and two anonymous reviewers for their helpful comments, which improved the manuscript. Funding for the project was provided by the Bergen Research Foundation Grant BFS2016REK01 (K. Våge and S. Semper), the Norwegian Research Council under Grant Agreement 231647 (K. Våge), and the U.S. National Science Foundation Grants OCE-1259618 and OCE-1756361 (R. S. Pickart and D. J. Torres), as well as OCE-1558742 (R. S. Pickart). The dataset is available on PANGAEA under https://doi.pangaea.de/10.1594/PANGAEA.903535.
    Keywords: Ocean ; Continental shelf/slope ; Ocean circulation ; Transport ; Intermediate waters ; In situ oceanic observations
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  • 18
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 32(13), (2019): 3883-3898, doi:10.1175/JCLI-D-18-0735.1.
    Description: While it has generally been understood that the production of Labrador Sea Water (LSW) impacts the Atlantic meridional overturning circulation (MOC), this relationship has not been explored extensively or validated against observations. To explore this relationship, a suite of global ocean–sea ice models forced by the same interannually varying atmospheric dataset, varying in resolution from non-eddy-permitting to eddy-permitting (1°–1/4°), is analyzed to investigate the local and downstream relationships between LSW formation and the MOC on interannual to decadal time scales. While all models display a strong relationship between changes in the LSW volume and the MOC in the Labrador Sea, this relationship degrades considerably downstream of the Labrador Sea. In particular, there is no consistent pattern among the models in the North Atlantic subtropical basin over interannual to decadal time scales. Furthermore, the strong response of the MOC in the Labrador Sea to LSW volume changes in that basin may be biased by the overproduction of LSW in many models compared to observations. This analysis shows that changes in LSW volume in the Labrador Sea cannot be clearly and consistently linked to a coherent MOC response across latitudes over interannual to decadal time scales in ocean hindcast simulations of the last half century. Similarly, no coherent relationships are identified between the MOC and the Labrador Sea mixed layer depth or the density of newly formed LSW across latitudes or across models over interannual to decadal time scales.
    Description: FL and MSL are thankful for the financial support from the National Science Foundation (NSF) Physical Oceanography Program (NSF-OCE-12-59102, NSF-OCE-12-59103). The NCAR contribution was supported by the National Oceanic and Atmospheric Administration (NOAA) Climate Program Office (CPO) under Climate Variability and Predictability Program (CVP) Grant NA13OAR4310138 and by the NSF Collaborative Research EaSM2 Grant OCE-1243015. NCAR is sponsored by the NSF. NPH is supported by NERC programs U.K. OSNAP (NE/K010875) and ACSIS (National Capability, NE/N018044/1). Y-OK is supported by NOAA CPO CVP (NA17OAR4310111) and NSF EaSM2 grant (OCE-1242989). AR is supported by NASA-ROSES Modeling, Analysis and Prediction 2016 NNX16AC93G-MAP. RZ is supported by NOAA/OAR. Argo data were collected and made freely available by the International Argo Program and the national programs that contribute to it (http://www.argo.ucsd.edu, http://argo.jcommops.org). The Argo Program is part of the Global Ocean Observing System (http://doi.org/10.17882/42182). Data from the RAPID-MOCHA-WBTS array funded by NERC, NSF and NOAA are freely available from www.rapid.ac.uk/rapidmoc. We thank Stephen Griffies for providing access to the GFDL-MOM025 COREII simulation output and Matthew Harrison and Xiaoqin Yan for their comments on the manuscript. We also thank the anonymous reviewers for their valuable comments.
    Description: 2020-06-11
    Keywords: North Atlantic Ocean ; Deep convection ; Meridional overturning circulation ; Model comparison
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  • 19
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(9), (2019): 2237-2254, doi: 10.1175/JPO-D-18-0181.1.
    Description: A cluster of 45 drifters deployed in the Bay of Bengal is tracked for a period of four months. Pair dispersion statistics, from observed drifter trajectories and simulated trajectories based on surface geostrophic velocity, are analyzed as a function of drifter separation and time. Pair dispersion suggests nonlocal dynamics at submesoscales of 1–20 km, likely controlled by the energetic mesoscale eddies present during the observations. Second-order velocity structure functions and their Helmholtz decomposition, however, suggest local dispersion and divergent horizontal flow at scales below 20 km. This inconsistency cannot be explained by inertial oscillations alone, as has been reported in recent studies, and is likely related to other nondispersive processes that impact structure functions but do not enter pair dispersion statistics. At scales comparable to the deformation radius LD, which is approximately 60 km, we find dynamics in agreement with Richardson’s law and observe local dispersion in both pair dispersion statistics and second-order velocity structure functions.
    Description: This research was supported by the Air Sea Interaction Regional Initiative (ASIRI) under ONR Grant N00014-13-1-0451 (SE and AM) and ONR Grant N00014-13-1-0477 (VH and LC). Additionally, AM and SE thank NSF (Grant OCE-I434788) and ONR (Grant N00014-16-1-2470) for support; VH and LC were further supported by ONR Grant N00014-15-1-2286 and NOAA GDP Grant NA10OAR4320156. We thank Joe LaCasce, Dhruv Balwada, and one anonymous reviewer for helpful comments and discussions that significantly improved this manuscript. The authors thank the captain and crew of the R/V Roger Revelle. The SVP-type drifters are part of the Global Drifter Program and supported by ONR Grant N00014-15-1-2286 and NOAA GDP Grant NA10OAR4320156 and are available under http://www.aoml.noaa.gov/phod/dac/. The Ssalto/Duacs altimeter products were produced and distributed by the Copernicus Marine and Environment Monitoring Service (CMEMS, http://www.marine.copernicus.eu).
    Keywords: Dispersion ; Fronts ; Mesoscale processes ; Subgrid-scale processes ; Trajectories ; Turbulence
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  • 20
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 36(10), (2019): 1997-2014, doi: 10.1175/JTECH-D-19-0029.1.
    Description: While land-based high-frequency (HF) radars are the only instruments capable of resolving both the temporal and spatial variability of surface currents in the coastal ocean, recent high-resolution views suggest that the coastal ocean is more complex than presently deployed radar systems are able to reveal. This work uses a hybrid system, having elements of both phased arrays and direction finding radars, to improve the azimuthal resolution of HF radars. Data from two radars deployed along the U.S. East Coast and configured as 8-antenna grid arrays were used to evaluate potential direction finding and signal, or emitter, detection methods. Direction finding methods such as maximum likelihood estimation generally performed better than the well-known multiple signal classification (MUSIC) method given identical emitter detection methods. However, accurately estimating the number of emitters present in HF radar observations is a challenge. As MUSIC’s direction-of-arrival (DOA) function permits simple empirical tests that dramatically aid the detection process, MUSIC was found to be the superior method in this study. The 8-antenna arrays were able to provide more accurate estimates of MUSIC’s noise subspace than typical 3-antenna systems, eliminating the need for a series of empirical parameters to control MUSIC’s performance. Code developed for this research has been made available in an online repository.
    Description: This analysis was supported by NSF Grants OCE-1657896 and OCE-1736930 to Kirincich, OCE-1658475 to Emery and Washburn and OCE-1736709 to Flament. Flament is also supported by NOAA’s Integrated Ocean Observing System through Award NA11NOS0120039. The authors thank Lindsey Benjamin, Alma Castillo, Ken Constantine, Benedicte Dousset, Ian Fernandez, Mael Flament, Dave Harris, Garrett Hebert, Ben Hodges, Victoria Futch, Matt Guanci, and Philip Moravcik for assistance in building, deploying, and operating the radars.
    Description: 2020-04-11
    Keywords: Ocean ; Coastal flows ; Algorithms ; Radars/Radar observations ; Remote sensing
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  • 21
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 32(8), (2019): 2185-2205. doi:10.1175/JCLI-D-18-0538.1.
    Description: Much attention has been paid to the climatic impacts of changes in the Kuroshio Extension, instead of the Kuroshio in the East China Sea (ECS). This study, however, reveals the prominent influences of the lateral shift of the Kuroshio at interannual time scale in late spring [April–June (AMJ)] on the sea surface temperature (SST) and precipitation in summer around the ECS, based on high-resolution satellite observations and ERA-Interim. A persistent offshore displacement of the Kuroshio during AMJ can result in cold SST anomalies in the northern ECS and the Japan/East Sea until late summer, which correspondingly causes anomalous cooling of the lower troposphere. Consequently, the anomalous cold SST in the northern ECS acts as a key driver to robustly enhance the precipitation from the Yangtze River delta to Kyushu in early summer (May–August) and over the central ECS in late summer (July–September). In view of the moisture budget analysis, two different physical processes modulated by the lateral shift of the Kuroshio are identified to account for the distinct responses of precipitation in early and late summer, respectively. First, the anomalous cold SST in the northern ECS induced by the Kuroshio offshore shift is likely conducive to the earlier arrival of the mei-yu–baiu front at 30°–32°N and its subsequent slower northward movement, which may prolong the local rainy season, leading to the increased rain belt in early summer. Second, the persistent cold SST anomalies in late summer strengthen the near-surface baroclinicity and the associated strong atmospheric fronts embedded in the extratropical cyclones over the central ECS, which in turn enhances the local rainfall.
    Description: We appreciate three anonymous reviewers for their thoughtful and constructive comments. This work is supported by the National Key Research and Development Program of China (2016YFA0601804), the National Natural Science Foundation of China (NSFC) Projects (91858102, 41490643, 41490640, 41506009, U1606402) and the OUC–WHOI joint research program (21366).
    Description: 2019-10-01
    Keywords: Continental shelf/slope ; Atmosphere-ocean interaction ; Boundary currents ; Precipitation ; Interannual variability
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  • 22
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(4), (2019): 1035-1053, doi:10.1175/JPO-D-18-0136.1.
    Description: Ocean stratification and the vertical extent of the mixed layer influence the rate at which the ocean and atmosphere exchange properties. This process has direct impacts for anthropogenic heat and carbon uptake in the Southern Ocean. Submesoscale instabilities that evolve over space (1–10 km) and time (from hours to days) scales directly influence mixed layer variability and are ubiquitous in the Southern Ocean. Mixed layer eddies contribute to mixed layer restratification, while down-front winds, enhanced by strong synoptic storms, can erode stratification by a cross-frontal Ekman buoyancy flux. This study investigates the role of these submesoscale processes on the subseasonal and interannual variability of the mixed layer stratification using four years of high-resolution glider data in the Southern Ocean. An increase of stratification from winter to summer occurs due to a seasonal warming of the mixed layer. However, we observe transient decreases in stratification lasting from days to weeks, which can arrest the seasonal restratification by up to two months after surface heat flux becomes positive. This leads to interannual differences in the timing of seasonal restratification by up to 36 days. Parameterizing the Ekman buoyancy flux in a one-dimensional mixed layer model reduces the magnitude of stratification compared to when the model is run using heat and freshwater fluxes alone. Importantly, the reduced stratification occurs during the spring restratification period, thereby holding important implications for mixed layer dynamics in climate models as well as physical–biological coupling in the Southern Ocean.
    Description: MdP acknowledges numerous research visits to the Department of Marine Science, University of Gothenburg, and a visit to Woods Hole Oceanographic Institution, which greatly enhanced this work. We thank SANAP and the captain and crew of the S.A. Agulhas II for their assistance in the deployment and retrieval of the gliders. We acknowledge the work of SAMERC-STS for housing, managing, and piloting the gliders. SS was supported by NRF-SANAP Grant SNA14071475720 and a Wallenberg Academy Fellowship (WAF 2015.0186). Lastly, SS thanks the numerous technical assistance, advice, and IOP hosting provided by Geoff Shilling and Craig Lee of the Applied Physics Laboratory, University of Washington.
    Description: 2020-04-11
    Keywords: Atmosphere-ocean interaction ; Fronts ; Oceanic mixed layer ; In situ oceanic observations ; Interannual variability ; Seasonal cycle
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(6), (2019): 1639-1649, doi: 10.1175/JPO-D-18-0154.1.
    Description: Using a recently developed asymptotic theory of internal solitary wave propagation over a sloping bottom in a rotating ocean, some new qualitative and quantitative features of this process are analyzed for internal waves in a two-layer ocean. The interplay between different singularities—terminal damping due to radiation and disappearing quadratic nonlinearity, and reaching an “internal beach” (e.g., zero lower-layer depth)—is discussed. Examples of the adiabatic evolution of a single solitary wave over a uniformly sloping bottom under realistic conditions are considered in more detail and compared with numerical solutions of the variable-coefficient, rotation-modified Korteweg–de Vries (rKdV) equation.
    Description: LAO is thankful to Yu. Stepanyants for broad discussions of mutual benefit. KRH was supported by Grant N00014-18-1-2542 from the Office of Naval Research.
    Description: 2020-06-13
    Keywords: Internal waves ; Differential equations ; Nonlinear models ; Ocean models
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  • 24
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society, 100(5), (2019): 897-908, doi:10.1175/BAMS-D-19-0130.1.
    Description: As states, cities, tribes, and private interests cope with climate damages and seek to increase preparedness and resilience, they will need to navigate myriad choices and options available to them. Making these choices in ways that identify pathways for climate action that support their development objectives will require constructive public dialogue, community participation, and flexible and ongoing access to science- and experience-based knowledge. In 2016, a Federal Advisory Committee (FAC) was convened to recommend how to conduct a sustained National Climate Assessment (NCA) to increase the relevance and usability of assessments for informing action. The FAC was disbanded in 2017, but members and additional experts reconvened to complete the report that is presented here. A key recommendation is establishing a new nonfederal “climate assessment consortium” to increase the role of state/local/tribal government and civil society in assessments. The expanded process would 1) focus on applied problems faced by practitioners, 2) organize sustained partnerships for collaborative learning across similar projects and case studies to identify effective tested practices, and 3) assess and improve knowledge-based methods for project implementation. Specific recommendations include evaluating climate models and data using user-defined metrics; improving benefit–cost assessment and supporting decision-making under uncertainty; and accelerating application of tools and methods such as citizen science, artificial intelligence, indicators, and geospatial analysis. The recommendations are the result of broad consultation and present an ambitious agenda for federal agencies, state/local/tribal jurisdictions, universities and the research sector, professional associations, nongovernmental and community-based organizations, and private-sector firms.
    Description: This report would not have been possible without the support and participation of numerous organizations and individuals. We thank New York State Governor Andrew M. Cuomo for announcing in his 2018 State of the State agenda that the IAC would be reconvened. The New York State Energy Research and Development Authority (Contract ID 123416), Columbia University’s Earth Institute, and the American Meteorological Society provided essential financial support and much more, including sage advice and moral support from John O’Leary, Shara Mohtadi, Steve Cohen, Alex Halliday, Peter deMenocal, Keith Seitter, Paul Higgins, and Bill Hooke. We thank the attendees of a workshop, generously funded by the Kresge Foundation in November of 2017, that laid a foundation for the idea to establish a civil-society-based assessment consortium. During the course of preparing the report, IAC members consulted with individuals too numerous to list here—state, local, and tribal officials; researchers; experts in nongovernmental and community-based organizations; and professionals in engineering, architecture, public health, adaptation, and other areas. We are so grateful for their time and expertise. We thank the members and staff of the National Academy of Sciences, Engineering, and Medicine’s Committee to Advise the U.S. Global Change Research Program for providing individual comments on preliminary recommendations during several discussions in open sessions of their meetings. The following individuals provided detailed comments on an earlier version of this report, which greatly sharpened our thinking and recommendations: John Balbus, Tom Dietz, Phil Duffy, Baruch Fischhoff, Brenda Hoppe, Melissa Kenney, Linda Mearns, Claudia Nierenberg, Kathleen Segerson, Soroosh Sorooshian, Chris Weaver, and Brian Zuckerman. Mary Black provided insightful copy editing of several versions of the report. We also thank four anonymous reviewers for their effort and care in critiquing and improving the report. It is the dedication, thoughtful feedback, expertise, care, and commitment of all these people and more that not only made this report possible, but allow us all to continue to support smart and insightful actions in a changing climate. We are grateful as authors and as global citizens. Author contributions: RM, SA, KB, MB, AC, JD, PF, KJ, AJ, KK, JK, ML, JM, RP, TR, LS, JS, JW, and DZ were members of the IAC and shared in researching, discussing, drafting, and approving the report. BA, JF, AG, LJ, SJ, PK, RK, AM, RM, JN, WS, JS, PT, GY, and RZ contributed to specific sections of the report.
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(6), (2019):1463-1483, doi: 10.1175/JPO-D-18-0213.1.
    Description: A set of float trajectories, deployed at 1500- and 2500-m depths throughout the deep Gulf of Mexico from 2011 to 2015, are analyzed for mesoscale processes under the Loop Current (LC). In the eastern basin, December 2012–June 2014 had 〉40 floats per month, which was of sufficient density to allow capturing detailed flow patterns of deep eddies and topographic Rossby waves (TRWs), while two LC eddies formed and separated. A northward advance of the LC front compresses the lower water column and generates an anticyclone. For an extended LC, baroclinic instability eddies (of both signs) develop under the southward-propagating large-scale meanders of the upper-layer jet, resulting in a transfer of eddy kinetic energy (EKE) to the lower layer. The increase in lower-layer EKE occurs only over a few months during meander activity and LC eddy detachment events, a relatively short interval compared with the LC intrusion cycle. Deep EKE of these eddies is dispersed to the west and northwest through radiating TRWs, of which examples were found to the west of the LC. Because of this radiation of EKE, the lower layer of the eastern basin becomes relatively quiescent, particularly in the northeastern basin, when the LC is retracted and a LC eddy has departed. A mean west-to-east, anticyclone–cyclone dipole flow under a mean LC was directly comparable to similar results from a previous moored LC array and also showed connections to an anticlockwise boundary current in the southeastern basin.
    Description: The authors were supported by the Department of the Interior, Bureau of Ocean Energy Management (BOEM), Contract M08PC20043 to Leidos, Inc., Raleigh, NC. The authors also wish to acknowledge the enthusiastic support of Dr. Alexis Lugo-Fernández, the BOEM Contracting Officer’s Technical Representative, during the study into the Deep Circulation of the Gulf of Mexico, using Lagrangian Methods. Thanks go to the captains and crews of the R/V Pelican and B/O Justo Sierra, J. Malbrough (LUMCON), J. Singer (Leidos), J. Valdes (WHOI), B. Guest (WHOI), and the CANEK group (CICESE).
    Description: 2020-05-29
    Keywords: Bottom currents ; Eddies ; Instability ; Lagrangian circulation/transport ; Mesoscale processes ; Topographic effects
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 36(4), (2019): 733-744, doi:10.1175/JTECH-D-18-0050.1.
    Description: Sea-Bird Scientific SBE 41CP CTDs are used on autonomous floats in the global Argo ocean observing program to measure the temperature and salinity of the upper ocean. While profiling, the sensors are subject to dynamic errors as they profile through vertical gradients. Applying dynamic corrections to the temperature and conductivity data reduces these errors and improves sensor accuracy. A series of laboratory experiments conducted in a stratified tank are used to characterize dynamic errors and determine corrections. The corrections are adapted for Argo floats, and recommendations for future implementation are presented.
    Description: 2020-04-23
    Keywords: Data processing ; In situ oceanic observations ; Instrumentation/sensors ; oceanic ; Profilers, oceanic
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  • 27
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Weather Climate and Society 11(3), (2019):465-487, doi: 10.1175/WCAS-D-18-0134.1.
    Description: As states, cities, tribes, and private interests cope with climate damages and seek to increase preparedness and resilience, they will need to navigate myriad choices and options available to them. Making these choices in ways that identify pathways for climate action that support their development objectives will require constructive public dialogue, community participation, and flexible and ongoing access to science- and experience-based knowledge. In 2016, a Federal Advisory Committee (FAC) was convened to recommend how to conduct a sustained National Climate Assessment (NCA) to increase the relevance and usability of assessments for informing action. The FAC was disbanded in 2017, but members and additional experts reconvened to complete the report that is presented here. A key recommendation is establishing a new nonfederal “climate assessment consortium” to increase the role of state/local/tribal government and civil society in assessments. The expanded process would 1) focus on applied problems faced by practitioners, 2) organize sustained partnerships for collaborative learning across similar projects and case studies to identify effective tested practices, and 3) assess and improve knowledge-based methods for project implementation. Specific recommendations include evaluating climate models and data using user-defined metrics; improving benefit–cost assessment and supporting decision-making under uncertainty; and accelerating application of tools and methods such as citizen science, artificial intelligence, indicators, and geospatial analysis. The recommendations are the result of broad consultation and present an ambitious agenda for federal agencies, state/local/tribal jurisdictions, universities and the research sector, professional associations, nongovernmental and community-based organizations, and private-sector firms.
    Description: This report would not have been possible without the support and participation of numerous organizations and individuals. We thank New York State Governor Andrew M. Cuomo for announcing in his 2018 State of the State agenda that the IAC would be reconvened. The New York State Energy Research and Development Authority (Contract ID 123416), Columbia University’s Earth Institute, and the American Meteorological Society provided essential financial support and much more, including sage advice and moral support from John O’Leary, Shara Mohtadi, Steve Cohen, Alex Halliday, Peter deMenocal, Keith Seitter, Paul Higgins, and Bill Hooke. We thank the attendees of a workshop, generously funded by the Kresge Foundation in November of 2017, that laid a foundation for the idea to establish a civil-society-based assessment consortium. During the course of preparing the report, IAC members consulted with individuals too numerous to list here—state, local, and tribal officials; researchers; experts in nongovernmental and community-based organizations; and professionals in engineering, architecture, public health, adaptation, and other areas. We are so grateful for their time and expertise. We thank the members and staff of the National Academy of Sciences, Engineering, and Medicine’s Committee to Advise the U.S. Global Change Research Program for providing individual comments on preliminary recommendations during several discussions in open sessions of their meetings. The following individuals provided detailed comments on an earlier version of this report, which greatly sharpened our thinking and recommendations: John Balbus, Tom Dietz, Phil Duffy, Baruch Fischhoff, Brenda Hoppe, Melissa Kenney, Linda Mearns, Claudia Nierenberg, Kathleen Segerson, Soroosh Sorooshian, Chris Weaver, and Brian Zuckerman. Mary Black provided insightful copy editing of several versions of the report. We also thank four anonymous reviewers for their effort and care in critiquing and improving the report. It is the dedication, thoughtful feedback, expertise, care, and commitment of all these people and more that not only made this report possible, but allow us all to continue to support smart and insightful actions in a changing climate. We are grateful as authors and as global citizens. Author contributions: RM, SA, KB, MB, AC, JD, PF, KJ, AJ, KK, JK, ML, JM, RP, TR, LS, JS, JW, and DZ were members of the IAC and shared in researching, discussing, drafting, and approving the report. BA, JF, AG, LJ, SJ, PK, RK, AM, RM, JN, WS, JS, PT, GY, and RZ contributed to specific sections of the report.
    Description: 2020-05-21
    Keywords: North America ; Climate prediction ; Planning ; Policy ; Risk assessment ; Societal impacts
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  • 28
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It 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 116(25), (2019):12343-12352, doi:10.1073/pnas.1901080116.
    Description: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
    Description: We thank Dr. David Nes (Texas Tech University) for providing sterols and Dr. Matthieu Legendre and Dr. Chantal Abergel (CNRS, Marseille) for access to the P. celtis sequences. Drs. Irina Arkhipova, Mark Hahn, Judith Luborsky, and Ann Bucklin commented on the manuscript. The research was supported by a USA-UK Fulbright Scholarship and a Royal Society grant (to D.C.L.), the Boston University Superfund Research Program [NIH Grant 5P42ES007381 (to J.J.S. and J.V.G.) and NIH Grant 5U41HG003345 (to J.V.G.)], the European Regional Development Fund and Welsh Government Project BEACON (S.L.K.), the Woods Hole Center for Oceans and Human Health [NIH Grant P01ES021923 and National Science Foundation Grant OCE-1314642 (to J.J.S.)], and NIH Grant R01GM53753 (to T.L.P.).
    Description: 2019-12-05
    Keywords: cytochrome P450 ; virus ; evolution ; domains of life ; redox partner
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  • 29
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(6), (2019):1619-1637, doi:10.1175/JPO-D-18-0175.1.
    Description: Although the hydrodynamics of river meanders are well studied, the influence of curvature on flow in estuaries, with alternating tidal flow and varying water levels and salinity gradients, is less well understood. This paper describes a field study on curvature effects in a narrow salt-marsh creek with sharp bends. The key observations, obtained during times of negligible stratification, are 1) distinct differences between secondary flow during ebb and flood, with helical circulation as in rivers during ebb and a reversed circulation during flood, and 2) maximum (ebb and flood) streamwise velocities near the inside of the bend, unlike typical river bend flow. The streamwise velocity structure is explained by the lack of a distinct point bar and the relatively deep cross section in the estuary, which means that curvature-induced inward momentum redistribution is not overcome by outward redistribution by frictional and topographic effects. Through differential advection of the along-estuary salinity gradient, the laterally sheared streamwise velocity generates lateral salinity differences, with the saltiest water near the inside during flood. The resulting lateral baroclinic pressure gradient force enhances the standard helical circulation during ebb but counteracts it during flood. This first leads to a reversed secondary circulation during flood in the outer part of the cross section, which triggers a positive feedback mechanism by bringing slower-moving water from the outside inward along the surface. This leads to a reversal of the vertical shear in the streamwise flow, and therefore in the centrifugal force, which further enhances the reversed secondary circulation.
    Description: This project was funded by NSF Grant OCE-1634490. During this work W.M. Kranenburg was supported as USGS Postdoctoral Scholar at Woods Hole Oceanographic Institution. A.M.P. Garcia was supported by the Michael J. Kowalski Fellowship in Ocean Science and Engineering (AMPG), and the Diversity Fellowship of the MIT Office of the Dean of Graduate Education (AMPG). The authors thank Jay Sisson for the technical support and Peter Traykovski for providing the bathymetric data. Also, the suggestions for improvement by Dr. K. Blanckaert and an anonymous reviewer are thankfully acknowledged.
    Keywords: Estuaries ; Advection ; Baroclinic flows ; Barotropic flows
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  • 30
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 100(5), (2019): 909-912, doi: 10.1175/BAMS-D-18-0319.1.
    Description: The open availability and wide accessibility of digital scientific resources, such as articles and datasets, is becoming the norm for twenty-first-century science. Geoscience researchers are now being asked by funding agencies and scientific publishers to archive and cite data to support open access but often struggle to understand, interpret, and fulfill these requirements. To fulfill the promise of new open data initiatives, 1) scientific resources (e.g., data and software) must be collected and documented properly; 2) repository services, including preservation and storage capabilities, must be maintained, supported, and improved over time; and 3) governance institutions must be established. These issues were discussed in the Geoscience Digital Data Resource and Repository Service (GeoDaRRS) workshop,1 held in August 2018, at NCAR. The workshop brought together more than 60 geoscience researchers, technology experts, scientific publishers, funders, and data repository personnel to discuss data management challenges and opportunities within the geosciences. This included exploring whether new services are needed to complement existing data facilities, particularly in the areas of 1) data management planning support resources and 2) repository services for geoscience researchers who have data that do not fit in any existing repository. More details on the workshop agenda and recommendations are available in the final workshop report (Mayernik et al. 2018).
    Description: The National Science Foundation (NSF) provided the funding support for this workshop. We also thank Cecilia Banner and Elizabeth Faircloth of NCAR for administrative and logistical support.
    Description: 2020-06-04
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  • 31
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(6), (2019): 1561-1575, doi:10.1175/JPO-D-19-0002.1.
    Description: Within the pycnocline, where diapycnal mixing is suppressed, both the vertical movement (uplift) of isopycnal surfaces and upward motion along sloping isopycnals supply nutrients to the euphotic layer, but the relative importance of each of these mechanisms is unknown. We present a method for decomposing vertical velocity w into two components in a Lagrangian frame: vertical velocity along sloping isopycnal surfaces and the adiabatic vertical velocity of isopycnal surfaces . We show that , where is the isopycnal slope and is the geometric aspect ratio of the flow, and that accounts for 10%–25% of the total vertical velocity w for isopycnal slopes representative of the midlatitude pycnocline. We perform the decomposition of w in a process study model of a midlatitude eddying flow field generated with a range of isopycnal slopes. A spectral decomposition of the velocity components shows that while is the largest contributor to vertical velocity, is of comparable magnitude at horizontal scales less than about 10 km, that is, at submesoscales. Increasing the horizontal grid resolution of models is known to increase vertical velocity; this increase is disproportionately due to better resolution of , as is shown here by comparing 1- and 4-km resolution model runs. Along-isopycnal vertical transport can be an important contributor to the vertical flux of tracers, including oxygen, nutrients, and chlorophyll, although we find weak covariance between vertical velocity and nutrient anomaly in our model.
    Description: MAF was supported by a National Defense Science and Engineering Graduate Fellowship and AM by NSF OCE-I434788. The authors thank Glenn Flierl and Ruth Curry for helpful conversations, and three anonymous reviewers for comments that improved the manuscript.
    Description: 2020-06-11
    Keywords: Baroclinic flows ; Mesoscale processes ; Small scale processes ; Subgrid-scale processes ; Vertical motion
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  • 32
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 36(9), (2019): 1789-1812, doi:10.1175/JTECH-D-18-0223.1.
    Description: Temporal vertical eddy viscosity coefficient (VEVC) in an Ekman layer model is estimated using an adjoint method. Twin experiments are carried out to investigate the influences of several factors on inversion results, and the conclusions of twin experiments are 1) the adjoint method is a capable method to estimate different kinds of temporal distributions of VEVCs; 2) the gradient descent algorithm is better than CONMIN and L-BFGS for the present problem, although the posterior two algorithms perform better on convergence efficiency; 3) inversion results are sensitive to initial guesses; 4) the model is applicable to different wind conditions; 5) the inversion result with thick boundary layer depth (BLD) is slightly better than thin BLD; 6) inversion results are more sensitive to observations in upper layers than those in lower layers; 7) inversion results are still acceptable when data noise exists, indicating the method can sustain noise to a certain degree; 8) a regularization method is proved to be useful to improve the results for present problem; and 9) the present method can tolerate the existence of balance errors due to the imperfection of governing equations. The methodology is further validated in practical experiments where Ekman currents are derived from Bermuda Testbed Mooring data and assimilated. Modeled Ekman currents coincide well with observed ones, especially for upper layers. The results demonstrate that the assumptions of depth dependence and time dependence are equally important for VEVCs. The feasibility of the typical Ekman model, the imperfection of Ekman balance equations, and the deficiencies of the present method are discussed. This method provides a potential way to realize the time variations of VEVCs in ocean models.
    Description: The authors thank the seven reviewers for the constructive suggestions which have greatly improved the manuscript. Financial support is provided by the National Key Research and Development Plan of China (Grants 2017YFA0604100 and 2017YFC1404000), the National Natural Science Foundation of China (Grants 41876086 and 41806012), Scientific Research Fund of the Second Institute of Oceanography, MNR (Grant JG1819), and the Fundamental Research Funds for the Central Universities of China. Jicai thanks the support of China Scholarship Council for the visiting research in WHOI, and he also thanks the host of WHOI. BTM data are provided by Ocean Physics Laboratory, University of California, Santa Barbara (http://opl.ucsb.edu).
    Description: 2020-03-10
    Keywords: Data assimilation ; Parameterization
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  • 33
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. 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 116 (35), (2019): 17187-17192, doi:10.1073/pnas.1903067116.
    Description: Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on 〉2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.
    Description: We thank D. McGillicuddy, G. Lawson, and G. Flierl for helpful discussions while developing this work and 2 anonymous reviewers whose feedback significantly improved the manuscript. We also thank C. Fischer and the OCEARCH team for their support of this research. This work was funded by awards to C.D.B. from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology; the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution; and the National Aeronatics and Space Administration (NASA) Earth and Space Science Fellowship. C.D.B. and P.G. acknowledge support from the NASA New Investigator Program Award 80NSSC18K0757, and P.G. acknowledges support from NSF Award OCE-1558809. This research is partially supported by funding to S.R.T. as part of the Audacious Project, a collaborative endeavor, housed at TED. We thank donors to the Woods Hole Oceanographic Institution (WHOI) ProjectWHOI crowdfunding campaign: The Secret Lives of Sharks. Computational support was provided by the Amazon Web Services Cloud Credits for Research program. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Description: 2020-02-06
    Keywords: remote sensing ; oceanographic model ; satellite telemetry ; marine predator ; mesopelagic
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  • 34
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. 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 116 (35), (2019): 17207-17212, doi:10.1073/pnas.1900325116.
    Description: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of 〉80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.
    Description: Olivia M. J. Dagnaud assisted during fieldwork. S. V. Lalonde and E. A. Sperling provided helpful comments on an early version of the manuscript. We thank N. J. Planavsky and an anonymous reviewer for their constructive feedback. M.S.W.H. was supported by an NSERC PGS-D and student research grants from National Geographic, the APS Lewis and Clark Fund, Northern Science Training Program, McGill University Graduate Research Enhancement and Travel Awards, Geological Society of America, Mineralogical Association of Canada, and Stanford University. P.W.C. acknowledges support from the University of Colorado Boulder, the Agouron Institute Geobiology postdoctoral Fellowship program, a Natural Sciences and Engineering Council of Canada Postgraduate Scholarship–Doctoral Program scholarship, and the NSTP. Y.P. was supported by the Strategic Priority Research Program of CAS (XDB26000000). T.J.H. thanks Maureen E. Auro for laboratory assistance and the NSF for supporting isotope research in the NIRVANA Labs.
    Description: 2020-02-12
    Keywords: Proterozoic ; primary productivity ; Great Oxidation Event ; triple-oxygen isotopes ; nutrient limitation
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  • 35
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. 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 116(45), (2019): 22518-22525, doi:10.1073/pnas.1913714116.
    Description: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.
    Description: This work was funded by National Science Foundation Grants OCE-1401217 and COL-T354A55 to S.J.F. and OCE-1400805 to V.G. Graduate student participation in the project received support from University of Southern California Provost’s Fellowship to H.L. Samples were provided by the International Ocean Discovery Program. We are grateful for the efforts of the Expedition 354 Science Party, Carl Johnson, and Zongguang Liu. C.F.-L. and A.G. were supported by IODP-France. We thank Colin Osborne and Maria Vorontsova for helpful discussions.
    Description: 2020-04-21
    Keywords: carbon cycle ; wood ; lignin ; Himalaya ; Bengal Fan
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  • 36
    Publication Date: 2023-02-23
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 32(5) (2019): 1551-1571. doi:10.1175/JCLI-D-18-0444.1.
    Description: Previous studies have documented a poleward shift in the subsiding branches of Earth’s Hadley circulation since 1979 but have disagreed on the causes of these observed changes and the ability of global climate models to capture them. This synthesis paper reexamines a number of contradictory claims in the past literature and finds that the tropical expansion indicated by modern reanalyses is within the bounds of models’ historical simulations for the period 1979–2005. Earlier conclusions that models were underestimating the observed trends relied on defining the Hadley circulation using the mass streamfunction from older reanalyses. The recent observed tropical expansion has similar magnitudes in the annual mean in the Northern Hemisphere (NH) and Southern Hemisphere (SH), but models suggest that the factors driving the expansion differ between the hemispheres. In the SH, increasing greenhouse gases (GHGs) and stratospheric ozone depletion contributed to tropical expansion over the late twentieth century, and if GHGs continue increasing, the SH tropical edge is projected to shift further poleward over the twenty-first century, even as stratospheric ozone concentrations recover. In the NH, the contribution of GHGs to tropical expansion is much smaller and will remain difficult to detect in a background of large natural variability, even by the end of the twenty-first century. To explain similar recent tropical expansion rates in the two hemispheres, natural variability must be taken into account. Recent coupled atmosphere–ocean variability, including the Pacific decadal oscillation, has contributed to tropical expansion. However, in models forced with observed sea surface temperatures, tropical expansion rates still vary widely because of internal atmospheric variability.
    Description: We thank Ori Adam, Nick Davis, Isaac Held, Tim Merlis, Lorenzo Polvani, and one anonymous reviewer for helpful comments and suggestions. We thank U.S. CLIVAR and the International Space Science Institute (ISSI) for funding working groups that stimulated this project. We thank all members of the working groups for helpful discussions, and the U.S. CLIVAR and ISSI offices and their sponsoring agencies (NASA,NOAA,NSF,DOE, ESA, Swiss Confederation, Swiss Academy of Sciences, and University of Bern) for supporting these groups and activities.We acknowledge WCRP’sWorking Group on CoupledModelling, which is responsible for CMIP, and we thank the climate modeling groups (Table 2) for producing and making available their model output. For CMIP, the U.S. DOE PCMDI provides coordinating support and led development of software infrastructure in partnership with the Global Organization for Earth System Science Portals.
    Description: 2019-08-06
    Keywords: Hadley circulation ; Climate models ; Reanalysis data ; Multidecadal variability ; Pacific decadal oscillation ; Trends
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  • 37
    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 Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17666-17672. doi:10.1073/pnas.1907871116.
    Description: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.
    Description: We are indebted to J. Eckert for his support with FE-EMPA; to K. Aquinho and E. Codillo for providing samples from Zambales; to K. Aquinho for Raman analysis of some of the samples from Zambales and Mt. Dent; to H. Dick for providing access to his thin section collection; to the curators of the IODP core repositories for providing access to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) samples; and to the captains and crews of the many cruises without whom the collection of these samples would not have been possible. Reviews by Peter Kelemen and an anonymous referee greatly improved this manuscript. This study is supported with funds provided by the National Science Foundation (NSF-OCE Award 1634032 to F.K. and J.S.S.).
    Description: 2020-02-19
    Keywords: Abiotic methane ; Fluid inclusions ; Serpentinization ; Methane seeps ; Carbon cycling
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  • 38
    Publication Date: 2022-10-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It 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 116(20), (2019):9925-9930, doi:10.1073/pnas.1818349116.
    Description: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (〉30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.
    Description: We thank John Baross and Rika Anderson for helpful discussions and feedback on this project. We also thank the chief scientists of the research cruise, Al Devol and Bess Ward, as well as the captain and crew of the R/V Thomas G. Thompson. This work was supported through a NASA Earth and Space Sciences Graduate Research Fellowship to J.K.S. and National Science Foundation Grant OCE-1138368 (to G.R.).
    Description: 2019-10-29
    Keywords: Oxygen deficient zones ; Arsenic ; Chemoautotrophy ; Dissimilatory arsenate reduction ; Marine metagenome
    Repository Name: Woods Hole Open Access Server
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  • 39
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. 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 116 (24), (2019):11646-11651, doi:10.1073/pnas.1900371116.
    Description: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from pCO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.
    Description: We thank Rebecca Wright and Erik Buitenhuis at University of East Anglia, Norwich, for providing updated runs from the NEMO-PlankTOM5 model. T.D. was supported by NSF Grant OCE-1658392. C.L.Q. thanks the UK Natural Environment Research Council for supporting the SONATA Project (Grant NE/P021417/1). P.L. was supported by the Max Planck Society for the Advancement of Science. J.H. was supported under Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys) Grant VH-NG-1301. S.B. and R.S. were supported by the H2020 project CRESCENDO “Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach,” which received funding from the European Union’s Horizon 2020 research and innovation program under Grant No 641816. SOCAT is an international effort, endorsed by the International Ocean Carbon Coordination Project, the Surface Ocean-Lower Atmosphere Study, and the Integrated Marine Biosphere Research program, to deliver a uniformly quality-controlled surface ocean CO2 database. The many researchers and funding agencies responsible for the collection of data and quality control are thanked for their contributions to SOCAT.
    Description: 2019-11-28
    Keywords: Carbon dioxide ; Ocean carbon sink ; Terrestrial carbon sink ; Climate variability ; Carbon budget
    Repository Name: Woods Hole Open Access Server
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  • 40
    Publication Date: 2019-04-02
    Description: Bacteria are surrounded by a protective exoskeleton, peptidoglycan (PG), a cross-linked mesh-like macromolecule consisting of glycan strands interlinked by short peptides. Because PG completely encases the cytoplasmic membrane, cleavage of peptide cross-links is a prerequisite to make space for incorporation of nascent glycan strands for its successful expansion during cell growth. In most bacteria, the peptides consist of l-alanine, d-glutamate, meso-diaminopimelic acid (mDAP) and d-alanine (d-Ala) with cross-links occurring either between d-Ala and mDAP or two mDAP residues. In Escherichia coli, the d-Ala−mDAP cross-links whose cleavage by specialized endopeptidases is crucial for expansion of PG predominate. However, a small proportion of mDAP−mDAP cross-links also exist, yet their role in the context of PG expansion or the hydrolase(s) capable of catalyzing their cleavage is not known. Here, we identified an ORF of unknown function, YcbK (renamed MepK), as an mDAP−mDAP cross-link cleaving endopeptidase working in conjunction with other elongation-specific endopeptidases to make space for efficient incorporation of nascent PG strands into the sacculus. E. coli mutants lacking mepK and another d-Ala−mDAP–specific endopeptidase (mepS) were synthetic sick, and the defects were abrogated by lack of l,d-transpeptidases, enzymes catalyzing the formation of mDAP cross-links. Purified MepK was able to cleave the mDAP cross-links of soluble muropeptides and of intact PG sacculi. Overall, this study describes a PG hydrolytic enzyme with a hitherto unknown substrate specificity that contributes to expansion of the PG sacculus, emphasizing the fundamental importance of cross-link cleavage in bacterial peptidoglycan synthesis.
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  • 41
    Publication Date: 2019-11-12
    Description: As monofacial, single-junction solar cells approach their fundamental limits, there has been significant interest in tandem solar cells in the presence of concentrated sunlight or tandem bifacial solar cells with back-reflected albedo. The bandgap sequence and thermodynamic efficiency limits of these complex cell configurations require sophisticated numerical calculation. Therefore, the analyses of specialized cases are scattered throughout the literature. In this paper, we show that a powerful graphical approach called the normalized “Shockley–Queisser (S-Q) triangle” (i.e., imp=1−vmp) is sufficient to calculate the bandgap sequence and efficiency limits of arbitrarily complex photovoltaic (PV) topologies. The results are validated against a wide variety of specialized cases reported in the literature and are accurate within a few percent. We anticipate that the widespread use of the S-Q triangle will illuminate the deeper physical principles and design trade-offs involved in the design of bifacial tandem solar cells under arbitrary concentration and series resistance.
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  • 42
    Publication Date: 2019-02-14
    Description: Previous studies have shown that insulin and IGF-1 signaling in the brain, especially the hypothalamus, is important for regulation of systemic metabolism. Here, we develop mice in which we have specifically inactivated both insulin receptors (IRs) and IGF-1 receptors (IGF1Rs) in the hippocampus (Hippo-DKO) or central amygdala (CeA-DKO) by stereotaxic delivery of AAV-Cre into IRlox/lox/IGF1Rlox/loxmice. Consequently, both Hippo-DKO and CeA-DKO mice have decreased levels of the GluA1 subunit of glutamate AMPA receptor and display increased anxiety-like behavior, impaired cognition, and metabolic abnormalities, including glucose intolerance. Hippo-DKO mice also display abnormal spatial learning and memory whereas CeA-DKO mice have impaired cold-induced thermogenesis. Thus, insulin/IGF-1 signaling has common roles in the hippocampus and central amygdala, affecting synaptic function, systemic glucose homeostasis, behavior, and cognition. In addition, in the hippocampus, insulin/IGF-1 signaling is important for spatial learning and memory whereas insulin/IGF-1 signaling in the central amygdala controls thermogenesis via regulation of neural circuits innervating interscapular brown adipose tissue.
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  • 43
    Publication Date: 2019-06-17
    Description: The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.
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  • 44
    Publication Date: 2019-04-15
    Description: There is a gap between how many scientists communicate and how most people understand and interpret messages. This article argues that the extensive science communications literature needs to be joined by the health literacy literature and anthropological work on cultural variations in hearing and understanding messages. Rapid changes and differences in how people in the United States get information are also discussed. Better understanding of how people get and perceive messages, and how access to information and to health services affects their behavior, should be an iterative and interdisciplinary effort. Community involvement in developing communication strategies is strongly encouraged.
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  • 45
    Publication Date: 2019-09-30
    Description: Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
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  • 46
    Publication Date: 2019-09-16
    Description: Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a–tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.
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  • 47
    Publication Date: 2019-07-01
    Description: Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.
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  • 48
    Publication Date: 2019-08-21
    Description: Organic electrosynthesis can transform the chemical industry by introducing electricity-driven processes that are more energy efficient and that can be easily integrated with renewable energy sources. However, their deployment is severely hindered by the difficulties of controlling selectivity and achieving a large energy conversion efficiency at high current density due to the low solubility of organic reactants in practical electrolytes. This control can be improved by carefully balancing the mass transport processes and electrocatalytic reaction rates at the electrode diffusion layer through pulsed electrochemical methods. In this study, we explore these methods in the context of the electrosynthesis of adiponitrile (ADN), the largest organic electrochemical process in industry. Systematically exploring voltage pulses in the timescale between 5 and 150 ms led to a 20% increase in production of ADN and a 250% increase in relative selectivity with respect to the state-of-the-art constant voltage process. Moreover, combining this systematic experimental investigation with artificial intelligence (AI) tools allowed us to rapidly discover drastically improved electrosynthetic conditions, reaching improvements of 30 and 325% in ADN production rates and selectivity, respectively. This powerful AI-enhanced experimental approach represents a paradigm shift in the design of electrified chemical transformations, which can accelerate the deployment of more sustainable electrochemical manufacturing processes.
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  • 49
    Publication Date: 2019-04-08
    Description: In most environments, the visual system is confronted with many relevant objects simultaneously. That is especially true during reading. However, behavioral data demonstrate that a serial bottleneck prevents recognition of more than one word at a time. We used fMRI to investigate how parallel spatial channels of visual processing converge into a serial bottleneck for word recognition. Participants viewed pairs of words presented simultaneously. We found that retinotopic cortex processed the two words in parallel spatial channels, one in each contralateral hemisphere. Responses were higher for attended than for ignored words but were not reduced when attention was divided. We then analyzed two word-selective regions along the occipitotemporal sulcus (OTS) of both hemispheres (subregions of the visual word form area, VWFA). Unlike retinotopic regions, each word-selective region responded to words on both sides of fixation. Nonetheless, a single region in the left hemisphere (posterior OTS) contained spatial channels for both hemifields that were independently modulated by selective attention. Thus, the left posterior VWFA supports parallel processing of multiple words. In contrast, activity in a more anterior word-selective region in the left hemisphere (mid OTS) was consistent with a single channel, showing (i) limited spatial selectivity, (ii) no effect of spatial attention on mean response amplitudes, and (iii) sensitivity to lexical properties of only one attended word. Therefore, the visual system can process two words in parallel up to a late stage in the ventral stream. The transition to a single channel is consistent with the observed bottleneck in behavior.
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  • 50
    Publication Date: 2019-06-24
    Description: Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD is unknown. Histone H2B monoubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40, and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment 6.01,P= 1.67 × 10−03), some of whom had abnormal laterality associated with ciliary dysfunction. InXenopus, knockdown ofrnf20andrnf40results in abnormal heart looping, defective development of left–right (LR) asymmetry, and impaired cilia motility. Rnf20, Rnf40, and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level inXenopusembryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and nonciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factorRfx3. Rnf20 knockdown results in decreased levels ofrfx3mRNA inXenopus, and exogenousrfx3can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at theRfx3locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.
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  • 51
    Publication Date: 2019-12-16
    Description: Plasticity theory aims at describing the yield loci and work hardening of a material under general deformation states. Most of its complexity arises from the nontrivial dependence of the yield loci on the complete strain history of a material and its microstructure. This motivated 3 ingenious simplifications that underpinned a century of developments in this field: 1) yield criteria describing yield loci location; 2) associative or nonassociative flow rules defining the direction of plastic flow; and 3) effective stress–strain laws consistent with the plastic work equivalence principle. However, 2 key complications arise from these simplifications. First, finding equations that describe these 3 assumptions for materials with complex microstructures is not trivial. Second, yield surface evolution needs to be traced iteratively, i.e., through a return mapping algorithm. Here, we show that these assumptions are not needed in the context of sequence learning when using recurrent neural networks, diverting the above-mentioned complications. This work offers an alternative to currently established plasticity formulations by providing the foundations for finding history- and microstructure-dependent constitutive models through deep learning.
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  • 52
    Publication Date: 2019-08-12
    Description: Two-dimensional monolayer materials, with thicknesses of up to several atoms, can be obtained from almost every layer-structured material. It is believed that the catalogs of known 2D materials are almost complete, with fewer new graphene-like materials being discovered. Here, we report 2D graphene-like monolayers from monoxides such as BeO, MgO, CaO, SrO, BaO, and rock-salt structured monochlorides such as LiCl, and NaCl using first-principle calculations. Two-dimensional materials containing d-orbital atoms such as HfO, CdO, and AgCl are predicted. Adopting the same strategy, 2D graphene-like monolayers from mononitrides such as scandium nitride (ScN) and monoselenides such as cadmium selenide (CdSe) are discovered. Stress engineering is found to help stabilize 2D monolayers, through canceling the imaginary frequency of phonon dispersion relation. These 2D monolayers show high dynamic, thermal, kinetic, and mechanic stabilities due to atomic hybridization, and electronic delocalization.
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  • 53
    Publication Date: 2019-03-08
    Description: Materials that can be switched between low and high thermal conductivity states would advance the control and conversion of thermal energy. Employing in situ time-domain thermoreflectance (TDTR) and in situ synchrotron X-ray scattering, we report a reversible, light-responsive azobenzene polymer that switches between high (0.35 W m−1K−1) and low thermal conductivity (0.10 W m−1K−1) states. This threefold change in the thermal conductivity is achieved by modulation of chain alignment resulted from the conformational transition between planar (trans) and nonplanar (cis) azobenzene groups under UV and green light illumination. This conformational transition leads to changes in the π-π stacking geometry and drives the crystal-to-liquid transition, which is fully reversible and occurs on a time scale of tens of seconds at room temperature. This result demonstrates an effective control of the thermophysical properties of polymers by modulating interchain π-π networks by light.
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  • 54
    Publication Date: 2019-05-01
    Description: The Hippo pathway is involved in regulating contact inhibition of proliferation and organ size control and responds to various physical and biochemical stimuli. It is a kinase cascade that negatively regulates the activity of cotranscription factors YAP and TAZ, which interact with DNA binding transcription factors including TEAD and activate the expression of target genes. In this study, we show that the palmitoylation of TEAD, which controls the activity and stability of TEAD proteins, is actively regulated by cell density independent of Lats, the key kinase of the Hippo pathway. The expression of fatty acid synthase and acetyl-CoA carboxylase involved in de novo biosynthesis of palmitate is reduced by cell density in an Nf2/Merlin-dependent manner. Depalmitoylation of TEAD is mediated by depalmitoylases including APT2 and ABHD17A. Palmitoylation-deficient TEAD4 mutant is unstable and degraded by proteasome through the activity of the E3 ubiquitin ligase CHIP. These findings show that TEAD activity is tightly controlled through the regulation of palmitoylation and stability via the orchestration of FASN, depalmitoylases, and E3 ubiquitin ligase in response to cell contact.
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  • 55
    Publication Date: 2019-02-19
    Description: Foraging is a goal-directed behavior that balances the need to explore the environment for resources with the need to exploit those resources. InDrosophila melanogaster, distinct phenotypes have been observed in relation to theforaginggene (for), labeled the rover and sitter. Adult rovers explore their environs more extensively than do adult sitters. We explored whether this distinction would be conserved in humans. We made use of a distinction from regulatory mode theory between those who “get on with it,” so-called locomotors, and those who prefer to ensure they “do the right thing,” so-called assessors. In this logic, rovers and locomotors share similarities in goal pursuit, as do sitters and assessors. We showed that genetic variation inPRKG1, the human ortholog offor, is associated with preferential adoption of a specific regulatory mode. Next, participants performed a foraging task to see whether genetic differences associated with distinct regulatory modes would be associated with distinct goal pursuit patterns. Assessors tended to hug the boundary of the foraging environment, much like behaviors seen inDrosophilaadult sitters. In a patchy foraging environment, assessors adopted more cautious search strategies maximizing exploitation. These results show that distinct patterns of goal pursuit are associated with particular genotypes ofPRKG1, the human ortholog offor.
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  • 56
    Publication Date: 2019-09-23
    Description: Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here, we describe the sequence characteristics of mutations induced by ultraviolet (UV) light, a major mutagen in several human cancers, in terms of extended (longer than trinucleotide) patterns as well as variability of the signature across chromatin states. Promoter regions display a distinct UV signature with reduced TCG 〉 TTG transitions, and genome-wide mapping of UVB-induced DNA photoproducts (pyrimidine dimers) showed that this may be explained by decreased damage formation at hypomethylated promoter CpG sites. Further, an extended signature model encompassing additional information from longer contextual patterns improves modeling of UV mutations, which may enhance discrimination between drivers and passenger events. Our study presents a refined picture of the UV signature and underscores that the characteristics of a single mutational process may vary across the genome.
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  • 57
    Publication Date: 2019-02-27
    Description: Drugs that reverse epigenetic silencing, such as the DNA methyltransferase inhibitor (DNMTi) 5-azacytidine (AZA), have profound effects on transcription and tumor cell survival. AZA is an approved drug for myelodysplastic syndromes and acute myeloid leukemia, and is under investigation for different solid malignant tumors. AZA treatment generates self, double-stranded RNA (dsRNA), transcribed from hypomethylated repetitive elements. Self dsRNA accumulation in DNMTi-treated cells leads to type I IFN production and IFN-stimulated gene expression. Here we report that cell death in response to AZA treatment occurs through the 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway. OASs are IFN-induced enzymes that synthesize the RNase L activator 2-5A in response to dsRNA. Cells deficient in RNase L or OAS1 to 3 are highly resistant to AZA, as are wild-type cells treated with a small-molecule inhibitor of RNase L. A small-molecule inhibitor of c-Jun NH2-terminal kinases (JNKs) also antagonizes RNase L-dependent cell death in response to AZA, consistent with a role for JNK in RNase L-induced apoptosis. In contrast, the rates of AZA-induced and RNase L-dependent cell death were increased by transfection of 2-5A, by deficiencies in ADAR1 (which edits and destabilizes dsRNA), PDE12 or AKAP7 (which degrade 2-5A), or by ionizing radiation (which induces IFN-dependent signaling). Finally, OAS1 expression correlates with AZA sensitivity in the NCI-60 set of tumor cell lines, suggesting that the level of OAS1 can be a biomarker for predicting AZA sensitivity of tumor cells. These studies may eventually lead to pharmacologic strategies for regulating the antitumor activity and toxicity of AZA and related drugs.
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  • 58
    Publication Date: 2019-09-12
    Description: Analyses of thermal diffusivity data on complex insulators and on strongly correlated electron systems hosted in similar complex crystal structures suggest that quantum chaos is a good description for thermalization processes in these systems, particularly in the high-temperature regime where the many phonon bands and their interactions dominate the thermal transport. Here we observe that for these systems diffusive thermal transport is controlled by a universal Planckian timescale τ∼ℏ/kBT and a unique velocity vE. Specifically, vE≈vph for complex insulators, and vph≲vE≪vF in the presence of strongly correlated itinerant electrons (vph and vF are the phonon and electron velocities, respectively). For the complex correlated electron systems we further show that charge diffusivity, while also reaching the Planckian relaxation bound, is largely dominated by the Fermi velocity of the electrons, hence suggesting that it is only the thermal (energy) diffusivity that describes chaos diffusivity.
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  • 59
    Publication Date: 2019-03-12
    Description: SalmonellaTyphimurium can invade and survive within macrophages where the bacterium encounters a range of host environmental conditions. Like many bacteria,S.Typhimurium rapidly responds to changing environments by the use of second messengers such as cyclic di-GMP (c-di-GMP). Here, we generate a fluorescent biosensor to measure c-di-GMP concentrations in thousands of individual bacteria during macrophage infection and to define the sensor enzymes important to c-di-GMP regulation. Three sensor phosphodiesterases were identified as critical to maintaining low c-di-GMP concentrations generated after initial phagocytosis by macrophages. Maintenance of low c-di-GMP concentrations by these phosphodiesterases was required to promote survival within macrophages and virulence for mice. Attenuation ofS. Typhimurium virulence was due to overproduction of c-di-GMP−regulated cellulose, as deletion of the cellulose synthase machinery restored virulence to a strain lacking enzymatic activity of the three phosphodiesterases. We further identified that the cellulose-mediated reduction in survival was constrained to a slow-replicating persister population ofS.Typhimurium induced within the macrophage intracellular environment. As utilization of glucose has been shown to be required forS.Typhimurium macrophage survival, one possible hypothesis is that this persister population requires the glucose redirected to the synthesis of cellulose to maintain a slow-replicating, metabolically active state.
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  • 60
    Publication Date: 2019-05-24
    Description: IgA is the most abundantly produced antibody in the body and plays a crucial role in gut homeostasis and mucosal immunity. IgA forms a dimer that covalently associates with the joining (J) chain, which is essential for IgA transport into the mucosa. Here, we demonstrate that the marginal zone B and B-1 cell-specific protein (MZB1) interacts with IgA through the α-heavy-chain tailpiece dependent on the penultimate cysteine residue and prevents the intracellular degradation of α-light-chain complexes. Moreover, MZB1 promotes J-chain binding to IgA and the secretion of dimeric IgA. MZB1-deficient mice are impaired in secreting large amounts of IgA into the gut in response to acute inflammation and develop severe colitis. Oral administration of a monoclonal IgA significantly ameliorated the colitis, accompanied by normalization of the gut microbiota composition. The present study identifies a molecular chaperone that promotes J-chain binding to IgA and reveals an important mechanism that controls the quantity, quality, and function of IgA.
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  • 61
    Publication Date: 2019-02-25
    Description: Raindrop impact on infected plants can disperse micron-sized propagules of plant pathogens (e.g., spores of fungi). Little is known about the mechanism of how plant pathogens are liberated and transported due to raindrop impact. We used high-speed photography to observe thousands of dry-dispersed spores of the rust fungus Puccinia triticina being liberated from infected wheat plants following the impact of a single raindrop. We revealed that an air vortex ring was formed during the raindrop impact and carried the dry-dispersed spores away from the surface of the host plant. The maximum height and travel distance of the airborne spores increased with the aid of the air vortex. This unique mechanism of vortex-induced dispersal dynamics was characterized to predict trajectories of spores. Finally, we found that the spores transported by the air vortex can reach beyond the laminar boundary layer of leaves, which would enable the long-distance transport of plant pathogens through the atmosphere.
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  • 62
    Publication Date: 2019-11-18
    Description: The avian predentary is a small skeletal structure located rostral to the paired dentaries found only in Mesozoic ornithuromorphs. The evolution and function of this enigmatic element is unknown. Skeletal tissues forming the predentary and the lower jaws in the basal ornithuromorph Yanornis martini are identified using computed-tomography, scanning electron microscopy, and histology. On the basis of these data, we propose hypotheses for the development, structure, and function of this element. The predentary is composed of trabecular bone. The convex caudal surface articulates with rostromedial concavities on the dentaries. These articular surfaces are covered by cartilage, which on the dentaries is divided into 3 discrete patches: 1 rostral articular cartilage and 2 symphyseal cartilages. The mechanobiology of avian cartilage suggests both compression and kinesis were present at the predentary–dentary joint, therefore suggesting a yet unknown form of avian cranial kinesis. Ontogenetic processes of skeletal formation occurring within extant taxa do not suggest the predentary originates within the dentaries, nor Meckel’s cartilage. We hypothesize that the predentary is a biomechanically induced sesamoid that arose within the soft connective tissues located rostral to the dentaries. The mandibular canal hosting the alveolar nerve suggests that the dentary teeth and predentary of Yanornis were proprioceptive. This whole system may have increased foraging efficiency. The Mesozoic avian predentary apparently coevolved with an edentulous portion of the premaxilla, representing a unique kinetic morphotype that combined teeth with a small functional beak and persisted successfully for ∼60 million years.
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  • 63
    Publication Date: 2019-01-17
    Description: Human feet have evolved to facilitate bipedal locomotion, losing an opposable digit that grasped branches in favor of a longitudinal arch (LA) that stiffens the foot and aids bipedal gait. Passive elastic structures are credited with supporting the LA, but recent evidence suggests that plantar intrinsic muscles (PIMs) within the foot actively contribute to foot stiffness. To test the functional significance of the PIMs, we compared foot and lower limb mechanics with and without a tibial nerve block that prevented contraction of these muscles. Comparisons were made during controlled limb loading, walking, and running in healthy humans. An inability to activate the PIMs caused slightly greater compression of the LA when controlled loads were applied to the lower limb by a linear actuator. However, when greater loads were experienced during ground contact in walking and running, the stiffness of the LA was not altered by the block, indicating that the PIMs’ contribution to LA stiffness is minimal, probably because of their small size. With the PIMs blocked, the distal joints of the foot could not be stiffened sufficiently to provide normal push-off against the ground during late stance. This led to an increase in stride rate and compensatory power generated by the hip musculature, but no increase in the metabolic cost of transport. The results reveal that the PIMs have a minimal effect on the stiffness of the LA when absorbing high loads, but help stiffen the distal foot to aid push-off against the ground when walking or running bipedally.
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  • 64
    Publication Date: 2019-05-08
    Description: Scalable nanomanufacturing enables the commercialization of nanotechnology, particularly in applications such as nanophotonics, silicon photonics, photovoltaics, and biosensing. Nanoimprinting lithography (NIL) was the first scalable process to introduce 3D nanopatterning of polymeric films. Despite efforts to extend NIL’s library of patternable media, imprinting of inorganic semiconductors has been plagued by concomitant generation of crystallography defects during imprinting. Here, we use an electrochemical nanoimprinting process—called Mac-Imprint—for directly patterning electronic-grade silicon with 3D microscale features. It is shown that stamps made of mesoporous metal catalysts allow for imprinting electronic-grade silicon without the concomitant generation of porous silicon damage while introducing mesoscale roughness. Unlike most NIL processes, Mac-Imprint does not rely on plastic deformation, and thus, it allows for replicating hard and brittle materials, such as silicon, from a reusable polymeric mold, which can be manufactured by almost any existing microfabrication technique.
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  • 65
    Publication Date: 2019-12-10
    Description: Electrochemical reduction of CO2to multicarbon products is a significant challenge, especially for molecular complexes. We report here CO2reduction to multicarbon products based on a Ru(II) polypyridyl carbene complex that is immobilized on an N-doped porous carbon (RuPC/NPC) electrode. The catalyst utilizes the synergistic effects of the Ru(II) polypyridyl carbene complex and the NPC interface to steer CO2reduction toward C2 production at low overpotentials. In 0.5 M KHCO3/CO2aqueous solutions, Faradaic efficiencies of 31.0 to 38.4% have been obtained for C2 production at −0.87 to −1.07 V (vs. normal hydrogen electrode) with 21.0 to 27.5% for ethanol and 7.1 to 12.5% for acetate. Syngas is also produced with adjustable H2/CO mole ratios of 2.0 to 2.9. The RuPC/NPC electrocatalyst maintains its activity during 3-h CO2-reduction periods.
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  • 66
    Publication Date: 2019-06-24
    Description: We present a mechanism for the anomalous behavior of the specific heat in low-temperature amorphous solids. The analytic solution of a mean-field model belonging to the same universality class as high-dimensional glasses, the spherical perceptron, suggests that there exists a cross-over temperature above which the specific heat scales linearly with temperature, while below it, a cubic scaling is displayed. This relies on two crucial features of the phase diagram: (i) the marginal stability of the free-energy landscape, which induces a gapless phase responsible for the emergence of a power-law scaling; and (ii) the vicinity of the classical jamming critical point, as the cross-over temperature gets lowered when approaching it. This scenario arises from a direct study of the thermodynamics of the system in the quantum regime, where we show that, contrary to crystals, the Debye approximation does not hold.
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  • 67
    Publication Date: 2019-09-23
    Description: The condensation of half-light half-matter exciton polaritons in semiconductor optical cavities is a striking example of macroscopic quantum coherence in a solid-state platform. Quantum coherence is possible only when there are strong interactions between the exciton polaritons provided by their excitonic constituents. Rydberg excitons with high principal value exhibit strong dipole–dipole interactions in cold atoms. However, polaritons with the excitonic constituent that is an excited state, namely Rydberg exciton polaritons (REPs), have not yet been experimentally observed. Here, we observe the formation of REPs in a single crystal CsPbBr3 perovskite cavity without any external fields. These polaritons exhibit strong nonlinear behavior that leads to a coherent polariton condensate with a prominent blue shift. Furthermore, the REPs in CsPbBr3 are highly anisotropic and have a large extinction ratio, arising from the perovskite’s orthorhombic crystal structure. Our observation not only sheds light on the importance of many-body physics in coherent polariton systems involving higher-order excited states, but also paves the way for exploring these coherent interactions for solid-state quantum optical information processing.
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  • 68
    Publication Date: 2019-06-18
    Description: A major obstacle to vaccination against antigenically variable viruses is skewing of antibody responses to variable immunodominant epitopes. For influenza virus hemagglutinin (HA), the immunodominance of the variable head impairs responses to the highly conserved stem. Here, we show that head immunodominance depends on the physical attachment of head to stem. Stem immunogenicity is enhanced by immunizing with stem-only constructs or by increasing local HA concentration in the draining lymph node. Surprisingly, coimmunization of full-length HA and stem alters stem-antibody class switching. Our findings delineate strategies for overcoming immunodominance, with important implications for human vaccination.
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  • 69
    Publication Date: 2019-10-07
    Description: All cells, including nonexcitable cells, maintain a discrete transmembrane potential (Vmem), and have the capacity to modulate Vmem and respond to their own and neighbors’ changes in Vmem. Spatiotemporal variations have been described in developing embryonic tissues and in some cases have been implicated in influencing developmental processes. Yet, how such changes in Vmem are converted into intracellular inputs that in turn regulate developmental gene expression and coordinate patterned tissue formation, has remained elusive. Here we document that the Vmem of limb mesenchyme switches from a hyperpolarized to depolarized state during early chondrocyte differentiation. This change in Vmem increases intracellular Ca2+ signaling through Ca2+ influx, via CaV1.2, 1 of L-type voltage-gated Ca2+ channels (VGCCs). We find that CaV1.2 activity is essential for chondrogenesis in the developing limbs. Pharmacological inhibition by an L-type VGCC specific blocker, or limb-specific deletion of CaV1.2, down-regulates expression of genes essential for chondrocyte differentiation, including Sox9, Col2a1, and Agc1, and thus disturbs proper cartilage formation. The Ca2+-dependent transcription factor NFATc1, which is a known major transducer of intracellular Ca2+ signaling, partly rescues Sox9 expression. These data reveal instructive roles of CaV1.2 in limb development, and more generally expand our understanding of how modulation of membrane potential is used as a mechanism of developmental regulation.
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  • 70
    Publication Date: 2019-08-19
    Description: An important feature of human cognition is the ability to flexibly and efficiently adapt behavior in response to continuously changing contextual demands. We leverage a large-scale dataset from Lumosity, an online cognitive-training platform, to investigate how cognitive processes involved in cued switching between tasks are affected by level of task practice across the adult lifespan. We develop a computational account of task switching that specifies the temporal dynamics of activating task-relevant representations and inhibiting task-irrelevant representations and how they vary with extended task practice across a number of age groups. Practice modulates the level of activation of the task-relevant representation and improves the rate at which this information becomes available, but has little effect on the task-irrelevant representation. While long-term practice improves performance across all age groups, it has a greater effect on older adults. Indeed, extensive task practice can make older individuals functionally similar to less-practiced younger individuals, especially for cognitive measures that focus on the rate at which task-relevant information becomes available.
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  • 71
    Publication Date: 2019-12-06
    Description: The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.
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  • 72
    Publication Date: 2019-04-16
    Description: While studying spontaneous mutations at the maize bronze (bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new bz mutations from several Bz stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable bz mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous wx mutations [Wessler S (1997) The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linked sh locus. These events occurred with a frequency of 2–4 × 10−5 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like Hopscotch, Magellan, and Bs2, a Bs1 variant, were described previously; others, like Foto and Focou in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of Hopscotch, Magellan, and Bs2 occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
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  • 73
    Publication Date: 2019-07-24
    Description: A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
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  • 74
    Publication Date: 2019-07-24
    Description: Our understanding of the rotary-coupling mechanism of F1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkán-Kacsó and Marcus [S. Volkán-Kacsó, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed γ-rotation angle dependence of the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) exchange rates of F1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and Pi along a well-defined pathway.
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  • 75
    Publication Date: 2019-07-24
    Description: Eukaryotic cells express transcription factor (TF) paralogues that bind to nearly identical DNA sequences in vitro but bind at different genomic loci and perform different functions in vivo. Predicting how 2 paralogous TFs bind in vivo using DNA sequence alone is an important open problem. Here, we analyzed 2 yeast bHLH TFs, Cbf1p and Tye7p, which have highly similar binding preferences in vitro, yet bind at almost completely nonoverlapping target loci in vivo. We dissected the determinants of specificity for these 2 proteins by making a number of chimeric TFs in which we swapped different domains of Cbf1p and Tye7p and determined the effects on in vivo binding and cellular function. From these experiments, we learned that the Cbf1p dimer achieves its specificity by binding cooperatively with other Cbf1p dimers bound nearby. In contrast, we found that Tye7p achieves its specificity by binding cooperatively with 3 other DNA-binding proteins, Gcr1p, Gcr2p, and Rap1p. Remarkably, most promoters (63%) that are bound by Tye7p do not contain a consensus Tye7p binding site. Using this information, we were able to build simple models to accurately discriminate bound and unbound genomic loci for both Cbf1p and Tye7p. We then successfully reprogrammed the human bHLH NPAS2 to bind Cbf1p in vivo targets and a Tye7p target intergenic region to be bound by Cbf1p. These results demonstrate that the genome-wide binding targets of paralogous TFs can be discriminated using sequence information, and provide lessons about TF specificity that can be applied across the phylogenetic tree.
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  • 76
    Publication Date: 2019-02-04
    Description: Much contemporary rhetoric regards the prospects and pitfalls of using artificial intelligence techniques to automate an increasing range of tasks, especially those once considered the purview of people alone. These accounts are often wildly optimistic, understating outstanding challenges while turning a blind eye to the human labor that undergirds and sustains ostensibly “automated” services. This long-standing focus on purely automated methods unnecessarily cedes a promising design space: one in which computational assistance augments and enriches, rather than replaces, people’s intellectual work. This tension between human agency and machine automation poses vital challenges for design and engineering. In this work, we consider the design of systems that enable rich, adaptive interaction between people and algorithms. We seek to balance the often-complementary strengths and weaknesses of each, while promoting human control and skillful action. We share case studies of interactive systems we have developed in three arenas—data wrangling, exploratory analysis, and natural language translation—that integrate proactive computational support into interactive systems. To improve outcomes and support learning by both people and machines, we describe the use of shared representations of tasks augmented with predictive models of human capabilities and actions. We conclude with a discussion of future prospects and scientific frontiers for intelligence augmentation research.
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  • 77
    Publication Date: 2019-03-25
    Description: Phosphorylation of histone H2AX is a major contributor to efficient DNA repair. We recently reported neurobehavioral deficits in mice lacking H2AX. Here we establish that this neural failure stems from impairment of mitochondrial function and repression of the mitochondrial biogenesis gene PGC-1α. H2AX loss leads to reduced levels of the major subunits of the mitochondrial respiratory complexes in mouse embryonic fibroblasts and in the striatum, a brain region particularly vulnerable to mitochondrial damage. These defects are substantiated by disruption of the mitochondrial shape in H2AX mutant cells. Ectopic expression of PGC-1α restores mitochondrial oxidative phosphorylation complexes and mitigates cell death. H2AX knockout mice display increased neuronal death in the brain when challenged with 3-nitropronionic acid, which targets mitochondria. This study establishes a role for H2AX in mitochondrial homeostasis associated with neuroprotection.
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  • 78
    Publication Date: 2019-06-18
    Description: BRUCE/Apollon is a membrane-associated inhibitor of apoptosis protein that is essential for viability and has ubiquitin-conjugating activity. On initiation of apoptosis, the ubiquitin ligase Nrdp1/RNF41 promotes proteasomal degradation of BRUCE. Here we demonstrate that BRUCE together with the proteasome activator PA28γ causes proteasomal degradation of LC3-I and thus inhibits autophagy. LC3-I on the phagophore membrane is conjugated to phosphatidylethanolamine to form LC3-II, which is required for the formation of autophagosomes and selective recruitment of substrates. SIP/CacyBP is a ubiquitination-related protein that is highly expressed in neurons and various tumors. Under normal conditions, SIP inhibits the ubiquitination and degradation of BRUCE, probably by blocking the binding of Nrdp1 to BRUCE. On DNA damage by topoisomerase inhibitors, Nrdp1 causes monoubiquitination of SIP and thus promotes apoptosis. However, on starvation, SIP together with Rab8 enhances the translocation of BRUCE into the recycling endosome, formation of autophagosomes, and degradation of BRUCE by optineurin-mediated autophagy. Accordingly, deletion of SIP in cultured cells reduces the autophagic degradation of damaged mitochondria and cytosolic protein aggregates. Thus, by stimulating proteasomal degradation of LC3-I, BRUCE also inhibits autophagy. Conversely, SIP promotes autophagy by blocking BRUCE-dependent degradation of LC3-I and by enhancing autophagosome formation and autophagic destruction of BRUCE. These actions of BRUCE and SIP represent mechanisms that link the regulation of autophagy and apoptosis under different conditions.
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  • 79
    Publication Date: 2019-01-11
    Description: Coordinated dynamics of individual components in active matter are an essential aspect of life on all scales. Establishing a comprehensive, causal connection between intracellular, intercellular, and macroscopic behaviors has remained a major challenge due to limitations in data acquisition and analysis techniques suitable for multiscale dynamics. Here, we combine a high-throughput adaptive microscopy approach with machine learning, to identify key biological and physical mechanisms that determine distinct microscopic and macroscopic collective behavior phases which develop as Bacillus subtilis swarms expand over five orders of magnitude in space. Our experiments, continuum modeling, and particle-based simulations reveal that macroscopic swarm expansion is primarily driven by cellular growth kinetics, whereas the microscopic swarming motility phases are dominated by physical cell–cell interactions. These results provide a unified understanding of bacterial multiscale behavioral complexity in swarms.
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  • 80
    Publication Date: 2019-05-03
    Description: The quantum Hall effect has recently been generalized from transport of conserved charges to include transport of other approximately conserved-state variables, including spin and valley, via spin- or valley-polarized boundary states with different chiralities. Here, we report a class of quantum Hall effect in Bernal- or ABA-stacked trilayer graphene (TLG), the quantum parity Hall (QPH) effect, in which boundary channels are distinguished by even or odd parity under the system’s mirror reflection symmetry. At the charge neutrality point, the longitudinal conductance σxx is first quantized to 4e2/h at a small perpendicular magnetic field B⊥, establishing the presence of four edge channels. As B⊥ increases, σxx first decreases to 2e2/h, indicating spin-polarized counterpropagating edge states, and then, to approximately zero. These behaviors arise from level crossings between even- and odd-parity bulk Landau levels driven by exchange interactions with the underlying Fermi sea, which favor an ordinary insulator ground state in the strong B⊥ limit and a spin-polarized state at intermediate fields. The transitions between spin-polarized and -unpolarized states can be tuned by varying Zeeman energy. Our findings demonstrate a topological phase that is protected by a gate-controllable symmetry and sensitive to Coulomb interactions.
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  • 81
    Publication Date: 2019-02-28
    Description: The Hedgehog-signaling pathway is an important target in cancer research and regenerative medicine; yet, on the cellular level, many steps are still poorly understood. Extensive studies of the bulk behavior of the key proteins in the pathway established that during signal transduction they dynamically localize in primary cilia, antenna-like solitary organelles present on most cells. The secreted Hedgehog ligand Sonic Hedgehog (SHH) binds to its receptor Patched1 (PTCH1) in primary cilia, causing its inactivation and delocalization from cilia. At the same time, the transmembrane protein Smoothened (SMO) is released of its inhibition by PTCH1 and accumulates in cilia. We used advanced, single molecule-based microscopy to investigate these processes in live cells. As previously observed for SMO, PTCH1 molecules in cilia predominantly move by diffusion and less frequently by directional transport, and spend a fraction of time confined. After treatment with SHH we observed two major changes in the motional dynamics of PTCH1 in cilia. First, PTCH1 molecules spend more time as confined, and less time freely diffusing. This result could be mimicked by a depletion of cholesterol from cells. Second, after treatment with SHH, but not after cholesterol depletion, the molecules that remain in the diffusive state showed a significant increase in the diffusion coefficient. Therefore, PTCH1 inactivation by SHH changes the diffusive motion of PTCH1, possibly by modifying the membrane microenvironment in which PTCH1 resides.
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  • 82
    Publication Date: 2019-05-30
    Description: We introduce a mathematical framework that allows one to carry out multiscalar and multigroup spatial exploratory analysis across urban regions. By producing coefficients that integrate information across all scales and that are normalized with respect to theoretical maximally segregated configurations, this framework provides a practical and powerful tool for the comparative empirical analysis of urban segregation. We illustrate our method with a study of ethnic mixing in the Los Angeles metropolitan area.
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  • 83
    Publication Date: 2019-04-19
    Description: Graphene-based nanodevices have been developed rapidly and are now considered a strong contender for postsilicon electronics. However, one challenge facing graphene-based transistors is opening a sizable bandgap in graphene. The largest bandgap achieved so far is several hundred meV in bilayer graphene, but this value is still far below the threshold for practical applications. Through in situ electrical measurements, we observed a semiconducting character in compressed trilayer graphene by tuning the interlayer interaction with pressure. The optical absorption measurements demonstrate that an intrinsic bandgap of 2.5 ± 0.3 eV could be achieved in such a semiconducting state, and once opened could be preserved to a few GPa. The realization of wide bandgap in compressed trilayer graphene offers opportunities in carbon-based electronic devices.
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  • 84
    Publication Date: 2019-01-17
    Description: Shape, size, and composition are the most fundamental design features, enabling highly complex functionalities. Despite recent advances, the independent control of shape, size, and chemistry of macromolecules remains a synthetic challenge. We report a scalable methodology to produce large, well-defined macromolecules with programmable shape, size, and chemistry that combines reactor engineering principles and controlled polymerizations. Specifically, bottlebrush polymers with conical, ellipsoidal, and concave architectures are synthesized using two orthogonal polymerizations. The chemical versatility is highlighted by the synthesis of a compositional asymmetric cone. The strong agreement between predictions and experiments validates the precision that this methodology offers.
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  • 85
    Publication Date: 2019-05-30
    Description: Neural stem cells (NSCs) are primary progenitor cells in the early developmental stage in the brain that initiate a diverse lineage of differentiated neurons and glia. Radial glial cells (RGCs), a type of neural stem cell in the ventricular zone, are essential for nurturing and delivering new immature neurons to the appropriate cortical target layers. Here we report that Anoctamin 1 (ANO1)/TMEM16A, a Ca2+-activated chloride channel, mediates the Ca2+-dependent process extension of RGCs. ANO1 is highly expressed and functionally active in RGCs of the mouse embryonic ventricular zone. Knockdown of ANO1 suppresses RGC process extension and protrusions, whereas ANO1 overexpression stimulates process extension. Among various trophic factors, brain-derived neurotrophic factor (BDNF) activates ANO1, which is required for BDNF-induced process extension in RGCs. More importantly, Ano1-deficient mice exhibited disrupted cortical layers and reduced cortical thickness. We thus conclude that the regulation of RGC process extension by ANO1 contributes to the normal formation of mouse embryonic brain.
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  • 86
    Publication Date: 2019-06-12
    Description: Ion exchange, as a postsynthetic transformation strategy, offers more flexibilities in controlling material compositions and structures beyond direct synthetic methodology. Observation of such transformation kinetics on the single-particle level with rich spatial and spectroscopic information has never been achieved. We report the quantitative imaging of anion exchange kinetics in individual single-crystalline halide perovskite nanoplates using confocal photoluminescence microscopy. We have systematically observed a symmetrical anion exchange pathway on the nanoplates with dependence on reaction time and plate thickness, which is governed by the crystal structure and the diffusion-limited transformation mechanism. Based on a reaction–diffusion model, the halide diffusion coefficient was estimated to be on the order of10−14cm2⋅s−1. This diffusion-controlled mechanism leads to the formation of 2D perovskite heterostructures with spatially resolved coherent interface through the precisely controlled anion exchange reaction, offering a design protocol for tailoring functionalities of semiconductors at the nano-/microscale.
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  • 87
    Publication Date: 2019-02-06
    Description: Successful efforts to activate T cells capable of recognizing weak cancer-associated self-antigens have employed altered peptide antigens to activate T cell responses capable of cross-reacting on native tumor-associated self. A limitation of this approach is the requirement for detailed knowledge about the altered self-peptide ligands used in these vaccines. In the current study we considered allorecognition as an approach for activating CTL capable of recognizing weak or self-antigens in the context of self-MHC. Nonself antigen-presenting molecules typically contain polymorphisms that influence interactions with the bound peptide and TCR interface. Recognition of these nonself structures results in peptide-dependent alloimmunity. Alloreactive T cells target their inducing alloantigens as well as third-party alloantigens but generally fail to target self-antigens. Certain residues located on the alpha-1/2 domains of class I antigen-presenting molecules primarily interface with TCR. These residues are more conserved within and across species than are residues that determine peptide antigen binding properties. Class I variants designed with amino acid substitutions at key positions within the conserved helical structures are shown to provide strong activating signals to alloreactive CD8 T cells while avoiding changes in naturally bound peptide ligands. Importantly, CTL activated in this manner can break self-tolerance by reacting to self-peptides presented by native MHC. The ability to activate self-tolerant T cells capable of cross-reacting on self-peptide-MHC in vivo represents an approach for inducing autoimmunity, with possible application in cancer vaccines.
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  • 88
    Publication Date: 2019-10-09
    Description: Episodic memories hinge upon our ability to process a wide range of multisensory information and bind this information into a coherent, memorable representation. On a neural level, these 2 processes are thought to be supported by neocortical alpha/beta desynchronization and hippocampal theta/gamma synchronization, respectively. Intuitively, these 2 processes should couple to successfully create and retrieve episodic memories, yet this hypothesis has not been tested empirically. We address this by analyzing human intracranial electroencephalogram data recorded during 2 associative memory tasks. We find that neocortical alpha/beta (8 to 20 Hz) power decreases reliably precede and predict hippocampal “fast” gamma (60 to 80 Hz) power increases during episodic memory formation; during episodic memory retrieval, however, hippocampal “slow” gamma (40 to 50 Hz) power increases reliably precede and predict later neocortical alpha/beta power decreases. We speculate that this coupling reflects the flow of information from the neocortex to the hippocampus during memory formation, and hippocampal pattern completion inducing information reinstatement in the neocortex during memory retrieval.
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  • 89
    Publication Date: 2019-10-14
    Description: Human cells express up to 9 active DNA cytosine deaminases with functions in adaptive and innate immunity. Many cancers manifest an APOBEC mutation signature and APOBEC3B (A3B) is likely the main enzyme responsible. Although significant numbers of APOBEC signature mutations accumulate in tumor genomes, the majority of APOBEC-catalyzed uracil lesions are probably counteracted in an error-free manner by the uracil base excision repair pathway. Here, we show that A3B-expressing cells can be selectively killed by inhibiting uracil DNA glycosylase 2 (UNG) and that this synthetic lethal phenotype requires functional mismatch repair (MMR) proteins and p53. UNG knockout human 293 and MCF10A cells elicit an A3B-dependent death. This synthetic lethal phenotype is dependent on A3B catalytic activity and reversible by UNG complementation. A3B expression in UNG-null cells causes a buildup of genomic uracil, and the ensuing lethality requires processing of uracil lesions (likely U/G mispairs) by MSH2 and MLH1 (likely noncanonical MMR). Cancer cells expressing high levels of endogenous A3B and functional p53 can also be killed by expressing an UNG inhibitor. Taken together, UNG-initiated base excision repair is a major mechanism counteracting genomic mutagenesis by A3B, and blocking UNG is a potential strategy for inducing the selective death of tumors.
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  • 90
    Publication Date: 2019-10-07
    Description: Antibiotics induce large and highly variable changes in the intestinal microbiome even at sublethal concentrations, through mechanisms that remain elusive. Using gnotobiotic zebrafish, which allow high-resolution examination of microbial dynamics, we found that sublethal doses of the common antibiotic ciprofloxacin cause severe drops in bacterial abundance. Contrary to conventional views of antimicrobial tolerance, disruption was more pronounced for slow-growing, aggregated bacteria than for fast-growing, planktonic species. Live imaging revealed that antibiotic treatment promoted bacterial aggregation and increased susceptibility to intestinal expulsion. Intestinal mechanics therefore amplify the effects of antibiotics on resident bacteria. Microbial dynamics are captured by a biophysical model that connects antibiotic-induced collapses to gelation phase transitions in soft materials, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.
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  • 91
    Publication Date: 2019-11-11
    Description: Receptor-activity–modifying proteins (RAMPs) are single transmembrane-spanning proteins which serve as molecular chaperones and allosteric modulators of G-protein–coupled receptors (GPCRs) and their signaling pathways. Although RAMPs have been previously studied in the context of their effects on Family B GPCRs, the coevolution of RAMPs with many GPCR families suggests an expanded repertoire of potential interactions. Using bioluminescence resonance energy transfer-based and cell-surface expression approaches, we comprehensively screen for RAMP interactions within the chemokine receptor family and identify robust interactions between RAMPs and nearly all chemokine receptors. Most notably, we identify robust RAMP interaction with atypical chemokine receptors (ACKRs), which function to establish chemotactic gradients for directed cell migration. Specifically, RAMP3 association with atypical chemokine receptor 3 (ACKR3) diminishes adrenomedullin (AM) ligand availability without changing G-protein coupling. Instead, RAMP3 is required for the rapid recycling of ACKR3 to the plasma membrane through Rab4-positive vesicles following either AM or SDF-1/CXCL12 binding, thereby enabling formation of dynamic spatiotemporal chemotactic gradients. Consequently, genetic deletion of either ACKR3 or RAMP3 in mice abolishes directed cell migration of retinal angiogenesis. Thus, RAMP association with chemokine receptor family members represents a molecular interaction to control receptor signaling and trafficking properties.
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  • 92
    Publication Date: 2019-10-14
    Description: KRAS mutations occur in ∼35% of colorectal cancers and promote tumor growth by constitutively activating the mitogen-activated protein kinase (MAPK) pathway. KRAS mutations at codons 12, 13, or 61 are thought to prevent GAP protein-stimulated GTP hydrolysis and render KRAS-mutated colorectal cancers unresponsive to epidermal growth factor receptor (EGFR) inhibitors. We report here that KRAS G13-mutated cancer cells are frequently comutated with NF1 GAP but NF1 is rarely mutated in cancers with KRAS codon 12 or 61 mutations. Neurofibromin protein (encoded by the NF1 gene) hydrolyzes GTP directly in complex with KRAS G13D, and KRAS G13D-mutated cells can respond to EGFR inhibitors in a neurofibromin-dependent manner. Structures of the wild type and G13D mutant of KRAS in complex with neurofibromin (RasGAP domain) provide the structural basis for neurofibromin-mediated GTP hydrolysis. These results reveal that KRAS G13D is responsive to neurofibromin-stimulated hydrolysis and suggest that a subset of KRAS G13-mutated colorectal cancers that are neurofibromin-competent may respond to EGFR therapies.
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  • 93
    Publication Date: 2019-11-18
    Description: Oil and gas well leakage is of public concern primarily due to the perceived risks of aquifer contamination and greenhouse gas (GHG) emissions. This study examined well leakage data from the British Columbia Oil and Gas Commission (BC OGC) to identify leakage pathways and initially quantify incident rates of leakage and GHG emissions from leaking wells. Three types of leakage are distinguished: “surface casing vent flow” (SCVF), “outside the surface casing leakage” (OSCL), and “cap leakage” (CL). In British Columbia (BC), the majority of reported incidents involve SCVF of gases, which does not pose a risk of aquifer contamination but does contribute to GHG emissions. Reported liquid leakage of brines and hydrocarbons is rarer. OSCL and CL of gas are more serious problems due to the risk of long-term leakage from abandoned wells; some were reported to be leaking gas several decades after they were permanently abandoned. According to the requirements of provincial regulation, 21,525 have been tested for leakage. In total, 2,329 wells in BC have had reported leakage during the lifetime of the well. This represents 10.8% of all wells in the assumed test population. However, it seems likely that wells drilled and/or abandoned before 2010 have unreported leakage. In BC, the total GHG emission from gas SCVF is estimated to reach about 75,000 t/y based on the existing inventory calculation; however, this number is likely higher due to underreporting.
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  • 94
    Publication Date: 2019-05-29
    Description: The primary cilium permits compartmentalization of specific signaling pathways, including elements of the Hedgehog (Hh) pathway. Hh transcriptional activity is thought to be negatively regulated by constitutively high ciliary cAMP maintained by the Gα(s)-coupled GPCR, GPR161. However, cilia also sequester many other Gα(s)-coupled GPCRs with unknown potential to regulate Hh. Here we used biosensors optimized for ciliary cAMP and strategies to isolate signals in the cilium from the cell body and neighboring cells. We found that ciliary cAMP was not elevated relative to cellular cAMP, inconsistent with constitutive cAMP production. Gα(s)-coupled GPCRs (e.g., the 5-HT6 serotonin and D1R dopamine receptor) had reduced ability to generate cAMP upon trafficking to the ciliary membrane. However, activation of the Hh pathway restored or amplified GPCR function to permit cAMP elevation selectively in the cilium. Hh therefore enables its own local GPCR-dependent cAMP regulatory circuit. Considering that GPCRs comprise much of the druggable genome, these data suggest alternative strategies to modify Hh signaling.
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  • 95
    Publication Date: 2019-09-11
    Description: The elucidation of the detailed mechanism used by F0 to convert proton gradient to torque and rotational motion presents a major puzzle despite significant biophysical and structural progress. Although the conceptual model has advanced our understanding of the working principles of such systems, it is crucial to explore the actual mechanism using structure-based models that actually reproduce a unidirectional proton-driven rotation. Our previous work used a coarse-grained (CG) model to simulate the action of F0. However, the simulations were based on a very tentative structural model of the interaction between subunit a and subunit c. Here, we again use a CG model but with a recent cryo-EM structure of cF1F0 and also explore the proton path using our water flooding and protein dipole Langevin dipole semimacroscopic formalism with its linear response approximation version (PDLD/S-LRA) approaches. The simulations are done in the combined space defined by the rotational coordinate and the proton transport coordinate. The study reproduced the effect of the protomotive force on the rotation of the F0 while establishing the electrostatic origin of this effect. Our landscape reproduces the correct unidirectionality of the synthetic direction of the F0 rotation and shows that it reflects the combined electrostatic coupling between the proton transport path and the c-ring conformational change. This work provides guidance for further studies in other proton-driven mechanochemical systems and should lead (when combined with studies of F1) to a complete energy transduction picture of the F0F1-ATPase system.
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  • 96
    Publication Date: 2019-03-08
    Description: Apicomplexan parasites replicate within a protective organelle, called the parasitophorous vacuole (PV). TheToxoplasma gondiiPV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the network’s functions. Here, we identify the parasite-secreted kinase WNG1 (With-No-Gly-loop) as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATP-binding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several of which are essential for the formation of a functional intravacuolar network. Moreover, we show that WNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family ofToxoplasmakinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV development during parasite infection.
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  • 97
    Publication Date: 2019-01-23
    Description: Pre-mRNA splicing must occur with extremely high fidelity. Spliceosomes assemble onto pre-mRNA guided by specific sequences (5′ splice site, 3′ splice site, and branchpoint). When splice sites are mutated, as in many hereditary diseases, the spliceosome can aberrantly select nearby pseudo- or “cryptic” splice sites, often resulting in nonfunctional protein. How the spliceosome distinguishes authentic splice sites from cryptic splice sites is poorly understood. We performed aCaenorhabditis elegansgenetic screen to find cellular factors that affect the frequency with which the spliceosome uses cryptic splice sites and identified two alleles in core spliceosome component Prp8 that alter cryptic splicing frequency. Subsequent complementary genetic and structural analyses in yeast implicate these alleles in the stability of the spliceosome’s catalytic core. However, despite a clear effect on cryptic splicing, high-throughput mRNA sequencing of theseprp-8mutantC. elegansreveals that overall alternative splicing patterns are relatively unchanged. Our data suggest the spliceosome evolved intrinsic mechanisms to reduce the occurrence of cryptic splicing and that these mechanisms are distinct from those that impact alternative splicing.
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  • 98
    Publication Date: 2019-08-13
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  • 99
    Publication Date: 2019-04-08
    Description: Kirigami-inspired metamaterials are attracting increasing interest because of their ability to achieve extremely large strains and shape changes via out-of-plane buckling. While in flat kirigami sheets, the ligaments buckle simultaneously as Euler columns, leading to a continuous phase transition; here, we demonstrate that kirigami shells can also support discontinuous phase transitions. Specifically, we show via a combination of experiments, numerical simulations, and theoretical analysis that, in cylindrical kirigami shells, the snapping-induced curvature inversion of the initially bent ligaments results in a pop-up process that first localizes near an imperfection and then, as the deformation is increased, progressively spreads through the structure. Notably, we find that the width of the transition zone as well as the stress at which propagation of the instability is triggered can be controlled by carefully selecting the geometry of the cuts and the curvature of the shell. Our study significantly expands the ability of existing kirigami metamaterials and opens avenues for the design of the next generation of responsive surfaces as demonstrated by the design of a smart skin that significantly enhances the crawling efficiency of a simple linear actuator.
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  • 100
    Publication Date: 2019-12-16
    Description: Kirigami (cutting and/or folding) offers a promising strategy to reconfigure metamaterials. Conventionally, kirigami metamaterials are often composed of passive cut unit cells to be reconfigured under mechanical forces. The constituent stimuli-responsive materials in active kirigami metamaterials instead will enable potential mechanical properties and functionality, arising from the active control of cut unit cells. However, the planar features of hinges in conventional kirigami structures significantly constrain the degrees of freedom (DOFs) in both deformation and actuation of the cut units. To release both constraints, here, we demonstrate a universal design of implementing folds to reconstruct sole-cuts–based metamaterials. We show that the supplemented folds not only enrich the structural reconfiguration beyond sole cuts but also enable more DOFs in actuating the kirigami metasheets into 3 dimensions (3D) in response to environmental temperature. Utilizing the multi-DOF in deformation of unit cells, we demonstrate that planar metasheets with the same cut design can self-fold into programmable 3D kirigami metastructures with distinct mechanical properties. Last, we demonstrate potential applications of programmable kirigami machines and easy-turning soft robots.
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