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  • 1
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e27205, doi:10.1371/journal.pone.0027205.
    Description: Heat shock protein 70 (Hsp70) is a molecular chaperone providing tolerance to heat and other challenges at the cellular and organismal levels. We sequenced a genomic cluster containing three hsp70 family genes linked with major histocompatibility complex (MHC) class III region from an extremely heat tolerant animal, camel (Camelus dromedarius). Two hsp70 family genes comprising the cluster contain heat shock elements (HSEs), while the third gene lacks HSEs and should not be induced by heat shock. Comparison of the camel hsp70 cluster with the corresponding regions from several mammalian species revealed similar organization of genes forming the cluster. Specifically, the two heat inducible hsp70 genes are arranged in tandem, while the third constitutively expressed hsp70 family member is present in inverted orientation. Comparison of regulatory regions of hsp70 genes from camel and other mammals demonstrates that transcription factor matches with highest significance are located in the highly conserved 250-bp upstream region and correspond to HSEs followed by NF-Y and Sp1 binding sites. The high degree of sequence conservation leaves little room for putative camel-specific regulatory elements. Surprisingly, RT-PCR and 5′/3′-RACE analysis demonstrated that all three hsp70 genes are expressed in camel's muscle and blood cells not only after heat shock, but under normal physiological conditions as well, and may account for tolerance of camel cells to extreme environmental conditions. A high degree of evolutionary conservation observed for the hsp70 cluster always linked with MHC locus in mammals suggests an important role of such organization for coordinated functioning of these vital genes.
    Description: This work was supported by the Russian Foundation for Basic Research, project 09-04-00643 and 09-04-00660, project from ‘‘Genofond dynamics’’ program, and Grant of the Program of Molecular and Cellular Biology RAN to Dr. Evgen’ev; and by the Ministry of Education and Science of Russian Federation (State contract 14.740.11.0757 and Russia President Grant to young scientists MK-1418.2010.4. The research was supported by State Contract N16.552.11.7034 of Ministry of Education and Science.
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e38249, doi:10.1371/journal.pone.0038249.
    Description: Arsenic (As) exposure is a significant worldwide environmental health concern. Chronic exposure via contaminated drinking water has been associated with an increased incidence of a number of diseases, including reproductive and developmental effects. The goal of this study was to identify adverse outcomes in a mouse model of early life exposure to low-dose drinking water As (10 ppb, current U.S. EPA Maximum Contaminant Level). C57B6/J pups were exposed to 10 ppb As, via the dam in her drinking water, either in utero and/or during the postnatal period. Birth outcomes, the growth of the F1 offspring, and health of the dams were assessed by a variety of measurements. Birth outcomes including litter weight, number of pups, and gestational length were unaffected. However, exposure during the in utero and postnatal period resulted in significant growth deficits in the offspring after birth, which was principally a result of decreased nutrients in the dam's breast milk. Cross-fostering of the pups reversed the growth deficit. Arsenic exposed dams displayed altered liver and breast milk triglyceride levels and serum profiles during pregnancy and lactation. The growth deficits in the F1 offspring resolved following separation from the dam and cessation of exposure in male mice, but did not resolve in female mice up to six weeks of age. Exposure to As at the current U.S. drinking water standard during critical windows of development induces a number of adverse health outcomes for both the dam and offspring. Such effects may contribute to the increased disease risks observed in human populations.
    Description: This work was supported by National Institute of Environmental Health Sciences at the National Institutes of Health grants 1F32 ES019070 (CDK-H) and P42 ES007373 (BPJ, JWH, RIE and CDK-H, Dartmouth Superfund Research Program Project Grant, Project 2 and Pilot Project).
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42535, doi:10.1371/journal.pone.0042535.
    Description: Some beaked whale species are susceptible to the detrimental effects of anthropogenic noise. Most studies have concentrated on the effects of military sonar, but other forms of acoustic disturbance (e.g. shipping noise) may disrupt behavior. An experiment involving the exposure of target whale groups to intense vessel-generated noise tested how these exposures influenced the foraging behavior of Blainville’s beaked whales (Mesoplodon densirostris) in the Tongue of the Ocean (Bahamas). A military array of bottom-mounted hydrophones was used to measure the response based upon changes in the spatial and temporal pattern of vocalizations. The archived acoustic data were used to compute metrics of the echolocation-based foraging behavior for 16 targeted groups, 10 groups further away on the range, and 26 nonexposed groups. The duration of foraging bouts was not significantly affected by the exposure. Changes in the hydrophone over which the group was most frequently detected occurred as the animals moved around within a foraging bout, and their number was significantly less the closer the whales were to the sound source. Non-exposed groups also had significantly more changes in the primary hydrophone than exposed groups irrespective of distance. Our results suggested that broadband ship noise caused a significant change in beaked whale behavior up to at least 5.2 kilometers away from the vessel. The observed change could potentially correspond to a restriction in the movement of groups, a period of more directional travel, a reduction in the number of individuals clicking within the group, or a response to changes in prey movement.
    Description: The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).
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  • 7
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 10 (2012): e1001234, doi:10.1371/journal.pbio.1001234.
    Description: Since the first discovery of deep-sea hydrothermal vents along the Galápagos Rift in 1977, numerous vent sites and endemic faunal assemblages have been found along mid-ocean ridges and back-arc basins at low to mid latitudes. These discoveries have suggested the existence of separate biogeographic provinces in the Atlantic and the North West Pacific, the existence of a province including the South West Pacific and Indian Ocean, and a separation of the North East Pacific, North East Pacific Rise, and South East Pacific Rise. The Southern Ocean is known to be a region of high deep-sea species diversity and centre of origin for the global deep-sea fauna. It has also been proposed as a gateway connecting hydrothermal vents in different oceans but is little explored because of extreme conditions. Since 2009 we have explored two segments of the East Scotia Ridge (ESR) in the Southern Ocean using a remotely operated vehicle. In each segment we located deep-sea hydrothermal vents hosting high-temperature black smokers up to 382.8°C and diffuse venting. The chemosynthetic ecosystems hosted by these vents are dominated by a new yeti crab (Kiwa n. sp.), stalked barnacles, limpets, peltospiroid gastropods, anemones, and a predatory sea star. Taxa abundant in vent ecosystems in other oceans, including polychaete worms (Siboglinidae), bathymodiolid mussels, and alvinocaridid shrimps, are absent from the ESR vents. These groups, except the Siboglinidae, possess planktotrophic larvae, rare in Antarctic marine invertebrates, suggesting that the environmental conditions of the Southern Ocean may act as a dispersal filter for vent taxa. Evidence from the distinctive fauna, the unique community structure, and multivariate analyses suggest that the Antarctic vent ecosystems represent a new vent biogeographic province. However, multivariate analyses of species present at the ESR and at other deep-sea hydrothermal vents globally indicate that vent biogeography is more complex than previously recognised.
    Description: The ChEsSo research programme was funded by a NERC Consortium Grant (NE/DO1249X/1) and supported by the Census of Marine Life and the Sloan Foundation, and the Total Foundation for Biodiversity (Abyss 2100)(SVTH) all of which are gratefully acknowledged. We also acknowledge NSF grant ANT-0739675 (CG and TS), NERC PhD studentships NE/D01429X/1(LH, LM, CNR), NE/H524922/1(JH) and NE/F010664/1 (WDKR), a Cusanuswerk doctoral fellowship, and a Lesley & Charles Hilton-Brown Scholarship, University of St. Andrews (PHBS).
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  • 8
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e44015, doi:10.1371/journal.pone.0044015.
    Description: Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented – Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.
    Description: This work was funded by grants from the John D and Catherine T MacArthur Foundation and the Alfred P Sloan Foundation to the Encyclopedia of Life and the National Science Foundation Data Net Program 0830976 and Global Names Project DBI-1062387.
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  • 9
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42872, doi:10.1371/journal.pone.0042872.
    Description: The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
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  • 10
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28353, doi:10.1371/journal.pone.0028353.
    Description: Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9) hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL) or near the sea-floor with little diel change. At least 43% (420/974) of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h) between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean.
    Description: The work was funded by the Office of Naval Research and the National Ocean Partnership Program (US), by a consortium consisting of the Canary Islands Government, the Spanish Ministry of Environment and the Spanish Ministry of Defense, and by the European environmental funding LIFE-INDEMARES program for the inventory and designation of the Natura 2000 network in marine areas of the Spanish territory, headed by Fundacion Biodiversidad, with additional support from the Cabildo Insular of El Hierro. PA is currently supported by the National Research Project: Cetacean, Oceanography and Biodiversity from La Palma and El Hierro (CGL2009-13112) of the Spanish Ministry of Science and NAS by a Marie Curie fellowship from the 7th European Frame Program. MJ was supported by grants from the Strategic Environmental Research Development Program and from the National Ocean Partnership Program. PTM was supported by frame grants from the National Danish Science Foundation.
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  • 11
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28257, doi:10.1371/journal.pone.0028257.
    Description: Cytochrome P450 1 (CYP1) genes are biomarkers for aryl hydrocarbon receptor (AHR) agonists and may be involved in some of their toxic effects. CYP1s other than the CYP1As are poorly studied in birds. Here we characterize avian CYP1B and CYP1C genes and the expression of the identified CYP1 genes and AHR1, comparing basal and induced levels in chicken and quail embryos. We cloned cDNAs of chicken CYP1C1 and quail CYP1B1 and AHR1. CYP1Cs occur in several bird genomes, but we found no CYP1C gene in quail. The CYP1C genomic region is highly conserved among vertebrates. This region also shares some synteny with the CYP1B region, consistent with CYP1B and CYP1C genes deriving from duplication of a common ancestor gene. Real-time RT-PCR analyses revealed similar tissue distribution patterns for CYP1A4, CYP1A5, CYP1B1, and AHR1 mRNA in chicken and quail embryos, with the highest basal expression of the CYP1As in liver, and of CYP1B1 in eye, brain, and heart. Chicken CYP1C1 mRNA levels were appreciable in eye and heart but relatively low in other organs. Basal transcript levels of the CYP1As were higher in quail than in chicken, while CYP1B1 levels were similar in the two species. 3,3′,4,5,5′-Pentachlorobiphenyl induced all CYP1s in chicken; in quail a 1000-fold higher dose induced the CYP1As, but not CYP1B1. The apparent absence of CYP1C1 in quail, and weak expression and induction of CYP1C1 in chicken suggest that CYP1Cs have diminishing roles in tetrapods; similar tissue expression suggests that such roles may be met by CYP1B1. Tissue distribution of CYP1B and CYP1C transcripts in birds resembles that previously found in zebrafish, suggesting that these genes serve similar functions in diverse vertebrates. Determining CYP1 catalytic functions in different species should indicate the evolving roles of these duplicated genes in physiological and toxicological processes.
    Description: Funding to MEJ and BB was from the Carl Tryggers Stiftelse and The Swedish Research Council Formas. Funding for BRW and JJS was from the United States National Institutes of Health (National Institute of Environmental Health Sciences), grants R01ES015912 and P42ES007381 to JJS.
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  • 12
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.
    Description: Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of 〈0.05, and a total of 136 proteins were differentially abundant (p〈0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.
    Description: This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito.
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  • 13
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e43039, doi:10.1371/journal.pone.0043039.
    Description: The transition metal, copper (Cu), is an enzymatic cofactor required for a wide range of biochemical processes. Its essentiality is demonstrated by Menkes disease, an X-linked copper deficiency disorder characterized by defects in nervous-, cardiovascular- and skeletal systems, and is caused by mutations in the ATP7A copper transporter. Certain ATP7A mutations also cause X-linked Spinal Muscular Atrophy type 3 (SMAX3), which is characterized by neuromuscular defects absent an underlying systemic copper deficiency. While an understanding of these ATP7A-related disorders would clearly benefit from an animal model that permits tissue-specific deletion of the ATP7A gene, no such model currently exists. In this study, we generated a floxed mouse model allowing the conditional deletion of the Atp7a gene using Cre recombinase. Global deletion of Atp7a resulted in morphological and vascular defects in hemizygous male embryos and death in utero. Heterozygous deletion in females resulted in a 50% reduction in live births and a high postnatal lethality. These studies demonstrate the essential role of the Atp7a gene in mouse embryonic development and establish a powerful model for understanding the tissue-specific roles of ATP7A in copper metabolism and disease.
    Description: This work was supported by National Institutes of Health Grants DK59893 and DK093386 to M.J.P., and DK44464 to J.D.G.
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e27693, doi:10.1371/journal.pone.0027693.
    Description: Atlantic bluefin tuna (Thunnus thynnus) is considered to be overfished, but the status of its populations has been debated, partly because of uncertainties regarding the effects of mixing on fishing grounds. A better understanding of spatial structure and mixing may help fisheries managers to successfully rebuild populations to sustainable levels while maximizing catches. We formulate a new seasonally and spatially explicit fisheries model that is fitted to conventional and electronic tag data, historic catch-at-age reconstructions, and otolith microchemistry stock-composition data to improve the capacity to assess past, current, and future population sizes of Atlantic bluefin tuna. We apply the model to estimate spatial and temporal mixing of the eastern (Mediterranean) and western (Gulf of Mexico) populations, and to reconstruct abundances from 1950 to 2008. We show that western and eastern populations have been reduced to 17% and 33%, respectively, of 1950 spawning stock biomass levels. Overfishing to below the biomass that produces maximum sustainable yield occurred in the 1960s and the late 1990s for western and eastern populations, respectively. The model predicts that mixing depends on season, ontogeny, and location, and is highest in the western Atlantic. Assuming that future catches are zero, western and eastern populations are predicted to recover to levels at maximum sustainable yield by 2025 and 2015, respectively. However, the western population will not recover with catches of 1750 and 12,900 tonnes (the “rebuilding quotas”) in the western and eastern Atlantic, respectively, with or without closures in the Gulf of Mexico. If future catches are double the rebuilding quotas, then rebuilding of both populations will be compromised. If fishing were to continue in the eastern Atlantic at the unregulated levels of 2007, both stocks would continue to decline. Since populations mix on North Atlantic foraging grounds, successful rebuilding policies will benefit from trans-Atlantic cooperation.
    Description: This work was supported by grants from the TAG A Giant Foundation, the Monterey Bay Aquarium Foundation, the Lenfest Ocean Program, Washington, DC, USA, the Canadian Fisheries and Oceans International Governance Strategies Fund and the National Oceanic and Atmospheric Administration (NOAA) of the United States.
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e28949, doi:10.1371/journal.pone.0028949.
    Description: Shotgun mass spectrometry was used to detect proteins in the harmful alga, Aureococcus anophagefferens, and monitor their relative abundance across nutrient replete (control), phosphate-deficient (−P) and −P refed with phosphate (P-refed) conditions. Spectral counting techniques identified differentially abundant proteins and demonstrated that under phosphate deficiency, A. anophagefferens increases proteins involved in both inorganic and organic phosphorus (P) scavenging, including a phosphate transporter, 5′-nucleotidase, and alkaline phosphatase. Additionally, an increase in abundance of a sulfolipid biosynthesis protein was detected in −P and P-refed conditions. Analysis of the polar membrane lipids showed that cellular concentrations of the sulfolipid sulphoquinovosyldiacylglycerol (SQDG) were nearly two-fold greater in the −P condition versus the control condition, while cellular phospholipids were approximately 8-fold less. Transcript and protein abundances were more tightly coupled for gene products involved in P metabolism compared to those involved in a range of other metabolic functions. Comparison of protein abundances between the −P and P-refed conditions identified differences in the timing of protein degradation and turnover. This suggests that culture studies examining nutrient starvation responses will be valuable in interpreting protein abundance patterns for cellular nutritional status and history in metaproteomic datasets.
    Description: Research for this work was supported by a National Oceanic and Atmospheric Administration ECOHAB grant (#NA09NOS4780206) and National Science Foundation grant (#OCE-0723667) and a STAR Research Assistance Agreement No. R-83041501-0 awarded by the U.S. Environmental Protection Agency. Further support came from the Woods Hole Coastal Ocean Institute. LLW was supported by a Environmental Protection Agency STAR Fellowship (#FP916901). EMB was supported by a National Science Foundation (NSF) Graduate Research Fellowship (#2007037200) and an Environmental Protection Agency STAR Fellowship (#F6E20324).
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Computational Biology 7 (2011): e1002318, doi:10.1371/journal.pcbi.1002318.
    Description: Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.
    Description: This study was funded by NIH and DOE grants.
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e29813, doi:10.1371/journal.pone.0029813.
    Description: Melanopsin, the receptor molecule that underlies light sensitivity in mammalian ‘circadian’ receptors, is homologous to invertebrate rhodopsins and has been proposed to operate via a similar signaling pathway. Its downstream effectors, however, remain elusive. Melanopsin also expresses in two distinct light-sensitive cell types in the neural tube of amphioxus. This organism is the most basal extant chordate and can help outline the evolutionary history of different photoreceptor lineages and their transduction mechanisms; moreover, isolated amphioxus photoreceptors offer unique advantages, because they are unambiguously identifiable and amenable to single-cell physiological assays. In the present study whole-cell patch clamp recording, pharmacological manipulations, and immunodetection were utilized to investigate light transduction in amphioxus photoreceptors. A Gq was identified and selectively localized to the photosensitive microvillar membrane, while the pivotal role of phospholipase C was established pharmacologically. The photocurrent was profoundly depressed by IP3 receptor antagonists, highlighting the importance of IP3 receptors in light signaling. By contrast, surrogates of diacylglycerol (DAG), as well as poly-unsaturated fatty acids failed to activate a membrane conductance or to alter the light response. The results strengthen the notion that calcium released from the ER via IP3-sensitive channels may fulfill a key role in conveying - directly or indirectly - the melanopsin-initiated light signal to the photoconductance; moreover, they challenge the dogma that microvillar photoreceptors and phoshoinositide-based light transduction are a prerogative of invertebrate eyes.
    Description: This work was supported by the National Science Foundation of the USA (grant 0918930).
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e45138, doi:10.1371/journal.pone.0045138.
    Description: A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic -outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.
    Description: This work was supported by the National Science Foundation (DEB-0919064 and IOS-1052262
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e29659, doi:10.1371/journal.pone.0029659.
    Description: Evidence that infectious diseases cause wildlife population extirpation or extinction remains anecdotal and it is unclear whether the impacts of a pathogen at the individual level can scale up to population level so drastically. Here, we quantify the response of a Common eider colony to emerging epidemics of avian cholera, one of the most important infectious diseases affecting wild waterfowl. We show that avian cholera has the potential to drive colony extinction, even over a very short period. Extinction depends on disease severity (the impact of the disease on adult female survival) and disease frequency (the number of annual epidemics per decade). In case of epidemics of high severity (i.e., causing 〉30% mortality of breeding females), more than one outbreak per decade will be unsustainable for the colony and will likely lead to extinction within the next century; more than four outbreaks per decade will drive extinction to within 20 years. Such severity and frequency of avian cholera are already observed, and avian cholera might thus represent a significant threat to viability of breeding populations. However, this will depend on the mechanisms underlying avian cholera transmission, maintenance, and spread, which are currently only poorly known.
    Description: The study was supported by the Canadian Wildlife Service-Environment Canada (http://www.ec.gc.ca/), Nunavut Wildlife Management Board (http:// www.nwmb.com/), Greenland Institute of Natural Resources (http://www.natur.gl/), Polar Continental Shelf Project (http://polar.nrcan.gc.ca/), Fonds Que´be´cois de la Recherche sur la Nature et les Technologies (http://www.fqrnt.gouv.qc.ca/), Canadian Network of Centres of Excellence ArcticNet (http://www.arcticnet.ulaval. ca/), Natural Sciences and Engineering Research Council of Canada (http://www.nserc-crsng.gc.ca/), and the Department of Indian Affairs and Northern Canada (http://www.ainc-inac.gc.ca/).
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e39971, doi:10.1371/journal.pone.0039971.
    Description: Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing 〉80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
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    Publication Date: 1997-12-01
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    Publication Date: 1997-09-01
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    Publication Date: 1997-06-01
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    Publication Date: 1997-04-01
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    Publication Date: 1997-02-01
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    Publication Date: 1997-04-01
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    Publication Date: 1997-09-01
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    Publication Date: 1997-05-01
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    Publication Date: 1997-05-01
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    Publication Date: 1997-03-01
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    Publication Date: 1997-02-01
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    Publication Date: 1997-08-01
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    Publication Date: 1997-07-01
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    Publication Date: 1997-03-01
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    Publication Date: 1997-05-01
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    Publication Date: 1997-08-01
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    Publication Date: 1997-06-01
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  • 56
    Publication Date: 2012-03-09
    Description: The role played by the required level of statistical significance in the scientific method should not be seen as analogous to that played by the standard of proof in the legal process.
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    Publication Date: 2012-03-09
    Description: The Supreme Court ruled in Matrixx that statistical significance is not necessary to show that a drug caused an adverse reaction. Five circuit court decisions holding otherwise preceded this decision. This paper examines the extent to which the Supreme Court’s reasoning differed from those of the circuit courts.
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    Publication Date: 2012-03-09
    Description: Unlike the evaluation of single items of scientific evidence, the formal study and analysis of the joint evaluation of several distinct items of forensic evidence has to date received some punctual, rather than systematic, attention. Questions about the (i) relationships among a set of (usually unobservable) propositions and a set of (observable) items of scientific evidence, (ii) the joint probative value of a collection of distinct items of evidence as well as (iii) the contribution of each individual item within a given group of pieces of evidence still represent fundamental areas of research. To some degree, this is remarkable since both, forensic science theory and practice, yet many daily inference tasks, require the consideration of multiple items if not masses of evidence. A recurrent and particular complication that arises in such settings is that the application of probability theory, i.e. the reference method for reasoning under uncertainty, becomes increasingly demanding. The present paper takes this as a starting point and discusses graphical probability models, i.e. Bayesian networks, as framework within which the joint evaluation of scientific evidence can be approached in some viable way. Based on a review of existing main contributions in this area, the article here aims at presenting instances of real case studies from the author’s institution in order to point out the usefulness and capacities of Bayesian networks for the probabilistic assessment of the probative value of multiple and interrelated items of evidence. A main emphasis is placed on underlying general patterns of inference, their representation as well as their graphical probabilistic analysis. Attention is also drawn to inferential interactions, such as redundancy, synergy and directional change. These distinguish the joint evaluation of evidence from assessments of isolated items of evidence. Together, these topics present aspects of interest to both, domain experts and recipients of expert information, because they have bearing on how multiple items of evidence are meaningfully and appropriately set into context.
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    Publication Date: 2012-03-09
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    Publication Date: 2012-03-09
    Description: In its first foray into the labyrinth that causation in personal injury has become, the U.K. Supreme Court recently held obiter that statistical evidence alone could not establish causation. But in an earlier toxic tort case, the High Court had relied on epidemiological evidence to identify a cluster of birth defects arising in the vicinity of a contaminated land site. This recent British experience is then discussed within the wider context of the forensic role of ‘naked statistics’.
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    Publication Date: 2012-03-09
    Description: Scales of conclusion in forensic interpretation play an important role in the interface between scientific work at a forensic laboratory and different bodies of the jurisdictional system of a country. Of particular importance is the use of a unified scale that allows interpretation of different kinds of evidence in one common framework. The logical approach to forensic interpretation comprises the use of the likelihood ratio as a measure of evidentiary strength. While fully understood by forensic scientists, the likelihood ratio may be hard to interpret for a person not trained in natural sciences or mathematics. Translation of likelihood ratios to an ordinal scale including verbal counterparts of the levels is therefore a necessary procedure for communicating evidence values to the police and in the courtroom. In this paper, we present a method to develop an ordinal scale for the value of evidence that can be applied to any type of forensic findings. The method is built on probabilistic reasoning about the interpretation of findings and the number of scale levels chosen is a compromise between a pragmatic limit and mathematically well-defined distances between levels. The application of the unified scale is illustrated by a number of case studies.
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    Publication Date: 2012-03-09
    Description: In personal injury litigation, claimants may seek their compensation for future losses or expenses as a lump sum that is determined by the product of a multiplicand and a multiplier. The multiplicand represents the annual loss in earnings and other benefits, as assessed at the trial date, while the multiplier discounts future pecuniary values into a single present-day lump sum amount. At present, multipliers in the UK are calculated using actuarial methods and based on assumed mortality and interest rates. However, it is entirely possible that these assumptions are incorrect, and if they are, then all claimants who rely on the same set of actuarial multipliers will be affected. In this article, we investigate how the uncertainty surrounding mortality and interest rate assumptions affects the precision of actuarial multipliers. With the aid of stochastic models, we estimate the possible range of values that an actuarial multiplier can take.
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    Publication Date: 2012-03-10
    Description: In this article we report and discuss a contextual problem solving task that was proposed to a class of 8th grade (13–14-year-old) students. These students had been developing a reasonable experience in the use of the spreadsheet to model relations within contextual problems and chose to use this tool to solve the mentioned problem, engaging in the process of translating relations between variables and combining them in chained models, while working with fractions, multiples and expressions. We intend to highlight the role of the spreadsheet in students’ processes of variable identification and translation of the problem conditions, their numerical approaches to algebraic models and their experimental forms of finding solutions to equations.
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    Publication Date: 2012-03-10
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  • 65
    Publication Date: 2012-03-10
    Description: This theoretical study is an attempt to explore the potential of the dynamic and interactive mathematics learning environments (DIMLE) in relation to the technological pedagogical content knowledge (TPACK) framework. DIMLE are developed with intent to support learning mathematics through free exploration in a less constrained environment. A typical DIMLE software package has interactivity and dynamism as key affordances; these are especially suitable for enhancing learning and teaching with technology of the essentially dynamic mathematics concepts. Moreover, we propose that DIMLE and their affordances should be studied under the TPACK framework because this framework is explicit in considering technology-supported mathematics learning as a qualitative add-on as contrasted to what would be a simple totalling of technological, pedagogical and mathematical knowledge. As an example, we focus in our discussion on using a DIMLE in order to support learner in development of the limit concept.
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  • 66
    Publication Date: 2012-03-10
    Description: The present article reports a study concerning the analysis of 19 activity plans (we call them ‘scenarios’) developed by mathematics teacher educators-in-training for the pedagogical use of digital tools. The development of these scenarios took place during their training program and was designed as an activity for increasing reflection, for expressing creative pedagogical ideas and for an active engagement in the design of curricula enriched with the use of technology. Our analysis showed that the trainee teacher educators deconstructed and reconstructed respective parts of the formal curriculum regarding the mathematical concepts they chose to embody in their scenarios.
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  • 67
    Publication Date: 2012-03-10
    Description: In this research we present the use of some technologies in problem solving activities (at different secondary school grades), aimed at finding a model for a geometric configuration, and representing this model in various ways: through a construction, through a Cartesian graph, etc. The task is part of a teaching experiment, in which students used paper and pencil, and technological tools: a sensor and a calculator (at a lower grade), GeoGebra and TI-Nspire (at a higher grade). We show results in terms of the passage from static to dynamic representations and back, to observe how technology may foster dynamic thinking for students solving mathematical problems. Data suggest that the dynamic features of technology support the genesis of conjectures, and their validation or refutation, along with the choice of independent and dependent variables. Results are used to prepare materials for teacher training in an e-learning Moodle platform (Comenius EdUmatics Project).
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  • 68
    Publication Date: 2012-02-22
    Description: SUMMARY In the absence of seismological measurements, observations of the topography and gravity fields of solid planets are the primary constraints on their internal structure. To compute the synthetic geoid and topography induced by the dynamics of planetary interiors, we introduce a 3-D numerical tool describing mantle convection beneath an elastic lithosphere. Although the energy conservation is treated in the whole spherical domain, the deformation aspect is solved using a hybrid technique (finite volume method for the viscous flow, spectral method for elastic deformation). The mechanical coupling is achieved via the imposition of the traction at the surface of the viscous flow as a basal boundary condition for the elastic deformation. We present both response functions and full thermal convection cases computed with our new method for planetary bodies of varying dimensions: the filtering effect of the lithosphere on the dynamic topography and geoid is specific for each planetary body, justifying the importance of such a tool. Furthermore, since our approach specifically focuses on the mechanical coupling at the base of the lithosphere, it will permit future, more elaborate, rheological treatments. It also enables to discriminate between the radial and tangential components of the viscous traction. The latter is found to have a significant influence on the elastic deformation. The effect on geoid is prominent. More specifically, while a thin elastic lithosphere is usually considered to play little role on the dynamic topography and geoid of Venus, a ∼35 per cent reduction is obtained for geoid height in the numerical example we propose. On a planet with thicker elastic lithosphere such as Mars, the consequence of this filtering effect is to rule out the possibility of a dynamical support for the Tharsis Rise, even for the lowest admissible values of elastic thickness in this region.
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  • 69
    Publication Date: 2012-02-22
    Description: SUMMARY The Central Iran plateau appears aseismic during the last few millenniums based on instrumental and historical seismic records. Nevertheless, it is sliced by several strike-slip faults that are hundreds of kilometres long. These faults display along-strike, horizontal offsets of intermittent gullies that suggest the occurrence of earthquakes in the Holocene. Establishing this is crucial for accurately assessing the regional seismic hazard. The first palaeoseismic study performed on the 200-km long, NS striking Anar fault shows that this right-lateral fault hosted three large ( M w ≈ 7) earthquakes during the Holocene or possibly Uppermost Pleistocene for the older one. These three seismic events are recorded within a sedimentary succession, which is not older than 15 ka, suggesting an average recurrence of at most 5 ka. The six optically stimulated luminescence ages available provide additional constraints and allow estimating that the three earthquakes have occurred within the following time intervals: 4.4 ± 0.8, 6.8 ± 1 and 9.8 ± 2 ka. The preferred age of the more recent event, ranging between 3600 and 5200 yr, suggests that the fault is approaching the end of its seismic cycle and the city of Anar could be under the threat of a destructive earthquake in the near future. In addition, our results confirm a previous minimum slip rate estimate of 0.8 ± 0.1 mm yr −1 for the Anar fault indicating that the westernmost prominent right-lateral faults of the Central Iran plateau are characterized by slip rates close to 1 mm yr −1 . These faults, which have repeatedly produced destructive earthquakes with large magnitudes and long recurrence interval of several thousands of years during the Holocene, show that the Central Iran plateau does not behave totally as a rigid block and that its moderate internal deformation is nonetheless responsible for a significant seismic hazard.
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  • 70
    Publication Date: 2012-03-13
    Description: SUMMARY Passive seismic interferometry is a new promising methodology for seismic exploration. Interferometry allows information about the subsurface structure to be extracted from ambient seismic noise. In this study, we apply the cross-correlation technique to approximately 25 hr of recordings of ambient seismic noise at the Ketzin experimental CO 2 storage site, Germany. Common source gathers were generated from the ambient noise for all available receivers along two seismic lines by cross-correlation of noise records. This methodology isolates the interstation Green's functions that can be directly compared to active source gathers. We show that the retrieved response includes surface waves, refracted waves and reflected waves. We use the dispersive behaviour of the retrieved surface waves to infer geological properties in the shallow subsurface and perform passive seismic imaging of the subsurface structure by processing the retrieved reflected waves.
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    Topics: Geosciences
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  • 71
    Publication Date: 2012-03-13
    Print ISSN: 1471-678X
    Electronic ISSN: 1471-6798
    Topics: Mathematics
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  • 72
    Publication Date: 2012-03-14
    Description: SUMMARY Normal mode observations play an important role in studying broad-scale lateral variations in the Earth. Such studies require the calculation of accurate synthetic spectra in realistic earth models, and this remains a computationally challenging problem. Here, we describe a new implementation of the direct solution method for calculating normal mode spectra in laterally heterogeneous earth models. In this iterative direct solution method , the mode-coupling equations are solved in the frequency-domain using the preconditioned biconjugate gradient algorithm, and the time-domain solution is recovered using a numerical inverse Fourier transform. A number of example calculations are presented to demonstrate the accuracy and efficiency of the method for performing large ‘full coupling’ calculations as compared to methods based on matrix diagonalization and the traditional direct solution method.
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 73
    Publication Date: 2012-03-14
    Description: Telomeres, the ends of linear chromosomes, safeguard against genome instability. The enzyme responsible for extension of the telomere 3' terminus is the ribonucleoprotein telomerase. Whereas telomerase activity can be reconstituted in vitro with only the telomerase RNA (hTR) and telomerase reverse transcriptase (TERT), additional components are required in vivo for enzyme assembly, stability and telomere extension activity. One such associated protein, dyskerin, promotes hTR stability in vivo and is the only component to co-purify with active, endogenous human telomerase. We used oligonucleotide-based affinity purification of hTR followed by native gel electrophoresis and in-gel telomerase activity detection to query the composition of telomerase at different purification stringencies. At low salt concentrations (0.1 M NaCl), affinity-purified telomerase was ‘supershifted’ with an anti-dyskerin antibody, however the association with dyskerin was lost after purification at 0.6 M NaCl, despite the retention of telomerase activity and a comparable yield of hTR. The interaction of purified hTR and dyskerin in vitro displayed a similar salt-sensitive interaction. These results demonstrate that endogenous human telomerase, once assembled and active, does not require dyskerin for catalytic activity. Native gel electrophoresis may prove useful in the characterization of telomerase complexes under various physiological conditions.
    Keywords: Protein-nucleic acid interaction, Miscellaneous/other
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  • 74
    Publication Date: 2012-03-14
    Description: We describe an inexpensive and efficient method for generating functional pools of Dicer-substrate small interfering RNAs (siRNAs) in a single reaction tube. The method exploits a highly active form of the enzyme Dicer from Giardia lamblia , which is capable of accurately processing double-stranded RNA (dsRNA) into 25–27 nt RNA pools during in vitro transcription. The small RNAs produced function as substrates of human Dicer in vitro and induce gene silencing with potency equivalent to traditional siRNAs when introduced into mammalian cells. The overall reaction is simple, can be carried out in any laboratory with access to a PCR machine, and is amenable to high-throughput processes.
    Keywords: Microarray Technology, Nucleic Acid Enzymology
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  • 75
    Publication Date: 2012-03-14
    Description: Microglial cells are the main HIV-1 targets in the central nervous system (CNS) and constitute an important reservoir of latently infected cells. Establishment and persistence of these reservoirs rely on the chromatin structure of the integrated proviruses. We have previously demonstrated that the cellular cofactor CTIP2 forces heterochromatin formation and HIV-1 gene silencing by recruiting HDAC and HMT activities at the integrated viral promoter. In the present work, we report that the histone demethylase LSD1 represses HIV-1 transcription and viral expression in a synergistic manner with CTIP2. We show that recruitment of LSD1 at the HIV-1 proximal promoter is associated with both H3K4me3 and H3K9me3 epigenetic marks. Finally, our data suggest that LSD1-induced H3K4 trimethylation is linked to hSET1 recruitment at the integrated provirus.
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  • 76
    Publication Date: 2012-03-14
    Description: This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base–base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.
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  • 77
    Publication Date: 2012-03-14
    Description: Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.
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  • 78
    Publication Date: 2012-03-14
    Description: RNA tetraloops can recognize receptors to mediate long-range interactions in stable natural RNAs. In vitro selected GNRA tetraloop/receptor interactions are usually more ‘G/C-rich’ than their ‘A/U-rich’ natural counterparts. They are not as widespread in nature despite comparable biophysical and chemical properties. Moreover, while AA, AC and GU dinucleotide platforms occur in natural GAAA/11 nt receptors, the AA platform is somewhat preferred to the others. The apparent preference for ‘A/U-rich’ GNRA/receptor interactions in nature might stem from an evolutionary adaptation to avoid folding traps at the level of the larger molecular context. To provide evidences in favor of this hypothesis, several riboswitches based on natural and artificial GNRA receptors were investigated in vitro for their ability to prevent inter-molecular GNRA/receptor interactions by trapping the receptor sequence into an alternative intra-molecular pseudoknot. Extent of attenuation determined by native gel-shift assays and co-transcriptional assembly is correlated to the G/C content of the GNRA receptor. Our results shed light on the structural evolution of natural long-range interactions and provide design principles for RNA-based attenuator devices to be used in synthetic biology and RNA nanobiotechnology.
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  • 79
    Publication Date: 2012-03-14
    Description: Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here we present biochemical and genetic evidence to suggest that Pso2 is a robust DNA hairpin opening nuclease in budding yeast. Pso2 (SNM1A in mammals) belongs to a small group of proteins thought to function predominantly during interstrand crosslink (ICL) repair. In this study, we characterized the nuclease activity of Pso2 toward a variety of DNA substrates. Unexpectedly, Pso2 was found to be an efficient, structure-specific DNA hairpin opening endonuclease. This activity was further shown to be required in vivo for repair of chromosomal breaks harboring closed hairpin ends. These findings provide the first evidence that Pso2 may function outside ICL repair and open the possibility that Pso2 may function at least in part during ICL repair by processing DNA intermediates including DNA hairpins or hairpin-like structures.
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  • 80
    Publication Date: 2012-03-14
    Description: The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to N 6 -(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H. influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the position occupied by mom in Mu they carry an unrelated gene that encodes a protein with homology to DNA adenine N 6 -methyltransferases ( hin1523 , nma1821 , hia5 , respectively). Products of the hin1523 , hia5 and nma1821 genes modify adenine residues to N 6 -methyladenine, both in vitro and in vivo . All of these enzymes catalyzed extensive DNA methylation; most notably the Hia5 protein caused the methylation of 61% of the adenines in DNA. Kinetic analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes. Their potential ‘sequence specificity’ could be summarized as AB or BA (where B = C, G or T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation.
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  • 81
    Publication Date: 2012-03-14
    Description: The influenza A virus genome consists of eight viral RNAs (vRNAs) that form viral ribonucleoproteins (vRNPs). Even though evidence supporting segment-specific packaging of vRNAs is accumulating, the mechanism ensuring selective packaging of one copy of each vRNA into the viral particles remains largely unknown. We used electron tomography to show that the eight vRNPs emerge from a common ‘transition zone’ located underneath the matrix layer at the budding tip of the virions, where they appear to be interconnected and often form a star-like structure. This zone appears as a platform in 3D surface rendering and is thick enough to contain all known packaging signals. In vitro , all vRNA segments are involved in a single network of intermolecular interactions. The regions involved in the strongest interactions were identified and correspond to known packaging signals. A limited set of nucleotides in the 5' region of vRNA 7 was shown to interact with vRNA 6 and to be crucial for packaging of the former vRNA. Collectively, our findings support a model in which the eight genomic RNA segments are selected and packaged as an organized supramolecular complex held together by direct base pairing of the packaging signals.
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  • 82
    Publication Date: 2012-03-14
    Description: Anti-miRs are oligonucleotide inhibitors complementary to miRNAs that have been used extensively as tools to gain understanding of specific miRNA functions and as potential therapeutics. We showed previously that peptide nucleic acid (PNA) anti-miRs containing a few attached Lys residues were potent miRNA inhibitors. Using miR-122 as an example, we report here the PNA sequence and attached amino acid requirements for efficient miRNA targeting and show that anti-miR activity is enhanced substantially by the presence of a terminal-free thiol group, such as a Cys residue, primarily due to better cellular uptake. We show that anti-miR activity of a Cys-containing PNA is achieved by cell uptake through both clathrin-dependent and independent routes. With the aid of two PNA analogues having intrinsic fluorescence, thiazole orange (TO)-PNA and [bis- o -(aminoethoxy)phenyl]pyrrolocytosine (BoPhpC)-PNA, we explored the subcellular localization of PNA anti-miRs and our data suggest that anti-miR targeting of miR-122 may take place in or associated with endosomal compartments. Our findings are valuable for further design of PNAs and other oligonucleotides as potent anti-miR agents.
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  • 83
    Publication Date: 2012-03-14
    Description: Translation initiation factor eIF3 acts as the key orchestrator of the canonical initiation pathway in eukaryotes, yet its structure is greatly unexplored. We report the 2.2 Å resolution crystal structure of the complex between the yeast seven-bladed β-propeller eIF3i/TIF34 and a C-terminal α-helix of eIF3b/PRT1, which reveals universally conserved interactions. Mutating these interactions displays severe growth defects and eliminates association of eIF3i/TIF34 and strikingly also eIF3g/TIF35 with eIF3 and 40S subunits in vivo . Unexpectedly, 40S-association of the remaining eIF3 subcomplex and eIF5 is likewise destabilized resulting in formation of aberrant pre-initiation complexes (PICs) containing eIF2 and eIF1, which critically compromises scanning arrest on mRNA at its AUG start codon suggesting that the contacts between mRNA and ribosomal decoding site are impaired. Remarkably, overexpression of eIF3g/TIF35 suppresses the leaky scanning and growth defects most probably by preventing these aberrant PICs to form. Leaky scanning is also partially suppressed by eIF1, one of the key regulators of AUG recognition, and its mutant sui1 G107R but the mechanism differs. We conclude that the C-terminus of eIF3b/PRT1 orchestrates co-operative recruitment of eIF3i/TIF34 and eIF3g/TIF35 to the 40S subunit for a stable and proper assembly of 48S pre-initiation complexes necessary for stringent AUG recognition on mRNAs.
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  • 84
    Publication Date: 2012-03-14
    Description: The misreplication of damaged DNA is an important biological process that produces numerous adverse effects on human health. This report describes the synthesis and characterization of a non-natural nucleotide, designated 3-ethynyl-5-nitroindolyl-2'-deoxyriboside triphosphate (3-Eth-5-NITP), as a novel chemical reagent that can probe and quantify the misreplication of damaged DNA. We demonstrate that this non-natural nucleotide is efficiently inserted opposite an abasic site, a commonly formed and potentially mutagenic non-instructional DNA lesion. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore using ‘click’ chemistry. This reaction provides a facile way to quantify the extent of nucleotide incorporation opposite non-instructional DNA lesions. In addition, the incorporation of 3-Eth-5-NITP is highly selective for an abasic site, and occurs even in the presence of a 50-fold molar excess of natural nucleotides. The biological applications of using 3-Eth-5-NITP as a chemical probe to monitor and quantify the misreplication of non-instructional DNA lesions are discussed.
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  • 85
    Publication Date: 2012-03-16
    Description: SUMMARY We report on a unique set of infrasound observations from a single earthquake, the 2011 January 3 Circleville earthquake ( M w 4.7, depth of 8 km), which was recorded by nine infrasound arrays in Utah. Based on an analysis of the signal arrival times and backazimuths at each array, we find that the infrasound arrivals at six arrays can be associated to the same source and that the source location is consistent with the earthquake epicentre. Results of propagation modelling indicate that the lack of associated arrivals at the remaining three arrays is due to path effects. Based on these findings we form the working hypothesis that the infrasound is generated by body waves causing the epicentral region to pump the atmosphere, akin to a baffled piston. To test this hypothesis, we have developed a numerical seismoacoustic model to simulate the generation of epicentral infrasound from earthquakes. We model the generation of seismic waves using a 3-D finite difference algorithm that accounts for the earthquake moment tensor, source time function, depth and local geology. The resultant acceleration–time histories on a 2-D grid at the surface then provide the initial conditions for modelling the near-field infrasonic pressure wave using the Rayleigh integral. Finally, we propagate the near-field source pressure through the Ground-to-Space atmospheric model using a time-domain Parabolic Equation technique. By comparing the resultant predictions with the six epicentral infrasound observations from the 2011 January 3, Circleville earthquake, we show that the observations agree well with our predictions. The predicted and observed amplitudes are within a factor of 2 (on average, the synthetic amplitudes are a factor of 1.6 larger than the observed amplitudes). In addition, arrivals are predicted at all six arrays where signals are observed, and importantly not predicted at the remaining three arrays. Durations are typically predicted to within a factor of 2, and in some cases much better. These results suggest that measured infrasound from the Circleville earthquake is consistent with the generation of infrasound from body waves in the epicentral region.
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    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 86
    Publication Date: 2012-03-16
    Description: SUMMARY We present new dedicated core surface field models spanning the decade from 2000.0 to 2010.0. These models, called gufm-sat , are based on CHAMP, Ørsted and SAC-C satellite observations along with annual differences of processed observatory monthly means. A spatial parametrization of spherical harmonics up to degree and order 24 and a temporal parametrization of sixth-order B-splines with 0.25 yr knot spacing is employed. Models were constructed by minimizing an absolute deviation measure of misfit along with measures of spatial and temporal complexity at the core surface. We investigate traditional quadratic or maximum entropy regularization in space, and second or third time derivative regularization in time. Entropy regularization allows the construction of models with approximately constant spectral slope at the core surface, avoiding both the divergence characteristic of the crustal field and the unrealistic rapid decay typical of quadratic regularization at degrees above 12. We describe in detail aspects of the models that are relevant to core dynamics. Secular variation and secular acceleration are found to be of lower amplitude under the Pacific hemisphere where the core field is weaker. Rapid field evolution is observed under the eastern Indian Ocean associated with the growth and drift of an intense low latitude flux patch. We also find that the present axial dipole decay arises from a combination of subtle changes in the southern hemisphere field morphology.
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  • 87
    Publication Date: 2012-03-16
    Description: SUMMARY We present a novel frequency-domain inverse solution to recover the 3-D electrical conductivity distribution in the mantle. The solution is based on analysis of local C -responses. It exploits an iterative gradient-type method—limited-memory quasi-Newton method—for minimizing the penalty function consisting of data misfit and regularization terms. The integral equation code is used as a forward engine to calculate responses and data misfit gradients during inversion. An adjoint approach is implemented to compute misfit gradients efficiently. Further improvements in computational load come from parallelizing the scheme with respect to frequencies, and from setting the most time-consuming part of the forward calculations—calculation of Green’s tensors—apart from the inversion loop. Convergence, performance, and accuracy of our 3-D inverse solution are demonstrated with a synthetic numerical example. A companion paper applies the strategy set forth here to real data.
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  • 88
    Publication Date: 2012-02-02
    Description: This paper presents a benchmarking, performance analysis and optimization study of the OP2 ‘active’ library, which provides an abstraction framework for the parallel execution of unstructured mesh applications. OP2 aims to decouple the scientific specification of the application from its parallel implementation, and thereby achieve code longevity and near-optimal performance through re-targeting the application to execute on different multi-core/many-core hardware. Runtime performance results are presented for a representative unstructured mesh application on a variety of many-core processor systems, including traditional X86 architectures from Intel (Xeon based on the older Penryn and current Nehalem micro-architectures) and GPU offerings from NVIDIA (GTX260, Tesla C2050). Our analysis demonstrates the contrasting performance between the use of CPU (OpenMP) and GPU (CUDA) parallel implementations for the solution of an industrial-sized unstructured mesh consisting of about 1.5 million edges. Results show the significance of choosing the correct partition and thread-block configuration, the factors limiting the GPU performance and insights into optimizations for improved performance.
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  • 89
    Publication Date: 2012-02-02
    Description: In this paper, we describe the integrated power, area and thermal modeling framework in the structural simulation toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also provides functionality to update the leakage power as temperature changes. We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP) and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering that temperature variation increases total power dissipation, we demonstrate the importance of considering temperature variation in the design flow. With this power, area and thermal modeling capability, the SST can be used for hardware/software co-design of future exascale systems.
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  • 90
    Publication Date: 2012-02-02
    Description: With the advent of heterogeneous computing systems consisting of multi-core central processing units (CPUs) and many-core graphics processing units (GPUs), robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper, we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated running costs and carbon emissions. We give a case study for these metrics applied to Bristol University Docking engine, a molecular mechanics-based docking application that has been ported to open computing language at the University of Bristol. Results are included for both AMD and NVIDIA GPUs, and for a highly optimized code on the latest x86 CPUs.
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  • 91
    Publication Date: 2012-02-02
    Description: Java embedded systems often include Java middleware classes installed on the client device. For higher performance, they can be compiled into machine code before runtime using an ahead-of-time compiler (AOTC). There are many approaches to AOTC, yet a bytecode-to-C (b-to-C) AOTC which translates the bytecode into the C code and then compiles it using an existing optimizing compiler such as gcc would be the most straightforward one. This paper explores a few important design and optimization issues of a b-to-C AOTC, including the compilation form for the translated C code, the call interfaces among translated and interpreted Java methods, and Java-specific optimizations by the AOTC that can complement the gcc optimizations. We evaluate these issues with our b-to-C AOTC implemented on the MIPS platform for the Sun's CDC VM to understand their performance impact.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 92
    Publication Date: 2012-02-02
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 93
    Publication Date: 2012-02-07
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
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  • 94
    Publication Date: 2012-02-08
    Description: Let K be a convex body in R n . We introduce a new affine invariant, which we call K , that can be found in three different ways: as a limit of normalized L p -affine surface areas; as the relative entropy of the cone measure of K and the cone measure of K °; as the limit of the volume difference of K and L p -centroid bodies. We investigate properties of K and of related new invariant quantities. In particular, we show new affine isoperimetric inequalities and we show an ‘information inequality’ for convex bodies.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
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  • 95
    Publication Date: 2012-02-08
    Description: We establish the precise bounds for the amount of determinacy provable in second-order arithmetic. We show that, for every natural number n , second-order arithmetic can prove that determinacy holds for Boolean combinations of n many classes, but it cannot prove that all finite Boolean combinations of classes are determined. More specifically, we prove that , but that , where is the n th level in the difference hierarchy of classes. We also show some conservativity results that imply that reversals for the theorems above are not possible. We prove that, for every true 1 4 sentence T (as, for instance, -DET) and every and .
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
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  • 96
    Publication Date: 2012-02-11
    Description: Longitudinal or hierarchical data are often observed in forestry, which can pose both challenges and opportunities when performing statistical analyses. The current standard approach for analysing these types of data is mixed-effects models under the frequentist paradigm. Bayesian techniques have several advantages when compared with traditional approaches, but their use in forestry has been relatively limited. In this paper, we propose a Bayesian solution to non-linear mixed-effects models for longitudinal data in forestry. We demonstrate the Bayesian modelling process using individual tree height–age data for balsam fir ( Abies balsamea (L.)) collected from eastern Maine. Due to its frequent utilization in modelling dominant tree height growth over time, we choose to examine models based on the Chapman–Richards function. We established four different model formulations, each having varying subject-specific parameters, which we estimated using both frequentist and Bayesian approaches. We found the estimation results to be quite close between the two methods. In addition, an important feature of the Bayesian method is the unified manner in which estimation and prediction are handled. Specifically, local parameters can be predicted for a new dataset after setting the posterior distributions from the estimation stage as new priors in the prediction phase.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 97
    Publication Date: 2012-02-11
    Description: This study compares the financial return of converting old-growth boreal stands into even-aged stands to that of two approaches of selection cutting in Quebec (Canada). In this region, old-growth stands are usually harvested by completely removing the canopy while protecting the abundant advance regeneration, an approach known as careful logging around advance growth (CLAAG). These approaches were compared using a time frame of over 200 years. Consideration is given to the majority of the operating costs leading to end products. The financial analysis integrates Monte Carlo simulations, making it possible to consider the uncertainty associated with variables. The net present values (NPVs) are then associated with a distribution of probabilities. The results show that the probabilities of obtaining positive NPVs are high for all treatments, suggesting that selection cutting approaches can be appropriate alternatives to CLAAG for some stands. Depending on the criteria used, the CLAAG cut or one of the selection cuts show the best performances. In fact, the results of the financial study show that in the future, selection cutting approaches will be more profitable than CLAAG but still less than present CLAAG operations. This occurs because, according to the current yield curves and rotation ages, future stands managed with CLAAG will have smaller and less valuable trees than in the primary forest and in stands managed with the selection system.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 98
    Publication Date: 2012-02-11
    Description: There is a growing interest in the feasibility of establishing ‘Carbon’ forests where carbon sinks are created by maintaining forest stands out to considerable ages. In New Zealand, Pinus radiata (D. Don) is usually grown over 25- to 30-year rotations; the main aim of this paper is to examine the potential to maintain stands to 60 years or more. There were over 140 permanent sample plots in New Zealand that were maintained for at least 50 years. These data were examined to verify that growth can be sustained over this period. Net basal area per hectare and mean-top-height are graphically demonstrated to follow expected growth paths with no signs of senescence occurring. Stems per hectare loss is shown to be sometimes high, especially with dense stockings, but virtually all dying trees are small suppressed stems, so the impact on basal area yield at maturity is minimal. It is concluded that growing radiata pine on a rotation of 60 years is feasible, and it may be possible to use much longer rotations.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 99
    Publication Date: 2012-02-11
    Description: The effects of site preparation practices (drainage, mounding and fertilization) on the fluxes from the soil surface of carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) were studied on an organic-rich peaty gley soil at Harwood Forest, north-east England. Drained plots had significantly higher CO 2 fluxes but significantly lower CH 4 fluxes compared with undrained plots, while N 2 O emissions were not affected by drainage. Mounding caused significantly higher CH 4 emissions, while it significantly reduced N 2 O emissions. Fertilization caused significant increases in emissions of CO 2 , CH 4 and N 2 O. In terms of overall greenhouse warming potential, drainage and fertilization increased CO 2 -equivalent emissions by ~18–29 and 7–23 per cent, respectively, while mounding reduced CO 2 -equivalent emissions by ~8 per cent in year 1, but had no effect on emissions in year 2 of study. Soil temperature was the main environmental variable controlling CO 2 emissions, while CH 4 was controlled primarily by water table depth. Nitrous oxide emissions responded to changes in soil temperature and water table depth. In the short term, drainage and fertilization contributed to accelerating greenhouse gas emissions significantly, although their long-term effects are likely moderated by accelerating carbon accumulation in the tree biomass. Long-term studies are required to assess the cumulative impacts of site preparation practices during the whole rotation cycle.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 100
    Publication Date: 2012-02-11
    Description: As signatories to the United Nation Framework Convention on Climate Change, the US has been estimating standing dead tree (SDT) carbon (C) stocks using a model based on live tree attributes. The USDA Forest Service began sampling SDTs nationwide in 1999. With comprehensive field data now available, the objective of this study was to compare field- and model-based estimates of SDT C stocks across the US to evaluate potential directions for improving National Greenhouse Gas Inventory (NGHGI) reporting and C dynamics research. Field inventory data indicated that most forests have relatively little SDT C stocks (〈1 Mg/ha), whereas large SDT C stocks (〉25 Mg/ha) are infrequent. Models used for past NGHGIs to predict SDT C stocks do not accurately reflect what was observed in inventory plots, resulting in an overestimation (~100 per cent) of SDT C stocks at the national scale. These results indicate that the current estimate of the Nation’s total forest C stock is overestimated by ~4.2 per cent due to overestimation of SDT C stocks that are a relatively small component of the total forest C stock. A field-based approach is suggested for use in future C reporting efforts to reduce estimation bias.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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