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  • Genetics  (74)
  • Climate
  • Southern Ocean
  • American Association for the Advancement of Science (AAAS)  (84)
  • Frontiers Media  (8)
  • 2020-2022
  • 2015-2019  (92)
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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.
    Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.
    Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).
    Keywords: Jellyfish bloom ; Genetics ; Acoustics ; Nanomia ; North Norwegian fjords ; Gelatinous zooplankton
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  • 2
    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 Sloyan, B. M., Wilkin, J., Hill, K. L., Chidichimo, M. P., Cronin, M. F., Johannessen, J. A., Karstensen, J., Krug, M., Lee, T., Oka, E., Palmer, M. D., Rabe, B., Speich, S., von Schuckmann, K., Weller, R. A., & Yu, W. Evolving the physical global ocean observing system for research and application services through international coordination. Frontiers in Marine Science, 6, (2019): 449, doi:10.3389/fmars.2019.00449.
    Description: Climate change and variability are major societal challenges, and the ocean is an integral part of this complex and variable system. Key to the understanding of the ocean’s role in the Earth’s climate system is the study of ocean and sea-ice physical processes, including its interactions with the atmosphere, cryosphere, land, and biosphere. These processes include those linked to ocean circulation; the storage and redistribution of heat, carbon, salt and other water properties; and air-sea exchanges of heat, momentum, freshwater, carbon, and other gasses. Measurements of ocean physics variables are fundamental to reliable earth prediction systems for a range of applications and users. In addition, knowledge of the physical environment is fundamental to growing understanding of the ocean’s biogeochemistry and biological/ecosystem variability and function. Through the progress from OceanObs’99 to OceanObs’09, the ocean observing system has evolved from a platform centric perspective to an integrated observing system. The challenge now is for the observing system to evolve to respond to an increasingly diverse end user group. The Ocean Observations Physics and Climate panel (OOPC), formed in 1995, has undertaken many activities that led to observing system-related agreements. Here, OOPC will explore the opportunities and challenges for the development of a fit-for-purpose, sustained and prioritized ocean observing system, focusing on physical variables that maximize support for fundamental research, climate monitoring, forecasting on different timescales, and society. OOPC recommendations are guided by the Framework for Ocean Observing which emphasizes identifying user requirements by considering time and space scales of the Essential Ocean Variables. This approach provides a framework for reviewing the adequacy of the observing system, looking for synergies in delivering an integrated observing system for a range of applications and focusing innovation in areas where existing technologies do not meet these requirements.
    Description: BS received support from the Centre for Southern Hemisphere Oceans Research, a collaboration between the CSIRO and the Qingdao National Laboratory for Marine Science and Technology and the Australian Government Department of the Environment and CSIRO through the Australian Climate Change Science Programme and by the National Environmental Science Program. JK was supported by the European Union’s Horizon 2020 Research and Innovation Programme under the grant agreement no. 633211 (AtlantOS). MP was supported by the Met Office Hadley Centre Climate Programme funded by the BEIS and Defra. SS was supported by the Ecole Normale Supérieure, CNRS, and Ifremer funded by the European Union’s Horizon 2020 Research and Innovation Programme under the grant agreement no. 633211 (AtlantOS), CNES, and ANR grants.
    Keywords: Observing system evaluation ; Observing system design ; Sustained observations ; Observing networks ; Observation platforms ; Climate ; Weather ; Operational services
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  • 3
    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 Benway, H. M., Lorenzoni, L., White, A. E., Fiedler, B., Levine, N. M., Nicholson, D. P., DeGrandpre, M. D., Sosik, H. M., Church, M. J., O'Brien, T. D., Leinen, M., Weller, R. A., Karl, D. M., Henson, S. A., & Letelier, R. M. Ocean time series observations of changing marine ecosystems: An era of integration, synthesis, and societal applications. Frontiers in Marine Science, 6, (2019): 393, doi:10.3389/fmars.2019.00393.
    Description: Sustained ocean time series are critical for characterizing marine ecosystem shifts in a time of accelerating, and at times unpredictable, changes. They represent the only means to distinguish between natural and anthropogenic forcings, and are the best tools to explore causal links and implications for human communities that depend on ocean resources. Since the inception of sustained ocean observations, ocean time series have withstood many challenges, most prominently availability of uninterrupted funding and retention of trained personnel. This OceanObs’19 review article provides an overarching vision for sustained ocean time series observations for the next decade, focusing on the growing challenges of maintaining sustained ocean time series, including ship-based and autonomous coastal and open-ocean platforms, as well as remote sensing. In addition to increased diversification of funding sources to include the private sector, NGOs, and other groups, more effective engagement of stakeholders and other end-users will be critical to ensure the sustainability of ocean time series programs. Building a cohesive international time series network will require dedicated capacity to coordinate across observing programs and leverage existing infrastructure and platforms of opportunity. This review article outlines near-term observing priorities and technology needs; explores potential mechanisms to broaden ocean time series data applications and end-user communities; and describes current tools and future requirements for managing increasingly complex multi-platform data streams and developing synthesis products that support science and society. The actionable recommendations outlined herein ultimately form the basis for a robust, sustainable, fit-for-purpose time series network that will foster a predictive understanding of changing ocean systems for the benefit of society.
    Description: This work was led by HB in the Ocean Carbon and Biogeochemistry (OCB) Project Office, which is supported by the NSF OCE (1558412) and the NASA (NNX17AB17G).
    Keywords: Ocean time series ; Marine ecosystems ; Climate ; End-users ; Synthesis ; Sustained observations
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  • 4
    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 Capotondi, A., Jacox, M., Bowler, C., Kavanaugh, M., Lehodey, P., Barrie, D., Brodie, S., Chaffron, S., Cheng, W., Dias, D. F., Eveillard, D., Guidi, L., Iudicone, D., Lovenduski, N. S., Nye, J. A., Ortiz, I., Pirhalla, D., Buil, M. P., Saba, V., Sheridan, S., Siedlecki, S., Subramanian, A., de Vargas, C., Di Lorenzo, E., Doney, S. C., Hermann, A. J., Joyce, T., Merrifield, M., Miller, A. J., Not, F., & Pesant, S. Observational needs supporting marine ecosystems modeling and forecasting: from the global ocean to regional and coastal systems. Frontiers in Marine Science, 6, (2019): 623, doi:10.3389/fmars.2019.00623.
    Description: Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.
    Description: This study was supported by the NOAA’s Climate Program Office’s Modeling, Analysis, Predictions, and Projections (MAPP) Program through grants NA17OAR4310106, NA17OAR4310104, NA17OAR4310108, NA17OAR4310109, NA17OAR4310110, NA17OAR4310111, NA17OAR4310112, and NA17OAR4310113. This manuscript is a product of the NOAA/MAPP Marine Prediction Task Force. The Tara Oceans consortium acknowledges support from the CNRS Research Federation FR2022 Global Ocean Systems Ecology and Evolution, and OCEANOMICS (grant agreement ‘Investissement d’Avenir’ ANR-11-BTBR-0008). This is article number 95 of the Tara Oceans consortium. MK and SD acknowledge support from NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the NOAA Integrated Ocean Observing System (IOOS) Program Office. WC, IO, and AH acknowledge partial support from the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063, Contribution No. 2019-1029. This study received support from the European H2020 International Cooperation project MESOPP (Mesopelagic Southern Ocean Prey and Predators), grant agreement no. 692173.
    Keywords: Marine ecosystems ; Modeling and forecasting ; Seascapes ; Genetics ; Acoustics
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  • 5
    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 Newman, L., Heil, P., Trebilco, R., Katsumata, K., Constable, A., van Wijk, E., Assmann, K., Beja, J., Bricher, P., Colemans, R., Costa, D., Diggs, S., Farneti, R., Fawcett, S., Gille, S. T., Hendry, K. R., Henley, S., Hofmann, E., Maksym, T., MazIoff, M., Meijers, A., Meredith, M. M., Moreau, S., Ozsor, B., Robertson, R., Schloss, I., Schofield, O., Shi, J., Sikes, E., Smith, I. J., Swart, S., Wahlin, A., Williams, G., Williams, M. J. M., Herraiz-Borreguero, L., Kern, S., Liesers, J., Massom, R. A., Melbourne-Thomas, J., Miloslavich, P., & Spreen, G. Delivering sustained, coordinated, and integrated observations of the Southern Ocean for global impact. Frontiers in Marine Science, 6, (2019): 433, doi:10.3389/fmars.2019.00433.
    Description: The Southern Ocean is disproportionately important in its effect on the Earth system, impacting climatic, biogeochemical, and ecological systems, which makes recent observed changes to this system cause for global concern. The enhanced understanding and improvements in predictive skill needed for understanding and projecting future states of the Southern Ocean require sustained observations. Over the last decade, the Southern Ocean Observing System (SOOS) has established networks for enhancing regional coordination and research community groups to advance development of observing system capabilities. These networks support delivery of the SOOS 20-year vision, which is to develop a circumpolar system that ensures time series of key variables, and delivers the greatest impact from data to all key end-users. Although the Southern Ocean remains one of the least-observed ocean regions, enhanced international coordination and advances in autonomous platforms have resulted in progress toward sustained observations of this region. Since 2009, the Southern Ocean community has deployed over 5700 observational platforms south of 40°S. Large-scale, multi-year or sustained, multidisciplinary efforts have been supported and are now delivering observations of essential variables at space and time scales that enable assessment of changes being observed in Southern Ocean systems. The improved observational coverage, however, is predominantly for the open ocean, encompasses the summer, consists of primarily physical oceanographic variables, and covers surface to 2000 m. Significant gaps remain in observations of the ice-impacted ocean, the sea ice, depths 〉2000 m, the air-ocean-ice interface, biogeochemical and biological variables, and for seasons other than summer. Addressing these data gaps in a sustained way requires parallel advances in coordination networks, cyberinfrastructure and data management tools, observational platform and sensor technology, two-way platform interrogation and data-transmission technologies, modeling frameworks, intercalibration experiments, and development of internationally agreed sampling standards and requirements of key variables. This paper presents a community statement on the major scientific and observational progress of the last decade, and importantly, an assessment of key priorities for the coming decade, toward achieving the SOOS vision and delivering essential data to all end-users.
    Description: PH was supported by the Australian Government’s Cooperative Research Centers Program through the Antarctica Climate and Ecosystems Cooperative Research Centre, and the International Space Science Institute’s team grant #406. This work contributes to the Australian Antarctica Science projects 4301 and 4390.
    Keywords: Southern Ocean ; observations ; modeling ; ocean–climate interactions ; ecosystem-based management ; long-term monitoring ; international coordination
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  • 6
    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 Foltz, G. R., Brandt, P., Richter, I., Rodriguez-Fonsecao, B., Hernandez, F., Dengler, M., Rodrigues, R. R., Schmidt, J. O., Yu, L., Lefevre, N., Da Cunha, L. C., Mcphaden, M. J., Araujo, M., Karstensen, J., Hahn, J., Martin-Rey, M., Patricola, C. M., Poli, P., Zuidema, P., Hummels, R., Perez, R. C., Hatje, V., Luebbecke, J. F., Palo, I., Lumpkin, R., Bourles, B., Asuquo, F. E., Lehodey, P., Conchon, A., Chang, P., Dandin, P., Schmid, C., Sutton, A., Giordani, H., Xue, Y., Illig, S., Losada, T., Grodsky, S. A., Gasparinss, F., Lees, T., Mohino, E., Nobre, P., Wanninkhof, R., Keenlyside, N., Garcon, V., Sanchez-Gomez, E., Nnamchi, H. C., Drevillon, M., Storto, A., Remy, E., Lazar, A., Speich, S., Goes, M., Dorrington, T., Johns, W. E., Moum, J. N., Robinson, C., Perruches, C., de Souza, R. B., Gaye, A. T., Lopez-Paragess, J., Monerie, P., Castellanos, P., Benson, N. U., Hounkonnou, M. N., Trotte Duha, J., Laxenairess, R., & Reul, N. The tropical Atlantic observing system. Frontiers in Marine Science, 6(206), (2019), doi:10.3389/fmars.2019.00206.
    Description: he tropical Atlantic is home to multiple coupled climate variations covering a wide range of timescales and impacting societally relevant phenomena such as continental rainfall, Atlantic hurricane activity, oceanic biological productivity, and atmospheric circulation in the equatorial Pacific. The tropical Atlantic also connects the southern and northern branches of the Atlantic meridional overturning circulation and receives freshwater input from some of the world’s largest rivers. To address these diverse, unique, and interconnected research challenges, a rich network of ocean observations has developed, building on the backbone of the Prediction and Research Moored Array in the Tropical Atlantic (PIRATA). This network has evolved naturally over time and out of necessity in order to address the most important outstanding scientific questions and to improve predictions of tropical Atlantic severe weather and global climate variability and change. The tropical Atlantic observing system is motivated by goals to understand and better predict phenomena such as tropical Atlantic interannual to decadal variability and climate change; multidecadal variability and its links to the meridional overturning circulation; air-sea fluxes of CO2 and their implications for the fate of anthropogenic CO2; the Amazon River plume and its interactions with biogeochemistry, vertical mixing, and hurricanes; the highly productive eastern boundary and equatorial upwelling systems; and oceanic oxygen minimum zones, their impacts on biogeochemical cycles and marine ecosystems, and their feedbacks to climate. Past success of the tropical Atlantic observing system is the result of an international commitment to sustained observations and scientific cooperation, a willingness to evolve with changing research and monitoring needs, and a desire to share data openly with the scientific community and operational centers. The observing system must continue to evolve in order to meet an expanding set of research priorities and operational challenges. This paper discusses the tropical Atlantic observing system, including emerging scientific questions that demand sustained ocean observations, the potential for further integration of the observing system, and the requirements for sustaining and enhancing the tropical Atlantic observing system.
    Description: MM-R received funding from the MORDICUS grant under contract ANR-13-SENV-0002-01 and the MSCA-IF-EF-ST FESTIVAL (H2020-EU project 797236). GF, MG, RLu, RP, RW, and CS were supported by NOAA/OAR through base funds to AOML and the Ocean Observing and Monitoring Division (OOMD; fund reference 100007298). This is NOAA/PMEL contribution #4918. PB, MDe, JH, RH, and JL are grateful for continuing support from the GEOMAR Helmholtz Centre for Ocean Research Kiel. German participation is further supported by different programs funded by the Deutsche Forschungsgemeinschaft, the Deutsche Bundesministerium für Bildung und Forschung (BMBF), and the European Union. The EU-PREFACE project funded by the EU FP7/2007–2013 programme (Grant No. 603521) contributed to results synthesized here. LCC was supported by the UERJ/Prociencia-2018 research grant. JOS received funding from the Cluster of Excellence Future Ocean (EXC80-DFG), the EU-PREFACE project (Grant No. 603521) and the BMBF-AWA project (Grant No. 01DG12073C).
    Keywords: Tropical Atlantic Ocean ; Observing system ; Weather ; Climate ; Hurricanes ; Biogeochemistry ; Ecosystems ; Coupled model bias
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  • 7
    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 [citation], doi:[doi]. Swart, S., Gille, S. T., Delille, B., Josey, S., Mazloff, M., Newman, L., Thompson, A. F., Thomson, J., Ward, B., du Plessis, M. D., Kent, E. C., Girton, J., Gregor, L., Heil, P., Hyder, P., Pezzi, L. P., de Souza, R. B., Tamsitt, V., Weller, R. A., & Zappa, C. J. Constraining Southern Ocean air-sea-ice fluxes through enhanced observations. Frontiers in Marine Science, 6, (2019): 421, doi:10.3389/fmars.2019.00421.
    Description: Air-sea and air-sea-ice fluxes in the Southern Ocean play a critical role in global climate through their impact on the overturning circulation and oceanic heat and carbon uptake. The challenging conditions in the Southern Ocean have led to sparse spatial and temporal coverage of observations. This has led to a “knowledge gap” that increases uncertainty in atmosphere and ocean dynamics and boundary-layer thermodynamic processes, impeding improvements in weather and climate models. Improvements will require both process-based research to understand the mechanisms governing air-sea exchange and a significant expansion of the observing system. This will improve flux parameterizations and reduce uncertainty associated with bulk formulae and satellite observations. Improved estimates spanning the full Southern Ocean will need to take advantage of ships, surface moorings, and the growing capabilities of autonomous platforms with robust and miniaturized sensors. A key challenge is to identify observing system sampling requirements. This requires models, Observing System Simulation Experiments (OSSEs), and assessments of the specific spatial-temporal accuracy and resolution required for priority science and assessment of observational uncertainties of the mean state and direct flux measurements. Year-round, high-quality, quasi-continuous in situ flux measurements and observations of extreme events are needed to validate, improve and characterize uncertainties in blended reanalysis products and satellite data as well as to improve parameterizations. Building a robust observing system will require community consensus on observational methodologies, observational priorities, and effective strategies for data management and discovery.
    Description: SS was funded by a Wallenberg Academy Fellowship (WAF 2015.0186). EK was funded by the NERC ORCHESTRA Project (NE/N018095/1). LP was funded by the Advanced Studies in Oceanography of Medium and High Latitudes (CAPES 23038.004304/2014-28) and the Research Productivity Program (CNPq 304009/2016-4). BdS was a research associate at the F.R.S-FNRS. PeH was supported by the Australian Antarctic Science Projects 4301 and 4390, and the Australian Government’s Cooperative Research Centres Programme through the Antarctic Climate and Ecosystems Cooperative Research Centre and the International Space Science Institute Project 406. SG and MM were funded by National Science Foundation awards OCE-1658001 and PLR-1425989. AT was supported by NASA (NNX15AG42G) and NSF (OCE-1756956).
    Keywords: Air-sea/air-sea-ice fluxes ; Southern Ocean ; Ocean-atmosphere interaction ; Climate ; Ocean-ice interaction
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1090, doi:10.3389/fmicb.2015.01090.
    Description: Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
    Description: This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095 to AP.
    Keywords: Southern Ocean ; Amundsen Sea Polynya ; Phytoplankton bloom ; Phaeocystis ; Micromonas ; Microbial communities ; Metagenomics ; Genome reconstruction
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-22
    Description: The vast majority of genes in sexually reproducing eukaryotes can recombine during the production of gametes. This reshuffling generates new genotypes that may provide selective advantages. However, reshuffling does not occur among the few genes in the genomes of cytoplasmic organelles (chloroplasts and mitochondria). Instead, these organelles are almost always transmitted through maternal inheritance (1). Why is this phenomenon widespread and how is it achieved? On page 394 of this issue, Zhou et al. (2) solve part of this puzzle by identifying the enzyme that degrades sperm mitochondrial DNA after fertilization. Author: Alexander M. van der Bliek
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-25
    Description: Author: Laura M. Zahn
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 11
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-24
    Description: The 14-month El Niño climate event that ended this month brought impacts across the globe, from wildfires in Indonesia to drought in Peru. The main drivers of El Niño conditions, ocean temperatures in the central and eastern Pacific, were as high as 3°C above the average, making this event one of the three most intense El Niños on record. For the most part, forecasts of its impacts on weather patterns were borne out, but forecasters fared relatively poorly in California, which relies on El Niños to deliver rains to parched areas. Along the U.S. West Coast, the jet stream was shifted hundreds of kilometers north last winter, which had the effect of dousing the Pacific Northwest with extraordinary precipitation while Southern California experienced its fourth straight year of drought. Now, scientists are analyzing why their climate models were blindsided and how they can be improved. Author: Eli Kintisch
    Keywords: Climate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-17
    Description: Last summer the northern parts of the Greenland Ice Sheet experienced record melting as summer temperatures rose as high as 19°C (66°F), while southern Greenland was unusually cold, with just average melting. Now, scientists have linked the melt pattern with a 500-kilometer-wide, high-pressure vortex, known as a block, that loitered north of the island during June and July 2015, wreaking weather havoc. Such atmospheric blocks are expected to result from melting sea ice, some researchers say—a claim that has added fuel to a contentious dispute over the global influence of the warming Arctic. Until now, the dispute has focused on how disappearing sea ice might be favoring extreme midlatitude weather, such as floods in Texas or heat waves in Russia. The new study is one of three recent papers that have expanded the debate to the melting of Greenland. Author: Eli Kintisch
    Keywords: Climate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 13
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-17
    Description: "This missing science of heredity … is, in simple truth, ten times more important to humanity than all the chemistry and physics, all the technical and industrial science that ever has been or ever will be discovered," wrote H. G. Wells in 1903. Having dedicated more than 500 pages to the topic in his new book, The Gene, Siddhartha Mukherjee would seem to agree. The book examines human genetics, from its philosophical roots in the work of Aristotle, through Gregor Mendel's garden and Thomas Hunt Morgan's work on fruitflies, and including active work in genome editing. Author: Michael A. Goldman
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-03
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Genetics
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  • 16
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Description: Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far—one megabase or more—from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.
    Keywords: Genetics
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  • 17
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Genetics
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  • 18
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Description: The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type–specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.
    Keywords: Genetics
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-28
    Keywords: Genetics
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  • 20
    Publication Date: 2018-09-28
    Description: Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing–based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.
    Keywords: Genetics
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-04
    Description: Changes in gene regulatory networks (GRNs) underlie many phenotypic differences between species. However, the mechanisms of GRN evolution are still being debated (1–5). Explaining how GRNs originate, diversify, and maintain their identities despite regulatory element turnover is essential for developing mechanistic explanations for the origin, diversification, and conservation of homologous characters between species. Among the major outstanding questions in GRN evolution is whether individual cis-regulatory elements arise de novo through the gradual accumulation of mutations that increase the regulatory potential of existing DNA or whether cis-regulatory elements originate more rapidly through concerted processes. On page 1083 of this issue, Chuong et al. provide evidence that concerted processes, involving endogenous retroviruses (ERVs), which are remarkably abundant in mammalian genomes, have contributed to the evolution of the regulatory systems that control the mammalian immune system (6). Author: Vincent J. Lynch
    Keywords: Genetics
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-01
    Description: Ice sheets such as those on Greenland and Antarctica today not only respond to changing climate but can also cause climate to change. Their sizes have fluctuated substantially in the past. In particular, Antarctica was effectively ice-free until its ice cover began to expand rapidly at the Eocene-Oligocene boundary around 34 million years ago (see the figure). Recent research, including a report by Galeotti et al. on page 76 of this issue (1), helps to identify the mechanisms that led to this rapid ice sheet growth. Authors: Caroline H. Lear, Dan J. Lunt
    Keywords: Climate
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-10
    Keywords: Genetics
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-14
    Keywords: Genetics
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 27
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-20
    Keywords: Genetics
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-01
    Keywords: Genetics
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-10-26
    Keywords: Genetics
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Keywords: Genetics
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-11-09
    Description: Consumer genomics databases have reached the scale of millions of individuals. Recently, law enforcement authorities have exploited some of these databases to identify suspects via distant familial relatives. Using genomic data of 1.28 million individuals tested with consumer genomics, we investigated the power of this technique. We project that about 60% of the searches for individuals of European descent will result in a third-cousin or closer match, which theoretically allows their identification using demographic identifiers. Moreover, the technique could implicate nearly any U.S. individual of European descent in the near future. We demonstrate that the technique can also identify research participants of a public sequencing project. On the basis of these results, we propose a potential mitigation strategy and policy implications for human subject research.
    Keywords: Genetics
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  • 32
    Publication Date: 2018-07-06
    Description: Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
    Keywords: Genetics
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  • 33
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-08
    Keywords: Genetics
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  • 34
    Publication Date: 2015-01-17
    Description: Our understanding of when and how humans adapted to living on the Tibetan Plateau at altitudes above 2000 to 3000 meters has been constrained by a paucity of archaeological data. Here we report data sets from the northeastern Tibetan Plateau indicating that the first villages were established only by 5200 calendar years before the present (cal yr B.P.). Using these data, we tested the hypothesis that a novel agropastoral economy facilitated year-round living at higher altitudes since 3600 cal yr B.P. This successful subsistence strategy facilitated the adaptation of farmers-herders to the challenges of global temperature decline during the late Holocene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, F H -- Dong, G H -- Zhang, D J -- Liu, X Y -- Jia, X -- An, C B -- Ma, M M -- Xie, Y W -- Barton, L -- Ren, X Y -- Zhao, Z J -- Wu, X H -- Jones, M K -- New York, N.Y. -- Science. 2015 Jan 16;347(6219):248-50. doi: 10.1126/science.1259172. Epub 2014 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China. fhchen@lzu.edu.cn ghdong@lzu.edu.cn. ; Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China. ; Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130-48, USA. ; Center for Comparative Archaeology, Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA. ; Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining 810007, China. ; Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China. ; School of Archaeology and Museology, Peking University, Beijing 100871, China. ; McDonald Institute of Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25593179" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Agriculture/*history ; *Altitude ; Archaeology ; Climate ; History, Ancient ; Humans ; Radiometric Dating ; Temperature ; Tibet
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  • 35
    Publication Date: 2015-09-26
    Description: Antarctic ice-core data reveal that the atmosphere experienced abrupt centennial increases in CO2 concentration during the last deglaciation (~18 thousand to 11 thousand years ago). Establishing the role of ocean circulation in these changes requires high-resolution, accurately dated marine records. Here, we report radiocarbon data from uranium-thorium-dated deep-sea corals in the Equatorial Atlantic and Drake Passage over the past 25,000 years. Two major deglacial radiocarbon shifts occurred in phase with centennial atmospheric CO2 rises at 14.8 thousand and 11.7 thousand years ago. We interpret these radiocarbon-enriched signals to represent two short-lived (less than 500 years) "overshoot" events, with Atlantic meridional overturning stronger than that of the modern era. These results provide compelling evidence for a close coupling of ocean circulation and centennial climate events during the last deglaciation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Tianyu -- Robinson, Laura F -- Burke, Andrea -- Southon, John -- Spooner, Peter -- Morris, Paul J -- Ng, Hong Chin -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1537-41. doi: 10.1126/science.aac6159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bristol Isotope Group, School of Earth Sciences, University of Bristol, Bristol, UK. tc14502@bristol.ac.uk. ; Bristol Isotope Group, School of Earth Sciences, University of Bristol, Bristol, UK. ; Department of Earth and Environmental Sciences, University of St Andrews, St. Andrews, UK. ; School of Physical Sciences, University of California, Irvine, Irvine, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404835" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/*chemistry ; Atmosphere/*chemistry ; Climate ; *Global Warming ; *Ice Cover ; Oceans and Seas ; Radiometric Dating ; Thorium/analysis ; Uranium/analysis
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  • 36
    Publication Date: 2015-09-19
    Description: The indigenous people of Greenland, the Inuit, have lived for a long time in the extreme conditions of the Arctic, including low annual temperatures, and with a specialized diet rich in protein and fatty acids, particularly omega-3 polyunsaturated fatty acids (PUFAs). A scan of Inuit genomes for signatures of adaptation revealed signals at several loci, with the strongest signal located in a cluster of fatty acid desaturases that determine PUFA levels. The selected alleles are associated with multiple metabolic and anthropometric phenotypes and have large effect sizes for weight and height, with the effect on height replicated in Europeans. By analyzing membrane lipids, we found that the selected alleles modulate fatty acid composition, which may affect the regulation of growth hormones. Thus, the Inuit have genetic and physiological adaptations to a diet rich in PUFAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fumagalli, Matteo -- Moltke, Ida -- Grarup, Niels -- Racimo, Fernando -- Bjerregaard, Peter -- Jorgensen, Marit E -- Korneliussen, Thorfinn S -- Gerbault, Pascale -- Skotte, Line -- Linneberg, Allan -- Christensen, Cramer -- Brandslund, Ivan -- Jorgensen, Torben -- Huerta-Sanchez, Emilia -- Schmidt, Erik B -- Pedersen, Oluf -- Hansen, Torben -- Albrechtsen, Anders -- Nielsen, Rasmus -- R01-HG003229/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 18;349(6254):1343-7. doi: 10.1126/science.aab2319.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK. Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. ; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark. ; Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. ; National Institute of Public Health, University of Southern Denmark, 1353 Copenhagen, Denmark. Greenland Center for Health Research, University of Greenland, Nuuk, Greenland. ; National Institute of Public Health, University of Southern Denmark, 1353 Copenhagen, Denmark. Steno Diabetes Center, 2820 Gentofte, Denmark. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. ; Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK. Department of Anthropology, University College London, London WC1H 0BW, UK. ; Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark. Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark. Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. ; Department of Medicine, Lillebaelt Hospital, Vejle, Denmark. ; Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark. Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark. ; Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark. Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Faculty of Medicine, University of Aalborg, Aalborg, Denmark. ; School of Natural Sciences, University of California-Merced, Merced, CA 95343, USA. ; Faculty of Medicine, University of Aalborg, Aalborg, Denmark. Department of Cardiology, Aalborg University Hospital, 9100 Aalborg, Denmark. ; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu. ; The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu. ; Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA. Department of Statistics, University of California-Berkeley, Berkeley, CA 94720, USA. torben.hansen@sund.ku.dk albrecht@binf.ku.dk rasmus_nielsen@berkeley.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26383953" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/*genetics ; Alleles ; Arctic Regions ; Body Height/genetics ; Body Weight/genetics ; Chromosomes, Human, Pair 11/genetics ; Climate ; *Diet, High-Fat ; Fatty Acids, Omega-3/*administration & dosage/analysis ; Female ; Genetic Loci ; Genome, Human/genetics ; Genome-Wide Association Study ; Greenland ; Humans ; Inuits/*genetics ; Linkage Disequilibrium ; Male ; Membrane Lipids/analysis/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- New York, N.Y. -- Science. 2015 Jun 12;348(6240):1185. doi: 10.1126/science.348.6240.1185.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26068817" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Climate ; *Dinosaurs ; *Extinction, Biological ; *Geologic Sediments ; *Global Warming ; *Greenhouse Effect ; *Lakes ; Temperature
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  • 38
    Publication Date: 2015-10-10
    Description: The landforms of northern Gale crater on Mars expose thick sequences of sedimentary rocks. Based on images obtained by the Curiosity rover, we interpret these outcrops as evidence for past fluvial, deltaic, and lacustrine environments. Degradation of the crater wall and rim probably supplied these sediments, which advanced inward from the wall, infilling both the crater and an internal lake basin to a thickness of at least 75 meters. This intracrater lake system probably existed intermittently for thousands to millions of years, implying a relatively wet climate that supplied moisture to the crater rim and transported sediment via streams into the lake basin. The deposits in Gale crater were then exhumed, probably by wind-driven erosion, creating Aeolis Mons (Mount Sharp).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grotzinger, J P -- Gupta, S -- Malin, M C -- Rubin, D M -- Schieber, J -- Siebach, K -- Sumner, D Y -- Stack, K M -- Vasavada, A R -- Arvidson, R E -- Calef, F 3rd -- Edgar, L -- Fischer, W F -- Grant, J A -- Griffes, J -- Kah, L C -- Lamb, M P -- Lewis, K W -- Mangold, N -- Minitti, M E -- Palucis, M -- Rice, M -- Williams, R M E -- Yingst, R A -- Blake, D -- Blaney, D -- Conrad, P -- Crisp, J -- Dietrich, W E -- Dromart, G -- Edgett, K S -- Ewing, R C -- Gellert, R -- Hurowitz, J A -- Kocurek, G -- Mahaffy, P -- McBride, M J -- McLennan, S M -- Mischna, M -- Ming, D -- Milliken, R -- Newsom, H -- Oehler, D -- Parker, T J -- Vaniman, D -- Wiens, R C -- Wilson, S A -- New York, N.Y. -- Science. 2015 Oct 9;350(6257):aac7575. doi: 10.1126/science.aac7575.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Geologic and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Earth Science and Engineering, Imperial College London, London SW7 2AZ, UK. ; Malin Space Science Systems, Post Office Box 910148, San Diego, CA 92121, USA. ; Department of Earth and Planetary Sciences, University of California-Santa Cruz, Santa Cruz, CA 95064, USA. ; Department of Geological Sciences, Indiana University, Bloomington, IN 47405, USA. ; Department of Earth and Planetary Sciences, University of California-Davis, Davis, CA 95616, USA. ; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. ; Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA. ; Astrogeology Science Center, U.S. Geological Survey, Flagstaff, AZ 86001, USA. ; Center for Earth and Planetary Studies, National Air and Space Museum, Smithsonian Institution, Washington, DC 20560, USA. ; Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA. ; Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA. ; Laboratoire Planetologie et Geodynamique de Nantes-Le Centre National de la Recherche, Unite Mixte de Recherche 6112 and Universite de Nantes, 44322 Nantes, France. ; Planetary Science Institute, Tucson, AZ 85719, USA. ; Department of Geology, Western Washington University, Bellingham, WA 98225, USA. ; Department of Space Sciences, NASA Ames Research Center, Moffett Field, CA 94035, USA. ; NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA. ; Department of Earth and Planetary Science, University of California-Berkeley, Berkeley, CA 94720, USA. ; Laboratoire de Geologie de Lyon, Universite de Lyon, 69364 Lyon, France. ; Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA. ; Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada. ; Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100, USA. ; Department of Geological Sciences, University of Texas at Austin, Austin, TX 78712, USA. ; Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA. ; Department of Geological Sciences, Brown University, Providence, RI 02912, USA. ; Institute of Meteoritics, University of New Mexico, Albuquerque, NM 87131 USA. ; LZ Technology, NASA Johnson Space Center, Houston, TX 77058, USA. ; Space Remote Sensing, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26450214" target="_blank"〉PubMed〈/a〉
    Keywords: Climate ; Exhumation ; *Lakes ; *Mars ; Paleontology
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  • 39
    Publication Date: 2016-01-09
    Description: Human activity is leaving a pervasive and persistent signature on Earth. Vigorous debate continues about whether this warrants recognition as a new geologic time unit known as the Anthropocene. We review anthropogenic markers of functional changes in the Earth system through the stratigraphic record. The appearance of manufactured materials in sediments, including aluminum, plastics, and concrete, coincides with global spikes in fallout radionuclides and particulates from fossil fuel combustion. Carbon, nitrogen, and phosphorus cycles have been substantially modified over the past century. Rates of sea-level rise and the extent of human perturbation of the climate system exceed Late Holocene changes. Biotic changes include species invasions worldwide and accelerating rates of extinction. These combined signals render the Anthropocene stratigraphically distinct from the Holocene and earlier epochs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waters, Colin N -- Zalasiewicz, Jan -- Summerhayes, Colin -- Barnosky, Anthony D -- Poirier, Clement -- Galuszka, Agnieszka -- Cearreta, Alejandro -- Edgeworth, Matt -- Ellis, Erle C -- Ellis, Michael -- Jeandel, Catherine -- Leinfelder, Reinhold -- McNeill, J R -- Richter, Daniel deB -- Steffen, Will -- Syvitski, James -- Vidas, Davor -- Wagreich, Michael -- Williams, Mark -- Zhisheng, An -- Grinevald, Jacques -- Odada, Eric -- Oreskes, Naomi -- Wolfe, Alexander P -- New York, N.Y. -- Science. 2016 Jan 8;351(6269):aad2622. doi: 10.1126/science.aad2622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉British Geological Survey, Keyworth, Nottingham NG12 5GG, UK. ; Department of Geology, University of Leicester, University Road, Leicester LE1 7RH, UK. ; Scott Polar Research Institute, Cambridge University, Lensfield Road, Cambridge CB2 1ER, UK. ; Department of Integrative Biology, Museum of Paleontology, and Museum of Vertebrate Zoology, University of California-Berkeley, Berkeley, CA 94720, USA. ; Morphodynamique Continentale et Cotiere, Universite de Caen Normandie, Centre National de la Recherche Scientifique (CNRS), 24 Rue des Tilleuls, F-14000 Caen, France. ; Geochemistry and the Environment Division, Institute of Chemistry, Jan Kochanowski University, 15G Swietokrzyska Street, 25-406 Kielce, Poland. ; Departamento de Estratigrafia y Paleontologia, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Apartado 644, 48080 Bilbao, Spain. ; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK. ; Department of Geography and Environmental Systems, University of Maryland-Baltimore County, Baltimore, MD 21250, USA. ; Laboratoire d'Etudes en Geophysique et Oceanographie Spatiales (CNRS, Centre National d'Etudes Spatiales, Institut de Recherche pour le Developpement, Universite Paul Sabatier), 14 Avenue Edouard Belin, 31400 Toulouse, France. ; Department of Geological Sciences, Freie Universitat Berlin, Malteserstrasse 74-100/D, 12249 Berlin, Germany. ; Georgetown University, Washington, DC, USA. ; Nicholas School of the Environment, Duke University, Box 90233, Durham, NC 27516, USA. ; The Australian National University, Canberra, Australian Capital Territory 0200, Australia. ; Department of Geological Sciences, University of Colorado-Boulder, Box 545, Boulder, CO 80309-0545, USA. ; Marine Affairs and Law of the Sea Programme, The Fridtjof Nansen Institute, Lysaker, Norway. ; Department of Geodynamics and Sedimentology, University of Vienna, A-1090 Vienna, Austria. ; State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, Beijing Normal University, Beijing 100875, China. ; Institut de Hautes Etudes Internationales et du Developpement, Chemin Eugene Rigot 2, 1211 Geneve 11, Switzerland. ; Department of Geology, University of Nairobi, Nairobi, Kenya. ; Department of the History of Science, Harvard University, Cambridge, MA 02138, USA. ; Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26744408" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum/analysis ; *Biota ; Carbon Cycle ; Climate ; Construction Materials/analysis ; *Earth (Planet) ; Fossil Fuels/adverse effects ; Geologic Sediments/*chemistry ; *Human Activities ; Humans ; Ice/analysis ; Introduced Species ; Plastics/analysis ; Radioactive Fallout/analysis ; Radioisotopes/analysis
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  • 40
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 41
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-08-18
    Keywords: Genetics
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  • 42
    Publication Date: 2017-09-01
    Description: Copy number mutations implicate excess production of α-synuclein as a possibly causative factor in Parkinson’s disease (PD). Using an unbiased screen targeting endogenous gene expression, we discovered that the β2-adrenoreceptor (β2AR) is a regulator of the α-synuclein gene ( SNCA ). β2AR ligands modulate SNCA transcription through histone 3 lysine 27 acetylation of its promoter and enhancers. Over 11 years of follow-up in 4 million Norwegians, the β2AR agonist salbutamol, a brain-penetrant asthma medication, was associated with reduced risk of developing PD (rate ratio, 0.66; 95% confidence interval, 0.58 to 0.76). Conversely, a β2AR antagonist correlated with increased risk. β2AR activation protected model mice and patient-derived cells. Thus, β2AR is linked to transcription of α-synuclein and risk of PD in a ligand-specific fashion and constitutes a potential target for therapies.
    Keywords: Genetics
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  • 43
    Publication Date: 2017-08-18
    Description: To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided 〉50-fold "shotgun" cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell type–specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.
    Keywords: Genetics
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  • 44
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 45
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-09-01
    Keywords: Genetics
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  • 46
    Publication Date: 2017-09-01
    Description: Having the correct number of chromosomes is vital for normal development and health. Sex chromosome trisomy affects 0.1% of the human population and is associated with infertility. We show that during reprogramming to induced pluripotent stem cells (iPSCs), fibroblasts from sterile trisomic XXY and XYY mice lose the extra sex chromosome through a phenomenon we term trisomy-biased chromosome loss (TCL). Resulting euploid XY iPSCs can be differentiated into the male germ cell lineage and functional sperm that can be used in intracytoplasmic sperm injection to produce chromosomally normal, fertile offspring. Sex chromosome loss is comparatively infrequent during mouse XX and XY iPSC generation. TCL also applies to other chromosomes, generating euploid iPSCs from cells of a Down syndrome mouse model. It can also create euploid iPSCs from human trisomic patient fibroblasts. The findings have relevance to overcoming infertility and other trisomic phenotypes.
    Keywords: Genetics
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  • 47
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 48
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 49
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    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 50
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-02
    Keywords: Genetics
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  • 51
    Publication Date: 2017-06-16
    Description: The mechanistic target of rapamycin complex 1 (mTORC1) is recruited to the lysosome by Rag guanosine triphosphatases (GTPases) and regulates anabolic pathways in response to nutrients. We found that MiT/TFE transcription factors—master regulators of lysosomal and melanosomal biogenesis and autophagy—control mTORC1 lysosomal recruitment and activity by directly regulating the expression of RagD. In mice, this mechanism mediated adaptation to food availability after starvation and physical exercise and played an important role in cancer growth. Up-regulation of MiT/TFE genes in cells and tissues from patients and murine models of renal cell carcinoma, pancreatic ductal adenocarcinoma, and melanoma triggered RagD-mediated mTORC1 induction, resulting in cell hyperproliferation and cancer growth. Thus, this transcriptional regulatory mechanism enables cellular adaptation to nutrient availability and supports the energy-demanding metabolism of cancer cells.
    Keywords: Genetics
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  • 52
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    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 53
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    In: Science
    Publication Date: 2017-06-16
    Keywords: Genetics
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  • 54
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Genetics
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  • 55
    Publication Date: 2017-10-06
    Description: The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Here we provide an overview of the state of single-cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity.
    Keywords: Genetics
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  • 56
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-06
    Description: The stereotyped spatial architecture of the brain is both beautiful and fundamentally related to its function, extending from gross morphology to individual neuron types, where soma position, dendritic architecture, and axonal projections determine their roles in functional circuitry. Our understanding of the cell types that make up the brain is rapidly accelerating, driven in particular by recent advances in single-cell transcriptomics. However, understanding brain function, development, and disease will require linking molecular cell types to morphological, physiological, and behavioral correlates. Emerging spatially resolved transcriptomic methods promise to fill this gap by localizing molecularly defined cell types in tissues, with simultaneous detection of morphology, activity, or connectivity. Here, we review the requirements for spatial transcriptomic methods toward these goals, consider the challenges ahead, and describe promising applications.
    Keywords: Genetics
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  • 57
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-10-06
    Description: Single-cell multi-omics has recently emerged as a powerful technology by which different layers of genomic output—and hence cell identity and function—can be recorded simultaneously. Integrating various components of the epigenome into multi-omics measurements allows for studying cellular heterogeneity at different time scales and for discovering new layers of molecular connectivity between the genome and its functional output. Measurements that are increasingly available range from those that identify transcription factor occupancy and initiation of transcription to long-lasting and heritable epigenetic marks such as DNA methylation. Together with techniques in which cell lineage is recorded, this multilayered information will provide insights into a cell’s past history and its future potential. This will allow new levels of understanding of cell fate decisions, identity, and function in normal development, physiology, and disease.
    Keywords: Genetics
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  • 58
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-13
    Keywords: Genetics
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  • 59
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    In: Science
    Publication Date: 2018-04-13
    Keywords: Genetics
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  • 60
    Publication Date: 2018-04-20
    Description: The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families, structural variants were depleted within promoters and untranslated regions, and paternally inherited CRE-SVs were preferentially transmitted to affected offspring and not to their unaffected siblings. The association of paternal CRE-SVs was replicated in an independent sample of 1771 families. Our results suggest that rare inherited noncoding variants predispose children to ASD, with differing contributions from each parent.
    Keywords: Genetics
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  • 61
    Publication Date: 2017-11-17
    Description: Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.
    Keywords: Genetics
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  • 62
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-17
    Keywords: Genetics
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  • 63
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-23
    Keywords: Genetics
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  • 64
    Publication Date: 2018-04-13
    Description: Family trees have vast applications in fields as diverse as genetics, anthropology, and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. We collected 86 million profiles from publicly available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of human longevity and to provide insights into the geographical dispersion of families. We also report a simple digital procedure to overlay other data sets with our resource.
    Keywords: Genetics
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  • 65
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-22
    Keywords: Genetics
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  • 66
    Publication Date: 2017-12-22
    Description: Puccinia graminis f. sp. tritici ( Pgt ) causes wheat stem rust, a devastating fungal disease. The Sr35 resistance gene confers immunity against this pathogen’s most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and natural Pgt isolates to identify a fungal gene named AvrSr35 that is required for Sr35 avirulence. The AvrSr35 gene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin of Pgt isolates virulent on Sr35 is associated with the nonfunctionalization of the AvrSr35 gene by the insertion of a mobile element. The discovery of AvrSr35 provides a new tool for Pgt surveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-06-08
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-12
    Keywords: Genetics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-28
    Keywords: Genetics
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-28
    Keywords: Genetics
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 71
    Publication Date: 2017-04-28
    Description: The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.
    Keywords: Genetics
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  • 72
    Publication Date: 2017-05-05
    Description: Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.
    Keywords: Genetics
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  • 73
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 74
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 75
    Publication Date: 2017-05-05
    Description: Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection. However, it is not known whether deleterious alleles affect fitness independently, so that cumulative fitness loss depends exponentially on the number of deleterious alleles, or synergistically, so that each additional deleterious allele results in a larger decrease in relative fitness. Negative selection with synergistic epistasis should produce negative linkage disequilibrium between deleterious alleles and, therefore, an underdispersed distribution of the number of deleterious alleles in the genome. Indeed, we detected underdispersion of the number of rare loss-of-function alleles in eight independent data sets from human and fly populations. Thus, selection against rare protein-disrupting alleles is characterized by synergistic epistasis, which may explain how human and fly populations persist despite high genomic mutation rates.
    Keywords: Genetics
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  • 76
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-05
    Keywords: Genetics
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 77
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-02-10
    Keywords: Genetics
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 78
    Publication Date: 2018-02-10
    Description: The predisposition to neuropsychiatric disease involves a complex, polygenic, and pleiotropic genetic architecture. However, little is known about how genetic variants impart brain dysfunction or pathology. We used transcriptomic profiling as a quantitative readout of molecular brain-based phenotypes across five major psychiatric disorders—autism, schizophrenia, bipolar disorder, depression, and alcoholism—compared with matched controls. We identified patterns of shared and distinct gene-expression perturbations across these conditions. The degree of sharing of transcriptional dysregulation is related to polygenic (single-nucleotide polymorphism–based) overlap across disorders, suggesting a substantial causal genetic component. This comprehensive systems-level view of the neurobiological architecture of major neuropsychiatric illness demonstrates pathways of molecular convergence and specificity.
    Keywords: Genetics
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  • 79
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-26
    Keywords: Genetics
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  • 80
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-26
    Keywords: Genetics
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  • 81
    Publication Date: 2018-01-26
    Description: Sequence variants in the parental genomes that are not transmitted to a child (the proband) are often ignored in genetic studies. Here we show that nontransmitted alleles can affect a child through their impacts on the parents and other relatives, a phenomenon we call "genetic nurture." Using results from a meta-analysis of educational attainment, we find that the polygenic score computed for the nontransmitted alleles of 21,637 probands with at least one parent genotyped has an estimated effect on the educational attainment of the proband that is 29.9% ( P = 1.6 x 10 –14 ) of that of the transmitted polygenic score. Genetic nurturing effects of this polygenic score extend to other traits. Paternal and maternal polygenic scores have similar effects on educational attainment, but mothers contribute more than fathers to nutrition- and heath-related traits.
    Keywords: Genetics
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  • 82
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-12-09
    Description: A detailed, long-term ocean temperature record derived from corals on Christmas Island in Kiribati and other islands in the tropical Pacific shows that the extreme warmth of recent El Niño events reflects not just the natural ocean-atmosphere cycle but a new factor: global warming caused by human activity. Over the last 7000 years, El Niños, which warm the eastern Pacific, waxed and waned. Then, during the 20th century, their intensity began to climb. The trend is likely to continue, boding ever-more-destructive El Niños in the future. The finding helps settle a long-standing debate about the role of global warming in these events, which had been hard to resolve because records are short and spotty in the remote parts of the Pacific where El Niño hits hardest. Author: Christopher Pala
    Keywords: Climate
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  • 83
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-12-09
    Description: Forty years ago, Hays, Imbrie, and Shackleton in a paper in Science tested the hypothesis that small changes in Earth's orbital geometry—namely precession, obliquity, and eccentricity—were responsible for the waxing and waning of the great continental ice sheets during the Quaternary period, which began about 2.58 million years ago (1). The paper is considered to be the “smoking gun” in support of the astronomical hypothesis of the Ice Ages, which is over a century old and most often ascribed to Milutin Milankovitch (2). Author: David A. Hodell
    Keywords: Climate
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  • 84
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-04-01
    Description: Author: Beverly A. Purnell
    Keywords: Genetics
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  • 85
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-09
    Description: The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions.
    Keywords: Genetics
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  • 86
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-16
    Keywords: Genetics
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  • 87
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-16
    Keywords: Genetics
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  • 88
    Publication Date: 2018-03-16
    Description: Genetic association studies often examine features independently, potentially missing subpopulations with multiple phenotypes that share a single cause. We describe an approach that aggregates phenotypes on the basis of patterns described by Mendelian diseases. We mapped the clinical features of 1204 Mendelian diseases into phenotypes captured from the electronic health record (EHR) and summarized this evidence as phenotype risk scores (PheRSs). In an initial validation, PheRS distinguished cases and controls of five Mendelian diseases. Applying PheRS to 21,701 genotyped individuals uncovered 18 associations between rare variants and phenotypes consistent with Mendelian diseases. In 16 patients, the rare genetic variants were associated with severe outcomes such as organ transplants. PheRS can augment rare-variant interpretation and may identify subsets of patients with distinct genetic causes for common diseases.
    Keywords: Genetics
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  • 89
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-09
    Keywords: Genetics
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  • 90
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-08
    Keywords: Genetics
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  • 91
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-07
    Keywords: Genetics
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  • 92
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-12-09
    Description: Author: Julia Fahrenkamp-Uppenbrink
    Keywords: Climate
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