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  • Public Library of Science  (118,079)
  • American Physical Society (APS)  (74,345)
  • BioMed Central  (39,661)
  • 2010-2014  (232,085)
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  • 1
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    Multiple Sclerosis in the Mount Etna Region: Possible Role of Volcanogenic Trace Elements (2014)
    Public Library of Science
    Details
    Publication Date: 2017-04-04
    Description: Background: Trace elements have been hypothesised to be involved in the pathogenesis of Multiple Sclerosis and volcanic degassing is the major natural sources of trace elements. Both incidence of Multiple Sclerosis in Catania and volcanic activity of Mount Etna have been significantly increased during the last 30 years. Due to prevailing trade winds direction, volcanic gases from Etna summit craters are mostly blown towards the eastern and southern sectors of the volcano. Objective: To evaluate the possible association between Multiple Sclerosis and exposure to volcanogenic trace elements. Methods: We evaluated prevalence and incidence of Multiple Sclerosis in four communities (47,234 inhabitants) located in the eastern flank and in two communities (52,210 inhabitants) located in the western flank of Mount Etna, respectively the most and least exposed area to crater gas emissions. Results: A higher prevalence was found in the population of the eastern flank compared to the population of the western one (137.6/100,000 versus 94.3/100,000; p-value 0.04). We found a borderline significantly higher incidence risk during the incidence study period (1980–2009) in the population of the eastern flank 4.6/100,000 (95% CI 3.1–5.9), compared with the western population 3.2/100,000 (95% CI 2.4–4.2) with a RR of 1.41 (95% CI 0.97–2.05; p-value 0.06). Incidence risks have increased over the time in both populations reaching a peak of 6.4/100,000 in the eastern flank and of 4.4/100.000 in the western flank during 2000–2009. Conclusion: We found a higher prevalence and incidence of Multiple Sclerosis among populations living in the eastern flank of Mount Etna. According to our data a possible role of TE cannot be ruled out as possible co-factor in the MS pathogenesis. However larger epidemiological study are needed to confirm this hypothesis.
    Description: Published
    Description: e74259
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: JCR Journal
    Description: open
    Keywords: Mt. Etna volcano ; Multiple Sclerosis ; trace elements ; volcanic activity ; 05. General::05.08. Risk::05.08.01. Environmental risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Geosphere-biosphere interacions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica). (2014)
    Public Library of Science
    Details
    Publication Date: 2020-02-24
    Description: Hule and Rı´o Cuarto are maar lakes located 11 and 18 km N of Poa´s volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Rı´o Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).
    Description: Published
    Description: e102456
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: open
    Keywords: bio activity, volcanic lakes, costa rica ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Compositional discrimination of decompression and decomposition gas bubbles in bycaught seals and dolphins (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 8 (2013): e83994, doi:10.1371/journal.pone.0083994.
    Description: Gas bubbles in marine mammals entangled and drowned in gillnets have been previously described by computed tomography, gross examination and histopathology. The absence of bacteria or autolytic changes in the tissues of those animals suggested that the gas was produced peri- or post-mortem by a fast decompression, probably by quickly hauling animals entangled in the net at depth to the surface. Gas composition analysis and gas scoring are two new diagnostic tools available to distinguish gas embolisms from putrefaction gases. With this goal, these methods have been successfully applied to pathological studies of marine mammals. In this study, we characterized the flux and composition of the gas bubbles from bycaught marine mammals in anchored sink gillnets and bottom otter trawls. We compared these data with marine mammals stranded on Cape Cod, MA, USA. Fresh animals or with moderate decomposition (decomposition scores of 2 and 3) were prioritized. Results showed that bycaught animals presented with significantly higher gas scores than stranded animals. Gas composition analyses indicate that gas was formed by decompression, confirming the decompression hypothesis.
    Description: This study was funded by the Woods Hole Oceanographic Institution Marine Mammal Center, and Wick and Sloan Simmons.
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Decadal changes in zooplankton of the Northeast U.S. continental shelf (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e87720, doi:10.1371/journal.pone.0087720.
    Description: The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf (NEUS) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine (GOM), Georges Bank (GB), Southern New England (SNE), and Mid-Atlantic Bight (MAB). Results suggested that there was significant difference in long term variation between northern region (GOM and GB), and the MAB for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the MAB. The long term abundance of C. finmarchicus showed more fluctuation in the MAB than the GOM and GB, whereas the long term abundance of Cen. typicus was more variable in the GB than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index (GSNWI) in the GOM and GB, but the GSNWI only explained 12–15% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the GSNWI, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    A quantitative assessment of the role of the parasite Amoebophrya in the termination of Alexandrium fundyense blooms within a small coastal embayment (2014)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e81150, doi:10.1371/journal.pone.0081150.
    Description: Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). High prevalence of Amoebophrya spp. has been linked to the decline of some HABs in marine systems. The objective of this study was to evaluate the impact of Amoebophrya spp. on the dynamics of dinoflagellate blooms in Salt Pond (MA, USA), particularly the harmful species Alexandrium fundyense. The abundance of Amoebophrya life stages was estimated 3–7 days per week through the full duration of an annual A. fundyense bloom using fluorescence in situ hybridization coupled with tyramide signal amplification (FISH- TSA). More than 20 potential hosts were recorded including Dinophysis spp., Protoperidinium spp. and Gonyaulax spp., but the only dinoflagellate cells infected by Amoebophrya spp. during the sampling period were A. fundyense. Maximum A. fundyense concentration co-occurred with an increase of infected hosts, followed by a massive release of Amoebophrya dinospores in the water column. On average, Amoebophrya spp. infected and killed ~30% of the A. fundyense population per day in the end phase of the bloom. The decline of the host A. fundyense population coincided with a dramatic life-cycle transition from vegetative division to sexual fusion. This transition occurred after maximum infected host concentrations and before peak infection percentages were observed, suggesting that most A. fundyense escaped parasite infection through sexual fusion. The results of this work highlight the importance of high frequency sampling of both parasite and host populations to accurately assess the impact of parasites on natural plankton assemblages.
    Description: L. Velo-Sua´rez was supported by a Marie Curie International Outgoing Fellowship (IOF; grant agreement: MOHAB PIOF-GA-252260). This work was supported in part by NSF grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences grants 1P50-ES01274201 and 1P01ES021923-01 to D.M. Anderson and D.J. McGillicuddy through the Woods Hole Center for Oceans and Human Health, National Park Service Cooperative Agreement H238015504 to D.M. Anderson.
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Diving behavior of the reef manta ray links coral reefs with adjacent deep pelagic habitats (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88170, doi:10.1371/journal.pone.0088170.
    Description: Recent successful efforts to increase protection for manta rays has highlighted the lack of basic ecological information, including vertical and horizontal movement patterns, available for these species. We deployed pop-up satellite archival transmitting tags on nine reef manta rays, Manta alfredi, to determine diving behaviors and vertical habitat use. Transmitted and archived data were obtained from seven tagged mantas over deployment periods of 102–188 days, including three recovered tags containing 2.6 million depth, temperature, and light level data points collected every 10 or 15 seconds. Mantas frequented the upper 10 m during daylight hours and tended to occupy deeper water throughout the night. Six of the seven individuals performed a cumulative 76 deep dives (〉150 m) with one individual reaching 432 m, extending the known depth range of this coastal, reef-oriented species and confirming its role as an ecological link between epipelagic and mesopelagic habitats. Mean vertical velocities calculated from high-resolution dive data (62 dives 〉150 m) from three individuals suggested that mantas may use gliding behavior during travel and that this behavior may prove more efficient than continuous horizontal swimming. The behaviors in this study indicate manta rays provide a previously unknown link between the epi- and mesopelagic layers of an extremely oligotrophic marine environment and provide evidence of a third marine species that utilizes gliding to maximize movement efficiency.
    Description: inancial support was provided in part by KAUST baseline research funds (to MLB), KAUST award numbers USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).
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  • 7
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    Identification of cinnabarinic acid as novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e87877, doi:10.1371/journal.pone.0087877.
    Description: The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.
    Description: This work was supported in part by National Institutes of Health (NIH) grants OD000329 and R01AI40312 (to JMM), R01ES006272 (to MEH), P42ES007381 (Superfund Research Program at Boston University to JS, DHS and MEH), R21CA134882 (to JS), NIH Training Grant T32 GM007175 (MML), and the Harvey V. Berneking Living Trust. BK is supported by Career Development Awards from the NIH/National Institute of Diabetes and Digestive and Kidney Diseases (DK083334) and the NASPGHAN Foundation. JEM is a recipient of the Human Frontiers Science Program Long-Term Fellowship (LT000231/2011-L). JMM is a recipient of the NIH Director's Pioneer Award Program, part of the NIH Roadmap for Medical Research, through grant DPI OD00329.
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  • 8
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    Shifts in the microbial community composition of Gulf Coast beaches following beach oiling (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e74265, doi:10.1371/journal.pone.0074265.
    Description: Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.
    Description: Financial support for this work was provided by the University of Wisconsin-Milwaukee National Institute of Environmental Health Sciences program, grant ES-004184 to SLM and the Alfred P. Sloan Foundation's grant for the Rare Biosphere in the Built Environment MLS.
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  • 9
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    Vertebral bomb radiocarbon suggests extreme longevity in white sharks (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This article is distributed free of all copyright. The definitive version was published in PLoS One 9 (2014): e84006, doi:10.1371/journal.pone.0084006.
    Description: Conservation and management efforts for white sharks (Carcharodon carcharias) remain hampered by a lack of basic demographic information including age and growth rates. Sharks are typically aged by counting growth bands sequentially deposited in their vertebrae, but the assumption of annual deposition of these band pairs requires testing. We compared radiocarbon (Δ14C) values in vertebrae from four female and four male white sharks from the northwestern Atlantic Ocean (NWA) with reference chronologies documenting the marine uptake of 14C produced by atmospheric testing of thermonuclear devices to generate the first radiocarbon age estimates for adult white sharks. Age estimates were up to 40 years old for the largest female (fork length [FL]: 526 cm) and 73 years old for the largest male (FL: 493 cm). Our results dramatically extend the maximum age and longevity of white sharks compared to earlier studies, hint at possible sexual dimorphism in growth rates, and raise concerns that white shark populations are considerably more sensitive to human-induced mortality than previously thought.
    Description: This study was funded by the National Science Foundation (OCE 0825148 was awarded to SRT) and LLH was supported by the National Science Foundation Graduate Research Fellowship Program.
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  • 10
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    Strong depth-related zonation of megabenthos on a rocky continental margin (∼700–4000 m) off southern Tasmania, Australia (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e85872, doi:10.1371/journal.pone.0085872.
    Description: Assemblages of megabenthos are structured in seven depth-related zones between ~700 and 4000 m on the rocky and topographically complex continental margin south of Tasmania, southeastern Australia. These patterns emerge from analysis of imagery and specimen collections taken from a suite of surveys using photographic and in situ sampling by epibenthic sleds, towed video cameras, an autonomous underwater vehicle and a remotely operated vehicle (ROV). Seamount peaks in shallow zones had relatively low biomass and low diversity assemblages, which may be in part natural and in part due to effects of bottom trawl fishing. Species richness was highest at intermediate depths (1000–1300 m) as a result of an extensive coral reef community based on the bioherm-forming scleractinian Solenosmilia variabilis. However, megabenthos abundance peaked in a deeper, low diversity assemblage at 2000–2500 m. The S. variabilis reef and the deep biomass zone were separated by an extensive dead, sub-fossil S. variabilis reef and a relatively low biomass stratum on volcanic rock roughly coincident with the oxygen minimum layer. Below 2400 m, megabenthos was increasingly sparse, though punctuated by occasional small pockets of relatively high diversity and biomass. Nonetheless, megabenthic organisms were observed in the vast majority of photographs on all seabed habitats and to the maximum depths observed - a sandy plain below 3950 m. Taxonomic studies in progress suggest that the observed depth zonation is based in part on changing species mixes with depth, but also an underlying commonality to much of the seamount and rocky substrate biota across all depths. Although the mechanisms supporting the extraordinarily high biomass in 2000–2500 m depths remains obscure, plausible explanations include equatorwards lateral transport of polar production and/or a response to depth-stratified oxygen availability.
    Description: Components of this work were supported by the National Science Foundation, the Australian Department of Environment, Water, Heritage, and the Arts, the Australian Commonwealth Environmental Research Fund, a grant of ship time by the Australian National Research Facility, and the CSIRO Wealth from Oceans and Climate Adaptation Flagships.
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  • 11
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    Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88618, doi:10.1371/journal.pone.0088618.
    Description: The taxon Syndermata comprises the biologically interesting wheel animals (“Rotifera”: Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.
    Description: The work was funded by the Deutsche Forschungsgemeinschaft (DFG grant Ha2103/4-3, Priority Project "Deep Metazoan Phylogeny", SPP1174; www. dfg.de). Additional financial support came from the Center for Computational Sciences (SRFN) of Johannes Gutenberg University Mainz (http://www.csm.unimainz. de).
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  • 12
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    Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e97338, doi:10.1371/journal.pone.0097338.
    Description: Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
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  • 13
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    Capture of lipopolysaccharide (endotoxin) by the blood clot : a comparative study (2014)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e80192, doi:10.1371/journal.pone.0080192.
    Description: In vertebrates and arthropods, blood clotting involves the establishment of a plug of aggregated thrombocytes (the cellular clot) and an extracellular fibrillar clot formed by the polymerization of the structural protein of the clot, which is fibrin in mammals, plasma lipoprotein in crustaceans, and coagulin in the horseshoe crab, Limulus polyphemus. Both elements of the clot function to staunch bleeding. Additionally, the extracellular clot functions as an agent of the innate immune system by providing a passive anti-microbial barrier and microbial entrapment device, which functions directly at the site of wounds to the integument. Here we show that, in addition to these passive functions in immunity, the plasma lipoprotein clot of lobster, the coagulin clot of Limulus, and both the platelet thrombus and the fibrin clot of mammals (human, mouse) operate to capture lipopolysaccharide (LPS, endotoxin). The lipid A core of LPS is the principal agent of gram-negative septicemia, which is responsible for more than 100,000 human deaths annually in the United States and is similarly toxic to arthropods. Quantification using the Limulus Amebocyte Lysate (LAL) test shows that clots capture significant quantities of LPS and fluorescent-labeled LPS can be seen by microscopy to decorate the clot fibrils. Thrombi generated in the living mouse accumulate LPS in vivo. It is suggested that capture of LPS released from gram-negative bacteria entrapped by the blood clot operates to protect against the disease that might be caused by its systemic dispersal.
    Description: Grant # 0344360 from the National Science Foundation (PBA).
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  • 14
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    Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis (2014)
    BioMed Central
    In:  EPIC3BMC Genomics, BioMed Central, 15(1), pp. 1051
    Details
    Publication Date: 2015-01-05
    Description: BACKGROUND: Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient utilization on the subcellular basis, we assessed the transcriptomic responses of the life-cycle stages of the biogeochemically important microalgae Emiliania huxleyi to nitrogen limitation. Cells grown in batch cultures were harvested at 'early' and 'full' nitrogen limitation and were compared with non-limited cells. We applied microarray-based transcriptome profilings, covering ~10.000 known E. huxleyi gene models, and screened for expression patterns that indicate the subcellular responses. RESULTS: The diploid life-cycle stage scavenges nitrogen from external organic sources and -like diatoms- uses the ornithine-urea cycle to rapidly turn over cellular nitrogen. The haploid stage reacts similarly, although nitrogen scavenging is less pronounced and lipid oxidation is more prominent. Generally, polyamines and proline appear to constitute major organic pools that back up cellular nitrogen. Both stages induce a malate:quinone-oxidoreductase that efficiently feeds electrons into the respiratory chain and drives ATP generation with reduced respiratory carbon throughput. CONCLUSIONS: The use of the ornithine-urea cycle to budget the cellular nitrogen in situations of limitation resembles the responses observed earlier in diatoms. This suggests that underlying biochemical mechanisms are conserved among distant clades of marine phototrophic protists. The ornithine-urea cycle and proline oxidation appear to constitute a sensory-regulatory system that monitors and controls cellular nitrogen budgets under limitation. The similarity between the responses of the life-cycle stages, despite the usage of different genes, also indicates a strong functional consistency in the responses to nitrogen-limitation that appears to be owed to biochemical requirements. The malate:quinone-oxidoreductase is a genomic feature that appears to be absent from diatom genomes, and it is likely to strongly contribute to the uniquely high endurance of E. huxleyi under nutrient limitation.
    Repository Name: EPIC Alfred Wegener Institut
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    Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.
    Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
    Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.
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    VAMPS : a website for visualization and analysis of microbial population structures (2014)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.
    Description: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
    Description: Funding provided by the National Science Foundation [grant NSF/BDI 0960626 to SMH] and the Sloan Foundation through a collaborative project with the Microbiology of the Built Environment program.
    Keywords: Microbiome ; Microbial ecology ; Microbial diversity ; Data visualization ; Website ; Bacteria ; SSU rRNA ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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    Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e103536, doi:10.1371/journal.pone.0103536.
    Description: Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the United States National Science Foundation (OCE 0825148 to SRT and GBS).
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    Scientific names of organisms : attribution, rights, and licensing (2014)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.
    Description: As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.
    Keywords: Scientific names ; Taxonomy ; Copyright ; Intellectual property rights ; Name-based infrastructure ; Big data
    Repository Name: Woods Hole Open Access Server
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    Aggregation and Sedimentation of Thalassiosira weissflogii (diatom) in a Warmer and More Acidified Future Ocean (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112379, doi:10.1575/1912/6845.
    Description: Increasing Transparent Exopolymer Particle (TEP) formation during diatom blooms as a result of elevated temperature and pCO2 have been suggested to result in enhanced aggregation and carbon flux, therewith potentially increasing the sequestration of carbon by the ocean. We present experimental results on TEP and aggregate formation by Thalassiosira weissflogii (diatom) in the presence or absence of bacteria under two temperature and three pCO2 scenarios. During the aggregation phase of the experiment TEP formation was elevated at the higher temperature (20°C vs. 15°C), as predicted. However, in contrast to expectations based on the established relationship between TEP and aggregation, aggregation rates and sinking velocity of aggregates were depressed in warmer treatments, especially under ocean acidification conditions. If our experimental findings can be extrapolated to natural conditions, they would imply a reduction in carbon flux and potentially reduced carbon sequestration after diatom blooms in the future ocean.
    Description: This work was supported by National Science Foundation grants OCE-0926711 & OCE-1041038 to UP and Helmholtz Graduate School for Polar and Marine Research and Jacobs University Bremen to SS.
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    Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e92277, doi:10.1371/journal.pone.0092277.
    Description: Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were 〈5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.
    Description: This research was primarily funded by Fundação para a Ciência e a Tecnologia (FCT), Fundo Regional da Ciência, Tecnologia (FRCT), through research projects TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER], the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, and Proconvergencia Açores/EU Program]. We acknowledge funds provided by FCT to LARSyS Associated Laboratory and IMAR-University of the Azores/the Thematic Area D & E of the Strategic Project PEst-OE/EEI/LA0009/2011–1012 and 2013–2014 (OE & Compete) and by the FRCT - Government of the Azores pluriannual funding. MAS was supported by an FCT postdoctoral grant (SFRH/BPD/29841/2006) and is currently supported by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education through an FCT Investigator grant. RP was supported by an FCT doctoral grant (SFRH/BD/41192/2007) and by the research grant from the Azores Regional Fund for Science and Technology (M3.1.5/F/115/2012). IJ was supported by the Natural Sciences and Engineering Research Council (NSERC) and the Canada Foundation for Innovation (CFI) through their support of the Ocean Tracking Network. DJFR is funded by the United Kingdom Department of Energy and Climate Change as part of their Offshore Energy Strategic Environmental Assessment program. DT is funded by Natural Environment Research Council and Marine Scotland.
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    Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e94249, doi:10.1371/journal.pone.0094249.
    Description: The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
    Description: This work was partially funded by an Emerging Frontiers in Research and Innovation – Multicellular and Inter-kingdom Signaling (EFRI-MIKS) grant awarded by the US National Science Foundation to Joerg Graf and NIH RO1 GM095390 to JG and HGM.
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    Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats (2014)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 14 (2014): 6, doi:10.1186/1471-2148-14-6.
    Description: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
    Description: This work was supported in part by the Hudson River Foundation (grant 004/02A; final report available at http://www.hudsonriver.org/ls/), by National Institute of Environmental Health Sciences (NIEHS) grant P42ES007381 (Superfund Basic Research Program at Boston University), by grant F32HD062178 from the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHHD), and by the National Science Foundation (DEB-1120263). Data interpretation was aided by reference to a preliminary draft of the F. heteroclitus genome sequence, which was supported by funding from the National Science Foundation (collaborative research grants DEB-1120512, DEB-1265282, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398).
    Keywords: Local adaptation ; Pollution ; Molecular mechanism ; Resistance ; Tolerance ; Convergent evolution ; Population genetics
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    Comparisons of Shewanella strains based on genome annotations, modeling, and experiments (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Systems Biology 8 (2014): 31, doi:10.1186/1752-0509-8-31.
    Description: Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains. In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels – for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models. We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
    Description: This work was funded by a grant from the NSF (NSF 1053712) and was also supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy, and is a contribution of the PNNL Biofuels Scientific Focus Area (BSFA) and the PNNL Foundational Scientific Focus Area (FSFA).
    Keywords: Constraint-based model ; Electron acceptors ; Phenotype ; FBA
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    First autonomous bio-optical profiling float in the Gulf of Mexico reveals dynamic biogeochemistry in deep waters (2014)
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e101658, doi:10.1371/journal.pone.0101658.
    Description: Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (bbp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R2 = 0.62). Particulate backscattering, bbp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between bbp and chlorophyll (R2 = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R2 = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.
    Description: This project was funded by Bureau of Ocean Energy Management (BOEM) Contract M10PC00112 to Leidos, Inc. with subcontract to ASB (www.boem.gov).
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    Swimming speed of larval snail does not correlate with size and ciliary beat frequency (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e82764, doi:10.1371/journal.pone.0082764.
    Description: Many marine invertebrates have planktonic larvae with cilia used for both propulsion and capturing of food particles. Hence, changes in ciliary activity have implications for larval nutrition and ability to navigate the water column, which in turn affect survival and dispersal. Using high-speed high-resolution microvideography, we examined the relationship between swimming speed, velar arrangements, and ciliary beat frequency of freely swimming veliger larvae of the gastropod Crepidula fornicata over the course of larval development. Average swimming speed was greatest 6 days post hatching, suggesting a reduction in swimming speed towards settlement. At a given age, veliger larvae have highly variable speeds (0.8–4 body lengths s−1) that are independent of shell size. Contrary to the hypothesis that an increase in ciliary beat frequency increases work done, and therefore speed, there was no significant correlation between swimming speed and ciliary beat frequency. Instead, there are significant correlations between swimming speed and visible area of the velar lobe, and distance between centroids of velum and larval shell. These observations suggest an alternative hypothesis that, instead of modifying ciliary beat frequency, larval C. fornicata modify swimming through adjustment of velum extension or orientation. The ability to adjust velum position could influence particle capture efficiency and fluid disturbance and help promote survival in the plankton.
    Description: K.Y.K. Chan was supported by the Postdoctoral Scholar 1 Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. H. Jiang was supported by National Science Foundation grant NSF OCE-1129496 and an award from WHOI's Ocean Life Institute, and D.K. Padilla was supported by NSF IOS-0920032.
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    Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e93296, doi:10.1371/journal.pone.0093296.
    Description: Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.
    Description: This research was made possible by a grant from the National Science Foundation Biological Oceanography Program and the Brown University Undergraduate Teaching and Research Award Program.
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    Humpback whale populations share a core skin bacterial community : towards a health index for marine mammals? (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90785, doi:10.1371/journal.pone.0090785.
    Description: Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.
    Description: A.A. was funded by a WHOI Ocean Life Institute post-doctoral scholar award, and this research was supported by a grant to A.A. and T.J.M. from Woods Hole Oceanographic Institution's (WHOI) Marine Mammal Center.
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    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres (2014)
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    Publication Date: 2022-05-26
    Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380.
    Description: Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
    Description: This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The contributions of S.K. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security (DHS) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.
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    The microbiome in pediatric cystic fibrosis patients : the role of shared environment suggests a window of intervention (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 2 (2014): 14, doi:10.1186/2049-2618-2-14.
    Description: Cystic fibrosis (CF) is caused by mutations in the CFTR gene that predispose the airway to infection. Chronic infection by pathogens such as Pseudomonas aeruginosa leads to inflammation that gradually degrades lung function, resulting in morbidity and early mortality. In a previous study of CF monozygotic twins, we demonstrate that genetic modifiers significantly affect the establishment of persistent P. aeruginosa colonization in CF. Recognizing that bacteria other than P. aeruginosa contribute to the CF microbiome and associated pathology, we used deep sequencing of sputum from pediatric monozygotic twins and nontwin siblings with CF to characterize pediatric bacterial communities and the role that genetics plays in their evolution. We found that the microbial communities in sputum from pediatric patients living together were much more alike than those from pediatric individuals living apart, regardless of whether samples were taken from monozygous twins or from nontwin CF siblings living together, which we used as a proxy for dizygous twins. In contrast, adult communities were comparatively monolithic and much less diverse than the microbiome of pediatric patients. Taken together, these data and other recent studies suggest that as patients age, the CF microbiome becomes less diverse, more refractory to treatment and dominated by mucoid P. aeruginosa, as well as being associated with accelerated pulmonary decline. Our studies show that the microbiome of pediatric patients is susceptible to environmental influences, suggesting that interventions to preserve the community structure found in young CF patients might be possible, perhaps slowing disease progression.
    Description: This work was supported by the Flatley Foundation of Boston (to GAO, BAS and AHG), National Institutes of Health (NIH) grants P20 GM103413-10 and R01 HL074175-09 (to BAS), a Cystic Fibrosis Foundation Research Development Program grant (STANTO07R0), Cystic Fibrosis Foundation Research Development Program grant R025-CR07 (to DMG), NIH grants R01 HL068927-09 and R01 DK44003 (to GRC), Cystic Fibrosis Foundation grant CUTTIN06P0 (to GRC), NIH grant R01 AI091699 (to GAO) and NIH grant 4UH3DK083993 (to MLS).
    Keywords: Cystic fibrosis ; Microbiome ; Pseudomonas aeruginosa ; Sputum
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing (2014)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
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    Assessing the health of the U.S. west coast with a regional-scale application of the Ocean Health Index (2014)
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e98995, doi:10.1371/journal.pone.0098995.
    Description: Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions scoring from 65 (Washington) to 74 (Oregon). Highest scoring goals included tourism and recreation (99) and clean waters (87), while the lowest scoring goals were sense of place (48) and artisanal fishing opportunities (57). Surprisingly, even in this well-studied area data limitations precluded robust assessments of past trends in overall ocean health. Nonetheless, retrospective calculation of current status showed that many goals have declined, by up to 20%. In contrast, near-term future scores were on average 6% greater than current status across all goals and sub-regions. Application of hypothetical but realistic management scenarios illustrate how the Index can be used to predict and understand the tradeoffs among goals and consequences for overall ocean health. We illustrate and discuss how this index can be used to vet underlying assumptions and decisions with local stakeholders and decision-makers so that scores reflect regional knowledge, priorities and values. We also highlight the importance of ongoing and future monitoring that will provide robust data relevant to ocean health assessment.
    Description: Beau and Heather Wrigley generously provided the founding grant. Additional financial and in-kind support was provided by the Pacific Life Foundation, Thomas W. Haas Fund of the New Hampshire Charitable Foundation, the Oak Foundation, Akiko Shiraki Dynner Fund for Ocean Exploration and Conservation, Darden Restaurants Inc. Foundation, Conservation International, New England Aquarium, National Geographic, and the University of California Santa Barbara's National Center for Ecological Analysis and Synthesis, which supported the Ecosystem Health Working Group as part of the Science of Ecosystem-Based Management project funded by the David and Lucile Packard Foundation. Individual authors also acknowledge support from the U.S. National Science Foundation.
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    Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.
    Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
    Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.
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    The transcriptional response to oxidative stress during vertebrate development : effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e113158, doi:10.1371/journal.pone.0113158.
    Description: Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
    Description: This research was supported in part by National Institutes of Health grants R01ES016366 (MEH), R01ES006272 (MEH), R01ES015912 (JJS), and F32ES017585 (ART-L), the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a WHOI (Woods Hole Oceanographic Institution) Postdoctoral Scholar award, and the Walter A. and Hope Noyes Smith endowed chair (MEH). AGM and MJC were supported in part by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.
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    Genetic, morphological, and chemical patterns of plant hybridization (2014)
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    Publication Date: 2014-08-01
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    A new population of Darwin's fox (Lycalopex fulvipes) in the Valdivian Coastal Range (2014)
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    Publication Date: 2014-03-26
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    Conservation of biodiversity in private lands: are Chilean landowners willing to keep threatened species in their lands? (2014)
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    Publication Date: 2014-03-26
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    Temporal and spatial variation of the pollinator assemblages in Alstroemeria ligtu (Alstroemeriaceae) (2014)
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    Publication Date: 2014-03-26
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    Reptiles in Monterey pine plantations of the Coastal Range of Central Chile (2014)
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    Publication Date: 2014-11-06
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    Rolling Pampas agroecosystem: which landscape attributes are relevant for determining bird distributions? (2014)
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    Publication Date: 2014-03-26
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    Robles in Lagunas de Epulauquen, Argentina: previous and recent evidence of their distinctive character (2014)
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    Publication Date: 2014-12-01
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    Anuran larvae as prey and hosts of invertebrates in Neotropical aquatic habitats (2014)
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    Foliar micromorphology and anatomy of Ugni molinae Turcz. (Myrtaceae), with particular reference to schizogenous secretory cavities (2014)
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    Publication Date: 2014-11-18
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    Legal protection assessment of different inland wetlands in Chile (2014)
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    Publication Date: 2014-11-08
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    Density and abundance of Rhea pennata garleppi (Struthioniformes: Rheidae) in the Puna ecoregion of Argentina (2014)
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    Publication Date: 2014-09-04
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    Host plant specificity of the moth species Glena mielkei (Lepidoptera, Geometridae) in northern Chile (2014)
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    Publication Date: 2014-11-07
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    Multidisciplinary approach to assess the water self-depuration characteristics of Suquía River (Córdoba, Argentina) (2014)
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    Publication Date: 2014-09-03
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    Diet of the Chilean flamingo Phoenicopterus chilensis (Phoenicopteriformes: Phoenicopteridae) in a coastal wetland in Chiloé, southern Chile (2014)
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    Publication Date: 2014-08-16
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    Recent rates of carbon and nitrogen accumulation in peatlands of Isla Grande de Chiloé-Chile (2014)
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    Publication Date: 2014-11-05
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    At-sea abundance and distribution of skuas and jaegers (Charadriiformes: Stercorariidae) at coastal waters off central Chile (2014)
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    Publication Date: 2014-01-01
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    Pollination ecology and breeding system of two Calceolaria species in Chile (2014)
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    Pollination ecology and breeding system of two Calceolaria species in Chile (2014)
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    At-sea abundance and distribution of skuas and jaegers (Charadriiformes: Stercorariidae) at coastal waters off central Chile (2014)
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    Publication Date: 2014-01-01
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    Presence of the red jollytail, Brachygalaxias bullocki (Regan, 1908) (Galaxiformes: Galaxiidae), in freshwater forested wetlands from Chile (2014)
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    Publication Date: 2014-11-12
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    Cooperation and bacterial pathogenicity: an approach to social evolution (2014)
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    Publication Date: 2014-08-16
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    Phenological synchrony between the austral thrush Turdus falcklandii (Passeriformes: Turdidae) and its food resources within forests and prairies in southern Chile (2014)
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    Publication Date: 2014-09-03
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    Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum (2014)
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    Publication Date: 2014-12-08
    Description: Background: Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection. Results: A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK,cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes. Conclusion: This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Exact results for models of multichannel quantum nonadiabatic transitions (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): N. A. Sinitsyn We consider nonadiabatic transitions in explicitly time-dependent systems with Hamiltonians of the form Ĥ(t)=Â+B̂t+Ĉ/t, where t is time and Â, B̂, Ĉ are Hermitian N×N matrices. We show that in any model of this type, scattering matrix elements satisfy nontrivial exact constraints that follow fr... [Phys. Rev. A 90, 062509] Published Thu Dec 11, 2014
    Keywords: Atomic and molecular structure and dynamics
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    Parameter estimation in memory-assisted noisy quantum interferometry (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): P. Szańkowski, M. Trippenbach, and J. Chwedeńczuk We demonstrate that memory in an N-qubit system subjected to decoherence, is a potential resource for the slowdown of the entanglement decay. We show that this effect can be used to retain the sub-shot-noise sensitivity of the parameter estimation in quantum interferometry. We calculate quantum Fish... [Phys. Rev. A 90, 063619] Published Thu Dec 11, 2014
    Keywords: Matter waves and collective properties of cold atoms and molecules
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    Collisional trap losses of cold magnetically trapped Br atoms (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): J. Lam, C. J. Rennick, and T. P. Softley Near-threshold photodissociation of Br 2 from a supersonic beam produces slow bromine atoms that are trapped in the magnetic-field minimum formed between two opposing permanent magnets. Here we quantify the dominant trap-loss rate due to collisions with two sources of residual gas: the background lim... [Phys. Rev. A 90, 063419] Published Thu Dec 11, 2014
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
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    Quantum phase transition with a simple variational ansatz (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Y. Lutsyshyn, G. E. Astrakharchik, C. Cazorla, and J. Boronat We study the zero-temperature quantum phase transition between liquid and hcp solid 4 He. We use the variational method with a simple yet exchange-symmetric and fully explicit wave function. It is found that the optimized wave function undergoes spontaneous symmetry breaking and describes the quantum... [Phys. Rev. B 90, 214512] Published Thu Dec 11, 2014
    Keywords: Superfluidity and superconductivity
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    Meissner and mesoscopic superconducting states in 1–4 unit-cell FeSe films (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): L. Z. Deng, B. Lv, Z. Wu, Y. Y. Xue, W. H. Zhang, F. S. Li, L. L. Wang, X. C. Ma, Q. K. Xue, and C. W. Chu We report a detailed investigation on the superconductivity in eight 1–4 unit-cell (UC) FeSe films on SrTiO 3 substrates by measuring their magnetization and sheet resistance in a field between 5×10 −2 and 7×10 4  Oe over the last one and a half years as a function of temperature and frequency, from 2 t... [Phys. Rev. B 90, 214513] Published Thu Dec 11, 2014
    Keywords: Superfluidity and superconductivity
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    Cluster algorithm for Monte Carlo simulations of spin ice (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Hiromi Otsuka We present an algorithm for Monte Carlo simulations of a nearest-neighbor spin-ice model based on its cluster representation. To assess its performance, we estimate a relaxation time, and find that, in contrast to the Metropolis algorithm, our algorithm does not develop spin freezing. Also, to demon... [Phys. Rev. B 90, 220406] Published Thu Dec 11, 2014
    Keywords: Magnetism
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    Relative phase control over tunneling ionization of H_{2}^{+} with a synthesized ω-2ω laser pulse (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-12
    Description: Author(s): Hongbin Yao, Wei Guo, Mark R. Hoffmann, and Keli Han We demonstrate an efficient scheme for controlling the tunneling ionization of a H 2 + molecular ion. Our scheme is based on the idea that the tunneling ionization rate is highly dependent on the instantaneous magnitude of the electric field. By manipulating the relative phase of the synthesized 5-fs,... [Phys. Rev. A 90, 063418] Published Thu Dec 11, 2014
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
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    High-fidelity quantum memory utilizing inhomogeneous nuclear polarization in a quantum dot (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Wenkui Ding, Anqi Shi, J. Q. You, and Wenxian Zhang We numerically investigate the encoding and retrieval processes for quantum memory realized in a semiconductor quantum dot by focusing on the effect of inhomogeneously polarized nuclear spins whose polarization depends on the local hyperfine coupling strength. We find that the performance of quantum... [Phys. Rev. B 90, 235421] Published Thu Dec 11, 2014
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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    Unitary evolution and the distinguishability of quantum states (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Sam Morley-Short, Lawrence Rosenfeld, and Pieter Kok The study of quantum systems evolving from initial states to distinguishable, orthogonal final states is important for information processing applications such as quantum computing and quantum metrology. However, for most unitary evolutions and initial states the system does not evolve to an orthogo... [Phys. Rev. A 90, 062116] Published Thu Dec 11, 2014
    Keywords: Fundamental concepts
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    Markovian evolution of strongly coupled harmonic oscillators (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Chaitanya Joshi, Patrik Öhberg, James D. Cresser, and Erika Andersson We investigate how to model Markovian evolution of coupled harmonic oscillators, each of them interacting with a local environment. When the coupling between the oscillators is weak, dissipation may be modeled using local Lindblad terms for each of the oscillators in the master equation, as is commo... [Phys. Rev. A 90, 063815] Published Thu Dec 11, 2014
    Keywords: Quantum optics, physics of lasers, nonlinear optics, classical optics
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    Superfluidity and solid order in a two-component Bose gas with dipolar interactions in an optical lattice (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Yoshihito Kuno, Keita Suzuki, and Ikuo Ichinose In this paper, we study an extended bosonic t-J model in an optical lattice, which describes two-component hard-core bosons with nearest-neighbor pseudospin interactions and, also, inter- and intraspecies dipole-dipole interactions. In particular, we focus on the case in which two-component hard-cor... [Phys. Rev. A 90, 063620] Published Thu Dec 11, 2014
    Keywords: Matter waves and collective properties of cold atoms and molecules
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    Hierarchical stripe phases in IrTe_{2} driven by competition between Ir dimerization and Te bonding (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-12
    Description: Author(s): Jixia Dai, Kristjan Haule, J. J. Yang, Y. S. Oh, S-W. Cheong, and Weida Wu Layered 5d transition metal dichalcogenide (TMD) IrTe 2 is distinguished from the traditional TMDs (such as NbSe 2 ) by the existence of multiple charge-density wave (CDW)-like stripe phases and superconductivity at low temperatures. Despite intensive studies, there is still no consensus on the physica... [Phys. Rev. B 90, 235121] Published Thu Dec 11, 2014
    Keywords: Electronic structure and strongly correlated systems
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    Aperiodic compression and reconstruction of real-world material systems based on Wang tiles (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Martin Doškář, Jan Novák, and Jan Zeman The paper presents a concept to compress and synthesize complex material morphologies that is based on Wang tilings. Specifically, a microstructure is stored in a set of Wang tiles and its reconstruction is performed by means of a stochastic tiling algorithm. A substantial part of the study is devot... [Phys. Rev. E 90, 062118] Published Thu Dec 11, 2014
    Keywords: Statistical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
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    Isgur-Wise functions and unitary representations of the Lorentz group: The meson case with j=1/2 light cloud (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-12
    Description: Author(s): A. Le Yaouanc, L. Oliver, and J.-C. Raynal We pursue the group-theoretical method to study Isgur-Wise (IW) functions. We extend the general formalism, formerly applied to the baryon case j P =0 + (for Λ b →Λ c ℓν̅ ℓ ), to mesons with j P =1/2 - , i.e. B̅ →D(D (*) )ℓν. In this case, which is more involved from the angular momentum point of vi... [Phys. Rev. D 90, 114016] Published Thu Dec 11, 2014
    Keywords: Strong Interactions
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    Effect of direct bubble-bubble interactions on linear-wave propagation in bubbly liquids (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): D. Fuster, J. M. Conoir, and T. Colonius We study the influence of bubble-bubble interactions on the propagation of linear acoustic waves in bubbly liquids. Using the full model proposed by Fuster and Colonius [J. Fluid Mech. 688 , 253 (2011)JFLSA710.1017/jfm.2011.380], numerical simulations reveal that direct bubble-bubble interactions hav... [Phys. Rev. E 90, 063010] Published Thu Dec 11, 2014
    Keywords: Fluid Dynamics
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    Effect of hole doping on the magnetism of point defects in graphene: A theoretical study (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Felix Yndurain Using ab initio methods based on the density functional theory, we study the magnetic properties of different point defects in graphene. We consider separately, atomic hydrogen, atomic fluorine, and single vacancies. The three defects have completely different magnetic properties. A local spin one-h... [Phys. Rev. B 90, 245420] Published Thu Dec 11, 2014
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
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    Single-sided Marchenko focusing of compressional and shear waves (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Kees Wapenaar In time-reversal acoustics, waves recorded at the boundary of a strongly scattering medium are sent back into the medium to focus at the original source position. This requires that the medium can be accessed from all sides. We discuss a focusing method for media that can be accessed from one side o... [Phys. Rev. E 90, 063202] Published Thu Dec 11, 2014
    Keywords: Classical Physics
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    Standard Rulers, Candles, and Clocks from the Low-Redshift Universe (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Alan Heavens, Raul Jimenez, and Licia Verde A measure of how galaxies are spatially distributed can be determined in a new, more robust way. [Phys. Rev. Lett. 113, 241302] Published Thu Dec 11, 2014
    Keywords: Gravitation and Astrophysics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
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    Holographic p-wave superfluid (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Ya-Bo Wu, Jun-Wang Lu, Wen-Xin Zhang, Cheng-Yuan Zhang, Jian-Bo Lu, and Fang Yu In the probe limit, we numerically construct a holographic p-wave superfluid model in the four-dimensional (4D) and five-dimensional (5D) anti-de Sitter black holes coupled to a Maxwell-complex vector field. We find that, for the condensate with the fixed superfluid velocity, the results are similar... [Phys. Rev. D 90, 126006] Published Thu Dec 11, 2014
    Keywords: String Theory
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    Complexity and shock wave geometries (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): Douglas Stanford and Leonard Susskind In this paper we refine a conjecture relating the time-dependent size of an Einstein-Rosen bridge (ERB) to the computational complexity of the dual quantum state. Our refinement states that the complexity is proportional to the spatial volume of the ERB. More precisely, up to an ambiguous numerical ... [Phys. Rev. D 90, 126007] Published Thu Dec 11, 2014
    Keywords: String Theory
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    Breakdown of the Dipole Approximation in Strong-Field Ionization (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): A. Ludwig, J. Maurer, B. W. Mayer, C. R. Phillips, L. Gallmann, and U. Keller We report the breakdown of the electric dipole approximation in the long-wavelength limit in strong-field ionization with linearly polarized few-cycle mid-infrared laser pulses at intensities on the order of 10 13   W/cm 2 . Photoelectron momentum distributions were recorded by velocity map imaging and ... [Phys. Rev. Lett. 113, 243001] Published Thu Dec 11, 2014
    Keywords: Atomic, Molecular, and Optical Physics
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    Many-Body Localization in Dipolar Systems (2014)
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    Publication Date: 2014-12-12
    Description: Author(s): N. Y. Yao, C. R. Laumann, S. Gopalakrishnan, M. Knap, M. Müller, E. A. Demler, and M. D. Lukin Systems of strongly interacting dipoles offer an attractive platform to study many-body localized phases, owing to their long coherence times and strong interactions. We explore conditions under which such localized phases persist in the presence of power-law interactions and supplement our analytic... [Phys. Rev. Lett. 113, 243002] Published Thu Dec 11, 2014
    Keywords: Atomic, Molecular, and Optical Physics
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    High prevalence of dyslipidemia and associated risk factors among rural Chinese adults (2014)
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    Publication Date: 2014-12-13
    Description: Background: Dyslipidemia is a key independent modifiable risk factor for Cardiovascular Disease, which is a leading contributor to morbidity and mortality in most developed and developing countries. This study was designed to investigate the current epidemiological features of dyslipidemia among adults in rural China. Methods: Between January 2013 and August 2013, we conducted a cross-sectional study involving 11,956 subjects with age 〉=35 years in a general Chinese population. Permanent residents of the population were invited to participate in the study and the response rate was at 85.3%. Dyslipidemia was identified based on serum lipids levels following the standards proposed by the National Cholesterol Education Program Adult Treatment Panel III. Multivariate logistic regression analysis was used to evaluate the associated risk factors for dyslipidemia. Results: Within the study population, 16.4% had high TC, 13.8% had low HDL-C, 7.6% had high LDL-C, and 17.3% had high TG concentrations. Prevalence of lipid abnormality (including borderline dyslipidemia and dyslipidemia) was 47.8%, 13.8%, 25.7% and 30.7% for TC, HDL-C, LDL-C and TG, respectively. Detailed analysis indicated that 36.9% of this population had at least one type of dyslipidemia and 64.4% had at least one type of abnormal lipid concentration. Thus, this study observed an alarmingly higher prevalence of lipid abnormality, in a relatively large population, compared to previous studies. Further, we determined that not all of the risk factors studied, including age, gender, hypertension, diabetes mellitus, obesity, smoking, drinking, education level, marital status, and family income, influenced dyslipidemia to the same extent. Conclusions: Our present study, in a population of 11,956 adults in Liaoning Providence, demonstrated a very high prevalence of dyslipidemia, which represented an alarming rise since the publication of our previous study and other similar studies around the world, which report lower levels. We also examined various risk factors for dyslipidemia, many of which are modifiable risk factors for Cardiovascular Disease (CVD), to provide a comprehensive view that will help in designing strategies to slow the rapid spread and promote effective measures to treat dyslipidemia. Our ultimate goal is to prevent the increasing prevalence of lipid abnormality and reduce the burden of CVD in rural China.
    Electronic ISSN: 1476-511X
    Topics: Biology
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    Carbon defects as sources of the green and yellow luminescence bands in undoped GaN (2014)
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    Publication Date: 2014-12-13
    Description: Author(s): M. A. Reshchikov, D. O. Demchenko, A. Usikov, H. Helava, and Yu. Makarov In high-purity GaN grown by hydride vapor phase epitaxy, the commonly observed yellow luminescence (YL) band gives way to a green luminescence (GL) band at high excitation intensity. We propose that the GL band with a maximum at 2.4 eV is caused by transitions of electrons from the conduction band t... [Phys. Rev. B 90, 235203] Published Fri Dec 12, 2014
    Keywords: Semiconductors I: bulk
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    Study of the process e^{+}e^{-}→nn[over ¯] at the VEPP-2000 e^{+}e^{-} collider with the SND detector (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): M. N. Achasov et al. The process e + e - →nn̅ has been studied at the VEPP-2000 e + e - collider with the SND detector in the energy range from threshold up to 2 GeV. As a result of the experiment, the e + e - →nn̅ cross section and effective neutron form factor have been measured. [Phys. Rev. D 90, 112007] Published Fri Dec 12, 2014
    Keywords: Particle Experiment
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    Angular analysis of polarized top quark decay into B mesons in two different helicity systems (2014)
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    Publication Date: 2014-12-13
    Description: Author(s): S. Mohammad Moosavi Nejad and Mahboobe Balali We calculate the O (α s ) radiative corrections to the spin-dependent differential decay rates of the process t→b+W + . These are needed to study the angular distribution of the energy of hadrons produced in polarized top quark decays at next-to-leading order. In our previous work, we studied the angular... [Phys. Rev. D 90, 114017] Published Fri Dec 12, 2014
    Keywords: Strong Interactions
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    Unveiling the structural origin of the high carrier mobility of a molecular monolayer on boron nitride (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): Rui Xu, Daowei He, Yuhan Zhang, Bing Wu, Fengyuan Liu, Lan Meng, Jun-Fang Liu, Qisheng Wu, Yi Shi, Jinlan Wang, Jia-Cai Nie, Xinran Wang, and Lin He Very recently, it was demonstrated that the carrier mobility of a molecular monolayer dioctylbenzothienobenzothiophene (C 8 -BTBT) on boron nitride can reach 10 cm 2 /Vs, the highest among the previously reported monolayer molecular field-effect transistors. Here we show that the high-quality single cry... [Phys. Rev. B 90, 224106] Published Fri Dec 12, 2014
    Keywords: Structure, structural phase transitions, mechanical properties, defects
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    Erratum: Measurement of the inclusive semileptonic branching fraction B(B_{s}^{0}→X^{−}ℓ^{+}ν_{ℓ}) at Belle [Phys. Rev. D 87, 072008 (2013)] (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): C. Oswald et al. (Belle Collaboration) [Phys. Rev. D 90, 119901] Published Fri Dec 12, 2014
    Keywords: Errata
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    Lattice simulations with eight flavors of domain wall fermions in SU(3) gauge theory (2014)
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    Publication Date: 2014-12-13
    Description: Author(s): T. Appelquist, R. C. Brower, G. T. Fleming, J. Kiskis, M. F. Lin, E. T. Neil, J. C. Osborn, C. Rebbi, E. Rinaldi, D. Schaich, C. Schroeder, S. Syritsyn, G. Voronov, P. Vranas, E. Weinberg, and O. Witzel (Lattice Strong Dynamics (LSD) Collaboration) We study an SU(3) gauge theory with N f =8 degenerate flavors of light fermions in the fundamental representation. Using the domain wall fermion formulation, we investigate the light hadron spectrum, chiral condensate ⟨ψ̅ ψ⟩ and electroweak S parameter. We consider a range of light fermion mass... [Phys. Rev. D 90, 114502] Published Fri Dec 12, 2014
    Keywords: Lattice Methods
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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    Borromean structures in medium-heavy nuclei (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): D. Hove, D. V. Fedorov, H. O. U. Fynbo, A. S. Jensen, K. Riisager, N. T. Zinner, and E. Garrido Borromean nuclear cluster structures are expected at the corresponding drip lines. We locate the regions in the nuclear chart with the most promising constituents, it being protons and α particles and investigate in details the properties of the possible Borromean two-α systems in medium-heavy nucle... [Phys. Rev. C 90, 064311] Published Fri Dec 12, 2014
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
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  • 87
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    Intermediate-energy Coulomb excitation of ^{104}Sn: Moderate E2 strength decrease approaching ^{100}Sn (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): P. Doornenbal et al. The reduced transition probability B(E2)↑ of the first excited 2 + state in the nucleus 104 Sn was measured via Coulomb excitation in inverse kinematics at intermediate energies. A value of 0.173(28) e 2 b 2 was extracted from the absolute cross section on a Pb target. Feeding contributions in 104 Sn from... [Phys. Rev. C 90, 061302] Published Fri Dec 12, 2014
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
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  • 88
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    Prompt neutron multiplicity in correlation with fragments from spontaneous fission of ^{252}Cf (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): A. Göök, F.-J. Hambsch, and M. Vidali The spontaneous fission of 252 Cf serves as an excellent benchmark of prompt emission in fission since experimental data can be obtained without the need of an incident beam. With the purpose of providing experimental data on the prompt fission neutron properties in correlation with fission-fragment ... [Phys. Rev. C 90, 064611] Published Fri Dec 12, 2014
    Keywords: Nuclear Reactions
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
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  • 89
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    Dynamics and cosmological constraints on Brans-Dicke cosmology (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): Orest Hrycyna, Marek Szydłowski, and Michał Kamionka We investigate observational constraints on the Brans-Dicke cosmological model using observational data coming from distant supernovae type Ia, the Hubble function H(z) measurements, information coming from the Alcock-Paczyński test, and baryon acoustic oscillations. Our analysis is based on the mod... [Phys. Rev. D 90, 124040] Published Fri Dec 12, 2014
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 90
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    Glashow resonance as a window into cosmic neutrino sources (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): V. Barger, Lingjun Fu, J. G. Learned, D. Marfatia, S. Pakvasa, and T. J. Weiler The Glashow resonance at E ν =6.3  PeV is a measure of the ν̅ e content of the astrophysical neutrino flux. The fractional ν̅ e content depends on the neutrino production model at the cosmic neutrino source, and the environment at the source. Thus, the strength of the Glashow resonance e... [Phys. Rev. D 90, 121301] Published Fri Dec 12, 2014
    Keywords: Astrophysics & Cosmology
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 91
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    Regularized cosmological power spectrum and correlation function in modified gravity models (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): Atsushi Taruya, Takahiro Nishimichi, Francis Bernardeau, Takashi Hiramatsu, and Kazuya Koyama Based on the multipoint propagator expansion, we present resummed perturbative calculations for cosmological power spectra and correlation functions in the context of modified gravity. In a wide class of modified gravity models that have a screening mechanism to recover general relativity (GR) on sm... [Phys. Rev. D 90, 123515] Published Fri Dec 12, 2014
    Keywords: Cosmology
    Print ISSN: 0556-2821
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  • 92
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    Multiparticle processes and tamed ultraviolet divergences (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): Victor T. Kim and Grigorii B. Pivovarov A new approach to computing the amplitudes of multiparticle processes in renormalizable quantum field theories is presented. Its major feature is a separation of the renormalization from the computation. Within the suggested approach, new computational rules are formulated. According to the new rule... [Phys. Rev. D 90, 125009] Published Fri Dec 12, 2014
    Keywords: Field Theory, Formal Particle Theory
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 93
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    Dynamical collisional energy loss and transport properties of on- and off-shell heavy quarks in vacuum and in the quark gluon plasma (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): H. Berrehrah, P. B. Gossiaux, J. Aichelin, W. Cassing, and E. Bratkovskaya In this study we evaluate the dynamical collisional energy loss of heavy quarks, their interaction rate, as well as the different transport coefficients (drag and diffusion coefficients, q̂, etc). We calculate these different quantities for (i) perturbative partons (on-shell particles in the vacuum ... [Phys. Rev. C 90, 064906] Published Fri Dec 12, 2014
    Keywords: Relativistic Nuclear Collisions
    Print ISSN: 0556-2813
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  • 94
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    Nonequilibrium density matrix in quantum open systems: Generalization for simultaneous heat and charge steady-state transport (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): H. Ness We suggest a generalization of the expression of the nonequilibrium (NE) density matrix obtained by Hershfield's method for the cases where both heat and charge steady-state currents are present in a quantum open system. The finite-size quantum system, connected to two temperature and particle reser... [Phys. Rev. E 90, 062119] Published Fri Dec 12, 2014
    Keywords: Statistical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 95
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    Discussion on possible effects of the Barbero-Immirzi parameter at the TeV-scale particle physics (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): N. Panza, H. Rodrigues, D. Cocuroci, and J. A. Helayël-Neto In this paper, we analyze a curvature- and torsion-square quantum gravity action with an additional Holst term minimally coupled to a massive Dirac field in four dimensions. The main purpose here is to try to estimate and compare the value of the Barbero-Immirzi parameter with its currently known re... [Phys. Rev. D 90, 125007] Published Fri Dec 12, 2014
    Keywords: Field Theory, Formal Particle Theory
    Print ISSN: 0556-2821
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    Capturing the Landauer bound through the application of a detailed Jarzynski equality for entropic memory erasure (2014)
    American Physical Society (APS)
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    Publication Date: 2014-12-13
    Description: Author(s): Moupriya Das The states of an overdamped Brownian particle confined in a two-dimensional bilobal enclosure are considered to correspond to two binary values: 0 (left lobe) and 1 (right lobe). An ensemble of such particles represents bits of entropic information. An external bias is applied on the particles, equa... [Phys. Rev. E 90, 062120] Published Fri Dec 12, 2014
    Keywords: Statistical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
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    Intrinsically disordered proteins (IDPs) in trypanosomatids (2014)
    BioMed Central
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    Publication Date: 2014-12-14
    Description: Background: Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conformation and exist as dynamic ensembles in their native state. Due to their intrinsic adaptability, IDPs participate in many regulatory biological processes, including parasite immune escape. Using the information from trypanosomatids proteomes, we developed a pipeline for the identification, characterization and analysis of IDPs. The pipeline employs six disorder prediction methodologies and integrates structural and functional annotation information, subcellular location prediction and physicochemical properties. At the core of the IDP pipeline, there is a relational database that describes the protein disorder knowledge in a logically consistent manner. Results: The results obtained from the IDP pipeline showed that Leishmania and Trypanosoma species have approximately 70% and 55% IDPs, respectively. Our results indicate that IDPs in trypanosomatids contain disorder-promoting amino acids and order-promoting amino acids. The functional annotation analysis demonstrated enrichment of selected Gene Ontology terms. A relevant association was observed between the disordered residue numbers within predicted IDPs and their subcellular location, lack of transmembrane domains and lack of predicted function. We validated our computational findings with 2D electrophoresis designed for IDP identification and found that 100% of the identified protein spots were predicted in silico. Conclusions: Because there is no pipeline or database addressing IDPs in trypanosomatids, the pipeline described here represents the first attempt to establish possible correlations between protein function and structural disorder in these eukaryotes. Interestingly, all significant associations detected in the contingency analysis were observed when the protein disorder content reached approximately 40%. The exploratory data analysis allowed us to develop hypotheses regarding the IDPs' association with key biological features of these parasites, including transcription and transcriptional regulation, RNA processing and splicing, and cytoskeleton.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Comparative genomics reveals molecular features unique to the songbird lineage (2014)
    BioMed Central
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    Publication Date: 2014-12-14
    Description: Background: Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with this success, as well as with characteristic songbird traits such as vocal learning and the brain circuits that underlie this behavior, has proven difficult, in part due to the small number of avian genomes available until recently. Here we performed a comparative analysis of 48 avian genomes to identify genomic features that are unique to songbirds, as well as an initial assessment of function by investigating their tissue distribution and predicted protein domain structure. Results: Using BLAT alignments and gene synteny analysis, we curated a large set of Ensembl gene models that were annotated as novel or duplicated in the most commonly studied songbird, the Zebra finch (Taeniopygia guttata), and then extended this analysis to 47 additional avian and 4 non-avian genomes. We identified 10 novel genes uniquely present in songbird genomes. A refined map of chromosomal synteny disruptions in the Zebra finch genome revealed that the majority of these novel genes localized to regions of genomic instability associated with apparent chromosomal breakpoints. Analyses of in situ hybridization and RNA-seq data revealed that a subset of songbird-unique genes is expressed in the brain and/or other tissues, and that 2 of these (YTHDC2L1 and TMRA) are highly differentially expressed in vocal learning-associated nuclei relative to the rest of the brain. Conclusions: Our study reveals novel genes unique to songbirds, including some that may subserve their unique vocal control system, substantially improves the quality of Zebra finch genome annotations, and contributes to a better understanding of how genomic features may have evolved in conjunction with the emergence of the songbird lineage.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Methodology for the inference of gene function from phenotype data (2014)
    BioMed Central
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    Publication Date: 2014-12-14
    Description: Background: Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures. Results: We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function.We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes. Conclusions: We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and phenotypes that would be overlooked by a semantics-based approach. Future work will include the implementation of the described algorithms for a variety of other model organism databases, taking full advantage of the abundance of available high quality curated data.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Genetic associations of Nrf2-encoding NFE2L2 variants with Parkinson¿s disease ¿ a multicenter study (2014)
    BioMed Central
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    Publication Date: 2014-12-14
    Description: Background: The transcription factor Nrf2, encoded by the NFE2L2 gene, is an important regulator of the cellular protection against oxidative stress. Parkinson?s disease is a neurodegenerative disease highly associated with oxidative stress. In a previously published study, we reported associations of NFE2L2 haplotypes with risk and age at onset of idiopathic Parkinson?s disease in a Swedish discovery material and a Polish replication material. Here, we have extended the replication study and performed meta-analyses including the Polish material and four new independent European patient-control materials. Furthermore, all SNPs included in the haplotype windows were investigated individually for associations with Parkinson?s disease in meta-analyses including all six materials. Methods: Totally 1038 patients and 1600 control subjects were studied. Based on previous NFE2L2 haplotype associations with Parkinson?s disease, five NFE2L2 tag SNPs were genotyped by allelic discrimination and three functional NFE2L2 promoter SNPs were genotyped by sequencing. The impact of individual SNPs and haplotypes on risk and age at onset of Parkinson?s disease were investigated in each material individually and in meta-analyses of the obtained results. Results: Meta-analyses of NFE2L2 haplotypes showed association of haplotype GAGCAAAA, including the fully functional promoter haplotype AGC, with decreased risk (OR?=?0.8 per allele, p?=?0.012) and delayed onset (+1.1?years per allele, p?=?0.048) of Parkinson?s disease. These results support the previously observed protective effect of this haplotype in the first study. Further, meta-analyses of the SNPs included in the haplotypes revealed four NFE2L2 SNPs associated with age at onset of Parkinson?s disease (rs7557529 G?〉?A, ?1.0?years per allele, p?=?0.042; rs35652124 A?〉?G, ?1.1?years per allele, p?=?0.045; rs2886161 A?〉?G, ?1.2?years per allele, p?=?0.021; rs1806649 G?〉?A, +1.2?years per allele, p?=?0.029). One of these (rs35652124) is a functional SNP located in the NFE2L2 promoter. No individual SNP was associated with risk of Parkinson?s disease. Conclusion: Our results support the hypothesis that variation in the NFE2L2 gene, encoding a central protein in the cellular protection against oxidative stress, may contribute to the pathogenesis of Parkinson?s disease. Functional studies are now needed to explore these results further.
    Electronic ISSN: 1471-2350
    Topics: Biology , Medicine
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