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  • Nature Publishing Group  (15,145)
  • MDPI Publishing
  • 2020-2023  (5)
  • 2000-2004  (15,140)
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  • 1
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    Return to rapid ice loss in Greenland and record loss in 2019 detected by the GRACE-FO satellites (2020)
    Nature Publishing Group
    In:  EPIC3Communications Earth & Environment, Nature Publishing Group, 1(1), pp. 1-8
    Details
    Publication Date: 2022-06-20
    Description: Between 2003-2016, the Greenland ice sheet (GrIS) was one of the largest contributors to sea level rise, as it lost about 255 Gt of ice per year. This mass loss slowed in 2017 and 2018 to about 100 Gt yr−1. Here we examine further changes in rate of GrIS mass loss, by analyzing data from the GRACE-FO (Gravity Recovery and Climate Experiment – Follow On) satellite mission, launched in May 2018. Using simulations with regional climate models we show that the mass losses observed in 2017 and 2018 by the GRACE and GRACE-FO missions are lower than in any other two year period between 2003 and 2019, the combined period of the two missions. We find that this reduced ice loss results from two anomalous cold summers in western Greenland, compounded by snow-rich autumn and winter conditions in the east. For 2019, GRACE-FO reveals a return to high melt rates leading to a mass loss of 223 ± 12 Gt month−1 during the month of July alone, and a record annual mass loss of 532 ± 58 Gt yr−1.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Arctic glaciers record wavier circumpolar winds (2022)
    Nature Publishing Group
    In:  EPIC3Nature Climate Change, Nature Publishing Group, 12(3), pp. 249-255
    Details
    Publication Date: 2022-06-20
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Small sinking particles control anammox rates in the Peruvian oxygen minimum zone (2021)
    Nature Publishing Group
    In:  EPIC3Nature Communications, Nature Publishing Group, 12(1), pp. 1-12
    Details
    Publication Date: 2022-08-15
    Description: Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species (2022)
    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 601(7892), pp. 257-262
    Details
    Publication Date: 2022-08-11
    Description: The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1,2,3. However, recent culture-independent studies have suggested that the archaeon ‘Candidatus Methanoliparum’ alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4,5,6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    The impact of faulting complexity and type on earthquake rupture dynamics (2022)
    Nature Publishing Group
    Details
    Publication Date: 2022-10-31
    Description: The statistical properties of seismicity are known to be affected by several factors such as the rheological parameters of rocks. We analysed the earthquake double-couple as a function of the faulting type. Here we show that it impacts the moment tensors of earthquakes: thrust- faulting events are characterized by higher double-couple components with respect to strike- slip- and normal-faulting earthquakes. Our results are coherent with the stress dependence of the scaling exponent of the Gutenberg-Richter law, which is anticorrelated to the double- couple. We suggest that the structural and tectonic control of seismicity may have its origin in the complexity of the seismogenic source marked by the width of the cataclastic damage zone and by the slip of different fault planes during the same seismic event; the sharper and concentrated the slip as along faults, the higher the double-couple. This phenomenon may introduce bias in magnitude estimation, with possible impact on seismic forecasting.
    Description: Published
    Description: 258
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: double couple ; damage zone ; different fault type ; seismicity ; tectonics ; fault type ; seismicity ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Tropical climate changes at millennial and orbital timescales on the Bolivian Altiplano (2001)
    Nature Publishing Group
    In:  Nature, 409 (6821). pp. 698-701.
    Details
    Publication Date: 2017-01-04
    Description: Tropical South America is one of the three main centres of the global, zonal overturning circulation of the equatorial atmosphere (generally termed the 'Walker' circulation1). Although this area plays a key role in global climate cycles, little is known about South American climate history. Here we describe sediment cores and down-hole logging results of deep drilling in the Salar de Uyuni, on the Bolivian Altiplano, located in the tropical Andes. We demonstrate that during the past 50,000 years the Altiplano underwent important changes in effective moisture at both orbital (20,000-year) and millennial timescales. Long-duration wet periods, such as the Last Glacial Maximum—marked in the drill core by continuous deposition of lacustrine sediments—appear to have occurred in phase with summer insolation maxima produced by the Earth's precessional cycle. Short-duration, millennial events correlate well with North Atlantic cold events, including Heinrich events 1 and 2, as well as the Younger Dryas episode. At both millennial and orbital timescales, cold sea surface temperatures in the high-latitude North Atlantic were coeval with wet conditions in tropical South America, suggesting a common forcing.
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  • 7
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    A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont (2002)
    Nature Publishing Group
    In:  Nature, 417 (6884). pp. 63-67.
    Details
    Publication Date: 2017-07-07
    Description: According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and—indicated only by environmental DNA sequences—to the 'Korarchaeota'1, 2. Here we report the cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent. This archaeon cannot be attached to one of these groups and therefore must represent an unknown phylum which we name 'Nanoarchaeota' and species, which we name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only about 400 nm in diameter. They grow attached to the surface of a specific archaeal host, a new member of the genus Ignicoccus3. The distribution of the 'Nanoarchaeota' is so far unknown. Owing to their unusual ss rRNA sequence, members remained undetectable by commonly used ecological studies based on the polymerase chain reaction4. 'N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication.
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  • 8
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    Termination of global warmth at the Palaeocene/Eocene boundary through productivity feedback (2000)
    Nature Publishing Group
    In:  Nature, 407 (6801). pp. 171-174.
    Details
    Publication Date: 2017-01-04
    Description: The onset of the Palaeocene/Eocene thermal maximum (about 55 Myr ago) was marked by global surface temperatures warming by 5–7 °C over approximately 30,000 yr (ref. 1), probably because of enhanced mantle outgassing2, 3 and the pulsed release of approx1,500 gigatonnes of methane carbon from decomposing gas-hydrate reservoirs4, 5, 6, 7. The aftermath of this rapid, intense and global warming event may be the best example in the geological record of the response of the Earth to high atmospheric carbon dioxide concentrations and high temperatures. This response has been suggested to include an intensified flux of organic carbon from the ocean surface to the deep ocean and its subsequent burial through biogeochemical feedback mechanisms8. Here we present firm evidence for this view from two ocean drilling cores, which record the largest accumulation rates of biogenic barium—indicative of export palaeoproductivity—at times of maximum global temperatures and peak excursion values of delta13C. The unusually rapid return of delta13C to values similar to those before the methane release7 and the apparent coupling of the accumulation rates of biogenic barium to temperature, suggests that the enhanced deposition of organic matter to the deep sea may have efficiently cooled this greenhouse climate by the rapid removal of excess carbon dioxide from the atmosphere.
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  • 9
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    Conservation: Biogeography of the Indonesian coelacanths (2000)
    Nature Publishing Group
    In:  Nature, 403 (6765). p. 38.
    Details
    Publication Date: 2017-07-06
    Description: Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.
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  • 10
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    The effects of surfactants on spilling breaking waves (2003)
    Nature Publishing Group
    In:  Nature, 421 (6922). pp. 520-523.
    Details
    Publication Date: 2016-05-10
    Description: Breaking waves markedly increase the rates of air–sea transfer of momentum, energy and mass. In light to moderate wind conditions, spilling breakers with short wavelengths are observed frequently. Theory and laboratory experiments have shown that, as these waves approach breaking in clean water, a ripple pattern that is dominated by surface tension forms at the crest. Under laboratory conditions and in theory, the transition to turbulent flow is triggered by flow separation under the ripples, typically without leading to overturning of the free surface15. Water surfaces in nature, however, are typically contaminated by surfactant films that alter the surface tension and produce surface elasticity and viscosity16, 17. Here we present the results of laboratory experiments in which spilling breaking waves were generated mechanically in water with a range of surfactant concentrations. We find significant changes in the breaking process owing to surfactants. At the highest concentration of surfactants, a small plunging jet issues from the front face of the wave at a point below the wave crest and entraps a pocket of air on impact with the front face of the wave. The bubbles and turbulence created during this process are likely to increase air–sea transfer.
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  • 11
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    The ‘zero charge’ partitioning behaviour of noble gases during mantle melting (2003)
    Nature Publishing Group
    In:  Nature, 423 (6941). pp. 738-741.
    Details
    Publication Date: 2015-11-24
    Description: Noble-gas geochemistry is an important tool for understanding planetary processes from accretion to mantle dynamics and atmospheric formation. Central to much of the modelling of such processes is the crystal–melt partitioning of noble gases during mantle melting, magma ascent and near-surface degassing5. Geochemists have traditionally considered the 'inert' noble gases to be extremely incompatible elements, with almost 100 per cent extraction efficiency from the solid phase during melting processes. Previously published experimental data on partitioning between crystalline silicates and melts has, however, suggested that noble gases approach compatible behaviour, and a significant proportion should therefore remain in the mantle during melt extraction. Here we present experimental data to show that noble gases are more incompatible than previously demonstrated, but not necessarily to the extent assumed or required by geochemical models. Independent atomistic computer simulations indicate that noble gases can be considered as species of 'zero charge' incorporated at crystal lattice sites. Together with the lattice strain model9, 10, this provides a theoretical framework with which to model noble-gas geochemistry as a function of residual mantle mineralogy.
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  • 12
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    Genomic islands in pathogenic and environmental microorganisms (2004)
    Nature Publishing Group
    In:  Nature Reviews Microbiology, 2 (5). pp. 414-424.
    Details
    Publication Date: 2020-06-23
    Description: Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands — mobile genetic elements that contribute to rapid changes in virulence potential — are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species — genomic islands — are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.
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  • 13
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    Consumer versus resource control of species diversity and ecosystem functioning (2002)
    Nature Publishing Group
    In:  Nature Geoscience, 417 . pp. 848-851.
    Details
    Publication Date: 2017-02-28
    Description: A key question in ecology is which factors control species diversity in a community1, 2, 3. Two largely separate groups of ecologists have emphasized the importance of productivity or resource supply, and consumers or physical disturbance, respectively. These variables show unimodal relationships with diversity when manipulated in isolation4, 5, 6, 7, 8. Recent multivariate models9, 10, however, predict that these factors interact, such that the disturbance–diversity relationship depends on productivity, and vice versa. We tested these models in marine food webs, using field manipulations of nutrient resources and consumer pressure on rocky shores of contrasting productivity. Here we show that the effects of consumers and nutrients on diversity consistently depend on each other, and that the direction of their effects and peak diversity shift between sites of low and high productivity. Factorial meta-analysis of published experiments confirms these results across widely varying aquatic communities. Furthermore, our experiments demonstrate that these patterns extend to important ecosystem functions such as carbon storage and nitrogen retention. This suggests that human impacts on nutrient supply11 and food-web structure12, 13 have strong and interdependent effects on species diversity and ecosystem functioning, and must therefore be managed together.
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  • 14
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    When the Earth moved: How Earth scientists developed the theory of plate tectonics (2002)
    Nature Publishing Group
    In:  Nature, 417 . pp. 487-488.
    Details
    Publication Date: 2017-03-07
    Description: BOOK REVIEWED: Plate Tectonics: An Insider's History of the Modern Theory of the Earth / edited by Naomi Oreskes Westview Press: 2001. 448 pp.
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  • 15
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    Break-up of the Atlantic Deep Western Boundary Current into eddies at 8°S (2004)
    Nature Publishing Group
    In:  Nature, 432 . pp. 1018-1020.
    Details
    Publication Date: 2017-03-09
    Description: The existence in the ocean of deep western boundary currents, which connect the high-latitude regions where deep water is formed with upwelling regions as part of the global ocean circulation, was postulated more than 40 years ago1. These ocean currents have been found adjacent to the continental slopes of all ocean basins, and have core depths between 1,500 and 4,000 m. In the Atlantic Ocean, the deep western boundary current is estimated to carry (10–40) times 106 m3 s-1 of water2, 3, 4, 5, transporting North Atlantic Deep Water—from the overflow regions between Greenland and Scotland and from the Labrador Sea—into the South Atlantic and the Antarctic circumpolar current. Here we present direct velocity and water mass observations obtained in the period 2000 to 2003, as well as results from a numerical ocean circulation model, showing that the Atlantic deep western boundary current breaks up at 8° S. Southward of this latitude, the transport of North Atlantic Deep Water into the South Atlantic Ocean is accomplished by migrating eddies, rather than by a continuous flow. Our model simulation indicates that the deep western boundary current breaks up into eddies at the present intensity of meridional overturning circulation. For weaker overturning, continuation as a stable, laminar boundary flow seems possible.
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  • 16
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    In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor (2003)
    Nature Publishing Group
    In:  Nature, 424 . pp. 763-765.
    Details
    Publication Date: 2017-03-07
    Description: More than 50% of the Earth' s surface is sea floor below 3,000 m of water. Most of this major reservoir in the global carbon cycle and final repository for anthropogenic wastes is characterized by severe food limitation. Phytodetritus is the major food source for abyssal benthic communities, and a large fraction of the annual food load can arrive in pulses within a few days1, 2. Owing to logistical constraints, the available data concerning the fate of such a pulse are scattered3, 4 and often contradictory5, 6, 7, 8, 9, 10, hampering global carbon modelling and anthropogenic impact assessments. We quantified (over a period of 2.5 to 23 days) the response of an abyssal benthic community to a phytodetritus pulse, on the basis of 11 in situ experiments. Here we report that, in contrast to previous hypotheses5, 6, 7, 8, 9, 10, 11, the sediment community oxygen consumption doubled immediately, and that macrofauna were very important for initial carbon degradation. The retarded response of bacteria and Foraminifera, the restriction of microbial carbon degradation to the sediment surface, and the low total carbon turnover distinguish abyssal from continental-slope ‘deep-sea’ sediments.
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  • 17
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    Paleoceanographic implications of genetic variation in living North Atlantic Neogloboquadrina pachyderma (2003)
    Nature Publishing Group
    In:  Nature, 424 (6946). pp. 299-302.
    Details
    Publication Date: 2017-03-07
    Description: The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial–interglacial climate conditions in the North Atlantic Ocean1, 2, 3. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments1, 2, 4, 5. Recently discovered cryptic genetic diversity in planktonic foraminifers6, 7, 8 now poses significant questions for these studies. Here we report genetic evidence demonstrating that the apparent ‘single species’ shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a species-dependent incremental shift in right-coiling N. pachyderma shell calcite δ18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of δ18O records of right-coiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.
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  • 18
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    Palaeoceanography: Antarctic stratification and glacial CO2 (2001)
    Nature Publishing Group
    In:  Nature, 412 . pp. 605-606.
    Details
    Publication Date: 2017-02-28
    Description: One way of accounting for lowered atmospheric carbon dioxide concentrations during Pleistocene glacial periods is by invoking the Antarctic stratification hypothesis, which links the reduction in CO2 to greater stratification of ocean surface waters around Antarctica1, 2. As discussed by Sigman and Boyle3, this hypothesis assumes that increased stratification in the Antarctic zone (Fig. 1) was associated with reduced upwelling of deep waters around Antarctica, thereby allowing CO2 outgassing to be suppressed by biological production while also allowing biological production to decline, which is consistent with Antarctic sediment records4. We point out here, however, that the response of ocean eddies to increased Antarctic stratification can be expected to increase, rather than reduce, the upwelling rate of deep waters around Antarctica. The stratification hypothesis may have difficulty in accommodating eddy feedbacks on upwelling within the constraints imposed by reconstructions of winds and Antarctic-zone productivity in glacial periods.
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  • 19
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    Strong hemispheric coupling of glacial climate through continental freshwater discharge and ocean circulation (2004)
    Nature Publishing Group
    In:  Nature, 430 . pp. 851-856.
    Details
    Publication Date: 2017-03-07
    Description: The climate of the last glacial period was extremely variable, characterized by abrupt warming events in the Northern Hemisphere, accompanied by slower temperature changes in Antarctica and variations of global sea level. It is generally accepted that this millennial-scale climate variability was caused by abrupt changes in the ocean thermohaline circulation. Here we use a coupled ocean–atmosphere–sea ice model to show that freshwater discharge into the North Atlantic Ocean, in addition to a reduction of the thermohaline circulation, has a direct effect on Southern Ocean temperature. The related anomalous oceanic southward heat transport arises from a zonal density gradient in the subtropical North Atlantic caused by a fast wave-adjustment process. We present an extended and quantitative bipolar seesaw concept that explains the timing and amplitude of Greenland and Antarctic temperature changes, the slow changes in Antarctic temperature and its similarity to sea level, as well as a possible time lag of sea level with respect to Antarctic temperature during Marine Isotope Stage 3.
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  • 20
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    Oceanic respite for wandering albatrosses (2000)
    Nature Publishing Group
    In:  Nature, 406 . pp. 955-956.
    Details
    Publication Date: 2021-07-01
    Description: Birds taking time off from breeding head for their favourite long-haul destinations. What oceanic seabirds do outside their breeding periods is something of a mystery, although altogether these "sabbaticals' add up to more than half of their lifetime and are probably a key feature of their life history. Here we use geolocation systems based on light-intensity measurements to show that during these periods wandering albatrosses (Diomedea exulans) leave the foraging grounds that they frequent while breeding for specific, individual oceanic sectors and spend the rest of the year there — each bird probably returns to the same area throughout its life. This discovery of individual home-range preferences outside the breeding season has important implications for the conservation of albatrosses threatened by the development of longline fisheries.
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  • 21
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    Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic (2004)
    Nature Publishing Group
    In:  Nature, 429 . pp. 292-294.
    Details
    Publication Date: 2017-03-10
    Description: The role of iron in enhancing phytoplankton productivity in high nutrient, low chlorophyll oceanic regions was demonstrated first through iron-addition bioassay experiments1 and subsequently confirmed by large-scale iron fertilization experiments2. Iron supply has been hypothesized to limit nitrogen fixation and hence oceanic primary productivity on geological timescales3, providing an alternative to phosphorus as the ultimate limiting nutrient4. Oceanographic observations have been interpreted both to confirm and refute this hypothesis5, 6, but direct experimental evidence is lacking7. We conducted experiments to test this hypothesis during the Meteor 55 cruise to the tropical North Atlantic. This region is rich in diazotrophs8 and strongly impacted by Saharan dust input9. Here we show that community primary productivity was nitrogen-limited, and that nitrogen fixation was co-limited by iron and phosphorus. Saharan dust addition stimulated nitrogen fixation, presumably by supplying both iron and phosphorus10, 11. Our results support the hypothesis that aeolian mineral dust deposition promotes nitrogen fixation in the eastern tropical North Atlantic.
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  • 22
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    Deep Roots of the Messinian Salinity Crisis (2003)
    Nature Publishing Group
    In:  Nature, 422 . pp. 602-606.
    Details
    Publication Date: 2019-09-23
    Description: The Messinian salinity crisis—the desiccation of the Mediterranean Sea between 5.96 and 5.33 million years (Myr) ago1—was one of the most dramatic events on Earth during the Cenozoic era2. It resulted from the closure of marine gateways between the Atlantic Ocean and the Mediterranean Sea, the causes of which remain enigmatic. Here we use the age and composition of volcanic rocks to reconstruct the geodynamic evolution of the westernmost Mediterranean from the Middle Miocene epoch to the Pleistocene epoch (about 12.1–0.65 Myr ago). Our data show that a marked shift in the geochemistry of mantle-derived volcanic rocks, reflecting a change from subduction-related to intraplate-type volcanism, occurred between 6.3 and 4.8 Myr ago, largely synchronous with the Messinian salinity crisis. Using a thermomechanical model, we show that westward roll back of subducted Tethys oceanic lithosphere and associated asthenospheric upwelling provides a plausible mechanism for producing the shift in magma chemistry and the necessary uplift (approx1 km) along the African and Iberian continental margins to close the Miocene marine gateways, thereby causing the Messinian salinity crisis.
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  • 23
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    Managing fisheries in a changing climate (2004)
    Nature Publishing Group
    In:  Nature, 429 .
    Details
    Publication Date: 2017-03-10
    Description: No need to wait for more information: industrialized fishing is already wiping out stocks.
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  • 24
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    Polysaccharide aggregation as a potential sink of marine dissolved organic carbon (2004)
    Nature Publishing Group
    In:  Nature, 428 . pp. 929-932.
    Details
    Publication Date: 2019-09-23
    Description: The formation and sinking of biogenic particles mediate vertical mass fluxes and drive elemental cycling in the ocean1. Whereas marine sciences have focused primarily on particle production by phytoplankton growth, particle formation by the assembly of organic macromolecules has almost been neglected2, 3. Here we show, by means of a combined experimental and modelling study, that the formation of polysaccharide particles is an important pathway to convert dissolved into particulate organic carbon during phytoplankton blooms, and can be described in terms of aggregation kinetics. Our findings suggest that aggregation processes in the ocean cascade from the molecular scale up to the size of fast-settling particles, and give new insights into the cycling and export of biogeochemical key elements such as carbon, iron and thorium.
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    Effect of trace metal availability on coccolithophorid calcification (2004)
    Nature Publishing Group
    In:  Nature, 430 . pp. 673-676.
    Details
    Publication Date: 2019-09-23
    Description: The deposition of atmospheric dust into the ocean has varied considerably over geological time1, 2. Because some of the trace metals contained in dust are essential plant nutrients which can limit phytoplankton growth in parts of the ocean, it has been suggested that variations in dust supply to the surface ocean might influence primary production3, 4. Whereas the role of trace metal availability in photosynthetic carbon fixation has received considerable attention, its effect on biogenic calcification is virtually unknown. The production of both particulate organic carbon and calcium carbonate (CaCO3) drives the ocean's biological carbon pump. The ratio of particulate organic carbon to CaCO3 export, the so-called rain ratio, is one of the factors determining CO2 sequestration in the deep ocean. Here we investigate the influence of the essential trace metals iron and zinc on the prominent CaCO3-producing microalga Emiliania huxleyi. We show that whereas at low iron concentrations growth and calcification are equally reduced, low zinc concentrations result in a de-coupling of the two processes. Despite the reduced growth rate of zinc-limited cells, CaCO3 production rates per cell remain unaffected, thus leading to highly calcified cells. These results suggest that changes in dust deposition can affect biogenic calcification in oceanic regions characterized by trace metal limitation, with possible consequences for CO2 partitioning between the atmosphere and the ocean.
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    Directly measured mid-depth circulation in the northeastern North Atlantic Ocean (2002)
    Nature Publishing Group
    In:  Nature, 419 . pp. 603-607.
    Details
    Publication Date: 2017-03-07
    Description: The circulation of water masses in the northeastern North Atlantic Ocean has a strong influence on global climate owing to the northward transport of warm subtropical water to high latitudes1. But the ocean circulation at depths below the reach of satellite observations is difficult to measure, and only recently have comprehensive, direct observations of whole ocean basins been possible2, 3, 4. Here we present quantitative maps of the absolute velocities at two levels in the northeastern North Atlantic as obtained from acoustically tracked floats. We find that most of the mean flow transported northward by the Gulf Stream system at the thermocline level (about 600 m depth) remains within the subpolar region, and only relatively little enters the Rockall trough or the Nordic seas. Contrary to previous work5, 6, our data indicate that warm, saline water from the Mediterranean Sea reaches the high latitudes through a combination of narrow slope currents and mixing processes. At both depths under investigation, currents cross the Mid-Atlantic Ridge preferentially over deep gaps in the ridge, demonstrating that sea-floor topography can constrain even upper-ocean circulation patterns.
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    Global change: Monsoon linkages (2003)
    Nature Publishing Group
    In:  Nature, 421 (6921). pp. 324-325.
    Details
    Publication Date: 2016-07-19
    Description: An excellent sediment record from the Arabian Sea traces recent patterns in the activity of the Asian monsoon. It reveals both variability in monsoon strength and links with climatic events elsewhere. The monsoon is the main determinant of environmental conditions over much of Asia, and so affects the most densely populated region on Earth. Differential heating of the north Indian Ocean and the northwest Pacific, and of the Asian land-mass, cause the seasonal reversal of monsoon winds. In summer, these winds blow northwards over the northern Indian Ocean, carrying huge amounts of moisture over the neighbouring land. The ensuing heavy rainfall can have devastating consequences for human life and livelihood. Conversely, agriculture in Asia depends on monsoon rains; and the seasonal upwelling of nutrient-laden subsurface waters, driven by monsoon winds, is essential to the success of coastal fisheries.
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    Magmatic and amagmatic seafloor generation at the ultraslow-spreading Gakkel ridge, Arctic Ocean (2003)
    Nature Publishing Group
    In:  Nature, 423 (6943). pp. 956-961.
    Details
    Publication Date: 2016-07-19
    Description: A high-resolution mapping and sampling study of the Gakkel ridge was accomplished during an international ice-breaker expedition to the high Arctic and North Pole in summer 2001. For this slowest-spreading endmember of the global mid-ocean-ridge system, predictions were that magmatism should progressively diminish as the spreading rate decreases along the ridge, and that hydrothermal activity should be rare. Instead, it was found that magmatic variations are irregular, and that hydrothermal activity is abundant. A 300-kilometre-long central amagmatic zone, where mantle peridotites are emplaced directly in the ridge axis, lies between abundant, continuous volcanism in the west, and large, widely spaced volcanic centres in the east. These observations demonstrate that the extent of mantle melting is not a simple function of spreading rate: mantle temperatures at depth or mantle chemistry (or both) must vary significantly along-axis. Highly punctuated volcanism in the absence of ridge offsets suggests that first-order ridge segmentation is controlled by mantle processes of melting and melt segregation. The strong focusing of magmatic activity coupled with faulting may account for the unexpectedly high levels of hydrothermal activity observed.
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    Power from the deep (2002)
    Nature Publishing Group
    In:  Nature Biotechnology, 20 (8). pp. 788-789.
    Details
    Publication Date: 2019-10-22
    Description: normous amounts of potential energy lie buried in marine sediments in the form of reduced carbon compounds. The most familiar form of this vast energy reserve is petroleum, which drives the lion's share of today's energy economy. The next most obvious submarine energy reserve, even more abundant than petroleum, is methane. At deep-sea conditions of low temperature and high pressure, large amounts of this natural gas are found in sub-seafloor reservoirs of frozen methane hydrates [1]. Yet there is another abundant, but less obvious, marine energy reserve: sediment-associated organic carbon, which represents about 2% of the dry weight of marine sediments along continental margins. Is it possible to tap into this vast, dispersed form of submarine energy? If so, how? The answer, in part, is that microbes already have tapped into this large energy reserve. Now, in two papers, one in this issue [2] and the other in a previous issue of Science [3], researchers harness microbially generated power by constructing a fuel cell that can exploit the naturally occurring voltage gradient created by microbial activity in marine sediments.
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    Mantle thermal pulses below the Mid-Atlantic Ridge and temporal variations in the formation of oceanic lithosphere (2003)
    Nature Publishing Group
    In:  Nature, 423 (6939). pp. 499-505.
    Details
    Publication Date: 2019-02-26
    Description: A 20-Myr record of creation of oceanic lithosphere is exposed along a segment of the central Mid-Atlantic Ridge on an uplifted sliver of lithosphere. The degree of melting of the mantle that is upwelling below the ridge, estimated from the chemistry of the exposed mantle rocks, as well as crustal thickness inferred from gravity measurements, show oscillations of ∼3–4 Myr superimposed on a longer-term steady increase with time. The time lag between oscillations of mantle melting and crustal thickness indicates that the mantle is upwelling at an average rate of ∼25 mm yr-1, but this appears to vary through time. Slow-spreading lithosphere seems to form through dynamic pulses of mantle upwelling and melting, leading not only to along-axis segmentation but also to across-axis structural variability. Also, the central Mid-Atlantic Ridge appears to have become steadily hotter over the past 20 Myr, possibly owing to north–south mantle flow.
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    Harnessing microbially generated power on the seafloor (2002)
    Nature Publishing Group
    In:  Nature Biotechnology, 20 (8). pp. 821-825.
    Details
    Publication Date: 2019-10-22
    Description: In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.
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    Biogeography of the Indonesian coelacanths (2000)
    Nature Publishing Group
    In:  Nature, 403 (6765). p. 38.
    Details
    Publication Date: 2019-11-11
    Description: Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands1. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away2. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish2,3. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.
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    Turned out nice again (2000)
    Nature Publishing Group
    In:  Nature, 404 (6780). p. 814.
    Details
    Publication Date: 2021-02-25
    Description: Book review of: The Change in the Weather: People, Weather, and the Science of Climate by William K. Stevens Delacorte: 2000. 432 pp. $24.95
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    Earth science: The ultraslow difference (2003)
    Nature Publishing Group
    In:  Nature, 426 (6965). p. 401.
    Details
    Publication Date: 2017-03-07
    Description: The speed at which mid-ocean ridges grind out new ocean floor varies considerably. The slowest-spreading ridges are especially tough to study — but the latest data show that they are especially intriguing.
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    Bacterial growth and primary production along a north-south transect of the Atlantic Ocean (2002)
    Nature Publishing Group
    In:  Nature, 416 . pp. 168-171.
    Details
    Publication Date: 2017-02-28
    Description: The oceanic carbon cycle is mainly determined by the combined activities of bacteria and phytoplankton, but the interdependence of climate, the carbon cycle and the microbes is not well understood. To elucidate this interdependence, we performed high-frequency sampling of sea water along a north-south transect of the Atlantic Ocean. Here we report that the interaction of bacteria and phytoplankton is closely related to the meridional profile of water temperature, a variable directly dependent on climate. Water temperature was positively correlated with the ratio of bacterial production to primary production, and, more strongly, with the ratio of bacterial carbon demand to primary production. In warm latitudes (25 degrees N to 30 degrees S), we observed alternating patches of predominantly heterotrophic and autotrophic community metabolism. The calculated regression lines (for data north and south of the Equator) between temperature and the ratio of bacterial production to primary production give a maximum value for this ratio of 40% in the oligotrophic equatorial regions. Taking into account a bacterial growth efficiency of 30%, the resulting area of net heterotrophy (where the bacterial carbon demand for growth plus respiration exceeds phytoplankton carbon fixation) expands from 8 degrees N (27 degrees C) to 20 degrees S (23 degrees C). This suggests an output of CO2 from parts of the ocean to the atmosphere.
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    A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 695-702.
    Details
    Publication Date: 2017-02-28
    Description: Changes in iron supply to oceanic plankton are thought to have a significant effect on concentrations of atmospheric carbon dioxide by altering rates of carbon sequestration, a theory known as the 'iron hypothesis'. For this reason, it is important to understand the response of pelagic biota to increased iron supply. Here we report the results of a mesoscale iron fertilization experiment in the polar Southern Ocean, where the potential to sequester iron-elevated algal carbon is probably greatest. Increased iron supply led to elevated phytoplankton biomass and rates of photosynthesis in surface waters, causing a large drawdown of carbon dioxide and macronutrients, and elevated dimethyl sulphide levels after 13 days. This drawdown was mostly due to the proliferation of diatom stocks. But downward export of biogenic carbon was not increased. Moreover, satellite observations of this massive bloom 30 days later, suggest that a sufficient proportion of the added iron was retained in surface waters. Our findings demonstrate that iron supply controls phytoplankton growth and community composition during summer in these polar Southern Ocean waters, but the fate of algal carbon remains unknown and depends on the interplay between the processes controlling export, remineralisation and timescales of water mass subduction.
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    A marine microbial consortium apparently mediating abaerobic oxidation of methane (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 623-626.
    Details
    Publication Date: 2017-02-28
    Description: A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles, radiotracer experiments and stable carbon isotope data. But the elusive microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria. Here we provide microscopic evidence for a structured consortium of archaea and sulphate-reducing bacteria, which we identified by fluorescence in situ hybridization using specific 16S rRNA-targeted oligonucleotide probes. In this example of a structured archaeal-bacterial symbiosis, the archaea grow in dense aggregates of about 100 cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.
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    Rapid worldwide depletion of predatory fish communities (2003)
    Nature Publishing Group
    In:  Nature (423). pp. 280-283.
    Details
    Publication Date: 2017-03-07
    Description: Serious concerns have been raised about the ecological effects of industrialized fishing1, 2, 3, spurring a United Nations resolution on restoring fisheries and marine ecosystems to healthy levels4. However, a prerequisite for restoration is a general understanding of the composition and abundance of unexploited fish communities, relative to contemporary ones. We constructed trajectories of community biomass and composition of large predatory fishes in four continental shelf and nine oceanic systems, using all available data from the beginning of exploitation. Industrialized fisheries typically reduced community biomass by 80% within 15 years of exploitation. Compensatory increases in fast-growing species were observed, but often reversed within a decade. Using a meta-analytic approach, we estimate that large predatory fish biomass today is only about 10% of pre-industrial levels. We conclude that declines of large predators in coastal regions5 have extended throughout the global ocean, with potentially serious consequences for ecosystems5, 6, 7. Our analysis suggests that management based on recent data alone may be misleading, and provides minimum estimates for unexploited communities, which could serve as the 'missing baseline'8 needed for future restoration efforts.
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    Reduced calcification of marine plankton in response to increased atmospheric CO2 (2000)
    Nature Publishing Group
    In:  Nature, 407 . pp. 634-637.
    Details
    Publication Date: 2017-02-28
    Description: The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments1. This is important in regulating marine carbon cycling and ocean–atmosphere CO2 exchange2. The present rise in atmospheric CO2 levels3 causes significant changes in surface ocean pH and carbonate chemistry4. Such changes have been shown to slow down calcification in corals and coralline macroalgae5,6, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica . This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.
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    Glaciology: Enigmatic Arctic ice sheets (2001)
    Nature Publishing Group
    In:  Nature, 410 (6827). pp. 427-428.
    Details
    Publication Date: 2017-02-28
    Description: To what extent was the Arctic Ocean glaciated in the past? Heavily, according to data, gathered by a submarine, which show considerable ice-scouring of topography in parts of the ocean basin
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    Bending-related faulting and mantle serpentinization at the Middle America Trench (2003)
    Nature Publishing Group
    Details
    Publication Date: 2023-09-26
    Description: The dehydration of subducting oceanic crust and upper mantle has been inferred both to promote the partial melting leading to arc magmatism and to induce intraslab intermediate-depth earthquakes, at depths of 50–300 km. Yet there is still no consensus about how slab hydration occurs or where and how much chemically bound water is stored within the crust and mantle of the incoming plate. Here we document that bending-related faulting of the incoming plate at the Middle America trench creates a pervasive tectonic fabric that cuts across the crust, penetrating deep into the mantle. Faulting is active across the entire ocean trench slope, promoting hydration of the cold crust and upper mantle surrounding these deep active faults. The along-strike length and depth of penetration of these faults are also similar to the dimensions of the rupture area of intermediate-depth earthquakes.
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    Desperately seeking RNAs (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 799-799 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Many years ago RNA came in three flavors: messenger RNA, transfer RNA and ribosomal RNA. Now RNA has become the Baskin-Robbins of nucleic acids. Many different flavors of RNA seem to control the majority of processes in the cell and, in many cases, do so in a cell-specific and developmentally ...
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    URL: http://dx.doi.org/10.1038/nsmb0904-799
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    RNA regulators of transcription (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 803-804 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The role of noncoding RNAs in regulating cellular processes, once considered unusual, has become almost an expectation as more and more of these RNAs and their functions are uncovered. Within gene expression pathways, translation and its regulation constitute a hotbed of RNA-mediated activity. The ...
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    Two classes give lessons about CCA (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 807-808 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Throughout all three kingdoms of life, many genomes do not encode the universal CCA sequence found at the 3′ ends of tRNAs. Among eukaryotes a genome-encoded CCA triplet is especially rare. Transfer RNAs are usually composed of 76 nucleotides that fold into a four-arm cloverleaf structure ...
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    The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 850-856 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Biological membranes are notoriously resistant to structural analysis. Excellent candidates to tackle this problem in situ are membrane-containing viruses where the membrane is constrained by an icosahedral capsid. Cryo-EM and image reconstruction of bacteriophage PM2 revealed a membrane bilayer ...
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    A novel tunnel in mycobacterial type III polyketide synthase reveals the structural basis for generating diverse metabolites (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 894-900 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The superfamily of plant and bacterial type III polyketide synthases (PKSs) produces diverse metabolites with distinct biological functions. PKS18, a type III PKS from Mycobacterium tuberculosis, displays an unusual broad specificity for aliphatic long-chain acyl-coenzyme A (acyl-CoA) starter units ...
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    B2 RNA binds directly to RNA polymerase II to repress transcript synthesis (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 822-829 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] B2 RNA is a small noncoding RNA polymerase III transcript that represses mRNA transcription in response to heat shock in mouse cells. Here we define the mechanism by which B2 RNA inhibits RNA polymerase II (Pol II) transcription. Using a purified Pol II transcription system, we found that B2 RNA ...
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    Myosin VI walks hand-over-hand along actin (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 884-887 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Myosin VI is a molecular motor that can walk processively on actin filaments with a 36-nm step size. The walking mechanism of myosin VI is controversial because it takes very large steps without an apparent lever arm of required length. Therefore, myosin VI is argued to be the first exception to ...
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    Mechanochemical coupling of two substeps in a single myosin V motor (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 877-883 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Myosin V is a double-headed processive molecular motor that moves along an actin filament by taking 36-nm steps. Using optical trapping nanometry with high spatiotemporal resolution, we discovered that there are two possible pathways for the 36-nm steps, one with 12- and 24-nm substeps, in this ...
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    The ternary complex of antithrombin–anhydrothrombin–heparin reveals the basis of inhibitor specificity (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 863-867 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Antithrombin, the principal physiological inhibitor of the blood coagulation proteinase thrombin, requires heparin as a cofactor. We report the crystal structure of the rate-determining encounter complex formed between antithrombin, anhydrothrombin and an optimal synthetic 16-mer oligosaccharide. ...
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    The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 816-821 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Cells respond to changes in environmental conditions via orchestrated modifications in gene expression. For example, in response to heat shock, cells execute a program of gene-specific transcriptional activation and repression. Although the activation of genes upon heat shock has been widely ...
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    Reversing DNA damage with a directional bias (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 688-690 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The genome is under constant attack from chemical and physical agents that damage DNA. Cells can usually repair such damage by direct reversal via the action of a single protein, or via multi-step processes such as nucleotide, base or mismatch excision repair and recombinational repair. Alkylation ...
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    Toward understanding GPCR dimers (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 691-692 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] G-protein-coupled receptors (GPCRs) mediate cellular responses to the majority of hormones and neurotransmitters, as well as the senses of sight, smell and taste. Although they have been studied for 〉30 years, it was only recently that GPCR dimers were identified and accepted as physiological ...
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    Research Highlights (2004)
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    Nature structural & molecular biology 11 (2004), S. 696-696 
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    Source: Nature Archives 1869 - 2009
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    Notes: [Auszug] Gene silencing without RNAi RNA interference (RNAi) is a phenomenon in which double-stranded RNAs are processed into small interfering RNAs that degrade homologous mRNAs. While RNAi has generally been thought to act post- transcriptionally it can also act at the transcriptional level. For example, ...
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    Membrane-dependent conformational changes initiate cholesterol-dependent cytolysin oligomerization and intersubunit β-strand alignment (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 697-705 
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    Notes: [Auszug] Cholesterol-dependent cytolysins are bacterial protein toxins that bind to cholesterol-containing membranes, form oligomeric complexes and insert into the bilayer to create large aqueous pores. Membrane-dependent structural rearrangements required to initiate the oligomerization of perfringolysin O ...
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    Closed state of both binding domains of homodimeric mGlu receptors is required for full activity (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 706-713 
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    Source: Nature Archives 1869 - 2009
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    Notes: [Auszug] Membrane receptors, key components in signal transduction, often function as dimers. These include some G protein–coupled receptors such as metabotropic glutamate (mGlu) receptors that have large extracellular domains (ECDs) where agonists bind. How agonist binding in dimeric ECDs activates ...
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    Structural basis for Ca 2+ -induced activation of human PAD4 (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 777-783 
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    Notes: [Auszug] Peptidylarginine deiminase 4 (PAD4) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca2+-free wild-type PAD4, which shows that the polypeptide ...
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    Nucleosomes facilitate their own invasion (2004)
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    Nature structural & molecular biology 11 (2004), S. 763-769 
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    Source: Nature Archives 1869 - 2009
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    Notes: [Auszug] DNA wrapped in nucleosomes is sterically occluded, creating obstacles for polymerase, regulatory, remodeling, repair and recombination complexes, which require access to the wrapped DNA. How such complexes recognize and gain access to their DNA target sites is not known. Here we report the direct ...
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    Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 591-598 
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    Source: Nature Archives 1869 - 2009
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    Notes: [Auszug] Both the dendritic cell receptor DC-SIGN and the closely related endothelial cell receptor DC-SIGNR bind human immunodeficiency virus and enhance infection. However, biochemical and structural comparison of these receptors now reveals that they have very different physiological functions. By ...
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    Substrate recognition by the AAA+ chaperone ClpB (2004)
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    Nature structural & molecular biology 11 (2004), S. 607-615 
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    Notes: [Auszug] The AAA+ protein ClpB cooperates with the DnaK chaperone system to solubilize and refold proteins from an aggregated state. The substrate-binding site of ClpB and the mechanism of ClpB-dependent protein disaggregation are largely unknown. Here we identified a substrate-binding site of ClpB that is ...
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    Erratum: Cooperative organization in a macromolecular complex (2004)
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    Nature structural & molecular biology 11 (2004), S. 678-678 
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    Notes: [Auszug] Nat. Struct. Biol. 10, 718–724 (2003). A mistake was introduced when the electronic document of this manuscript was being converted for production. The mistake is in the peptide sequence corresponding to the 19 residues at the C terminus of p27Kip1 page 723, second column, line 2). The ...
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    Corrigendum: Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 678-678 
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    Notes: [Auszug] Nat. Struct. Biol. 10, 781–788 (2003). Two mistakes are found in the final version of this manuscript. The first is on page 784 (second column, line 19 from the bottom); the correct sentence should read: “... in which the base U33 forms hydrogen bonds with the main chain amide and ...
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    Opening the gate in potassium channels (2004)
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    Nature structural & molecular biology 11 (2004), S. 499-501 
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    Notes: [Auszug] Potassium ion channels are a large family of membrane proteins that provide an exquisitely selective pore for potassium ions to cross the lipid bilayer. Like most ion channels, potassium channel pores undergo a conformational change to open and close a gate in response to an activating stimulus. ...
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    The σ 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 544-550 
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    Notes: [Auszug] The σ70 subunit of RNA polymerase plays an essential role in transcription initiation. In addition, σ70 has a critical regulatory role during transcription elongation at the bacteriophage λ late promoter, λPR′. At this promoter, σ70 mediates a pause in early ...
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    Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 512-518 
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    Notes: [Auszug] Germline mutations in the BRCA1 tumor suppressor gene often result in a significant increase in susceptibility to breast and ovarian cancers. Although the molecular basis of their effects remains largely obscure, many mutations are known to target the highly conserved C-terminal BRCT repeats that ...
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    Structure and mechanism of the RNA polymerase II transcription machinery (2004)
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    Nature structural & molecular biology 11 (2004), S. 394-403 
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    Notes: [Auszug] Advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a marked increase in the understanding of the mechanism of transcription. Models for the specific assembly of the RNA polymerase II transcription machinery at a promoter, conformational changes ...
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    Structures of HIV-1 RT–DNA complexes before and after incorporation of the anti-AIDS drug tenofovir (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 469-474 
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    Notes: [Auszug] Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a ternary complex at a resolution of 3.0 Å of RT ...
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    Transition states for protein folding have native topologies despite high structural variability (2004)
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    Nature structural & molecular biology 11 (2004), S. 443-449 
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    Notes: [Auszug] We present a structural analysis of the folding transition states of three SH3 domains. Our results reveal that the secondary structure is not yet fully formed at this stage of folding and that the solvent is only partially excluded from the interior of the protein. Comparison of the members of the ...
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    Long live structural biology (2004)
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    Nature structural & molecular biology 11 (2004), S. 293-295 
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    Notes: [Auszug] In the January issue of Nature Structural & Molecular Biology, Stephen Harrison accurately communicates in a commentary the need to expand the length and timescale at which we study biological systems at atomic resolution. Expanding the number of systems being studied will certainly benefit our ...
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    Three-dimensional structure of a pre-catalytic human spliceosomal complex B (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 463-468 
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    Notes: [Auszug] Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have ...
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    Demystifying the editorial process (2004)
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    Nature structural & molecular biology 11 (2004), S. 291-291 
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    Notes: [Auszug] “What do you do with my manuscript once I've submitted it to your office?” This is one of the most commonly asked questions we get from authors. We understand the anxiety behind the question since we publish only about one out of every six papers submitted to the journal. No doubt some ...
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    Structures and technology for biologists (2004)
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    Nature structural & molecular biology 11 (2004), S. 296-297 
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    Notes: [Auszug] Structural genomics is a worldwide project that aims to obtain detailed experimental or inferred structural information representing the entire range of biological macromolecules (see http://www.isgo.org). It is a long-term project in which structural information, technology and infrastructure will ...
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    A novel ADP- and zinc-binding fold from function-directed in vitro evolution (2004)
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    Nature structural & molecular biology 11 (2004), S. 382-383 
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    Notes: [Auszug] A great challenge to biologists is to create proteins with novel folds and tailored functions. As an alternative to de novo protein design, we investigated the structure of a randomly generated protein targeted to bind ATP. The crystal structure reveals a novel α/β fold bound to its ...
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    PSI—phase 1 and beyond (2004)
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    Nature structural & molecular biology 11 (2004), S. 201-201 
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    Notes: [Auszug] Ten years ago, the growing impact of protein structure on biomedical research and significant advances in genome sequencing ushered in the new field of structural genomics. In 2000, following years of investments in structural biology through individual R01 grants, the National Institute of General ...
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    Too hot to splice (2004)
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    Nature structural & molecular biology 11 (2004), S. 208-209 
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    Notes: [Auszug] It has been nearly twenty years since the initial observation that heat shock causes a global shutdown of pre-mRNA splicing, but the molecular mechanisms underlying this inactivation have remained largely obscure. Early biochemical analyses, which included complementation of inactive in vitro ...
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    RNase III enzymes and the initiation of gene silencing (2004)
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    Nature structural & molecular biology 11 (2004), S. 214-218 
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    Notes: [Auszug] Our understanding of RNA interference has been enhanced by new data concerning RNase III molecules. The role of Dicer has previously been established in RNAi as the originator of 22-mers characteristic of silencing phenomena. Recently, a related RNAse III enzyme, Drosha, has surfaced as another ...
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    In praise of biochemistry (2004)
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    Nature structural & molecular biology 11 (2004), S. 107-107 
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    Notes: [Auszug] When asked to write a guest editorial on the importance of biochemistry Arthur Kornberg, one of the most revered biochemists of the 20th century, was concerned that what he wanted to say “would be as welcome as a skunk at a picnic. Structural, molecular and cell biology have been so ...
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    Happy motoring with ATP synthase (2004)
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    Nature structural & molecular biology 11 (2004), S. 110-112 
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    Notes: [Auszug] Purposeful generation and utilization of energy define living organisms. The central molecule of biological energetics is ATP, and the enzyme responsible for the majority of ATP synthesis in organisms from bacteria to man is ATP synthase. A rush of excitement ran through this field in 1997 when ...
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    Research Notes (2004)
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    Nature structural & molecular biology 11 (2004), S. 120-120 
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    Notes: [Auszug] Shine a light on me Researchers at the University of Hawaii at Manoa and UCLA have identified a set of unusual proteins in the reflective tissues of the Hawaiian bobtail squid. Reflectivity involves the redirection of natural sunlight or bioluminescence, and it's a strategy that is widely ...
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    Mapping structural differences between 30S ribosomal subunit assembly intermediates (2004)
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    Nature structural & molecular biology 11 (2004), S. 179-186 
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    Notes: [Auszug] Under appropriate conditions, functional Escherichia coli 30S ribosomal subunits assemble in vitro from purified components. However, at low temperatures, assembly stalls, producing an intermediate (RI) that sediments at 21S and is composed of 16S ribosomal RNA (rRNA) and a subset of ribosomal ...
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    Structure of a bifunctional DNA primase-polymerase (2004)
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    Nature structural & molecular biology 11 (2004), S. 157-162 
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    Notes: [Auszug] Genome replication generally requires primases, which synthesize an initial oligonucleotide primer, and DNA polymerases, which elongate the primer. Primase and DNA polymerase activities are combined, however, in newly identified replicases from archaeal plasmids, such as pRN1 from Sulfolobus ...
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    Reactive oxygen species impair Slo1 BK channel function by altering cysteine-mediated calcium sensing (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 171-178 
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    Notes: [Auszug] Vascular dysfunction is a hallmark of many diseases, including coronary heart disease, stroke and diabetes. The underlying mechanisms of these disorders, which are intimately associated with inflammation and oxidative stress caused by excess reactive oxygen species (ROS), have remained elusive. ...
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    Hsp90: from structure to phenotype (2004)
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    Nature structural & molecular biology 11 (2004), S. 1152-1155 
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    Notes: [Auszug] Hsp90 forms a central part of the cellular assembly (and, as recent work suggests, disassembly) machine. This chaperone machine aids in the folding, assembly-disassembly and activation of a wide range of substrate or client proteins, including many kinases and transcription factors as well as other ...
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    Research Highlights (2004)
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    Nature structural & molecular biology 11 (2004), S. 1165-1165 
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    Notes: [Auszug] Buried in a riboswitch Binding of small molecules, such as guanine, can alter the structure of RNA control elements found in the untranslated region of some genes. These structural alterations usually repress expression of the genes with which they are associated by affecting transcription, ...
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    Corrigendum: Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1253-1253 
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    Notes: [Auszug] Nat. Struct. Mol. Biol. 11, 412–419 (2004). Some of the enzymatic activity data for paraoxonase (PON1) reported in this article were biased by two factors. First, the gene encoding the H115Q mutant contained an additional H177R mutation introduced during PCR amplification. Although His177 is ...
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    Cell cycle-dependent regulation of yeast telomerase by Ku (2004)
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    Nature structural & molecular biology 11 (2004), S. 1198-1205 
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    Notes: [Auszug] The heterodimeric Ku complex affects telomere structure in diverse organisms. We report here that in the absence of Ku, the catalytic subunit of telomerase, Est2p, was not telomere-associated in G1 phase, and its association in late S phase was decreased. The telomere association of Est1p, a ...
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    Hsp70 and Hsp40 attenuate formation of spherical and annular polyglutamine oligomers by partitioning monomer (2004)
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    Nature structural & molecular biology 11 (2004), S. 1215-1222 
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    Notes: [Auszug] Protein conformational changes that result in misfolding, aggregation and amyloid fibril formation are a common feature of many neurodegenerative disorders. Studies with β-amyloid (Aβ), α-synuclein and other amyloid-forming proteins indicate that the assembly of misfolded protein ...
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    Human CD59 is a receptor for the cholesterol-dependent cytolysin intermedilysin (2004)
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    Nature structural & molecular biology 11 (2004), S. 1173-1178 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Cholesterol is believed to serve as the common receptor for the cholesterol-dependent cytolysins (CDCs). One member of this toxin family, Streptococcus intermedius intermedilysin (ILY), exhibits a narrow spectrum of cellular specificity that is seemingly inconsistent with this premise. We show here ...
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    URL: http://dx.doi.org/10.1038/nsmb862
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    Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1179-1185 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The Escherichia coli OxyR transcription factor is activated by cellular hydrogen peroxide through the oxidation of reactive cysteines. Although there is substantial evidence for specific disulfide bond formation in the oxidative activation of OxyR, the presence of the disulfide bond has remained ...
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    URL: http://dx.doi.org/10.1038/nsmb856
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    Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1068-1075 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Transcriptional silencing in mammals is often associated with promoter methylation. However, a considerable number of genomic methylated CpGs exist in transposable elements, which are frequently found in intronic regions. To determine whether intragenic methylation influences transcription ...
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    URL: http://dx.doi.org/10.1038/nsmb840
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    Take two (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1034-1035 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The genomic RNA of retroviruses, like that of many RNA viruses, leads a double life. On the one hand, the retroviral RNA must be incorporated into nascent virus particles in order to carry the viral genetic information to the new host cell. On the other hand, it serves as the mRNA for the Gag and ...
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    URL: http://dx.doi.org/10.1038/nsmb1104-1034
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    Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1142-1149 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained ...
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    URL: http://dx.doi.org/10.1038/nsmb838
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    Internal recognition through PDZ domain plasticity in the Par-6–Pals1 complex (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1122-1127 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] PDZ protein interaction domains are typically selective for C-terminal ligands, but non-C-terminal, 'internal' ligands have also been identified. The PDZ domain from the cell polarity protein Par-6 binds C-terminal ligands and an internal sequence from the protein Pals1/Stardust. The structure of ...
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    URL: http://dx.doi.org/10.1038/nsmb839
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    Observation of internal cleavage and ligation reactions of a ribozyme (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1107-1113 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] We have used single-molecule spectroscopy to untangle conformational dynamics and internal chemistry in the hairpin ribozyme. The active site of the ribozyme is stably formed by docking two internal loops, but upon cleavage undocking is accelerated by two orders of magnitude. The markedly different ...
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    URL: http://dx.doi.org/10.1038/nsmb842
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    Regulated interactions of mtHsp70 with Tim44 at the translocon in the mitochondrial inner membrane (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1084-1091 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Preproteins synthesized on cytosolic ribosomes, but destined for the mitochondrial matrix, pass through the presequence translocase of the inner membrane. Translocation is driven by the import motor, having at its core the essential chaperone mtHsp70 (Ssc1 in yeast). MtHsp70 is tethered to the ...
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    URL: http://dx.doi.org/10.1038/nsmb846
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    The dynamic response of upstream DNA to transcription-generated torsional stress (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 1092-1100 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The torsional stress caused by counter-rotation of the transcription machinery and template generates supercoils in a closed topological domain, but has been presumed to be too short-lived to be significant in an open domain. This report shows that transcribing RNA polymerases dynamically sustain ...
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    URL: http://dx.doi.org/10.1038/nsmb848
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    The politics of science (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 907-907 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] As the US 2004 presidential election approaches it is worth stepping back to review the administration's science and technology policies. Unfortunately, our review of the record leads us to conclude that the Bush administration has repeatedly let politics rather than scientific findings determine ...
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    URL: http://dx.doi.org/10.1038/nsmb1004-907
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    Grabbing E2 by the tail (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 908-909 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Ubiquitylation is a form of post-translational modification in which the small protein ubiquitin is ligated by its C terminus to a lysine side chain of the target protein. Many cellular proteins receive this modification and consequently experience a range of possible fates including, but not ...
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    URL: http://dx.doi.org/10.1038/nsmb1004-908
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    RNA editing of a human potassium channel modifies its inactivation (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 915-916 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Voltage-gated potassium channels such as Kv1.1 play a fundamental role in excitability. They open upon depolarization, thereby re-establishing the resting membrane potential that is changed by, for example, the opening of sodium channels during an action potential or nerve impulse. After opening, ...
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    URL: http://dx.doi.org/10.1038/nsmb1004-915
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    Research Highlights (2004)
    [s.l.] : Nature Publishing Group
    Nature structural & molecular biology 11 (2004), S. 917-917 
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    ISSN: 1545-9985
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Setting boundaries Pattern development in plants and animals begins with the division of groups of cells into distinct domains. The cells within each group acquire different developmental fates as a result of precise gene expression patterns. MicroRNAS (miRNAs), which are involved in regulation of ...
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    URL: http://dx.doi.org/10.1038/nsmb1004-917
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