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  • Public Library of Science  (34,238)
  • Oxford University Press  (33,612)
  • Copernicus  (13,616)
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  • 2010-2014  (78,746)
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  • 2000-2004  (10,516)
  • 1985-1989
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  • 1
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    In defense of globalization (2004)
    New York : Oxford University Press
    Details
    Keywords: Anti-globalization movement. ; Globalization, Economic aspects. ; Globalization, Social aspects.
    Notes: I. Coping with anti-globalization -- 1. Anti-globalization: why? -- 2. Globalization: socially, not just economically, benign -- 3. Globalization is good but not good enough -- 4. Non-government organizations -- II. Globalization's human face: trade and corporations -- 5. Poverty: enhanced or diminished? -- 6. Child labor: increased or reduced? -- 7. Women: harmed or helped? -- 8. Democracy at bay? -- 9. Culture imperiled or enriched? -- 10. Wages and labor standards at stake? -- 11. Environment in peril? -- 12. Corporations: predatory or beneficial? -- III. Other dimensions of globalization -- 13. The perils of Gung-Ho International Financial capitalism -- 14. International flows of humanity -- IV. Appropriate governance: making globalization work better -- 15. Appropriate governance: an overview -- 16. Coping with downsides -- 17. Accelerating the achievement of social agendas -- 18. Managing transitions: optimal, not maximal, speed -- V. In conclusion -- 19. And so, let us begin anew
    Pages: xi, 308 p.
    ISBN: 0-19-530391-1
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=129267
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  • 2
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    Memory and emotion (2004)
    Oxford ; New York : Oxford University Press
    Series in affective science  
    Details
    Keywords: Autobiographical memory. ; Brain, physiology. ; Emotions. ; Emotions, physiology. ; Memory, physiology. ; Mental Disorders, psychology. ; Psychiatry. ; Psychophysiology.
    Notes: Memory for emotional events / Daniel Reisberg and Friderike Heuer -- The neuroanatomy of emotional memory in humans / Tony W. Buchanan and Ralph Adolphs -- The biopsychology of trauma and memory / Jessica D. Payne ... [et al.] -- Forgetting trauma? / Richard J. McNally, Susan A. Clancy, and Heidi M. Barrett -- Selective memory effects in anxiety disorders : an overview of research findings and their implications / Colin MacLeod and Andrew Mathews -- Memory for emotional and nonemotional events in depression : a question of habit? / Paula Hertel -- Emotion, memory, and conscious awareness in schizophrenia / Jean-Marie Danion ... [et al.] -- Children's memories of emotional events / Robyn Fivush and Jessica McDermott Sales -- Aging and emotional memory / Mara Mather -- Emotion and eyewitness memory / Robin S. Edelstein ... [et al.] -- Emotional memory in survivors of the Holocaust : a qualitative study of oral testimony / Robert N. Kraft
    Pages: xiv, 413 p.
    ISBN: 0-19-518650-8
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=121006
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  • 3
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    Armies without nations : public violence and state formation in Central America, 1821-1960 (2004)
    Oxford ; New York : Oxford University Press
    Details
    Keywords: Central America, Politics and government. ; Political violence, Central America, History. ; State-sponsored terrorism, Central America, History.
    Notes: Part 1 : 1821-1939. Historical dimensions of public violence in Latin America -- Binding hatreds : public violence, state, and nation in Central American history -- Guatemala : organizing for war -- El Salvador : a democracy of violence -- Honduras : caudillos in search of an army -- Nicaragua : a new army finds its caudillo -- Costa Rica : caudillos in search of a state -- Part 2 : 1940-1960. Transformations -- Defining collaboration : the United States and Central America -- Guatemala : "Showcase of Latin America" -- El Salvador : distrustful collaborator -- Honduras : remaking an "armed rabble" -- Nicaragua : "Ready to receive orders from Uncle Sam" -- Costa Rica : an army renamed -- Conclusions -- Statistical appendix -- Notes
    Pages: x, 336 p.
    ISBN: 0-19-518573-0
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=121469
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  • 4
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    Sight unseen : an exploration of conscious and unconscious vision (2004)
    Oxford ; New York : Oxford University Press
    Details
    Keywords: Electronic books ; Vision disorders ; Visual perception
    Pages: ix, 135 p.
    ISBN: 1-423-70567-X
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=130746
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  • 5
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    Thinking about feeling : contemporary philosophers on emotions (2004)
    Oxford ; New York : Oxford University Press
    Series in affective science  
    Details
    Keywords: Emotions (Philosophy)
    Notes: Emotions, physiology, and intentionality.Primitive emotions /John Deigh --Emotion : biological fact or social construction /Jenefer Robinson --Embodied emotions /Jesse Prinz --Emotion, appraisal, and cognition.Emotions : what I know, what I'd like to think I know, and what I'd like to think /Ronald de Sousa --Emotions, thoughts, and feelings : emotions as engagements with the world /Robert C. Solomon --Emotions and feelings.Emotion, feeling, and knowledge of the world /Peter Goldie --Subjectivity and emotion /Cheshire Calhoun --Emotions and rationality.Emotions, rationality, and mind/body /Patricia Greenspan --Some considerations about intellectual desire and emotions /Michael Stocker --Emotions, action, and freedom.Emotion and action /Jon Elster --Emotions and freedom /Jerome Neu --Emotion and value.Emotions as judgments of value and importance /Martha Nussbaum --Feelings that matter /Annette Baier --Perturbations of desire : emotions disarming morality in the "Great song" of The Mahabharata /Purushottama Bilimoria --On theories of emotion.Is emotion a natural kind? /Paul E. Griffiths --Emotion as a subtle mental mode /Aaron Ben-Zeev --Enough already with "Theories of emotions" /Amelie Oksenberg Rorty.
    Pages: x, 297 p.
    ISBN: 0-19-530334-2
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=129793
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  • 6
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    The foundations of mind : origins of conceptual thought (2004)
    Oxford ; New York : Oxford University Press
    Oxford series in cognitive development  
    Details
    Keywords: Cognition in infants. ; Cognition, physiology, Infant. ; Concepts in infants. ; Thinking, physiology, Infant.
    Notes: How to build a baby : prologue -- Piaget's sensorimotor infant -- Kinds of representation : seeing and thinking -- Perceptual meaning analysis and image-schemas : the infant as interpreter -- Some image-schemas and their functions -- Some differences between percepts and concepts : the case of the basic level -- Some preverbal concepts -- Conceptual categories as induction machines -- Continuity in the conceptual system : acquisition, breakdown, and reorganization -- Recall of the past -- Language acquisition -- Consciousness and conclusions
    Pages: xiii, 359 p.
    ISBN: 0-19-530396-2
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=129820
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  • 7
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    Twentieth century sprawl : highways and the reshaping of the American Landscape ; Highways transformed America (2004)
    New York : Oxford University Press
    Details
    Keywords: Denver (Colo.), History, 20th century. ; Middlebury (Vt. : Town), History, 20th century. ; Smyrna (Rutherford County, Tenn.), History, 20th century. ; Cities and towns, United States, Growth, History, 20th century, Case studies. ; Interstate Highway System, History, 20th century. ; Roads, Government policy, United States, History, 20th century. ; Transportation, Automotive, United States, History, 20th century.
    Notes: Highway federalism -- Denver meets the automobile -- The decentralization of post-World War II Denver -- Automobiles and a small town -- Bridges, bypasses, and boulevards -- AutoCity : Smyrna, Tennessee
    Pages: xiv, 297 p.
    ISBN: 0-19-530264-8
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=129257
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  • 8
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    The human side of M & A : how CEOs leverage the most important asset in deal making ; Human side of M and A ; Human side of mergers and acquisitions ; Leveraging the most important factor in deal making (2004)
    New York : Oxford University Press
    Details
    Keywords: Consolidation and merger of corporations. ; Human capital. ; Organizational effectiveness.
    Pages: xi, 193 p.
    ISBN: 0-19-518406-8
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=120907
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  • 9
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    At war with ourselves : why America is squandering its chance to build a better world (2004)
    Oxford ; New York : Oxford University Press
    Details
    Keywords: United States, Foreign relations, Philosophy. ; United States, Foreign relations, 2001- ; Globalization, Political aspects. ; National characteristics, American.
    Pages: xiv, 288 p.
    Edition: [Pbk. ed.]
    ISBN: 0-19-518433-5
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=120929
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  • 10
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    When flesh becomes word : an anthology of early eighteenth-century libertine literature (2004)
    New York : Oxford University Press
    Details
    Keywords: English literature, 18th century. ; Erotic literature, English. ; Libertinism, Literary collections.
    Notes: British libertine literature before Fanny Hill (1749) -- 1: The school of Venus (1680) -- 2: The pleasure of a single life (1701), The fifteen comforts of Cuckoldom (1706), and the fifteen plagues of a maiden-head (1707) -- 3: Gonosologium Novum (1709) -- 4: Venus in the cloister (1725) -- 5: A dialogue between a married lady and a maid (1740) -- 6: A new description of merryland (1741) -- 7: The female husband (1746)
    Pages: xxxiii, 332 p.
    ISBN: 0-19-518577-3
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=120996
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  • 11
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    Playing the races : ethnic caricature and American literary realism (2004)
    New York : Oxford University Press
    Details
    Keywords: United States, Ethnic relations, History, 19th century. ; United States, Race relations, History, 19th century. ; American fiction, 19th century, History and criticism. ; Caricatures and cartoons, United States, History, 19th century. ; Ethnicity in literature. ; Race in literature. ; Realism in literature. ; Stereotype (Psychology) in literature.
    Notes: Introduction: the age of caricature, the age of realism -- William Dean Howells and the touch of exaggeration which typifies -- "I want a real coon": Twain and ethnic caricature -- A Jamesian art to be cultivated -- Edith Wharton's flamboyant copy -- The "curious realism" of Charles Chesnutt
    Pages: viii, 196 p.
    ISBN: 0-19-518578-1
    URL: http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=121496
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  • 12
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    Subsidence Detected by Multi-Pass Differential SAR Interferometry in the Cassino Plain (Central Italy): Joint Effect of Geological and Anthropogenic Factors? (2014)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-06-30
    Description: In the present work, the Differential SAR Interferometry (DInSAR) technique has been applied to study the surface movements affecting the sedimentary basin of Cassino municipality. Two datasets of SAR images, provided by ERS 1-2 and Envisat missions, have been acquired from 1992 to 2010. Such datasets have been processed independently each other and with different techniques nevertheless providing compatible results. DInSAR data show a subsidence rate mostly located in the northeast side of the city, with a subsidence rate decreasing from about 5–6 mm/yr in the period 1992–2000 to about 1–2 mm/yr between 2004 and 2010, highlighting a progressive reduction of the phenomenon. Based on interferometric results and geological/geotechnical observations, the explanation of the detected movements allows to confirm the anthropogenic (surface effect due to building construction) and geological causes (thickness and characteristics of the compressible stratum)
    Description: Published
    Description: 9676-9690
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: JCR Journal
    Description: open
    Keywords: Differential SAR Interferometry; SBAS; IPTA; Cassino plain; subsidence ; 04. Solid Earth::04.01. Earth Interior::04.01.02. Geological and geophysical evidences of deep processes
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 13
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    Using empirical orthogonal functions derived from remote sensing reflectance for the prediction of concentrations of phytoplankton pigments. (2014)
    Copernicus
    In:  EPIC3Ocean Science Discussions, Copernicus, 11(5), pp. 2073-2117, ISSN: 1812-0822
    Details
    Publication Date: 2014-10-14
    Description: The composition and abundance of algal pigments provide information on characteristics of a phytoplankton community in respect to its photoacclimation, overall biomass, and taxonomic composition. Particularly, these pigments play a major role in photoprotection and in the light-driven part of photosynthesis. Most phytoplankton pigments can be measured by High Performance Liquid Chromatography (HPLC) techniques to filtered water samples. This method, like others when water samples have to be analysed in the laboratory, is time consuming and therefore only a limited number of data points can be obtained. In order to receive information on phytoplankton pigment composition with a higher temporal and spatial resolution, we have developed a method to assess pigment concentrations from continuous optical measurements. The method applies an Empirical Orthogonal Function (EOF) analysis to remote sensing reflectance data derived from ship-based hyper-spectral underwater radiometric and from multispectral satellite data (using the MERIS Polymer product developed by Steinmetz et al., 2011) measured in the Eastern Tropical Atlantic. Subsequently we developed statistically linear models with measured (collocated) pigment concentrations as the response variable and EOF loadings as predictor variables. The model results, show that surface concentrations of a suite of pigments and pigment groups can be well predicted from the ship-based reflectance measurements, even when only a multi-spectral resolution is chosen (i.e. eight bands similar to those used by MERIS). Based on the MERIS reflectance data, concentrations of total and monovinyl chlorophyll a and the groups of photoprotective and photosynthetic carotenoids can be predicted with high quality. The fitted statistical model constructed on the satellite reflectance data as input was applied to one month of MERIS Polymer data to predict the concentration of those pigment groups for the whole Eastern Tropical Atlantic area. Bootstrapping explorations of cross-validation error indicate that the method can produce reliable predictions with relatively small data sets (e.g., 〈 50 collocated values of reflectance and pigment concentration). The method allows for the derivation of time series from continuous reflectance data of various pigment groups at various regions, which can be used to study variability and change of phytoplankton composition and photo-physiology.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , notRev
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  • 14
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    Multiple Sclerosis in the Mount Etna Region: Possible Role of Volcanogenic Trace Elements (2014)
    Public Library of Science
    Details
    Publication Date: 2017-04-04
    Description: Background: Trace elements have been hypothesised to be involved in the pathogenesis of Multiple Sclerosis and volcanic degassing is the major natural sources of trace elements. Both incidence of Multiple Sclerosis in Catania and volcanic activity of Mount Etna have been significantly increased during the last 30 years. Due to prevailing trade winds direction, volcanic gases from Etna summit craters are mostly blown towards the eastern and southern sectors of the volcano. Objective: To evaluate the possible association between Multiple Sclerosis and exposure to volcanogenic trace elements. Methods: We evaluated prevalence and incidence of Multiple Sclerosis in four communities (47,234 inhabitants) located in the eastern flank and in two communities (52,210 inhabitants) located in the western flank of Mount Etna, respectively the most and least exposed area to crater gas emissions. Results: A higher prevalence was found in the population of the eastern flank compared to the population of the western one (137.6/100,000 versus 94.3/100,000; p-value 0.04). We found a borderline significantly higher incidence risk during the incidence study period (1980–2009) in the population of the eastern flank 4.6/100,000 (95% CI 3.1–5.9), compared with the western population 3.2/100,000 (95% CI 2.4–4.2) with a RR of 1.41 (95% CI 0.97–2.05; p-value 0.06). Incidence risks have increased over the time in both populations reaching a peak of 6.4/100,000 in the eastern flank and of 4.4/100.000 in the western flank during 2000–2009. Conclusion: We found a higher prevalence and incidence of Multiple Sclerosis among populations living in the eastern flank of Mount Etna. According to our data a possible role of TE cannot be ruled out as possible co-factor in the MS pathogenesis. However larger epidemiological study are needed to confirm this hypothesis.
    Description: Published
    Description: e74259
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: JCR Journal
    Description: open
    Keywords: Mt. Etna volcano ; Multiple Sclerosis ; trace elements ; volcanic activity ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Geosphere-biosphere interacions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica). (2014)
    Public Library of Science
    Details
    Publication Date: 2020-02-24
    Description: Hule and Rı´o Cuarto are maar lakes located 11 and 18 km N of Poa´s volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Rı´o Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).
    Description: Published
    Description: e102456
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: open
    Keywords: bio activity, volcanic lakes, costa rica ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
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    Empirical sea ice thickness retrieval during the freeze up period from SMOS high incident angle observations (2014)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 8(2), pp. 439-451, ISSN: 1994-0416
    Details
    Publication Date: 2019-07-17
    Description: Sea ice thickness information is important for sea ice modelling and ship operations. Here a method to detect the thickness of sea ice up to 50 cm during the freeze-up season based on high incidence angle observations of the Soil Moisture and Ocean Salinity (SMOS) satellite working at 1.4 GHz is suggested. By comparison of thermodynamic ice growth data with SMOS brightness temperatures, a high correlation to intensity and an anticorrelation to the difference between vertically and horizontally polarised brightness temperatures at incidence angles between 40 and 50° are found and used to develop an empirical retrieval algorithm sensitive to thin sea ice up to 50 cm thickness. The algorithm shows high correlation with ice thickness data from airborne measurements and reasonable ice thickness patterns for the Arctic freeze-up period.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    SMOS derived sea ice thickness: algorithm baseline, product specifications and initial verification (2014)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 8(3), pp. 997-1018, ISSN: 1994-0416
    Details
    Publication Date: 2014-06-02
    Description: Following the launch of ESA's Soil Moisture and Ocean Salinity (SMOS) mission, it has been shown that brightness temperatures at a low microwave frequency of 1.4 GHz (L-band) are sensitive to sea ice properties. In the first demonstration study, sea ice thickness up to 50 cm has been derived using a semi-empirical algorithm with constant tie-points. Here, we introduce a novel iterative retrieval algorithm that is based on a thermodynamic sea ice model and a three-layer radiative transfer model, which explicitly takes variations of ice temperature and ice salinity into account. In addition, ice thickness variations within the SMOS spatial resolution are considered through a statistical thickness distribution function derived from high-resolution ice thickness measurements from NASA's Operation IceBridge campaign. This new algorithm has been used for the continuous operational production of a SMOS-based sea ice thickness data set from 2010 on. The data set is compared to and validated with estimates from assimilation systems, remote sensing data, and airborne electromagnetic sounding data. The comparisons show that the new retrieval algorithm has a considerably better agreement with the validation data and delivers a more realistic Arctic-wide ice thickness distribution than the algorithm used in the previous study (Kaleschke et al., 2012).
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    A data-constrained model for compatibility check of remotely sensed basal melting with the hydrography in front of Antarctic ice shelves (2014)
    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus, 8(1), pp. 919-951, ISSN: 1994-0440
    Details
    Publication Date: 2019-07-16
    Description: The ice shelf caverns around Antarctica are sources of cold and fresh water which contributes to the formation of Antarctic bottom water and thus to the ventilation of the deep basins of the World Ocean. While a realistic simulation of the cavern circulation requires high resolution, because of the complicated bottom topography and ice shelf morphology, the physics of melting and freezing at the ice shelf base is relatively simple. We have developed an analytically solvable box model of the cavern thermohaline state, using the formulation of melting and freezing as in Olbers and Hellmer (2010). There is high resolution along the cavern's path of the overturning circulation whereas the cross-path resolution is fairly coarse. The circulation in the cavern is prescribed and used as a tuning parameter to constrain the solution by attempting to match observed ranges for outflow temperature and salinity at the ice shelf front as well as of the mean basal melt rate. The method, tested for six Antarctic ice shelves, can be used for a quick estimate of melt/freeze rates and the overturning rate in particular caverns, given the temperature and salinity of the inflow and the above mentioned constrains for outflow and melting. In turn, the model can also be used for testing the compatibility of remotely sensed basal mass loss with observed cavern inflow characteristics.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    An update to the Surface Ocean CO2 Atlas (SOCAT version 2) (2014)
    Copernicus
    In:  EPIC3Earth System Science Data, Copernicus, 6(1), pp. 69-90, ISSN: 1866-3516
    Details
    Publication Date: 2015-03-19
    Description: The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Can sparse proxy data constrain the strength of the Atlantic meridional overturning circulation? (2014)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(1), pp. 419-432, ISSN: 1991-9603
    Details
    Publication Date: 2019-07-17
    Description: In a feasibility study, the potential of proxy data for the temperature and salinity during the Last Glacial Maximum (LGM, about 19 000 to 23 000 years before present) in constraining the strength of the Atlantic meridional overturning circulation (AMOC) with a general ocean circulation model was explored. The proxy data were simulated by drawing data from four different model simulations at the ocean sediment core locations of the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface (MARGO) project, and perturbing these data with realistic noise estimates. The results suggest that our method has the potential to provide estimates of the past strength of the AMOC even from sparse data, but in general, paleo-sea-surface temperature data without additional prior knowledge about the ocean state during the LGM is not adequate to constrain the model. On the one hand, additional data in the deep-ocean and salinity data are shown to be highly important in estimating the LGM circulation. On the other hand, increasing the amount of surface data alone does not appear to be enough for better estimates. Finally, better initial guesses to start the state estimation procedure would greatly improve the performance of the method. Indeed, with a sufficiently good first guess, just the sea-surface temperature data from the MARGO project promise to be sufficient for reliable estimates of the strength of the AMOC.
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    Compositional discrimination of decompression and decomposition gas bubbles in bycaught seals and dolphins (2014)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 8 (2013): e83994, doi:10.1371/journal.pone.0083994.
    Description: Gas bubbles in marine mammals entangled and drowned in gillnets have been previously described by computed tomography, gross examination and histopathology. The absence of bacteria or autolytic changes in the tissues of those animals suggested that the gas was produced peri- or post-mortem by a fast decompression, probably by quickly hauling animals entangled in the net at depth to the surface. Gas composition analysis and gas scoring are two new diagnostic tools available to distinguish gas embolisms from putrefaction gases. With this goal, these methods have been successfully applied to pathological studies of marine mammals. In this study, we characterized the flux and composition of the gas bubbles from bycaught marine mammals in anchored sink gillnets and bottom otter trawls. We compared these data with marine mammals stranded on Cape Cod, MA, USA. Fresh animals or with moderate decomposition (decomposition scores of 2 and 3) were prioritized. Results showed that bycaught animals presented with significantly higher gas scores than stranded animals. Gas composition analyses indicate that gas was formed by decompression, confirming the decompression hypothesis.
    Description: This study was funded by the Woods Hole Oceanographic Institution Marine Mammal Center, and Wick and Sloan Simmons.
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    Decadal changes in zooplankton of the Northeast U.S. continental shelf (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e87720, doi:10.1371/journal.pone.0087720.
    Description: The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf (NEUS) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine (GOM), Georges Bank (GB), Southern New England (SNE), and Mid-Atlantic Bight (MAB). Results suggested that there was significant difference in long term variation between northern region (GOM and GB), and the MAB for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the MAB. The long term abundance of C. finmarchicus showed more fluctuation in the MAB than the GOM and GB, whereas the long term abundance of Cen. typicus was more variable in the GB than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index (GSNWI) in the GOM and GB, but the GSNWI only explained 12–15% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the GSNWI, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.
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    A quantitative assessment of the role of the parasite Amoebophrya in the termination of Alexandrium fundyense blooms within a small coastal embayment (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e81150, doi:10.1371/journal.pone.0081150.
    Description: Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). High prevalence of Amoebophrya spp. has been linked to the decline of some HABs in marine systems. The objective of this study was to evaluate the impact of Amoebophrya spp. on the dynamics of dinoflagellate blooms in Salt Pond (MA, USA), particularly the harmful species Alexandrium fundyense. The abundance of Amoebophrya life stages was estimated 3–7 days per week through the full duration of an annual A. fundyense bloom using fluorescence in situ hybridization coupled with tyramide signal amplification (FISH- TSA). More than 20 potential hosts were recorded including Dinophysis spp., Protoperidinium spp. and Gonyaulax spp., but the only dinoflagellate cells infected by Amoebophrya spp. during the sampling period were A. fundyense. Maximum A. fundyense concentration co-occurred with an increase of infected hosts, followed by a massive release of Amoebophrya dinospores in the water column. On average, Amoebophrya spp. infected and killed ~30% of the A. fundyense population per day in the end phase of the bloom. The decline of the host A. fundyense population coincided with a dramatic life-cycle transition from vegetative division to sexual fusion. This transition occurred after maximum infected host concentrations and before peak infection percentages were observed, suggesting that most A. fundyense escaped parasite infection through sexual fusion. The results of this work highlight the importance of high frequency sampling of both parasite and host populations to accurately assess the impact of parasites on natural plankton assemblages.
    Description: L. Velo-Sua´rez was supported by a Marie Curie International Outgoing Fellowship (IOF; grant agreement: MOHAB PIOF-GA-252260). This work was supported in part by NSF grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences grants 1P50-ES01274201 and 1P01ES021923-01 to D.M. Anderson and D.J. McGillicuddy through the Woods Hole Center for Oceans and Human Health, National Park Service Cooperative Agreement H238015504 to D.M. Anderson.
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    Diving behavior of the reef manta ray links coral reefs with adjacent deep pelagic habitats (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88170, doi:10.1371/journal.pone.0088170.
    Description: Recent successful efforts to increase protection for manta rays has highlighted the lack of basic ecological information, including vertical and horizontal movement patterns, available for these species. We deployed pop-up satellite archival transmitting tags on nine reef manta rays, Manta alfredi, to determine diving behaviors and vertical habitat use. Transmitted and archived data were obtained from seven tagged mantas over deployment periods of 102–188 days, including three recovered tags containing 2.6 million depth, temperature, and light level data points collected every 10 or 15 seconds. Mantas frequented the upper 10 m during daylight hours and tended to occupy deeper water throughout the night. Six of the seven individuals performed a cumulative 76 deep dives (〉150 m) with one individual reaching 432 m, extending the known depth range of this coastal, reef-oriented species and confirming its role as an ecological link between epipelagic and mesopelagic habitats. Mean vertical velocities calculated from high-resolution dive data (62 dives 〉150 m) from three individuals suggested that mantas may use gliding behavior during travel and that this behavior may prove more efficient than continuous horizontal swimming. The behaviors in this study indicate manta rays provide a previously unknown link between the epi- and mesopelagic layers of an extremely oligotrophic marine environment and provide evidence of a third marine species that utilizes gliding to maximize movement efficiency.
    Description: inancial support was provided in part by KAUST baseline research funds (to MLB), KAUST award numbers USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).
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    Identification of cinnabarinic acid as novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e87877, doi:10.1371/journal.pone.0087877.
    Description: The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.
    Description: This work was supported in part by National Institutes of Health (NIH) grants OD000329 and R01AI40312 (to JMM), R01ES006272 (to MEH), P42ES007381 (Superfund Research Program at Boston University to JS, DHS and MEH), R21CA134882 (to JS), NIH Training Grant T32 GM007175 (MML), and the Harvey V. Berneking Living Trust. BK is supported by Career Development Awards from the NIH/National Institute of Diabetes and Digestive and Kidney Diseases (DK083334) and the NASPGHAN Foundation. JEM is a recipient of the Human Frontiers Science Program Long-Term Fellowship (LT000231/2011-L). JMM is a recipient of the NIH Director's Pioneer Award Program, part of the NIH Roadmap for Medical Research, through grant DPI OD00329.
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    Shifts in the microbial community composition of Gulf Coast beaches following beach oiling (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e74265, doi:10.1371/journal.pone.0074265.
    Description: Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.
    Description: Financial support for this work was provided by the University of Wisconsin-Milwaukee National Institute of Environmental Health Sciences program, grant ES-004184 to SLM and the Alfred P. Sloan Foundation's grant for the Rare Biosphere in the Built Environment MLS.
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    Vertebral bomb radiocarbon suggests extreme longevity in white sharks (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed free of all copyright. The definitive version was published in PLoS One 9 (2014): e84006, doi:10.1371/journal.pone.0084006.
    Description: Conservation and management efforts for white sharks (Carcharodon carcharias) remain hampered by a lack of basic demographic information including age and growth rates. Sharks are typically aged by counting growth bands sequentially deposited in their vertebrae, but the assumption of annual deposition of these band pairs requires testing. We compared radiocarbon (Δ14C) values in vertebrae from four female and four male white sharks from the northwestern Atlantic Ocean (NWA) with reference chronologies documenting the marine uptake of 14C produced by atmospheric testing of thermonuclear devices to generate the first radiocarbon age estimates for adult white sharks. Age estimates were up to 40 years old for the largest female (fork length [FL]: 526 cm) and 73 years old for the largest male (FL: 493 cm). Our results dramatically extend the maximum age and longevity of white sharks compared to earlier studies, hint at possible sexual dimorphism in growth rates, and raise concerns that white shark populations are considerably more sensitive to human-induced mortality than previously thought.
    Description: This study was funded by the National Science Foundation (OCE 0825148 was awarded to SRT) and LLH was supported by the National Science Foundation Graduate Research Fellowship Program.
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    Strong depth-related zonation of megabenthos on a rocky continental margin (∼700–4000 m) off southern Tasmania, Australia (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e85872, doi:10.1371/journal.pone.0085872.
    Description: Assemblages of megabenthos are structured in seven depth-related zones between ~700 and 4000 m on the rocky and topographically complex continental margin south of Tasmania, southeastern Australia. These patterns emerge from analysis of imagery and specimen collections taken from a suite of surveys using photographic and in situ sampling by epibenthic sleds, towed video cameras, an autonomous underwater vehicle and a remotely operated vehicle (ROV). Seamount peaks in shallow zones had relatively low biomass and low diversity assemblages, which may be in part natural and in part due to effects of bottom trawl fishing. Species richness was highest at intermediate depths (1000–1300 m) as a result of an extensive coral reef community based on the bioherm-forming scleractinian Solenosmilia variabilis. However, megabenthos abundance peaked in a deeper, low diversity assemblage at 2000–2500 m. The S. variabilis reef and the deep biomass zone were separated by an extensive dead, sub-fossil S. variabilis reef and a relatively low biomass stratum on volcanic rock roughly coincident with the oxygen minimum layer. Below 2400 m, megabenthos was increasingly sparse, though punctuated by occasional small pockets of relatively high diversity and biomass. Nonetheless, megabenthic organisms were observed in the vast majority of photographs on all seabed habitats and to the maximum depths observed - a sandy plain below 3950 m. Taxonomic studies in progress suggest that the observed depth zonation is based in part on changing species mixes with depth, but also an underlying commonality to much of the seamount and rocky substrate biota across all depths. Although the mechanisms supporting the extraordinarily high biomass in 2000–2500 m depths remains obscure, plausible explanations include equatorwards lateral transport of polar production and/or a response to depth-stratified oxygen availability.
    Description: Components of this work were supported by the National Science Foundation, the Australian Department of Environment, Water, Heritage, and the Arts, the Australian Commonwealth Environmental Research Fund, a grant of ship time by the Australian National Research Facility, and the CSIRO Wealth from Oceans and Climate Adaptation Flagships.
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    Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88618, doi:10.1371/journal.pone.0088618.
    Description: The taxon Syndermata comprises the biologically interesting wheel animals (“Rotifera”: Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.
    Description: The work was funded by the Deutsche Forschungsgemeinschaft (DFG grant Ha2103/4-3, Priority Project "Deep Metazoan Phylogeny", SPP1174; www. dfg.de). Additional financial support came from the Center for Computational Sciences (SRFN) of Johannes Gutenberg University Mainz (http://www.csm.unimainz. de).
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    Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e97338, doi:10.1371/journal.pone.0097338.
    Description: Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
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    Capture of lipopolysaccharide (endotoxin) by the blood clot : a comparative study (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e80192, doi:10.1371/journal.pone.0080192.
    Description: In vertebrates and arthropods, blood clotting involves the establishment of a plug of aggregated thrombocytes (the cellular clot) and an extracellular fibrillar clot formed by the polymerization of the structural protein of the clot, which is fibrin in mammals, plasma lipoprotein in crustaceans, and coagulin in the horseshoe crab, Limulus polyphemus. Both elements of the clot function to staunch bleeding. Additionally, the extracellular clot functions as an agent of the innate immune system by providing a passive anti-microbial barrier and microbial entrapment device, which functions directly at the site of wounds to the integument. Here we show that, in addition to these passive functions in immunity, the plasma lipoprotein clot of lobster, the coagulin clot of Limulus, and both the platelet thrombus and the fibrin clot of mammals (human, mouse) operate to capture lipopolysaccharide (LPS, endotoxin). The lipid A core of LPS is the principal agent of gram-negative septicemia, which is responsible for more than 100,000 human deaths annually in the United States and is similarly toxic to arthropods. Quantification using the Limulus Amebocyte Lysate (LAL) test shows that clots capture significant quantities of LPS and fluorescent-labeled LPS can be seen by microscopy to decorate the clot fibrils. Thrombi generated in the living mouse accumulate LPS in vivo. It is suggested that capture of LPS released from gram-negative bacteria entrapped by the blood clot operates to protect against the disease that might be caused by its systemic dispersal.
    Description: Grant # 0344360 from the National Science Foundation (PBA).
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    Post-seismic viscoelastic deformation and stress transfer after the 1960 M9.5 Valdivia, Chile earthquake : effects on the 2010 M8.8 Maule, Chile earthquake (2014)
    Oxford University Press
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    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
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    Ice sheet dynamics within an earth system model: downscaling, coupling and first results (2014)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(5), pp. 2003-2013, ISSN: 1991-9603
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    Publication Date: 2016-12-09
    Description: We present first results from a coupled model setup, consisting of the state-of-the-art ice sheet model RIMBAY (Revised Ice Model Based on frAnk pattYn), and the community earth system model COSMOS. We show that special care has to be provided in order to ensure physical distributions of the forcings as well as numeric stability of the involved models. We demonstrate that a suitable statistical downscaling is crucial for ice sheet stability, especially for southern Greenland where surface temperatures are close to the melting point. The downscaling of net snow accumulation is based on an empirical relationship between surface slope and rainfall. The simulated ice sheet does not show dramatic loss of ice volume for pre-industrial conditions and is comparable with present-day ice orography. A sensitivity study with high CO2 level is used to demonstrate the effects of dynamic ice sheets onto climate compared to the standard setup with prescribed ice sheets.
    Repository Name: EPIC Alfred Wegener Institut
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    Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.
    Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
    Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.
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    Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e103536, doi:10.1371/journal.pone.0103536.
    Description: Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the United States National Science Foundation (OCE 0825148 to SRT and GBS).
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    Aggregation and Sedimentation of Thalassiosira weissflogii (diatom) in a Warmer and More Acidified Future Ocean (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112379, doi:10.1575/1912/6845.
    Description: Increasing Transparent Exopolymer Particle (TEP) formation during diatom blooms as a result of elevated temperature and pCO2 have been suggested to result in enhanced aggregation and carbon flux, therewith potentially increasing the sequestration of carbon by the ocean. We present experimental results on TEP and aggregate formation by Thalassiosira weissflogii (diatom) in the presence or absence of bacteria under two temperature and three pCO2 scenarios. During the aggregation phase of the experiment TEP formation was elevated at the higher temperature (20°C vs. 15°C), as predicted. However, in contrast to expectations based on the established relationship between TEP and aggregation, aggregation rates and sinking velocity of aggregates were depressed in warmer treatments, especially under ocean acidification conditions. If our experimental findings can be extrapolated to natural conditions, they would imply a reduction in carbon flux and potentially reduced carbon sequestration after diatom blooms in the future ocean.
    Description: This work was supported by National Science Foundation grants OCE-0926711 & OCE-1041038 to UP and Helmholtz Graduate School for Polar and Marine Research and Jacobs University Bremen to SS.
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    Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates (2014)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
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    Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e92277, doi:10.1371/journal.pone.0092277.
    Description: Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were 〈5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.
    Description: This research was primarily funded by Fundação para a Ciência e a Tecnologia (FCT), Fundo Regional da Ciência, Tecnologia (FRCT), through research projects TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER], the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, and Proconvergencia Açores/EU Program]. We acknowledge funds provided by FCT to LARSyS Associated Laboratory and IMAR-University of the Azores/the Thematic Area D & E of the Strategic Project PEst-OE/EEI/LA0009/2011–1012 and 2013–2014 (OE & Compete) and by the FRCT - Government of the Azores pluriannual funding. MAS was supported by an FCT postdoctoral grant (SFRH/BPD/29841/2006) and is currently supported by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education through an FCT Investigator grant. RP was supported by an FCT doctoral grant (SFRH/BD/41192/2007) and by the research grant from the Azores Regional Fund for Science and Technology (M3.1.5/F/115/2012). IJ was supported by the Natural Sciences and Engineering Research Council (NSERC) and the Canada Foundation for Innovation (CFI) through their support of the Ocean Tracking Network. DJFR is funded by the United Kingdom Department of Energy and Climate Change as part of their Offshore Energy Strategic Environmental Assessment program. DT is funded by Natural Environment Research Council and Marine Scotland.
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    Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e94249, doi:10.1371/journal.pone.0094249.
    Description: The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
    Description: This work was partially funded by an Emerging Frontiers in Research and Innovation – Multicellular and Inter-kingdom Signaling (EFRI-MIKS) grant awarded by the US National Science Foundation to Joerg Graf and NIH RO1 GM095390 to JG and HGM.
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    First autonomous bio-optical profiling float in the Gulf of Mexico reveals dynamic biogeochemistry in deep waters (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e101658, doi:10.1371/journal.pone.0101658.
    Description: Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (bbp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R2 = 0.62). Particulate backscattering, bbp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between bbp and chlorophyll (R2 = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R2 = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.
    Description: This project was funded by Bureau of Ocean Energy Management (BOEM) Contract M10PC00112 to Leidos, Inc. with subcontract to ASB (www.boem.gov).
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    Magnetotelluric data, stable distributions and impropriety: an existential combination (2014)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
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    Swimming speed of larval snail does not correlate with size and ciliary beat frequency (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e82764, doi:10.1371/journal.pone.0082764.
    Description: Many marine invertebrates have planktonic larvae with cilia used for both propulsion and capturing of food particles. Hence, changes in ciliary activity have implications for larval nutrition and ability to navigate the water column, which in turn affect survival and dispersal. Using high-speed high-resolution microvideography, we examined the relationship between swimming speed, velar arrangements, and ciliary beat frequency of freely swimming veliger larvae of the gastropod Crepidula fornicata over the course of larval development. Average swimming speed was greatest 6 days post hatching, suggesting a reduction in swimming speed towards settlement. At a given age, veliger larvae have highly variable speeds (0.8–4 body lengths s−1) that are independent of shell size. Contrary to the hypothesis that an increase in ciliary beat frequency increases work done, and therefore speed, there was no significant correlation between swimming speed and ciliary beat frequency. Instead, there are significant correlations between swimming speed and visible area of the velar lobe, and distance between centroids of velum and larval shell. These observations suggest an alternative hypothesis that, instead of modifying ciliary beat frequency, larval C. fornicata modify swimming through adjustment of velum extension or orientation. The ability to adjust velum position could influence particle capture efficiency and fluid disturbance and help promote survival in the plankton.
    Description: K.Y.K. Chan was supported by the Postdoctoral Scholar 1 Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. H. Jiang was supported by National Science Foundation grant NSF OCE-1129496 and an award from WHOI's Ocean Life Institute, and D.K. Padilla was supported by NSF IOS-0920032.
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    Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e93296, doi:10.1371/journal.pone.0093296.
    Description: Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.
    Description: This research was made possible by a grant from the National Science Foundation Biological Oceanography Program and the Brown University Undergraduate Teaching and Research Award Program.
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    Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions (2014)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
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    Humpback whale populations share a core skin bacterial community : towards a health index for marine mammals? (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90785, doi:10.1371/journal.pone.0090785.
    Description: Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.
    Description: A.A. was funded by a WHOI Ocean Life Institute post-doctoral scholar award, and this research was supported by a grant to A.A. and T.J.M. from Woods Hole Oceanographic Institution's (WHOI) Marine Mammal Center.
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    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380.
    Description: Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
    Description: This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The contributions of S.K. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security (DHS) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.
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    The evolution of the four subunits of voltage-gated calcium channels : ancient roots, increasing complexity, and multiple losses (2014)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
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    Assessing the health of the U.S. west coast with a regional-scale application of the Ocean Health Index (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e98995, doi:10.1371/journal.pone.0098995.
    Description: Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions scoring from 65 (Washington) to 74 (Oregon). Highest scoring goals included tourism and recreation (99) and clean waters (87), while the lowest scoring goals were sense of place (48) and artisanal fishing opportunities (57). Surprisingly, even in this well-studied area data limitations precluded robust assessments of past trends in overall ocean health. Nonetheless, retrospective calculation of current status showed that many goals have declined, by up to 20%. In contrast, near-term future scores were on average 6% greater than current status across all goals and sub-regions. Application of hypothetical but realistic management scenarios illustrate how the Index can be used to predict and understand the tradeoffs among goals and consequences for overall ocean health. We illustrate and discuss how this index can be used to vet underlying assumptions and decisions with local stakeholders and decision-makers so that scores reflect regional knowledge, priorities and values. We also highlight the importance of ongoing and future monitoring that will provide robust data relevant to ocean health assessment.
    Description: Beau and Heather Wrigley generously provided the founding grant. Additional financial and in-kind support was provided by the Pacific Life Foundation, Thomas W. Haas Fund of the New Hampshire Charitable Foundation, the Oak Foundation, Akiko Shiraki Dynner Fund for Ocean Exploration and Conservation, Darden Restaurants Inc. Foundation, Conservation International, New England Aquarium, National Geographic, and the University of California Santa Barbara's National Center for Ecological Analysis and Synthesis, which supported the Ecosystem Health Working Group as part of the Science of Ecosystem-Based Management project funded by the David and Lucile Packard Foundation. Individual authors also acknowledge support from the U.S. National Science Foundation.
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    Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.
    Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
    Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.
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    The transcriptional response to oxidative stress during vertebrate development : effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e113158, doi:10.1371/journal.pone.0113158.
    Description: Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
    Description: This research was supported in part by National Institutes of Health grants R01ES016366 (MEH), R01ES006272 (MEH), R01ES015912 (JJS), and F32ES017585 (ART-L), the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a WHOI (Woods Hole Oceanographic Institution) Postdoctoral Scholar award, and the Walter A. and Hope Noyes Smith endowed chair (MEH). AGM and MJC were supported in part by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.
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    Multi-events earthquake early warning algorithm using a Bayesian approach (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    A Lagrangian advection scheme with shape matrix (LASM) for solving advection problems (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: A Lagrangian advection scheme with shape matrix (LASM) for solving advection problems Geoscientific Model Development, 7, 2951-2968, 2014 Author(s): L. Dong, B. Wang, and L. Liu A new Lagrangian advection scheme with shape matrix (LASM) is proposed to take advantage of the extreme low numerical diffusion of the Lagrangian methods. The tracer is discretized into finite parcels, which move along the downstream trajectories. Different from other Lagrangian schemes, the parcel shape is simulated explicitly by a linear transformation matrix. By doing so, the aliasing error in the Lagrangian schemes is largely reduced without introducing substantial interparcel mixing in the pure advection stage, because the flow information will be respected when remapping tracer density onto the fixed model grids. An adaptive interparcel mixing algorithm is constructed to ensure the validity of the linear approximation of the parcel shape, where the mixing is only triggered when it is necessary and resembles the physical mixing. The total tracer mass on the parcels is conserved exactly. The new scheme is validated by using several test cases.
    Print ISSN: 1991-959X
    Electronic ISSN: 1991-9603
    Topics: Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Technical Note: Reducing the spin-up time of integrated surface water–groundwater models (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: Technical Note: Reducing the spin-up time of integrated surface water–groundwater models Hydrology and Earth System Sciences, 18, 5169-5179, 2014 Author(s): H. Ajami, J. P. Evans, M. F. McCabe, and S. Stisen One of the main challenges in the application of coupled or integrated hydrologic models is specifying a catchment's initial conditions in terms of soil moisture and depth-to-water table (DTWT) distributions. One approach to reducing uncertainty in model initialization is to run the model recursively using either a single year or multiple years of forcing data until the system equilibrates with respect to state and diagnostic variables. However, such "spin-up" approaches often require many years of simulations, making them computationally intensive. In this study, a new hybrid approach was developed to reduce the computational burden of the spin-up procedure by using a combination of model simulations and an empirical DTWT function. The methodology is examined across two distinct catchments located in a temperate region of Denmark and a semi-arid region of Australia. Our results illustrate that the hybrid approach reduced the spin-up period required for an integrated groundwater–surface water–land surface model (ParFlow.CLM) by up to 50%. To generalize results to different climate and catchment conditions, we outline a methodology that is applicable to other coupled or integrated modeling frameworks when initialization from an equilibrium state is required.
    Print ISSN: 1027-5606
    Electronic ISSN: 1607-7938
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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  • 56
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    Extending periodic eddy covariance latent heat fluxes through tree sapflow measurements to estimate long-term total evaporation in a peat swamp forest (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: Extending periodic eddy covariance latent heat fluxes through tree sapflow measurements to estimate long-term total evaporation in a peat swamp forest Hydrology and Earth System Sciences Discussions, 11, 13607-13661, 2014 Author(s): A. D. Clulow, C. S. Everson, M. G. Mengistu, J. S. Price, A. Nickless, and G. P. W. Jewitt A combination of measurement and modelling was used to find a pragmatic solution to estimate the annual total evaporation (ET) from the rare and indigenous Nkazana Peat Swamp Forest (PSF) on the east coast of Southern Africa to improve the water balance estimates within the area. Total evaporation was measured during three window periods (between seven and nine days each) using an eddy covariance (EC) system on a telescopic mast above the forest canopy. Sapflow of an understory and an emergent tree was measured using a low maintenance heat pulse velocity system for an entire hydrological year (October 2009 to September 2010). An empirical model was derived, describing the relationship between the observed ET of the Nkazana PSF measured during two of the window periods ( R 2 = 0.92 and 0.90) which, overlapped with sapflow measurements, thereby providing hourly estimates of predicted ET of the Nkazana PSF for a year, totalling 1125 mm (while rainfall was 650 mm). In building the empirical model, it was found that including the understory tree sapflow provided no benefit to the model performance. In addition, the observed emergent tree sapflow relationship with observed ET between the two field campaigns was consistent and could be represented by a single empirical model ( R 2 = 0.90; RMSE = 0.08 mm). During the window periods of EC measurement, no single meteorological variable was found to describe the Nkazana PSF ET satisfactorily. However, in terms of evaporation models, the hourly FAO56 Penman–Monteith equation best described the observed ET from EC during the August 2009 ( R 2 = 0.75), November 2009 ( R 2 = 0.85) and March 2010 ( R 2 = 0.76) field campaigns, compared to the Priestley–Taylor model ( R 2 = 0.54, 0.74 and 0.62 during the respective field campaigns). From the empirical model of ET and the FAO56 Penman–Monteith equation, a monthly crop factor ( K c ) was derived for the Nkazana PSF providing a method of estimating long-term swamp forest ET from meteorological data. The monthly crop factor indicated two distinct periods. From February to May, it was between 1.2 and 1.4 compared with June to January, when the crop factor was 0.8 to 1.0. The derived monthly K c values were verified as accurate (to one significant digit) using historical data measured at the same site, also using EC, from a~previous study. The measurements provided insights into the microclimate within a subtropical peat swamp forest and the contrasting sapflow of emergent and understory trees. They showed that expensive, high maintenance equipment can be used during manageable window periods in conjunction with low maintenance systems, dedicated to individual trees, to derive a model to estimate long-term ET over remote heterogeneous forests. In addition, the contrast in ET and rainfall emphasises the reliance of the Nkazana PSF on groundwater.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    A catalogue of 2D photometric decompositions in the SDSS-DR7 spectroscopic main galaxy sample: preferred models and systematics (2014)
    Oxford University Press
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    Publication Date: 2014-12-12
    Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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    Stratospheric ozone depletion from future nitrous oxide increases (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: Stratospheric ozone depletion from future nitrous oxide increases Atmospheric Chemistry and Physics, 14, 12967-12982, 2014 Author(s): W. Wang, W. Tian, S. Dhomse, F. Xie, J. Shu, and J. Austin We have investigated the impact of the assumed nitrous oxide (N 2 O) increases on stratospheric chemistry and dynamics using a series of idealized simulations with a coupled chemistry-climate model (CCM). In a future cooler stratosphere the net yield of NO y from N 2 O is shown to decrease in a reference run following the IPCC A1B scenario, but NO y can still be significantly increased by extra increases of N 2 O over 2001–2050. Over the last decade of simulations, 50% increases in N 2 O result in a maximal 6% reduction in ozone mixing ratios in the middle stratosphere at around 10 hPa and an average 2% decrease in the total ozone column (TCO) compared with the control run. This enhanced destruction could cause an ozone decline in the first half of this century in the middle stratosphere around 10 hPa, while global TCO still shows an increase at the same time. The results from a multiple linear regression analysis and sensitivity simulations with different forcings show that the chemical effect of N 2 O increases dominates the N 2 O-induced ozone depletion in the stratosphere, while the dynamical and radiative effects of N 2 O increases are overall insignificant. The analysis of the results reveals that the ozone depleting potential of N 2 O varies with the time period and is influenced by the environmental conditions. For example, carbon dioxide (CO 2 ) increases can strongly offset the ozone depletion effect of N 2 O.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    Corrigendum to "Air-sea exchange and gas-particle partitioning of polycyclic aromatic hydrocarbons in the Mediterranean" published in Atmos. Chem. Phys., 14, 8905–8915, 2014 (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: Corrigendum to "Air-sea exchange and gas-particle partitioning of polycyclic aromatic hydrocarbons in the Mediterranean" published in Atmos. Chem. Phys., 14, 8905–8915, 2014 Atmospheric Chemistry and Physics, 14, 12965-12965, 2014 Author(s): M. D. Mulder, A. Heil, P. Kukučka, J. Klánová, J. Kuta, R. Prokeš, F. Sprovieri, and G. Lammel No abstract available.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide Atmospheric Chemistry and Physics, 14, 12951-12964, 2014 Author(s): A. W. Birdsall, C. R. Miner, L. E. Mael, and M. J. Elrod Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
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    Megacity emission plume characteristics in summer and winter investigated by mobile aerosol and trace gas measurements: the Paris metropolitan area (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: Megacity emission plume characteristics in summer and winter investigated by mobile aerosol and trace gas measurements: the Paris metropolitan area Atmospheric Chemistry and Physics, 14, 12931-12950, 2014 Author(s): S.-L. von der Weiden-Reinmüller, F. Drewnick, Q. J. Zhang, F. Freutel, M. Beekmann, and S. Borrmann For the investigation of megacity emission plume characteristics mobile aerosol and trace gas measurements were carried out in the greater Paris region in July 2009 and January–February 2010 within the EU FP7 MEGAPOLI project (Megacities: Emissions, urban, regional and Global Atmospheric POLlution and climate effects, and Integrated tools for assessment and mitigation). The deployed instruments measured physical and chemical properties of sub-micron aerosol particles, gas phase constituents of relevance for urban air pollution studies and meteorological parameters. The emission plume was identified based on fresh pollutant (e.g., particle-bound polycyclic aromatic hydrocarbons, black carbon, CO 2 and NO x ) concentration changes in combination with wind direction data. The classification into megacity influenced and background air masses allowed a characterization of the emission plume during summer and winter environmental conditions. On average, a clear increase of fresh pollutant concentrations in plume compared to background air masses was found for both seasons. For example, an average increase of 190% (+ 8.8 ng m −3 ) in summer and of 130% (+ 18.1 ng m −3 ) in winter was found for particle-bound polycyclic aromatic hydrocarbons in plume air masses. The aerosol particle size distribution in plume air masses was influenced by nucleation and growth due to coagulation and condensation in summer, while in winter only the latter process (i.e., particle growth) seemed to be initiated by urban pollution. The observed distribution of fresh pollutants in the emission plume – its cross sectional Gaussian-like profile and the exponential decrease of pollutant concentrations with increasing distance to the megacity – are in agreement with model results. Differences between model and measurements were found for plume center location, plume width and axial plume extent. In general, dilution was identified as the dominant process determining the axial variations within the Paris emission plume. For in-depth analysis of transformation processes occurring in the advected plume, simultaneous measurements at a suburban measurement site and a stationary site outside the metropolitan area using the mobile laboratory have proven to be most useful. Organic aerosol oxidation was observed in summer, while in winter transformation processes seemed to occur at a slower rate.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
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    A regional CO 2 observing system simulation experiment for the ASCENDS satellite mission (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: A regional CO 2 observing system simulation experiment for the ASCENDS satellite mission Atmospheric Chemistry and Physics, 14, 12897-12914, 2014 Author(s): J. S. Wang, S. R. Kawa, J. Eluszkiewicz, D. F. Baker, M. Mountain, J. Henderson, T. Nehrkorn, and T. S. Zaccheo Top–down estimates of the spatiotemporal variations in emissions and uptake of CO 2 will benefit from the increasing measurement density brought by recent and future additions to the suite of in situ and remote CO 2 measurement platforms. In particular, the planned NASA Active Sensing of CO 2 Emissions over Nights, Days, and Seasons (ASCENDS) satellite mission will provide greater coverage in cloudy regions, at high latitudes, and at night than passive satellite systems, as well as high precision and accuracy. In a novel approach to quantifying the ability of satellite column measurements to constrain CO 2 fluxes, we use a portable library of footprints (surface influence functions) generated by the Stochastic Time-Inverted Lagrangian Transport (STILT) model in combination with the Weather Research and Forecasting (WRF) model in a regional Bayesian synthesis inversion. The regional Lagrangian particle dispersion model framework is well suited to make use of ASCENDS observations to constrain weekly fluxes in North America at a high resolution, in this case at 1° latitude × 1° longitude. We consider random measurement errors only, modeled as a function of the mission and instrument design specifications along with realistic atmospheric and surface conditions. We find that the ASCENDS observations could potentially reduce flux uncertainties substantially at biome and finer scales. At the grid scale and weekly resolution, the largest uncertainty reductions, on the order of 50%, occur where and when there is good coverage by observations with low measurement errors and the a priori uncertainties are large. Uncertainty reductions are smaller for a 1.57 μm candidate wavelength than for a 2.05 μm wavelength, and are smaller for the higher of the two measurement error levels that we consider (1.0 ppm vs. 0.5 ppm clear-sky error at Railroad Valley, Nevada). Uncertainty reductions at the annual biome scale range from ~40% to ~75% across our four instrument design cases and from ~65% to ~85% for the continent as a whole. Tests suggest that the quantitative results are moderately sensitive to assumptions regarding a priori uncertainties and boundary conditions. The a posteriori flux uncertainties we obtain, ranging from 0.01 to 0.06 Pg C yr −1 across the biomes, would meet requirements for improved understanding of long-term carbon sinks suggested by a previous study.
    Print ISSN: 1680-7316
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    Estimating regional fluxes of CO 2 and CH 4 using space-borne observations of XCH 4 : XCO 2 (2014)
    Copernicus
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    Publication Date: 2014-12-09
    Description: Estimating regional fluxes of CO 2 and CH 4 using space-borne observations of XCH 4 : XCO 2 Atmospheric Chemistry and Physics, 14, 12883-12895, 2014 Author(s): A. Fraser, P. I. Palmer, L. Feng, H. Bösch, R. Parker, E. J. Dlugokencky, P. B. Krummel, and R. L. Langenfelds We use the GEOS-Chem global 3-D atmospheric chemistry transport model to interpret XCH 4 :XCO 2 column ratios retrieved from the Japanese Greenhouse Gases Observing Satellite (GOSAT). The advantage of these data over CO 2 and CH 4 columns retrieved independently using a full physics optimal estimation algorithm is that they are less prone to scattering-related regional biases. We show that the model is able to reproduce observed global and regional spatial (mean bias =0.7%) and temporal variations (global r 2 =0.92) of this ratio with a model bias 〈 2.5%. We also show that these variations are driven by emissions of CO 2 and CH 4 that are typically 6 months out of phase, which may reduce the sensitivity of the ratio to changes in either gas. To simultaneously estimate fluxes of CO 2 and CH 4 we use a maximum likelihood estimation approach. We use two approaches to resolve independent flux estimates of these two gases using GOSAT observations of XCH 4 :XCO 2 : (1) the a priori error covariance between CO 2 and CH 4 describing common source from biomass burning; and (2) also fitting independent surface atmospheric measurements of CH 4 and CO 2 mole fraction that provide additional constraints, improving the effectiveness of the observed GOSAT ratio to constrain flux estimates. We demonstrate the impact of these two approaches using numerical experiments. A posteriori flux estimates inferred using only the GOSAT ratios and taking advantage of the error covariance due to biomass burning are not consistent with the true fluxes in our experiments, as the inversion system cannot judge which species' fluxes to adjust. This reflects the weak dependence of XCH 4 :XCO 2 on biomass burning. We find that adding the surface data effectively provides an "anchor" to the inversion that dramatically improves the ability of the GOSAT ratios to infer both CH 4 and CO 2 fluxes. We show that the regional flux estimates inferred from GOSAT XCH 4 :XCO 2 ratios together with the surface mole fraction data during 2010 are typically consistent with or better than the corresponding values inferred from fitting XCH 4 or the full-physics XCO 2 data products, as judged by a posteriori uncertainties. We show that the fluxes inferred from the ratio measurements perform best over regions where there is a large seasonal cycle such as Tropical South America, for which we report a small but significant annual source of CO 2 compared to a small annual sink inferred from the XCO 2 data. We argue that given that the ratio measurements are less compromised by systematic error than the full physics data products, the resulting a~posteriori estimates and uncertainties provide a more faithful description of the truth. Based on our analysis we also argue that by using the ratios we may be reaching the current limits on the precision of these observed space-based data.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
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    Long-term variability of storm surge frequency in the Venice Lagoon: an update thanks to eighteenth century sea level observations (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: Long-term variability of storm surge frequency in the Venice Lagoon: an update thanks to eighteenth century sea level observations Natural Hazards and Earth System Sciences Discussions, 2, 7465-7486, 2014 Author(s): F. Raicich Sea level observations made in the Venice Lagoon between 1751 and 1792 have been recovered, consisting of two time series of daily data on high and low waters at Venice and Chioggia. From comparisons with modern observations the quality of the 18th century data appears to be good enough to allow a useful analysis. A composite time series of daily mean sea level is obtained by merging the 18th century data and 1872–2004 observations at Venice Punta della Salute. The absence of reliable information on vertical references prevents the connection of the two 18th century time series with each other and with modern observations. However, daily sea level anomalies relative to the mean sea level enable to recognize storm surge events, that appear to occur more frequently in the second half of the 18th century than in the late 19th and 20th centuries, particularly during the 1751–1769 period. The record-breaking storm surge of 4 November 1966 turns out to be a remarkable event also in comparison with the events extracted from the 18th century time series. Further work is required to fill the gap between the old and modern observations.
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
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    Ground-penetrating radar observations for estimating the vertical displacement of rotational landslides (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: Ground-penetrating radar observations for estimating the vertical displacement of rotational landslides Natural Hazards and Earth System Sciences Discussions, 2, 7487-7506, 2014 Author(s): C. Lissak, O. Maquaire, J.-P. Malet, F. Lavigne, C. Virmoux, C. Gomez, and R. Davidson The objective of this paper is to demonstrate the applicability of Ground Penetrating Radar (GPR) for monitoring the displacement of slow-moving landslides. GPR data is used to estimate the vertical movement of rotational slides in combination with other surveying techniques. The experimental site is located along the Normandy coast (North East France) here several rotational landslides are continuously affected by a seasonal kinematic pattern (low displacement rates of 0.01 to 0.10 m yr −1 ) and periodically by major acceleration events (high displacement of 1.0 to 7.0 m per event).
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
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    The H I-dominated low-surface-brightness galaxy KKR 17 (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    A multiwavelength study of the M dwarf binary YY Geminorum (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Global representation of tropical cyclone-induced ocean thermal changes using Argo data – Part 2: Estimating air–sea heat fluxes and ocean heat content changes (2014)
    Copernicus
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    Publication Date: 2014-12-13
    Description: Global representation of tropical cyclone-induced ocean thermal changes using Argo data – Part 2: Estimating air–sea heat fluxes and ocean heat content changes Ocean Science Discussions, 11, 2907-2937, 2014 Author(s): L. Cheng, J. Zhu, and R. L. Sriver We use Argo temperature data to examine changes in ocean heat content (OHC) and air–sea heat fluxes induced by tropical cyclones (TC)s on a global scale. A footprint technique that analyzes the vertical structure of cross-track thermal responses along all storm tracks during the period 2004–2012 is utilized (see part I). We find that TCs are responsible for 1.87 PW (11.05 W m −2 when averaging over the global ocean basin) of heat transfer annually from the global ocean to the atmosphere during storm passage (0–3 days) on a global scale. Of this total, 1.05 ± 0.20 PW (4.80 ± 0.85 W m −2 ) is caused by Tropical storms/Tropical depressions (TS/TD) and 0.82 ± 0.21 PW (6.25 ± 1.5 W m −2 ) is caused by hurricanes. Our findings indicate that ocean heat loss by TCs may be a substantial missing piece of the global ocean heat budget. Net changes in OHC after storm passage is estimated by analyzing the temperature anomalies during wake recovery following storm events (4–20 days after storm passage) relative to pre-storm conditions. Results indicate the global ocean experiences a 0.75 ± 0.25 PW (5.98 ± 2.1W m −2 ) net heat gain annually for hurricanes. In contrast, under TS/TD conditions, ocean experiences 0.41 ± 0.21 PW (1.90 ± 0.96 W m −2 ) net ocean heat loss, suggesting the overall oceanic thermal response is particularly sensitive to the intensity of the event. The net ocean heat uptake caused by all storms is 0.34 PW.
    Print ISSN: 1812-0806
    Electronic ISSN: 1812-0822
    Topics: Geosciences
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    Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer Atmospheric Measurement Techniques, 7, 4445-4453, 2014 Author(s): B. Xiang, D. D. Nelson, J. B. McManus, M. S. Zahniser, R. A. Wehr, and S. C. Wofsy We present field test results for a new spectroscopic instrument to measure atmospheric carbon dioxide (CO 2 ) with high precision (0.02 μmol mol −1 , or ppm at 1 Hz) and demonstrate high stability (within 0.1 ppm over more than 8 months), without the need for hourly, daily, or even monthly calibration against high-pressure gas cylinders. The technical novelty of this instrument (ABsolute Carbon dioxide, ABC) is the spectral null method using an internal quartz reference cell with known CO 2 column density. Compared to a previously described prototype, the field instrument has better stability and benefits from more precise thermal control of the optics and more accurate pressure measurements in the sample cell (at the mTorr level). The instrument has been deployed at a long-term ecological research site (the Harvard Forest, USA), where it has measured for 8 months without on-site calibration and with minimal maintenance, showing drift bounds of less than 0.1 ppm. Field measurements agree well with those of a commercially available cavity ring-down CO 2 instrument (Picarro G2301) run with a standard calibration protocol. This field test demonstrates that ABC is capable of performing high-accuracy, unattended, continuous field measurements with minimal use of reference gas cylinders.
    Print ISSN: 1867-1381
    Electronic ISSN: 1867-8548
    Topics: Geosciences
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    Meteorological factors controlling low-level continental pollutant outflow across a coast (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Meteorological factors controlling low-level continental pollutant outflow across a coast Atmospheric Chemistry and Physics, 14, 13295-13312, 2014 Author(s): D. L. Peake, H. F. Dacre, J. Methven, and O. Coceal Coastal outflow describes the horizontal advection of pollutants from the continental boundary layer (BL) across a coastline. The outflow can ventilate polluted continental BLs and thus regulate air quality in highly populated coastal regions. This paper investigates the factors controlling coastal outflow and quantifies their importance as a ventilation mechanism. Tracers in the Met Office Unified Model (MetUM) are used to examine the magnitude and variability of coastal outflow over the eastern United States during summer 2004. Over the 4 week period examined, ventilation of tracer from the continental BL via coastal outflow occurs with the same magnitude as vertical ventilation via convection and advection. The relative importance of tracer decay rate, cross-coastal advection rate, and a parameter based on the relative continental and marine BL heights on coastal outflow is assessed by reducing the problem to a time-dependent box model. The ratio of the advection rate and decay rate is a dimensionless parameter which determines whether tracers are long-lived or short-lived. Long- and short-lived tracers exhibit different behaviours with respect to coastal outflow. Short-lived tracers exhibit large diurnal variability in coastal outflow but long-lived tracers do not. For short-lived tracers, increasing the advection rate increases the diurnally averaged magnitude of coastal outflow, but this has the opposite effect for very long-lived tracers. By using the box-model solutions to interpret the MetUM simulations, a land width is determined which represents the distance inland over which emissions contribute significantly to coastal outflow. A land width of between 100 and 400 km is found to be representative for a tracer with a lifetime of 24 h.
    Print ISSN: 1680-7316
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    An efficient radiative cooling approximation for use in hydrodynamic simulations (2014)
    Oxford University Press
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    Publication Date: 2014-12-14
    Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Continental Portuguese Territory Flood Susceptibility Index – contribution for a vulnerability index (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Continental Portuguese Territory Flood Susceptibility Index – contribution for a vulnerability index Natural Hazards and Earth System Sciences Discussions, 2, 7521-7552, 2014 Author(s): R. Jacinto, N. Grosso, E. Reis, L. Dias, F. D. Santos, and P. Garrett This work defines a national flood susceptibility index for the Portuguese continental territory, by proposing the aggregation of different variables which represent natural conditions for permeability, runoff and accumulation. This index is part of the national vulnerability index developed in the scope of Flood Maps in Climate Change Scenarios (CIRAC) project, supported by the Portuguese Association of Insurers (APS). This approach expands on previous works by trying to bridge the gap between different floods mechanisms (e.g. progressive and flash floods) occurring at different spatial scales in the Portuguese territory through: (a) selecting homogeneously processed datasets, (b) aggregating their values to better translate the spatially continuous and cumulative influence in floods at multiple spatial scales. Results show a good ability to capture, in the higher susceptibility classes, different flood types: progressive floods and flash floods. Lower values are usually related to: mountainous areas, low water accumulation potential and more permeable soils. Validation with independent flood datasets confirmed these index characteristics, although some overestimation can be seen in the southern region of Alentejo where, due to a dense hydrographic network and an overall low slope, floods are not as frequent as a result of lower precipitation mean values. Future work will focus on: (i) including extreme precipitation datasets to represent the triggering factor, (ii) improving representation of smaller and stepper basins, (iii) optimizing variable weight definition process, (iii) developing more robust independent flood validation datasets.
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
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    Simple, affordable and sustainable borehole observatories for complex monitoring objectives (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Simple, affordable and sustainable borehole observatories for complex monitoring objectives Geoscientific Instrumentation, Methods and Data Systems Discussions, 4, 653-681, 2014 Author(s): A. Kopf, T. Freudenthal, V. Ratmeyer, M. Bergenthal, M. Lange, T. Fleischmann, S. Hammerschmidt, C. Seiter, and G. Wefer Seafloor drill rigs are remotely operated systems that provide a cost effective means to recover sedimentary records of the upper sub-seafloor deposits. Recent increases in their payload included downhole logging tools or autoclave coring systems. We here report on another milestone in using seafloor rigs: the development and installation of shallow borehole observatories. Three different systems have been developed for the MARUM-MeBo seafloor drill, which is operated by MARUM, University of Bremen, Germany. A simple design, the MeBoPLUG, separates the inner borehole from the overlying ocean by using o-ring seals at the conical threads of the drill pipe. The systems are self-contained and include data loggers, batteries, thermistors and a differential pressure sensor. A second design, the so-called MeBoCORK, is more sophisticated and also hosts an acoustic modem for data transfer and, if desired, fluid sampling capability using osmotic pumps. Of these MeBoCORKs, two systems have to be distinguished: the CORK-A (A = autonomous) can be installed by the MeBo alone and monitors pressure and temperature inside and above the borehole (the latter for reference). The CORK-B (B = bottom) has a higher payload and can additionally be equipped with geochemical, biological or other physical components. Owing to its larger size, it is installed by ROV and utilises a hotstab connection in the upper portion of the drill string. Either design relies on a hotstab connection from beneath which coiled tubing with a conical drop weight is lowered to couple to the formation. These tubes are fluid-saturated and either serve to transmit pore pressure signals or collect pore water in the osmo-sampler. The third design, the MeBoPUPPI ( P op- U p P ore P ressure I nstrument), is similar to the MeBoCORK-A and monitors pore pressure and temperature in a self-contained manner. Instead of transferring data upon command using an acoustic modem, the MeBoPUPPI contains a pop-up telemetry with Iridium link. After a predefined period, the data unit with satellite link is released, ascends to the sea surface, and remains there for up to two weeks while sending the long-term data sets to shore. In summer 2012, two MeBoPLUGs, one MeBoCORK-A and one MeBoCORK-B were installed with MeBo on German RV Sonne in the Nankai Trough area, Japan. We have successfully downloaded data from the CORKs, attesting that coupling to the formation worked and pressure records were elevated relative to the seafloor reference. In the near future, we will further deploy the first two MeBoPUPPIs. Recovery of all monitoring systems by ROV is planned for 2016.
    Electronic ISSN: 2193-0872
    Topics: Geosciences
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    Dye tracing for investigating flow and transport properties of hydrocarbon-polluted Rabots glaciär, Kebnekaise, Sweden (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Dye tracing for investigating flow and transport properties of hydrocarbon-polluted Rabots glaciär, Kebnekaise, Sweden Hydrology and Earth System Sciences Discussions, 11, 13711-13744, 2014 Author(s): C. C. Clason, C. Coch, J. Jarsjö, K. Brugger, P. Jansson, and G. Rosqvist Over 11 000 L of hydrocarbon pollution was deposited on the surface of Rabots glaciär on the Kebnekaise Massif, northern Sweden, following the crash of a Royal Norwegian Air Force aircraft in March 2012. An environmental monitoring programme was subsequently commissioned, including water, snow and ice sampling. The scientific programme further included a series of dye tracing experiments during the 2013 melt season, conducted to investigate flow pathways for pollutants through the glacier hydrological system, and to gain new insight to the internal hydrological system of Rabots glaciär. Results of dye tracing reveal a degree of homogeneity in the topology of the drainage system throughout July and August, with an increase in efficiency as the season progresses, as reflected by decreasing temporary storage and dispersivity. Early onset of melting likely led to formation of an efficient, discrete drainage system early in the melt season, subject to decreasing sinuosity and braiding as the season progressed. Analysis of turbidity-discharge hysteresis further supports the formation of discrete, efficient drainage, with clockwise diurnal hysteresis suggesting easy mobilisation of readily-available sediments in channels. Dye injection immediately downstream of the pollution source zone revealed prolonged storage of dye followed by fast, efficient release. Twinned with a low dye recovery, and supported by sporadic detection of hydrocarbons in the proglacial river, we suggest that meltwater, and thus pollutants in solution, may be released periodically from this zone of the glacier hydrological system. The here identified dynamics of dye storage, dispersion and breakthrough indicate that the ultimate fate and permanence of pollutants in the glacier system is likely to be governed by storage of pollutants in the firn layer and ice mass, or within the internal hydrological system, where it may refreeze. This shows that future studies on the fate of hydrocarbons in pristine, glaciated mountain environments should address the extent to which pollutants in solution act like water molecules or whether they are more susceptible to, for example, refreezing into the surrounding ice, becoming stuck in micro-fractures and pore spaces, or sorption onto subglacial sediments.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
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    Magnetic resonance tomography using elongated transmitter and in-loop receiver arrays for time-efficient 2-D imaging of subsurface aquifer structures (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Integrated velocity field from ground and satellite geodetic techniques: application to Arenal volcano (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Air temperature variability over three glaciers in the Ortles-Cevedale (Italian Alps): effects of glacier disintegration, intercomparison of calculation methods, and impacts on mass balance modeling (2014)
    Copernicus
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    Publication Date: 2014-12-16
    Description: Air temperature variability over three glaciers in the Ortles-Cevedale (Italian Alps): effects of glacier disintegration, intercomparison of calculation methods, and impacts on mass balance modeling The Cryosphere Discussions, 8, 6147-6192, 2014 Author(s): L. Carturan, F. Cazorzi, F. De Blasi, and G. Dalla Fontana Glacier mass balance models rely on accurate spatial calculation of input data, in particular air temperature. Lower temperatures (the so-called glacier cooling effect), and lower temperature variability (the so-called glacier damping effect) generally occur over glaciers, compared to ambient conditions. These effects, which depend on the geometric characteristics of glaciers and display a high spatial and temporal variability, have been mostly investigated on medium- to large-size glaciers so far, while observations on smaller ice bodies are scarce. Using a dataset from 8 on-glacier and 4 off-glacier weather stations, collected in summer 2010 and 2011, we analyzed the air temperature variability and wind regime over three different glaciers in the Ortles-Cevedale. The magnitude of the cooling effect and the occurrence of katabatic boundary layer (KBL) processes showed remarkable differences among the three ice bodies, suggesting the likely existence of important reinforcing mechanisms during glacier decay and disintegration. None of the methods proposed in the literature for calculating on-glacier temperature from off-glacier data fully reproduced our observations. Among them, the more physically-based procedure of Greuell and Böhm (1998) provided the best overall results where the KBL prevail, but it was not effective elsewhere (i.e. on smaller ice bodies and close to the glacier margins). The accuracy of air temperature estimations strongly impacted the results from a mass balance model which was applied to the three investigated glaciers. Most importantly, even small temperature deviations caused distortions in parameter calibration, thus compromising the model generalizability.
    Print ISSN: 1994-0432
    Electronic ISSN: 1994-0440
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    Galactic outflow and diffuse gas properties at z 〉= 1 using different baryonic feedback models (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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    Multiplex sequencing of pooled mitochondrial genomes--a crucial step toward biodiversity analysis using mito-metagenomics (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Easy quantitative assessment of genome editing by sequence trace decomposition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.
    Keywords: Targeted gene modification
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    Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients ( r 2 ) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
    Keywords: Nucleic acid structure, Protein-nucleic acid interaction
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    Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity ( T m ), nuclease stability, activity in vitro and in vivo , RNase H activation and cleavage patterns (both human and E. coli ) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro , while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo , the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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    qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction–modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.
    Keywords: Nucleic acid modification, Computational Methods
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    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
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    In silico prediction of splice-altering single nucleotide variants in the human genome (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
    Keywords: RNA characterisation and manipulation, Computational Methods
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    AGO2 and SETDB1 cooperate in promoter-targeted transcriptional silencing of the androgen receptor gene (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In mammals, RNA interference is primarily a post-transcriptional mechanism. Evidence has accumulated for additional role in transcriptional gene silencing (TGS) but the question for a good paradigm for small interfering antigene RNA (agRNA)-induced chromatin modification remains unanswered. Here, we show that SETDB1, a histone H3-lysine 9 (H3K9)-specific methyltransferase, cooperates with Argonaute-2 (AGO2) and plays an essential role in agRNA-induced TGS. The androgen receptor ( AR ) gene was transcriptionally silenced by agRNA targeted to its promoter, and we show that this repression was mitigated by knockdown of SETDB1 or AGO2 . Chromatin immunoprecipitation demonstrated that agRNA-driven AGO2 was first targeted to the AR promoter, followed by SETDB1. SIN3A and HDAC1/2, the components of the SIN3-HDAC complex, immunoprecipitated with SETDB1, and localized at the agRNA-targeted promoter. Agreeing with the presence of SETDB1, trimethyl-H3K9 was enriched in the AR promoter. Both EZH2 and trimethyl-H3K27 were also present in the targeted locus; accordingly, EZH2 immunoprecipitated with SETDB1. DNA methylation level was not significantly changed, suggesting the absence of de novo methylating activity in agRNA-induced AR promoter. Our results demonstrate that SETDB1, together with AGO2, plays an essential role in TGS through recruiting chromatin remodeler and/or other modifiers, consequently creating a repressive chromatin milieu at the targeted promoter.
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    The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.
    Print ISSN: 0305-1048
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    Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Keywords: Genomics
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    Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html .
    Keywords: Nucleic acid structure, Computational Methods
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    EDITORIAL: NAR AWARDS 2014 (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
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    Mesoscale modeling study of the interactions between aerosols and PBL meteorology during a haze episode in China Jing–Jin–Ji and its near surrounding region – Part 1: Aerosol distributions and meteorological features (2014)
    Copernicus
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    Publication Date: 2014-12-17
    Description: Mesoscale modeling study of the interactions between aerosols and PBL meteorology during a haze episode in China Jing–Jin–Ji and its near surrounding region – Part 1: Aerosol distributions and meteorological features Atmospheric Chemistry and Physics Discussions, 14, 31675-31717, 2014 Author(s): H. Wang, M. Xue, X. Y. Zhang, H. L. Liu, C. H. Zhou, S. C. Tan, H. Z. Che, B. Chen, and T. Li The urbanized region of Beijing–Tianjin–Hebei – often shortened to Jing–Jin–Ji and referred to as the 3JNS region in this paper – and its near surrounding region is becoming China's most polluted area by haze, exceeding even the Yangtze and Pearl river deltas. Aside from pollutant emission, the meteorology of the planetary boundary layer (PBL) is the most important factor affecting haze pollution. Focusing on July 2008, the aerosol optical properties and PBL meteorology features closely related with haze formation were simulated in 3JNS region using an online atmospheric chemical transport model. The relationship between regional PBL meteorology, PM 2.5 , and haze is discussed. Model results accurately simulated the aerosol optical depth (AOD), single scattering albedo (SSA) and asymmetry parameter (ASY), validate by comparison with observations from the MODerate Resolution Imaging Spectroradiometer (MODIS), the China Aerosol Remote Sensing NETwork (CARSNET) and the Aerosol Robotic NETwork (AERONET). Modeled PBL wind speeds showed reasonable agreement with those from the National Centers for Environmental Prediction (NCEP) Reanalysis 2. A monthly mean AOD value as high as 1.2 was found from both model and observations, with a daily mean larger than 2.0 during haze episodes in the 3JNS Region. Modeled and observed SSA values of 0.9–0.96 and ASY values of 0.72–0.74 demonstrated the high scattering characteristic of summer aerosols in this region. PBL wind speeds from modeled and NCEP data both showed a reversing trend of PM 2.5 variation, illustrating the importance of the "PBL window shadow" on haze formation. Turbulence diffusion and PBL height showed had opposite phases to surface PM 2.5 , indicating that lower PBL height and weaker PBL turbulence diffusion are essential to haze formation. It is noted that homogeneous air pressure does not occur at the surface but at an 85–950 hPa height during the haze episode. The momentum transmitting downward of the cold air from above the PBL to the low PBL and surface lead to an increase in surface wind speeds and haze dispersal.
    Print ISSN: 1680-7367
    Electronic ISSN: 1680-7375
    Topics: Geosciences
    Published by Copernicus on behalf of The European Geosciences Union (EGU).
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    Impact of seawater Ca 2+ on the calcification and calcite Mg/Ca of Amphistegina lessonii (2014)
    Copernicus
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    Publication Date: 2014-12-17
    Description: Impact of seawater Ca 2+ on the calcification and calcite Mg/Ca of Amphistegina lessonii Biogeosciences Discussions, 11, 17463-17489, 2014 Author(s): A. Mewes, G. Langer, S. Thoms, G. Nehrke, G.-J. Reichart, L. J. de Nooijer, and J. Bijma Mg/Ca ratios in foraminiferal tests are routinely used as paleo temperature proxy, but on long timescales, also hold the potential to reconstruct past seawater Mg/Ca. Impact of both temperature and seawater Mg/Ca on Mg incorporation in foraminifera have been quantified by a number of studies. The underlying mechanism responsible for Mg incorporation in foraminiferal calcite and its sensitivity to environmental conditions, however, is not fully identified. A recently published biomineralization model (Nehrke et al., 2013) proposes a combination of transmembrane transport and seawater leakage or vacuolization to link calcite Mg/Ca to seawater Mg/Ca and explains inter-species variability in Mg/Ca ratios. To test the assumptions of this model, we conducted a culture study in which seawater Mg/Ca was manipulated by varying [Ca 2+ ] and keeping [Mg 2+ ] constant. Foraminiferal growth rates, test thickness and calcite Mg/Ca of newly formed chambers were analyzed. Results showed optimum growth rates and test thickness at Mg/Ca closest to that of ambient seawater. Calcite Mg/Ca is positively correlated to seawater Mg/Ca, indicating that not absolute seawater [Ca 2+ ] and [Mg 2+ ], but the telative ratio controls Mg/Ca in tests. These results demonstrate that the calcification process cannot be based only on seawater vacuolization, supporting the mixing model proposed by Nehrke et al. (2013). Here we, however, suggest a transmembrane transport fractionation that is not as strong as suggested by Nehrke et al. (2013).
    Print ISSN: 1810-6277
    Electronic ISSN: 1810-6285
    Topics: Biology , Geosciences
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    DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R 2 N 2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (~170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6–7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.
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    Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3'-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H 2 O 2 ) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H 2 O 2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
    Keywords: Nucleic acid modification, Transcriptome Mapping - Monitoring Gene Expression
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    Rad51/Dmc1 paralogs and mediators oppose DNA helicases to limit hybrid DNA formation and promote crossovers during meiotic recombination (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: During meiosis programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination using the sister chromatid or the homologous chromosome (homolog) as a template. This repair results in crossover (CO) and non-crossover (NCO) recombinants. Only CO formation between homologs provides the physical linkages guiding correct chromosome segregation, which are essential to produce healthy gametes. The factors that determine the CO/NCO decision are still poorly understood. Using Schizosaccharomyces pombe as a model we show that the Rad51/Dmc1-paralog complexes Rad55-Rad57 and Rdl1-Rlp1-Sws1 together with Swi5-Sfr1 play a major role in antagonizing both the FANCM-family DNA helicase/translocase Fml1 and the RecQ-type DNA helicase Rqh1 to limit hybrid DNA formation and promote Mus81-Eme1-dependent COs. A common attribute of these protein complexes is an ability to stabilize the Rad51/Dmc1 nucleoprotein filament, and we propose that it is this property that imposes constraints on which enzymes gain access to the recombination intermediate, thereby controlling the manner in which it is processed and resolved.
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    Landscape of target:guide homology effects on Cas9-mediated cleavage (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: To study target sequence specificity, selectivity, and reaction kinetics of Streptococcus pyogenes Cas9 activity, we challenged libraries of random variant targets with purified Cas9::guide RNA complexes in vitro . Cleavage kinetics were nonlinear, with a burst of initial activity followed by slower sustained cleavage. Consistent with other recent analyses of Cas9 sequence specificity, we observe considerable (albeit incomplete) impairment of cleavage for targets mutated in the PAM sequence or in ‘seed’ sequences matching the proximal 8 bp of the guide. A second target region requiring close homology was located at the other end of the guide::target duplex (positions 13–18 relative to the PAM). Sequences flanking the guide+PAM region had measurable (albeit modest) effects on cleavage. In addition, the first-base Guanine constraint commonly imposed by gRNA expression systems has little effect on overall cleavage efficiency. Taken together, these studies provide an in vitro understanding of the complexities of Cas9–gRNA interaction and cleavage beyond the general paradigm of site determination based on the ‘seed’ sequence and PAM.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Identification of tri-phosphatase activity in the biogenesis of retroviral microRNAs and RNAP III-generated shRNAs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.
    Keywords: Synthetic Biology and Assembly Cloning, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al. , 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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  • 100
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    Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Distinct translational initiation mechanisms between prokaryotes and eukaryotes limit the exploitation of prokaryotic riboswitch repertoire for regulatory RNA circuit construction in mammalian application. Here, we explored programmed ribosomal frameshifting (PRF) as the regulatory gene expression platform for engineered ligand-responsive RNA devices in higher eukaryotes. Regulation was enabled by designed ligand-dependent conformational rearrangements of the two cis-acting RNA motifs of opposite activity in -1 PRF. Particularly, RNA elements responsive to trans-acting ligands can be tailored to modify co-translational RNA refolding dynamics of a hairpin upstream of frameshifting site to achieve reversible and adjustable -1 PRF attenuating activity. Combined with a ligand-responsive stimulator, synthetic RNA devices for synergetic translational-elongation control of gene expression can be constructed. Due to the similarity between co-transcriptional RNA hairpin folding and co-translational RNA hairpin refolding, the RNA-responsive ligand repertoire provided in prokaryotic systems thus becomes accessible to gene-regulatory circuit construction for synthetic biology application in mammalian cells.
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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