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  • Proceedings of the National Academy of Sciences  (6)
  • Biodiversity Research  (6)
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  • Proceedings of the National Academy of Sciences  (6)
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  • 1
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 16 ( 2019-04-16), p. 7760-7765
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 16 ( 2019-04-16), p. 7760-7765
    Abstract: China has been experiencing fine particle (i.e., aerodynamic diameters ≤ 2.5 µm; PM 2.5 ) pollution and acid rain in recent decades, which exert adverse impacts on human health and the ecosystem. Recently, ammonia (i.e., NH 3 ) emission reduction has been proposed as a strategic option to mitigate haze pollution. However, atmospheric NH 3 is also closely bound to nitrogen deposition and acid rain, and comprehensive impacts of NH 3 emission control are still poorly understood in China. In this study, by integrating a chemical transport model with a high-resolution NH 3 emission inventory, we find that NH 3 emission abatement can mitigate PM 2.5 pollution and nitrogen deposition but would worsen acid rain in China. Quantitatively, a 50% reduction in NH 3 emissions achievable by improving agricultural management, along with a targeted emission reduction (15%) for sulfur dioxide and nitrogen oxides, can alleviate PM 2.5 pollution by 11−17% primarily by suppressing ammonium nitrate formation. Meanwhile, nitrogen deposition is estimated to decrease by 34%, with the area exceeding the critical load shrinking from 17% to 9% of China’s terrestrial land. Nevertheless, this NH 3 reduction would significantly aggravate precipitation acidification, with a decrease of as much as 1.0 unit in rainfall pH and a corresponding substantial increase in areas with heavy acid rain. An economic evaluation demonstrates that the worsened acid rain would partly offset the total economic benefit from improved air quality and less nitrogen deposition. After considering the costs of abatement options, we propose a region-specific strategy for multipollutant controls that will benefit human and ecosystem health.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2012
    In:  Proceedings of the National Academy of Sciences Vol. 109, No. 18 ( 2012-05)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 18 ( 2012-05)
    Abstract: Similar application of paleoenvironmental records to many regions worldwide is possible, but there are caveats. Limitations on data accuracy and precision, irregular time series, variable spatial inferences, and unavailability of records may all constrain the transferability of the approach. Nevertheless, as global concerns turn strongly toward the impacts from climate and human activities within regions, this study demonstrates how we may use the wealth of information produced by paleoenvironmental methods more effectively to design sustainable management strategies ( 5 ). Compiling, scrutinizing, integrating, and modeling multidecadal paleoenvironmental records of ecosystem services should now be viewed as a major international scientific priority. An index for regulating services shows a decline starting in the 1970s during the period of the Cultural Revolution ( Fig. P1 ). The losses accelerated after Deng Xiaoping’s “opening-up” reforms in the 1980s and continue to the present time (2006). The decline of the index points strongly to agricultural intensification and industrial development as the main drivers of regulating service losses. Improved environmental regulation and environmental policies after the late 1980s may have partially stabilized losses of biodiversity and erosion regulating services. However, for water purification, there is strong evidence that thresholds ( 4 ) have already been transgressed. The records show clearly how the trade-off between economic growth and environmental degradation has evolved. The region has yet to reach a stage where economic development is decoupled from ecological degradation. Past success in the drive to alleviate rural poverty should be tempered against the likelihood of ecological failure in the near future. In the Chinese case study, lake sediment data derived from analyses of microfossils, geochemistry, mineral magnetism, and sediment accumulation rates give regional signals of changing biodiversity, soil stability, water quality, sediment quality, sediment regulation, and air quality for the past 200 y. Complementary data from official statistical records and climate models give regional trends for land use, population, gross domestic product, temperature, and precipitation. Following the Millennium Ecosystem Assessment Synthesis ( 3 ), we map the range of paleoenvironmental records onto the following categories of ecosystem services: “supporting (e.g., nutrient cycles),” “provisioning (e.g., food and fiber),” “regulating” (e.g., water purification), and “cultural” (e.g., recreational benefits). For subcategories, we identify or define 〉 50 representative processes or system states for which recognized types of paleoenvironmental proxy records exist. It seems that the “regulating services” category may have the greatest number of potential paleoenvironmental proxy records. Importantly, these records are often the least well monitored, especially in remote areas and developing nations. Sources of data for ecological change over the last few decades and centuries lie in natural archives, such as lake sediments. Such paleoenvironmental research has long been concerned with climate and human impacts on natural processes (e.g., ref. 2 ) but has yet to fully embrace the ecosystem service agenda that demands integration of social and ecological records. The aim of this work is to rectify this situation with a case study using paleoenvironmental and socioeconomic records from two lake catchments lying west of Nanjing in eastern China. Resources and processes provided by natural ecosystems offer numerous benefits known as ecosystem services; these services have become central to discussions about the sustainable management of natural resources ( 1 ). However, critical knowledge gaps exist in many regions worldwide, especially with regard to the dynamics of services that support and regulate ecosystems. Here we review the role of paleoenvironmental sequences to provide multidecadal information for ecosystem services, exemplified by a case study from the lower Yangtze basin. The Chinese study shows rapid losses of regulating services, especially since the 1980s, mirroring the rise in population and economic growth ( Fig. P1 ). The findings imply that land management practices are critically unsustainable.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 3
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 32 ( 2014-08-12)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 32 ( 2014-08-12)
    Abstract: Nonenzymatic RNA polymerization in early life is likely to introduce backbone heterogeneity with a mixture of 2′–5′ and 3′–5′ linkages. On the other hand, modern nucleic acids are dominantly composed of 3′–5′ linkages. RNA polymerase II (pol II) is a key modern enzyme responsible for synthesizing 3′–5′–linked RNA with high fidelity. It is not clear how modern enzymes, such as pol II, selectively recognize 3′–5′ linkages over 2′–5′ linkages of nucleic acids. In this work, we systematically investigated how phosphodiester linkages of nucleic acids govern pol II transcriptional efficiency and fidelity. Through dissecting the impacts of 2′–5′ linkage mutants in the pol II catalytic site, we revealed that the presence of 2′–5′ linkage in RNA primer only modestly reduces pol II transcriptional efficiency without affecting pol II transcriptional fidelity. In sharp contrast, the presence of 2′–5′ linkage in DNA template leads to dramatic decreases in both transcriptional efficiency and fidelity. These distinct effects reveal that pol II has an asymmetric (strand-specific) recognition of phosphodiester linkage. Our results provided important insights into pol II transcriptional fidelity, suggesting essential contributions of phosphodiester linkage to pol II transcription. Finally, our results also provided important understanding on the molecular basis of nucleic acid recognition and genetic information transfer during molecular evolution. We suggest that the asymmetric recognition of phosphodiester linkage by modern nucleic acid enzymes likely stems from the distinct evolutionary pressures of template and primer strand in genetic information transfer during molecular evolution.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 4
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 36 ( 2020-09-08), p. 21889-21895
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 36 ( 2020-09-08), p. 21889-21895
    Abstract: DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions. However, the slow mode has not been successfully characterized due to the limitation in the spatial and temporal resolutions of current experimental techniques. Using a newly developed scanning fluorescence resonance energy transfer (FRET)–fluorescence correlation spectroscopy (FCS) platform, we were able to observe both slow and fast modes of glycosylase AlkD translocating on double-stranded DNA (dsDNA), reaching the temporal resolution of microsecond and spatial resolution of subnanometer. The underlying molecular mechanism of the slow mode was further elucidated by Markov state model built from extensive all-atom molecular dynamics simulations. We found that in the slow mode, AlkD follows an asymmetric diffusion pathway, i.e., rotation followed by translation. Furthermore, the essential role of Y27 in AlkD diffusion dynamics was identified both experimentally and computationally. Our results provided mechanistic insights on how conformational dynamics of AlkD–dsDNA complex coordinate different diffusion modes to accomplish the search for DNA lesions with high efficiency and accuracy. We anticipate that the mechanism adopted by AlkD to search for DNA lesions could be a general one utilized by other glycosylases and DNA binding proteins.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 5
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 3 ( 2019-01-15), p. 845-853
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 3 ( 2019-01-15), p. 845-853
    Abstract: Bacterium Thermus thermophilus Argonaute (Ago; Tt Ago) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The Tt Ago active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically around it. An interesting challenge is to understand how they can collaboratively facilitate enzymatic catalysis. In Kluyveromyces polysporus Ago, a eukaryotic Ago, the evolutionarily symmetrical residues are arginine and histidine, both of which function to stabilize the plugged-in catalytic tetrad conformation. Surprisingly, our simulation results indicated that, in Tt Ago, only R545 is involved in the cleavage reaction by serving as a critical structural anchor to stabilize the catalytic tetrad Asp-Glu-Asp-Asp that is completed by the insertion of the glutamate finger, whereas R486 is not involved in target cleavage. The Tt Ago-mediated target DNA cleavage occurs in a substrate-assisted mechanism, in which the pro-Rp (Rp, a tetrahedral phosphorus center with “R-type” chirality) oxygen of scissile phosphate acts as a general base to activate the nucleophilic water. Our unexpected theoretical findings on distinct roles played by R545 and R486 in Tt Ago catalysis have been validated by single-point site-mutagenesis experiments, wherein the target cleavage is abolished for all mutants of R545. In sharp contrast, the cleavage activity is maintained for all mutants of R486. Our work provides mechanistic insights on the catalytic specificity of Ago proteins and could facilitate the design of new gene-editing tools in the long term.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 50 ( 2013-12-10)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 50 ( 2013-12-10)
    Abstract: Stimulus information is encoded in the spatial-temporal structures of external inputs to the neural system. The ability to extract the temporal information of inputs is fundamental to brain function. It has been found that the neural system can memorize temporal intervals of visual inputs in the order of seconds. Here we investigate whether the intrinsic dynamics of a large-size neural circuit alone can achieve this goal. The network models we consider have scale-free topology and the property that hub neurons are difficult to be activated. The latter is implemented by either including abundant electrical synapses between neurons or considering chemical synapses whose efficacy decreases with the connectivity of the postsynaptic neuron. We find that hub neurons trigger synchronous firing across the network, loops formed by low-degree neurons determine the rhythm of synchronous firing, and the hardness of exciting hub neurons avoids epileptic firing of the network. Our model successfully reproduces the experimentally observed rhythmic synchronous firing with long periods and supports the notion that the neural system can process temporal information through the dynamics of local circuits in a distributed way.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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