WorldWideScience

Sample records for macleodii deep ecotype

  1. Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes.

    Science.gov (United States)

    Neumann, Anna M; Balmonte, John P; Berger, Martine; Giebel, Helge-Ansgar; Arnosti, Carol; Voget, Sonja; Simon, Meinhard; Brinkhoff, Thorsten; Wietz, Matthias

    2015-10-01

    The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.

  2. Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island

    Directory of Open Access Journals (Sweden)

    Eduard eFadeev

    2016-03-01

    Full Text Available Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de-novo methods. In general, the de-novo assemblies clearly outperformed the reference-based or hybrid ones, covering>99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (~4.5Mbp allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to Alteromonas macleodii, typically found in surface waters (surface ecotype, this plasmid consists of an almost complete flexible genomic island, containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (deep ecotype. Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire flexible genomic island suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon.

  3. Switchgrass ecotypes alter microbial contribution to deep-soil C

    Science.gov (United States)

    Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

    2016-05-01

    Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

  4. Switchgrass ecotypes alter microbial contribution to deep-soil C

    Science.gov (United States)

    Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on mic...

  5. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis.

    Science.gov (United States)

    Ivars-Martínez, Elena; D'Auria, Giuseppe; Rodríguez-Valera, Francisco; Sânchez-Porro, Cristina; Ventosa, Antonio; Joint, Ian; Mühling, Martin

    2008-09-01

    Twenty-three isolates of the widely distributed marine bacteria Alteromonas macleodii have been analysed by multilocus sequence analysis combined with phylogenetic and multivariate statistical analyses. The strains originated from the Pacific Ocean, Mediterranean Sea, English Channel, Black Sea and Thailand. Using the nucleotide sequences of nine loci for each of the 23 isolates, a robust identification was achieved of different clades within the single species. Strains generally clustered with the depth in the water column from which the isolate originated. Strains also showed more recombination with isolates from the same vicinity, suggesting that genetic exchange plays a role in diversification of planktonic marine prokaryotes. This study thus shows for the first time for a large set of isolates of a species of planktonic marine prokaryotes that multilocus sequence analysis overcomes the problems associated with the analysis of individual marker genes or presence of extensive recombination events. It can thus achieve intraspecific identification to the level of genotypes and, by comparison with relevant environmental data, ecotypes.

  6. Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

    DEFF Research Database (Denmark)

    Gonzaga, Aitor; Martin-Cuadrado, Ana-Belen; López-Pérez, Mario

    2012-01-01

    involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least...... indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat....

  7. NCBI nr-aa BLAST: CBRC-TTRU-01-0453 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0453 ref|YP_002125639.1| hypothetical protein MADE_01331 [Alteromonas macleodii 'Deep... ecotype'] gb|ACG65645.1| hypothetical protein MADE_01331 [Alteromonas macleodii 'Deep ecotype'] YP_002125639.1 0.20 24% ...

  8. NCBI nr-aa BLAST: CBRC-GGAL-15-0007 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GGAL-15-0007 ref|ZP_01109341.1| gamma-glutamyltranspeptidase [Alteromonas macleodii 'Deep... ecotype'] gb|EAR06392.1| gamma-glutamyltranspeptidase [Alteromonas macleodii 'Deep ecotype'] ZP_01109341.1 0.39 31% ...

  9. NCBI nr-aa BLAST: CBRC-CREM-01-1371 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1371 ref|ZP_01109498.1| phosphopyruvate hydratase [Alteromonas macleodii 'Deep... ecotype'] gb|EAR06202.1| phosphopyruvate hydratase [Alteromonas macleodii 'Deep ecotype'] ZP_01109498.1 2e-88 70% ...

  10. Antivenom potential of ethanolic extract of Cordia macleodii bark against Naja venom

    Institute of Scientific and Technical Information of China (English)

    Pranay Soni; Surendra H. Bodakhe

    2014-01-01

    Objective: To evaluate the antivenom potential of ethanolic extract of bark of Cordia macleodii against Naja venom induced pharmacological effects such as lethality, hemorrhagic lesion, necrotizing lesion, edema, cardiotoxicity and neurotoxicity.Methods:Wistar strain rats were challenged with Naja venom and treated with the ethanolic extract of Cordia macleodii bark. The effectiveness of the extract to neutralize the lethalities ofNaja venom was investigated as recommended by WHO. Results: At the dose of 400 and 800 mg/kg ethanolic extract of Cordia macleodii bark significantly inhibited the Naja venom induced lethality, hemorrhagic lesion, necrotizing lesion and edema in rats. Ethanolic extract of Cordia macleodii bark was effective in neutralizing the coagulant and defibrinogenating activity of Naja venom. The cardiotoxic effects in isolated frog heart and neurotoxic activity studies on frog rectus abdominus muscle were also antagonized by ethanolic extract of Cordia macleodii bark.Conclusions:It is concluded that the protective effect of extract of Cordia macleodii against Naja venom poisoning may be mediated by the cardiotonic, proteolysin neutralization, anti-inflammatory, antiserotonic and antihistaminic activity. It is possible that the protective effect may also be due to precipitation of active venom constituents.

  11. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

    Directory of Open Access Journals (Sweden)

    Eric Daniel Becraft

    2015-06-01

    Full Text Available Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes, which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation, exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species

  12. Production and Reutilization of Fluorescent Dissolved Organic Matter by a Marine Bacterial Strain, Alteromonas macleodii

    Science.gov (United States)

    Goto, Shuji; Tada, Yuya; Suzuki, Koji; Yamashita, Youhei

    2017-01-01

    The recalcitrant fraction of marine dissolved organic matter (DOM) plays an important role in carbon storage on the earth’s surface. Bacterial production of recalcitrant DOM (RDOM) has been proposed as a carbon sequestration process. It is still unclear whether bacterial physiology can affect RDOM production. In this study, we conducted a batch culture using the marine bacterial isolate Alteromonas macleodii, a ubiquitous gammaproteobacterium, to evaluate the linkage between bacterial growth and DOM production. Glucose (1 mmol C L-1) was used as the sole carbon source, and the bacterial number, the DOM concentration in terms of carbon, and the excitation–emission matrices (EEMs) of DOM were monitored during the 168-h incubation. The incubation period was partitioned into the exponential growth (0–24 h) and stationary phases (24–168 h) based on the growth curve. Although the DOM concentration decreased during the exponential growth phase due to glucose consumption, it remained stable during the stationary phase, corresponding to approximately 4% of the initial glucose in terms of carbon. Distinct fluorophores were not evident in the EEMs at the beginning of the incubation, but DOM produced by the strain exhibited five fluorescent peaks during exponential growth. Two fluorescent peaks were similar to protein-like fluorophores, while the others could be categorized as humic-like fluorophores. All fluorophores increased during the exponential growth phase. The tryptophan-like fluorophore decreased during the stationary phase, suggesting that the strain reused the large exopolymer. The tyrosine-like fluorophore seemed to be stable during the stationary phase, implying that the production of tyrosine-containing small peptides through the degradation of exopolymers was correlated with the reutilization of the tyrosine-like fluorophore. Two humic-like fluorophores that showed emission maxima at the longer wavelength (525 nm) increased during the stationary phase

  13. Ecotype Zones for Minnesota and Iowa Prairie Lands

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This document contains a map of local ecotype seed harvest zones for Iowa and Minnesota. A local ecotype zone is defined as a geographic area with generally similar...

  14. Extracellular polysaccharide production by a novel osmotolerant marine strain of Alteromonas macleodii and its application towards biomineralization of silver.

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    Ananya Mehta

    Full Text Available The present study demonstrates exopolysaccharide production by an osmotolerant marine isolate and also describes further application of the purified polysaccharide for production of colloidal suspension of silver nanoparticles with narrow size distribution. Phylogenetic analysis based on 16S r RNA gene sequencing revealed close affinity of the isolate to Alteromonas macleodii. Unlike earlier reports, where glucose was used as the carbon source, lactose was found to be the most suitable substrate for polysaccharide production. The strain was capable of producing 23.4 gl(-1 exopolysaccharide with a productivity of 7.8 gl(-1 day(-1 when 15% (w/v lactose was used as carbon source. Furthermore, the purified polysaccharide was able to produce spherical shaped silver nanoparticles of around 70 nm size as characterized by Uv-vis spectroscopy, Dynamic light scattering and Transmission electron microscopy. These observations suggested possible commercial potential of the isolated strain for production of a polysaccharide which has the capability of synthesizing biocompatible metal nanoparticle.

  15. Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain.

    Science.gov (United States)

    Mitulla, Maximilian; Dinasquet, Julie; Guillemette, Ryan; Simon, Meinhard; Azam, Farooq; Wietz, Matthias

    2016-12-01

    Alginate is a major cell wall polysaccharide from marine macroalgae and nutrient source for heterotrophic bacteria. Alginate can form gel particles in contact with divalent cations as found in seawater. Here, we tested the hypothesis that alginate gel particles serve as carbon source and microhabitat for marine bacteria by adding sterile alginate particles to microcosms with seawater from coastal California, a habitat rich in alginate-containing macroalgae. Alginate particles were rapidly colonized and degraded, with three- to eightfold higher bacterial abundances and production among alginate particle-associated (PA) bacteria. 16S rRNA gene amplicon sequencing showed that alginate PA bacteria were enriched in OTUs related to Cryomorphaceae, Saprospiraceae (Bacteroidetes) and Phaeobacter (Alphaproteobacteria) towards the end of the experiment. In microcosms amended with alginate particles and the proficient alginolytic bacterium Alteromonas macleodii strain 83-1, this strain dominated the community and outcompeted Cryomorphaceae, Saprospiraceae and Phaeobacter, and PA hydrolytic activities were over 50% higher. Thus, alginolytic activity by strain 83-1 did not benefit non-alginolytic strains by cross-feeding on alginate hydrolysis or other metabolic products. Considering the global distribution and extensive biomass of alginate-containing macroalgae, the observed bacterial dynamics associated with the utilization and remineralization of alginate microhabitats promote the understanding of carbon cycling in macroalgae-rich waters worldwide. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Evaluation of Freeze Tolerance in Lancelot Plantain (Plantago lanceolata L. Ecotypes under Controlled Conditions

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    M. Janalizadeh

    2016-02-01

    Full Text Available Introduction Lancelot Plantain (Ribwort, narrow-leaf or English plantain is a deep-rooted, short-lived perennial herb from Plantaginaceae family which has been used for various medicinal purposes for centuries, especially in Europe and only more recently has been proposed as a forage plant. The leaf of plantain is highly palatable for grazing animals, providing mineral-rich forage. Recently two productive upright cultivars of plantain have been bred and introduced, Grasslands Lancelot and the more erect winter active Ceres Tonic. Plantain grows moderately in winter but its main growth periods beings in spring and autumn with opportunistic summer growth. Although it reveals suitable winter survival in natural conditions, but there is not a lot of information about cold tolerance of this plant. So it is important to recognize the freeze tolerance of narrow leaf plantain for successful planting and utilization in cold regions such as Mashhad in Khorasan Razavi Province (Northeast of Iran. Determining LT50 point or critical temperature for survival of plant is the most reliable and simple method for evaluating cold tolerance of plants. Another reliable method for freeze tolerance of plants is estimation of temperature at which 50 % of dry matter reduces (RDMT50. This experiment was carried out to evaluate freeze tolerance of five ecotypes of Lancelot plantain according to the LT50su and RDMT50 indices. Materials and Methods In order to evaluate freeze tolerance of Lancelot plantain, a factorial experiment based on completely randomized design with three replications was carried out under controlled conditions at college of agriculture, Ferdowsi University of Mashhad. Five ecotypes of Lancelot plantain (Bojnourd, Kalat, Mashhad, Ghayen and Birjand after three months growth and hardening in natural environment were transferred to a Thermo gradient freezer on January 20th, 2012 and exposed to eight freezing temperatures (Zero, -3, -6, -9, -12, -15, -18

  17. Varied growth response of cogongrass ecotypes to elevated CO2

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    G. Brett Runion

    2016-01-01

    Full Text Available Cogongrass [Imperata cylindrica (L. P. Beauv] is an invasive C4 perennial grass which is listed as one of the top ten worst weeds in the world and is a major problem in the Southeast US. Five cogongrass ecotypes (Florida, Hybrid, Louisiana, Mobile, and North Alabama collected across the Southeast and a red-tip ornamental variety were container grown for six months in open top chambers under ambient and elevated (ambient plus 200 ppm atmospheric CO2. Elevated CO2 increased average dry weight (13% which is typical for grasses. Elevated CO2 increased height growth and both nitrogen and water use efficiencies, but lowered tissue nitrogen concentration; again, these are typical plant responses to elevated CO2. The hybrid ecotype tended to exhibit the greatest growth (followed by Louisiana, North Alabama, and Florida ecotypes while the red-tip and Mobile ecotypes were smallest. Interactions of CO2 with ecotype generally showed that the hybrid, Louisiana, Florida, and/or North Alabama ecotypes showed a positive response to CO2 while the Mobile and red-tip ecotypes did not. Cogongrass is a problematic invasive weed in the southeastern U.S. and some ecotypes may become more so as atmospheric CO2 continues to rise.

  18. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

    DEFF Research Database (Denmark)

    Becraft, Eric D.; Wood, Jason M.; Rusch, Douglas B.

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes...

  19. Freeze tolerance differs between two ecotypes of Paspalum vaginatum (Poaceae

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    Liliana Teresa Fabbri

    2016-03-01

    Full Text Available Morphological and physiological responses to freezing were evaluated in two ecotypes of the perennial turfgrass Paspalum vaginatum. Leaf extension rate, number of active meristems, leaf water potential and net photosynthesis were measured on plants of both a commercial cultivar, 'Sea Isle 2000', and a wild ecotype from the Flooding Pampa grasslands of Argentina. Plants were propagated by cloning, cultivated in pots, and examined during 18 consecutive days under two treatments: a non-frozen control treatment (15.5±7 ºC and a frozen treatment with two stages: Stage 1 with four hours of freezing stress for 10 nights (-5ºC, and Stage 2 with 12 hours of freezing stress for eight nights (five nights at -5ºC and three nights at -8ºC. After these treatments, plants were returned to the outside environment to evaluate shoot injury and post-freezing recovery. Leaf water potential, net photosynthesis and leaf extension rate were significantly higher in the wild ecotype than in the commercial cultivar. Meristem density was reduced after freezing in both ecotypes, but was more pronounced in the commercial cultivar (98.5% than in the wild ecotype (80%. Thus, the two ecotypes coming from different environments, exhibited different morphological and physiological responses to exposure to freezing temperatures.

  20. Edaphic factors determining variation of two ecotypes of Leymus chinensis in North China

    Institute of Scientific and Technical Information of China (English)

    ZHOU Chan; YANG Yunfei

    2006-01-01

    To identify ecotypic variation of L. chinensis, the physiological characteristics and environmental factors were measured and assessed for grey-green and yellow-green ecotypes of L. chinensis grown in the salt-alkalized and aeolian sandy soils. Although both ecotypes presented a similar salt-alkaline tolerance under the experimental conditions, they differed in several aspects. The L. chinensis grown in the aeolian sandy soils had higher water potential and chlorophyll content and lower proline content in their leaves than those grown in the salt-alkalized habitat, and the grey-green ecotype of L. chinensis in both types of soils had higher water potential,chlorophyll and proline contents than the yellow-green ecotype. Besides, grey-green ecotypes had higher salt-alkaline tolerance than the yellow-green ecotype. The stepwise regression analysis showed that soil conductance and pH value were the main ecological factors affecting the physiology of L. chinensis. From the natural distribution of the two ecotypes, we considered that salt-alkaline in the soils is the leading factor in determining ecotypic variation of L. chinensis. The two ecotypes were first named grey-green and yellow-green ecotypes respectively.

  1. Genomic evidence of adaptive evolution in emergent Vibrio parahaemolyticus ecotypes

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    Jeffrey W. Turner

    2016-07-01

    Full Text Available Abstract The ubiquitous marine bacterium Vibrio parahaemolyticus is a leading cause of illness associated with seafood consumption. The emergence of two genetically distinct ecotypes (ST3 and ST36 has led to an alarming increase in the size and frequency of disease outbreaks. We conducted a genomic comparison of 30 V. parahaemolyticus genomes that represent a diverse collection of 15 genetically distinct ecotypes, including newly sequenced representatives of ST3 and ST36, isolated from both clinical and environmental sources. A multistep evolutionary analysis showed that genes associated with sensing and responding to environmental stimuli have evolved under positive selection, identifying examples of convergent evolution between ST3 and ST36. A comparison of predicted proteomes indicated that ST3 and ST36 ecotypes laterally acquired tens of novel genes associated with a variety of functions including dormancy, homeostasis and membrane transport. Genes identified in this study play an apparent role in environmental fitness and may confer cross protection against stressors encountered in the human host. Together, these results show the evolution of stress response is an important genetic mechanism correlated with the recent emergence of the ST3 and ST36 ecotypes.

  2. Circulation of four Anaplasma phagocytophilum ecotypes in Europe

    NARCIS (Netherlands)

    Jahfari, Setareh; Coipan, E Claudia; Fonville, Manoj; van Leeuwen, Arieke Docters; Hengeveld, Paul; Heylen, Dieter; Heyman, Paul; van Maanen, Cees; Butler, Catherine M|info:eu-repo/dai/nl/304832162; Földvári, Gábor; Szekeres, Sándor; van Duijvendijk, Gilian; Tack, Wesley; Rijks, Jolianne M|info:eu-repo/dai/nl/151266093; van der Giessen, Joke; Takken, Willem; van Wieren, Sipke E; Takumi, Katsuhisa; Sprong, Hein

    2014-01-01

    BACKGROUND: Anaplasma phagocytophilum is the etiological agent of granulocytic anaplasmosis in humans and animals. Wild animals and ticks play key roles in the enzootic cycles of the pathogen. Potential ecotypes of A. phagocytophilum have been characterized genetically, but their host range,

  3. Circulation of four Anaplasma phagocytophilum ecotypes in Europe

    NARCIS (Netherlands)

    Jahfari, S.; Coipan, E.C.; Fonville, M.; Leeuwen, van A.D.; Hengeveld, P.; Heylen, D.; Heyman, P.; Maanen, van C.; Butler, C.M.; Foldvari, G.; Szekeres, S.; Duijvendijk, van L.A.G.; Tack, W.; Rijks, J.M.; Giessen, van der J.; Takken, W.; Wieren, van S.E.; Takumi, K.; Sprong, H.

    2014-01-01

    Background: Anaplasma phagocytophilum is the etiological agent of granulocytic anaplasmosis in humans and animals. Wild animals and ticks play key roles in the enzootic cycles of the pathogen. Potential ecotypes of A. phagocytophilum have been characterized genetically, but their host range,

  4. Circulation of four Anaplasma phagocytophilum ecotypes in Europe

    NARCIS (Netherlands)

    Jahfari, Setareh; Coipan, E Claudia; Fonville, Manoj; van Leeuwen, Arieke Docters; Hengeveld, Paul; Heylen, Dieter; Heyman, Paul; van Maanen, Cees; Butler, Catherine M; Földvári, Gábor; Szekeres, Sándor; van Duijvendijk, Gilian; Tack, Wesley; Rijks, Jolianne M; van der Giessen, Joke; Takken, Willem; van Wieren, Sipke E; Takumi, Katsuhisa; Sprong, Hein

    2014-01-01

    BACKGROUND: Anaplasma phagocytophilum is the etiological agent of granulocytic anaplasmosis in humans and animals. Wild animals and ticks play key roles in the enzootic cycles of the pathogen. Potential ecotypes of A. phagocytophilum have been characterized genetically, but their host range, zoonoti

  5. Circulation of four Anaplasma phagocytophilum ecotypes in Europe

    NARCIS (Netherlands)

    Jahfari, S.; Coipan, E.C.; Fonville, M.; Leeuwen, van A.D.; Hengeveld, P.; Heylen, D.; Heyman, P.; Maanen, van C.; Butler, C.M.; Foldvari, G.; Szekeres, S.; Duijvendijk, van L.A.G.; Tack, W.; Rijks, J.M.; Giessen, van der J.; Takken, W.; Wieren, van S.E.; Takumi, K.; Sprong, H.

    2014-01-01

    Background: Anaplasma phagocytophilum is the etiological agent of granulocytic anaplasmosis in humans and animals. Wild animals and ticks play key roles in the enzootic cycles of the pathogen. Potential ecotypes of A. phagocytophilum have been characterized genetically, but their host range, zoonoti

  6. Accumulation and tolerance of lead in two contrasting ecotypes of Dianthus carthusianorum.

    Science.gov (United States)

    Wójcik, Małgorzata; Tukiendorf, Anna

    2014-04-01

    Dianthus carthusianorum is one of the dominant plant species colonising the Zn-Pb waste deposits in Bolesław, Southern Poland. It differs in terms of morphology and genetics from ecotypes inhabiting non-metal-polluted areas. The response of waste-heap (metallicolous, M) and reference (nonmetallicolous, NM) ecotypes of D. carthusianorum to Pb in hydroponics was investigated and compared in this study. The plants of the M ecotype were more tolerant to Pb than these of the NM ecotype in spite of accumulation of higher concentrations of Pb. In both ecotypes, about 70-78% of Pb was retained in roots. In non Pb-treated plants, a higher glutathione (GSH) level was found in the M ecotype. After the Pb exposure, the GSH level decreased and was similar in both ecotypes. Lead treatment induced synthesis of phytochelatins (PCs) only in the plant roots, with significantly higher concentrations thereof detected in the NM ecotype. Malate and citrate concentrations were higher in the M ecotype; however, they did not change significantly upon any Pb treatment in either ecotype. The results indicated that neither PCs nor organic acids were responsible for the enhanced Pb tolerance of the waste-heap plants.

  7. Cadmium Induced Changes of Proline in Two Ecotypes of Thlaspi Caerulescens

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    Zemanová V.

    2013-04-01

    Full Text Available A Thlaspi caerulescens (J. & C. PRESL was used to study the effect of cadmium on the content of free amino acids and ability accumulation of Cd in ecotypes of this plant species. In pot experiment two ecotypes T. caerulescens were used: Ganges ecotype from France and Mežica ecotype from Slovenia. The plants were grown in soil (chernozem – Suchdol spiked with NPK and three different concentration of Cd: 30, 60 and 90 mg/kg. The content of Cd was measured in the above-ground biomass and roots using ICP-OES. Accumulation of Cd was higher in the Mežica ecotype in contrast to the low Cd-accumulating the Ganges ecotype. Analyses of free amino acids contents were measured by GC-MS method. The content of free amino acids in above-ground biomass of the Mežica ecotype declined progressively with increasing concentrations of Cd. Opposite trend was observed in roots of this ecotype. The increase of free amino acids contents in above-ground biomass and roots of the Ganges ecotype were detected. The results of specific amino acids free proline showed increased content in plant biomass with increasing Cd contamination of soil. A statistically significant increase was observed between control plants (0 mg/kg Cd and variant Cd3 (90 mg/kg Cd for both ecotypes. The statistically significant decrease of free proline was observed in the Mežica ecotype roots. Opposite trend was observed in roots of Ganges ecotype - increasing trend of free proline content. These results indicate a correlation between content of Cd and content of free proline in different parts of the plant. We can speculate that the mechanism of Cd hyperaccumulation and metabolism of free proline are not identical in ecotypes of this species.

  8. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park.

    Science.gov (United States)

    Becraft, Eric D; Wood, Jason M; Rusch, Douglas B; Kühl, Michael; Jensen, Sheila I; Bryant, Donald A; Roberts, David W; Cohan, Frederick M; Ward, David M

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.

  9. WOOD ANATOMICAL STUDY AMONG THREE ECOTYPES OF Pinus merkusii IN SUMATRA AND THE POTENTIAL AS CLIMATE CHANGE INDICATOR

    Directory of Open Access Journals (Sweden)

    Yulia Sandri

    2016-09-01

    Full Text Available Recently, climate change is the one of most important environmental issue. Climate variability can be recorded by tree growing through the growth ring. Growth ring formed by cambial activity were examined in wood anatomy. In Sumatra, there are three ecotypes Pinus merkusii, namely ecotypes Kerinci, Tapanuli, and Aceh which can be distinguished morphologically. This study aims to knowing the wood anatomical characteristics of the three ecotypes and determine the potential as climate indicator. This study was conducted in October 2014 until June 2015. Sample of Kerinci ecotype was collected in Kerinci Seblat National Park, Tapanuli ecotype in Dolok Sibualbuali Natural Reserve and Aceh ecotype in Gunung Leuser National Park on a height of 130 cm using increment borer and cut on the main stem 5×5 cm for anatomical sample. Results from this study indicate that ecotype Kerinci and Tapanuli showed earlywood and latewood boundary exposing the clear growth ring, whereas in Aceh ecotype unclear. Tapanuli ecotype have the thickest tracheid diameter than ecotype Kerinci and Aceh. Ecotypes of Kerinci, Tapanuli, and Aceh has homoceluler and uniseriate ray where Aceh ecotype have the longest ray. Furthermore, Kerinci and Tapanuli ecotype have potential as climate indicator eventhough showed negative correlation, that Tapanuli ecotype show the best result and recommended in dendrochronology study.

  10. A genomic island linked to ecotype divergence in Atlantic cod

    DEFF Research Database (Denmark)

    Hansen, Jakob Hemmer; Eg Nielsen, Einar; Therkildsen, Nina O.;

    2013-01-01

    gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two......The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced....... Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high...

  11. Delineating ecotypes of marine photosynthetic picoeukaryotes in the wild

    Science.gov (United States)

    Limardo, A. J.; Sudek, S.; Rii, Y. M.; Church, M. J.; Wei, C. L.; Armbrust, E. V.; Worden, A. Z.

    2015-12-01

    Extremely small eukaryotic green algae are abundant primary producers found in diverse marine habitats. Over the last decade several studies have revealed extensive diversity within the "pico-prasinophytes" (≤2 µm diameter) that was previously unrecognized due to a lack of distinguishing morphological features. Using whole genome and marker gene analyses, distinct species have since been recognized within the Micromonas and Ostreococcus genera. Relatively little is known about environmental factors driving distributions of these species, but for Ostreococcus, laboratory studies suggested that differentiation reflects high- and low-light adapted ecotypes. Subsequent field studies indicated that Ostreococcus Clade OI and Clade OII rarely co-occur but partition according to distinct habitats - representing 'mesotrophic' and 'oligotrophic' ecotypes, respectively. Unlike Micromonas and Ostreococcus, Bathycoccus was presumed to be a single cosmopolitan species because identical 18S rRNA gene sequences are observed in cultured isolates and in environmental surveys. However, analysis of a targeted metagenome from a Bathycoccus population in the tropical Atlantic led to the hypothesis that Bathycoccus also harbors distinct ecotypes. Here, we have developed qPCR assays to enumerate the two Bathycoccus types which can be discriminated based on the internal transcribed spacer (ITS). Statistical analysis of qPCR and environmental data from >200 North Pacific Ocean samples shows that the two Bathycoccus clades are only somewhat analogous to oligotrophic and mesotrophic Ostreococcus clades. The two Bathycoccus clades co-occurred more than twice as often as the Ostreococcus clades. Additionally, while Bathycoccus BII and oligotrophic Ostreococcus OII were found at warm temperatures up to 26°C, BII extended into colder waters than OII. Similarly, Bathycoccus BI extended into warmer waters than mesotrophic Ostreococcus OI. Currently, we are analyzing metatranscriptomes to

  12. Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.

    Science.gov (United States)

    Francisco, Juan Carlos; Cohan, Frederick M; Krizanc, Danny

    2014-01-01

    Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway.

  13. Distribution and diversity of Prochlorococcus ecotypes in the Red Sea

    KAUST Repository

    Shibl, Ahmed A.

    2014-06-19

    Photosynthetic prokaryotes of the genus Prochlorococcus play a major role in global primary production in the world\\'s oligotrophic oceans. A recent study on pelagic bacterioplankton communities in the northern and central Red Sea indicated that the predominant cyanobacterial 16S rRNA gene sequence types were from Prochlorococcus cells belonging to a high-light-adapted ecotype (HL II). In this study, we analyzed microdiversity of Prochlorococcus sp. at multiple depths within and below the euphotic zone in the northern, central, and southern regions of the Red Sea, as well as in surface waters in the same locations, but in a different season. Prochlorococcus dominated the communities in clone libraries of the amplified 16S-23S rRNA internal transcribed spacer (ITS) region. Almost no differences were found between samples from coastal or open-water sites, but a high diversity of Prochlorococcus ecotypes was detected at 100-meter depth in the water column. In addition, an unusual dominance of HL II-related sequences was observed in deeper waters. Our results indicate that the Red Sea harbors diverse Prochlorococcus lineages, but no novel ecotypes, despite its unusual physicochemical properties. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  14. Recurrent evolution of life history ecotypes in sockeye salmon: implications for conservation and future evolution.

    Science.gov (United States)

    Wood, Chris C; Bickham, John W; John Nelson, R; Foote, Chris J; Patton, John C

    2008-05-01

    We examine the evolutionary history and speculate about the evolutionary future of three basic life history ecotypes that contribute to the biocomplexity of sockeye salmon (Oncorhynchus nerka). The 'recurrent evolution' (RE) hypothesis claims that the sea/river ecotype is ancestral, a 'straying' form with poorly differentiated (meta)population structure, and that highly structured populations of lake-type sockeye and kokanee have evolved repeatedly in parallel adaptive radiations between recurrent glaciations of the Pleistocene Epoch. Basic premises of this hypothesis are consistent with new, independent evidence from recent surveys of genetic variation in mitochondrial and microsatellite DNA: (1) sockeye salmon are most closely related to pink (O. gorbuscha) and chum (O. keta) salmon with sea-type life histories; (2) the sockeye life history ecotypes exist as polyphyletic lineages within large drainages and geographic regions; (3) the sea/river ecotype exhibits less genetic differentiation among populations than the lake or kokanee ecotypes both within and among drainages; and (4) genetic diversity is typically higher in the sea/river ecotype than in the lake and kokanee ecotypes. Anthropogenic modification of estuarine habitat and intensive coastal fisheries have likely reduced and fragmented historic metapopulations of the sea/river ecotype, particularly in southern areas. In contrast, the kokanee ecotype appears to be favoured by marine fisheries and predicted changes in climate.

  15. Physiological assessment of drought tolerance of two ecotypes of cumin (Cuminum cyminum L. under greenhouse conditions

    Directory of Open Access Journals (Sweden)

    2015-11-01

    Full Text Available Drought has adverse effects on plant growth and production. Plants respond to drought stress through biochemical and physiological processes. In the present study, physiological responses of two cumin (Cuminum cyminum L. ecotypes including Ravar and Gonbad, which belong to dry and sub-humid regions of Iran, respectively, were evaluated in a split-plot factorial experiment with three replications in controlled greenhouse conditions. Physiological traits such as relative water content, relative leaf water loss and electrolyte leakage were measured. Analysis of variance showed that there are considerable genetic variations for drought tolerance between the ecotypes. Drought stress decreased relative water content and relative leaf water loss rate, while electrolyte leakage was significantly increased in both ecotypes. Most of the significant changes were recorded in Gonbad ecotype. The Ravar ecotype demonstrated higher tolerance to drought stress, as compared to Gonbad ecotype, which can be due to compatibility of this genotype to water-deficit conditions. Therefore, this ecotype was recommended as a tolerant ecotype to drought stress. In conclusion, the investigated traits in this experiment were found to be valuable criteria in selection of drought-tolerant ecotypes at seedling stage under greenhouse conditions.

  16. Nutritional stress effects under different nitrogen sources on the genes in microalga Isochrysis zhangjiangensis and the assistance of Alteromonas macleodii in releasing the stress of amino acid deficiency.

    Science.gov (United States)

    Wu, Shuang; Zhou, Jiannan; Xin, Yanjuan; Xue, Song

    2015-10-01

    The expressions of nine nitrogen assimilation-associated genes, NRT2, NAR1, NIA2, NIR, GLN2, GLSF, GSN1, GDH, and AAT2, in the microalga Isochrysis zhangjiangensis were investigated to unveil the effects of limitations of various nitrogen sources (NaNO3 , NH4 Cl, NaNO2 , and an amino acid mixture) on the microalgae. The results demonstrated that the NRT2, NAR1, GLN2, GSN1, and AAT2 genes were highly expressed in lipid-rich microalgae under inorganic nitrogen-deficient conditions and they decreased after nitrogen resupply. Significant increases in the expressions of NAR1, GLN2, and GLSF were found in nitrate-depleted microalgae, whereas significant increases in the expressions of NRT2, NAR1, GLN2, and GSN1 were found in nitrite-depleted microalgae. Significant increases in the expressions of only NRT2 and GSN1 were found in ammonium-depleted microalgae (P < 0.05). Except for the NRT2, other genes were expressed at lower levels under amino acid-deficient conditions compared with amino acid-sufficient controls. The expression of the NIA2 gene decreased in nitrogen-depleted microalgae regardless of the initial nitrogen source. However, the results of fatty acid analyses showed that the features of fatty acid profiles followed a similar mode, in which the percentage compositions of C16:0 and C18:1Δ(9) increased in nitrogen-depleted cells and that of C16:1Δ(9) , C18:3Δ(9,12,15) , C18:4Δ(6,9,12,15) , and C18:5Δ(3,6,9,12,15) decreased, regardless of the type of nitrogen source applied. It was also found that the epiphytic bacterium Alteromonas macleodii played a particularly important role in releasing microalgae from the stress of amino acid deficiency. These findings also provide a foundation for regulating microalgal lipid production through manipulation of the nitrogen assimilation-associated genes.

  17. The adaptive value of phenotypic plasticity in two ecotypes of a marine gastropod

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    Butlin Roger K

    2010-10-01

    Full Text Available Abstract Background Few surveys have concentrated on studying the adaptive value of phenotypic plasticity within genetically-distinct conspecific ecotypes. Here, we conduct a test to assess the adaptive value that partial phenotypic plasticity may have for survival in the marine gastropod Littorina saxatilis. This species has evolved canalized ecotypes but, nevertheless, the ecotypes show some phenotypic plasticity for the traits under divergent selection between wave-exposed and high-predation habitats. Results We exposed juveniles of each ecotype to several environmental treatments under laboratory conditions in order to produce shape variation associated with plasticity. The two ecotypes from different treatments were then transplanted to the wave-exposed habitat and the survival rate was monitored. Ecotype explained the largest distinction in survival rate while treatment caused variation in survival rate within the ecotype released into its parental habitat which was correlated with plastic changes in shell shape. Snails that had experienced a treatment mimicking the environment of the transplantation location survived with the highest rate, while individuals from the contrary experimental treatment had lower survivorship. Conclusions We conclude that the partial plastic response shown in Littorina saxatilis has a significant impact on fitness, although this remains small compared to the overall adaptive difference between ecotypes.

  18. [Effects of exogenous Ca2+ on the growth and Zn accumulation of two Sedum alfredii Hance ecotypes].

    Science.gov (United States)

    Huang, Hua-gang; Li, Ting-xuan; Zhang, Xi-zhou; Tian, Sheng-ke; Yang, Xiao-e

    2008-04-01

    A hydroponic study was conducted to investigate the biomass, root morphology, and zinc (Zn), calcium (Ca) and sulfur (S) contents of two Sedum alfredii ecotypes under effects of different concentration calcium (Ca2+) addition. The results showed that with increasing exogenous Ca2+ concentration, the dry mass of the two S. alfredii ecotypes increased, and the shoot dry mass of hyperaccumulation ecotype increased significantly (P hyperaccumulation ecotype increased with increasing exogenous Ca2+ concentration, while those of non-hyperaccumulation ecotype were in adverse. The Zn accumulation in the root, stem and leaf of hyperaccumulation ecotype was increased with increasing exogenous Ca2+ concentration though the differences among Ca2+ treatments were not significant (P >0.05), while the Zn accumulation in the shoot of non-hyperaccumulation ecotype was significantly low (P hyperaccumulation ecotype had a significant positive correlation with the concentration of exogenous Ca2+ (P hyperaccumulation ecotype (P hyperaccumulation ecotype, while inhibited the Zn accumulation of non-hyperaccumulation ecotype. Appropriate concentration of exogenous Ca2+ could promote the growth of hyperaccumulation ecotype S. alfredii, and improve its ability of accumulating more zinc.

  19. Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences

    KAUST Repository

    Shibl, Ahmed A.

    2016-06-25

    The marine picocyanobacteria Prochlorococcus represent a significant fraction of the global pelagic bacterioplankton community. Specifically, in the surface waters of the Red Sea, they account for around 91% of the phylum Cyanobacteria. Previous work suggested a widespread presence of high-light (HL)-adapted ecotypes in the Red Sea with the occurrence of low-light (LL)-adapted ecotypes at intermediate depths in the water column. To obtain a more comprehensive dataset over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze the diversity of the Prochlorococcus rpoC1 gene from a total of 113 samples at various depths (up to 500 m) from 45 stations spanning the Red Sea basin from north to south. In addition, we analyzed 45 metagenomes from eight stations using hidden Markov models based on a set of reference Prochlorococcus genomes to (1) estimate the relative abundance of Prochlorococcus based on 16S rRNA gene sequences, and (2) identify and classify rpoC1 sequences as an assessment of the community structure of Prochlorococcus in the northern, central and southern regions of the basin without amplification bias. Analyses of metagenomic data indicated that Prochlorococcus occurs at a relative abundance of around 9% in samples from surface waters (25, 50, 75 m), 3% in intermediate waters (100 m) and around 0.5% in deep-water samples (200–500 m). Results based on rpoC1 sequences using both methods showed that HL II cells dominate surface waters and were also present in deep-water samples. Prochlorococcus communities in intermediate waters (100 m) showed a higher diversity and co-occurrence of low-light and high-light ecotypes. Prochlorococcus communities at each depth range (surface, intermediate, deep sea) did not change significantly over the sampled transects spanning most of the Saudi waters in the Red Sea. Statistical analyses of rpoC1 sequences from metagenomes indicated that the vertical distribution of Prochlorococcus in the water

  20. [Quality variation and ecotype division of Panax quinquefolium in China].

    Science.gov (United States)

    Huang, Lin-Fang; Suo, Feng-Mei; Song, Jing-Yuan; Wen, Mei-Jia; Jia, Guang-Lin; Xie, Cai-Xiang; Chen, Shi-Lin

    2013-04-01

    Quality variation and ecotype classification of Chinese herbal medicine are important scientific problems in Daodi herbal medicine research. The diversity of natural environmental conditions has led to form unique multi-Daodi, multi-product areas that produce particular Chinese herbal medicine. China is one of three big American ginseng (Panax quinquefolium L.) producing areas worldwide, with over 300 years of application and 40 years of cultivation history. Long-term production practice has led to the formation of three big advocate produce areas in China: Northeast province, Beijing and Shandong. P. quinquefolium L. grown under certain environmental conditions will develop long-term adaptations that will lead to more stable strains (different ecotypes). P. quinquefolium L., can vary greatly in quality; however, the ecological mechanisms causing this variation are still unclear. Root samples were collected from four-year-old cultivated P. quinquefolium L. plants in the three major genuine (Daodi) American ginseng-producing areas of Northeast province, Beijing and Shandong province, China. Ultra-performance liquid chromatography was used to analyze the contents of eight ginsenosides (Rg1, Re, Rb1, Rb2, Rb3, Rc, Rd, Rg2). Data for nine ecological factors, including temperature, moisture and sunlight, were obtained from the ecological database of Geographic Information System for Traditional Chinese Medicine. Soil samples from the sampling sites were collected. Effective boron and iron, available nitrogen and potassium, as well as other trace elements and soil nutrients, were determined by conventional soil physicochemical property assay methods. Analytical methods of biostatistics and numerical taxonomy were used to divide ecotypes of the three main Panax quinquefolium L. producing areas in China based on ginsenoside content, climate, soil and other ecological factors. To our knowledge, this is the first time that ecological division of P. quinquefolium L. producing

  1. Reproductive, morphological, and phytochemical responses of Arabidopsis thaliana ecotypes to enhanced UV-B radiation

    Energy Technology Data Exchange (ETDEWEB)

    Trumbull, V.L.; McCloud, E.S.; Paige, K.N. (Univ. of Illinois, Urbana, IL (United States))

    1994-06-01

    Two ecotypes of Arabidopsis thaliana, collected from Libya and Norway, were grown in the greenhouse under. UV-B doses of 0 and 10.5 kJ m[sup [minus]2] UV-B[sub BE]. The high UV-B dose simulated midsummer ambient conditions over Libya and a 40% reduction in stratospheric ozone over Norway. The Libyan ectotype, which originated from latitudes where solar UV-B is high, showed no UV-B induced damage to plant growth. However the Norwegian ecotype, which originated from latitudes where solar UV-B is low, showed a significant reduction in plant height, inflorescence weight, and rosette weight in response to enhanced UV-B. Although fruit and seed number for both ecotypes were unaffected by enhanced UV-B radiation the germination success of the seeds harvested from the irradiated Norwegian plants were significantly reduced. The two ecotypes also differed with respect to their accumulation of kaempferol, a putative UV-B protective filter. The Libyan ecotype increased kaempferol concentration by 38% over the 0 kJ treatment whereas the Norwegian ecotype increased by only 15%. These data suggest that, for these ecotypes, variation in UV-B sensitivity may be explained by the differential induction of UV-absorbing leaf pigments.

  2. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

    Directory of Open Access Journals (Sweden)

    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

  3. Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale.

    Science.gov (United States)

    Ravinet, Mark; Westram, Anja; Johannesson, Kerstin; Butlin, Roger; André, Carl; Panova, Marina

    2016-01-01

    Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel, and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However, the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this, we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities amongst ecotype pairs on three close islands (<10 km distance) connected by weak gene flow (Nm ~ 0.03) and with recent common ancestry (<10 000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared amongst all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.

  4. Evaluation of Freezing Tolerance of Three Ajowan (Trachyspermum ammi (Linn. Sprague Ecotypes in Controlled Conditions

    Directory of Open Access Journals (Sweden)

    Z Boroumand Rezazadeh

    2013-08-01

    Full Text Available Ajowan is one of the endemic plants in Khorasan province, and there is a little information on its tolerance to cold stress. In order to study freezing tolerance of ajowan, an experiment was conducted in faculty of agriculture, Ferdowsi University of Mashhad, based on factorial-completely randomized design with three replications and three ecotypes of ajowan (Neishabour, Birjand and Torbat-e-Heidarieh were imposed on eight freezing temperatures (0 (control, -1.5, -3, -4.5, -6,-7.5, -9 and -10.5 °C. Plants were grown in natural environment till 4-5 leaf stage, then for freezing treatments transferred to thermo-gradient freezer. The cell membrane stability was evaluated by electrolyte leakage index (EL and temperature for killing 50% of samples according to the electrolyte leakage (LT50el was determined. Furthermore, survival percentage, leaf number and dry weight, temperature for killing 50% of samples according to survival (LT50su and reduced dry matter temperature 50 (RDMT50 were determined after three weeks recovery in the glasshouse. Response of ajowan ecotypes for electrolyte leakage was different and birjand ecotype had the lowest %EL, whereas the slope of %EL in mentioned ecotype was lower than two other ecotypes. However there were no significant differences among ajowan ecotypes on LT50su. Decreasing temperature to -7.5 °C reduced survival percentage of Neishabour and Torbat-e-Heidarieh ecotypes to lower than 20 percent, whiles in this temperature Birjand’s survival percentage was about 60 percent. It seems that Birjand ecotype with the lowest electrolyte leakage, the highest survival and dry matter and the lowest LT50su was more tolerant than two other ecotypes.

  5. The effect of Chinese tallow tree (Sapium sebiferum) ecotype on soil-plant system carbon and nitrogen processes.

    Science.gov (United States)

    Zou, Jianwen; Rogers, William E; DeWalt, Saara J; Siemann, Evan

    2006-11-01

    The EICA hypothesis predicts that shifts in allocation of invasive plants give rise to higher growth rates and lower herbivore defense levels in their introduced range than conspecifics in their native range. These changes in traits of invasive plants may also affect ecosystem processes. We conducted an outdoor pot experiment with Chinese tallow tree (Sapium sebiferum, Euphorbiaceae) seedlings from its native (Jiangsu, China, native ecotype) and introduced ranges (Texas, USA, invasive ecotype) to compare their relative performances in its native range and to examine ecotype effects on soil processes with and without fertilization. Consistent with predictions, plant (shoot and root) mass was significantly greater and leaf defoliation tended to be higher, while the root:shoot ratio was lower for the invasive ecotype relative to the native ecotype. Seasonal amounts of soil-plant system CO(2) and N(2)O emissions were higher for the invasive ecotype than for the native ecotype. Soil respiration rates and N(2)O emission increases from fertilization were also greater for the invasive ecotype than for the native ecotype, while shoot-specific respiration rates (g CO(2)-C g(-1) C day(-1)) did not differ between ecotypes. Further, soil inorganic N (ammonium and nitrate) was higher, but soil total N was lower for soils with the invasive ecotype than soils with the native ecotype. Compared with native ecotypes, therefore, invasive ecotypes may have developed a competition advantage in accelerating soil processes and promoting more nitrogen uptake through soil-plant direct interaction. The results of this study suggest that soil and ecosystem processes accelerated by variation in traits of invasive plants may have implications for their invasiveness.

  6. Phylogenomics of the killer whale indicates ecotype divergence in sympatry.

    Science.gov (United States)

    Moura, A E; Kenny, J G; Chaudhuri, R R; Hughes, M A; Reisinger, R R; de Bruyn, P J N; Dahlheim, M E; Hall, N; Hoelzel, A R

    2015-01-01

    For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the 'marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists.

  7. Phenotypic plasticity in response to the social environment: effects of density and sex ratio on mating behaviour following ecotype divergence.

    Directory of Open Access Journals (Sweden)

    Kristina Karlsson

    Full Text Available The ability to express phenotypically plastic responses to environmental cues might be adaptive in changing environments. We studied phenotypic plasticity in mating behaviour as a response to population density and adult sex ratio in a freshwater isopod (Asellus aquaticus. A. aquaticus has recently diverged into two distinct ecotypes, inhabiting different lake habitats (reed Phragmites australis and stonewort Chara tomentosa, respectively. In field surveys, we found that these habitats differ markedly in isopod population densities and adult sex ratios. These spatially and temporally demographic differences are likely to affect mating behaviour. We performed behavioural experiments using animals from both the ancestral ecotype ("reed" isopods and from the novel ecotype ("stonewort" isopods population. We found that neither ecotype adjusted their behaviour in response to population density. However, the reed ecotype had a higher intrinsic mating propensity across densities. In contrast to the effects of density, we found ecotype differences in plasticity in response to sex ratio. The stonewort ecotype show pronounced phenotypic plasticity in mating propensity to adult sex ratio, whereas the reed ecotype showed a more canalised behaviour with respect to this demographic factor. We suggest that the lower overall mating propensity and the phenotypic plasticity in response to sex ratio have evolved in the novel stonewort ecotype following invasion of the novel habitat. Plasticity in mating behaviour may in turn have effects on the direction and intensity of sexual selection in the stonewort habitat, which may fuel further ecotype divergence.

  8. ABSCISIC ACID EFFECTS ON WATER AND PHOTOSYNTHETIC CHARACTERISTICS OF TWO ECOTYPES OF Atriplex halimus L.

    Directory of Open Access Journals (Sweden)

    Y. Bidai

    2016-05-01

    Full Text Available The aim of this study is to compare the water and photosynthetic characteristics of two xerophilic ecotypes of Atriplex halimus (L.. Seeds collected from two different sites Djelfa and Oran are germinated in controlled greenhouse. After 6 months, the plantlets were treated 21 days with increasing concentrations of abscisic acid (0M, 10-6 M and 10-3 M. The results show that ecotype of Djelfa reduced water loss through transpiration because of high stomatal resistance. Consequently the content of chlorophyll a and b decrease significantly compared to Oran ecotype which show an increase of the osmotic potential and relative water content. Osmotic adjustment to reduce dehydration and maintain a good photosynthesis seems efficient in Oran ecotype.

  9. Genetic and Ecotypic Differentiation in a Californian Plant Polyploid Complex (Grindelia, Asteraceae)

    OpenAIRE

    Abigail J Moore; Moore, William L.; Baldwin, Bruce G.

    2014-01-01

    Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations...

  10. Demographic characteristics of circumpolar caribou populations: ecotypes, ecological constraints, releases, and population dynamics

    OpenAIRE

    Mallory, F.F.; T.L. Hillis

    1998-01-01

    Data on the status of caribou {Rangifer tarandus) herds throughout the circumpolar region during the last 20 years were obtained from the literature and personal communication with researchers. Information was analysed in relation to ecotype (insular, montane, barren-ground, and woodland/forest), population status (increasing, stable, decreasing), herd size, human impact, and temporal change in number. The data support the conclusions (1) that each ecotype is exposed to different ecological c...

  11. Identification and Selection for Salt Tolerance in Alfalfa (Medicago sativa L. Ecotypes via Physiological Traits

    Directory of Open Access Journals (Sweden)

    Hassan MONIRIFAR

    2009-12-01

    Full Text Available Salt stress is a serious environmental problem throughout the world which may be partially relieved by breeding cultivars that can tolerate salt stress. Plant breeding may provide a relatively cost effective short-term solution to the salinity problem by producing cultivars able to remain productive at low to moderate levels of salinity. Five alfalfa cultivars, �Seyah-Roud�, �Ahar-Hourand�, �Oskou�, �Malekan� and �Sefida-Khan� were assessed for salt tolerance at mature plant stage. A greenhouse screening system was used to evaluate individual alfalfa plants grown in perlit medium, and irrigated with water containing different amounts of NaCl. Three salt levels were achieved by adding 0, 100 and 200 mM NaCl to Hoagland nutrient solution, respectively. Forage yield, sodium and potassium contents and K/Na ratio was determined. Also, leaf samples were analyzed for proline and chlorophyll contents. The ecotypes Seyha-Roud and �Sefida-Khan� had comparatively less sodium contents than �Oskou�, �Ahar-Hourand� and �Malekan� ecotypes, also potassium content increased under saline condition. Forage yield of different alfalfa ecotypes was significantly influenced by the salinity. The ecotypes �Malekan�, Ahar- Hourand and �Oskou� were successful in maintaining forage yield under salinity stress. Sodium contents increased due to salinity in all alfalfa ecotypes however ecotypes �Ahar-Hourand� and �Malekan� maintained the highest leaf Na concentration. They showed higher content of K than other ecotypes but had lower K/Na ratio. It was concluded that, two ecotypes �Malekan� and �Ahar-Hourand� were better.

  12. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers.

    Science.gov (United States)

    Sanarana, Yandisiwe; Visser, Carina; Bosman, Lydia; Nephawe, Khathutshelo; Maiwashe, Azwihangwisi; van Marle-Köster, Este

    2016-02-01

    The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

  13. Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka

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    B. H. Rudresh

    2015-08-01

    Full Text Available Aim: The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions. Materials and Methods: 210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel. Results: The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node. Conclusion: Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in

  14. Brood development of different carniolan bee ecotypes (Apis mellifera carnica Pollmann, 1879

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    Dragan Bubalo

    2002-09-01

    Full Text Available Brood development of different carniolan honeybee ecotypes (Apis mellifera carnica Pollmann, 1879 was carried out in condition of pannonian and alpine climate. The colonies on both experimental apiaries were divided in the three groups, each 12 queens, of alpine (Austria, subalpine (Slovenia and pannonian (Croatia ecotype. The experiment was designed to monitor development of brood, the total number of laid cells and colony strength. In particular part of the year, experimental ecotypes shown significant differences in area of unsealed and sealed brood in both climate. In the whole season there was not established significant difference between ecotypes regarding to development of drone brood. In pannonian climate, in comparison to alpine climate, the number of laid eggs was higher for all ecotypes. Pannonian ecotype did not recognize all food sources in the new environment, which could be seen in the lack of pollen in the colonies at the alpine climate during last two measuriments. The lack of pollen affected the weakening of the colonies laiter in the season.

  15. COMPARISON OF SLAUGHTER, CARCASS VALUES OF SUDAN GOAT ECOTYPES FED DIFFERENT LEVELS OF ENERGY/PROTEIN

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    A.A. TAMEEM ELDAR

    2012-07-01

    Full Text Available This experiment aimed to assess the slaughter and carcass values of different Sudan goat ecotypes (Nubian, Desert and Swiss Nubian fed different levels of energy/protein. Nine male goat kids (2-3 months and average weight 9.23 kg of either ecotypes were used in a 3x3x3 arrangement, fed three experimental diets A (control, B and C, with varying energy: protein 1:0.14, 1:0.16 and 1:0.18 respectively. The study showed that Nubian goats possessed heavier slaughter weight; empty body weight, warm and cold carcass weight than the Desert and Swiss Nubian goats in the ration B and C. Dressing percentage on both basis (slaughter weight and empty body weight of Nubian were higher for ration B and C. Warm carcass weights of all goat ecotypes increased directly with energy: protein ratio. Highest weight of leg, loin, rack and neck and shoulder were recorded by Nubian goats for ration B and C. It was concluded that, all ecotype kids respond well to increasing energy protein levels. According to the results obtained local goat ecotypes, mainly Nubian goats, responded well to improved nutrition, therefore results obtained can be applied for the local goat ecotypes studied to encourage goat meat consumption and exportation.

  16. Comparison of seasonal habitat selection between threatened woodland caribou ecotypes in central British Columbia

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    Elena S. Jones

    2007-04-01

    Full Text Available Woodland caribou (Rangifer tarandus caribou in British Columbia have been classified into ecotypes based on differences in use of habitat in winter. Although recovery planning focuses on ecotypes, habitat use and selection varies within ecotypes. Our objectives were to compare habitat use and selection among previously identified woodland caribou herds at the transition zone between northern (Moberly, Quintette, and Kennedy herds and mountain (Parsnip herd ecotypes in central British Columbia. We developed selection models for each herd in spring, calving, summer/fall, early and late winter. Topographic models best predicted selection by most herds in most seasons, but importance of vegetation-cover was highlighted by disproportionate use of specific vegetation-cover types by all caribou herds (e.g., in early winter, 75% of Kennedy locations were in pine-leading stands, 84% of Parsnip locations were in fir and fir-leading stands, and 87 and 96% of locations were in alpine for the Moberly and Quintette herds, respectively. Using a combination of GPS and VHF radio-collar locations, we documented some spatial overlap among herds within the year, but use of vegetation-cover types and selection of elevations, aspects, and vegetation-cover types differed among herds and within ecotypes in all seasons. Habitat use and selection were most similar between the two northern-ecotype herds residing on the eastern side of the Rocky Mountains. This research indicates that habitat use and selection by caribou herds in all seasons is more variable than ecotype classifications suggest and demonstrates the value of undertaking herd-specific mapping of critical habitat for woodland caribou.

  17. Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population.

    Directory of Open Access Journals (Sweden)

    Caroline B Turner

    Full Text Available In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+ and non-consuming (Cit- ecotypes, with Cit-bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit-lineage went extinct; cells with the Cit-phenotype dropped to levels below detection, and the Cit-clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit-ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit-type did not go extinct in any of these replays, and Cit-cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit-ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit-ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit-ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.

  18. Metabolic and biological profile of autochthonous Vitis vinifera L. ecotypes.

    Science.gov (United States)

    Impei, Stefania; Gismondi, Angelo; Canuti, Lorena; Canini, Antonella

    2015-05-01

    Vitis vinifera L. is a plant species rich in phenolic compounds that are usually associated with the health benefits of wine and grape consumption in the diet. Anthocyanins, catechins, flavonol, phenolic acids and stilbenes are key molecular constituents of the Vitis berries, affecting the quality of grape products. The purpose of this work was to identify the metabolic profiles of 37 genetically certified V. vinifera Latial accessions. In particular, qualitative and quantitative analyses of specific secondary metabolites and total phenolic and tannin contents were performed by LC-MS and spectrophotometric analysis. In addition, since plant molecules are well-known for their free radical scavenging properties, the antioxidant effects of the sample extracts were evaluated through two different antiradical assays: DPPH and FRAP tests. Finally, a preliminary screening of the antiproliferative activity of each specimen on HCT-116 human colorectal cancer cells was conducted. All the results showed a great variety and amount of phenolic compounds in all accessions; moreover, we observed a significant correlation in the extracts between the metabolite concentration and bioactivity. Besides, some samples presented extraordinary biological effects, such as reduction of tumor cell growth not associated with cytotoxicity, supporting their use as possible future adjuvants for cancer therapy. In conclusion, the present research increased the scientific knowledge about Italian autochthonous vine ecotypes in order to valorize them and support their reintroduction in the local economic system.

  19. Divergence is focused on few genomic regions early in speciation: incipient speciation of sunflower ecotypes.

    Science.gov (United States)

    Andrew, Rose L; Rieseberg, Loren H

    2013-09-01

    Early in speciation, as populations undergo the transition from local adaptation to incipient species, is when a number of transient, but potentially important, processes appear to be most easily detected. These include signatures of selective sweeps that can point to asymmetry in selection between habitats, divergence hitchhiking, and associations of adaptive genes with environments. In a genomic comparison of ecotypes of the prairie sunflower, Helianthus petiolaris, occurring at Great Sand Dunes National Park and Preserve (Colorado), we found that selective sweeps were mainly restricted to the dune ecotype and that there was variation across the genome in whether proximity to the nondune population constrained or promoted divergence. The major regions of divergence were few and large between ecotypes, in contrast with an interspecific comparison between H. petiolaris and a sympatric congener, Helianthus annuus. In general, the large regions of divergence observed in the ecotypic comparison swamped locus-specific associations with environmental variables. In both comparisons, regions of high divergence occurred in portions of the genetic map with high marker density, probably reflecting regions of low recombination. The difference in genomic distributions of highly divergent regions between ecotypic and interspecific comparisons highlights the value of studies spanning the spectrum of speciation in related taxa.

  20. Evaluation of Fall Planting Dates of Cumin (Cuminum cyminum L. Ecotypes in Mashhad Conditions

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    Z Khorasani

    2012-07-01

    Full Text Available In order to study the effects of fall planting dates on yield and yield components of six cumin (Cuminum cyminum L. ecotypes an experiment was arranged in a randomized complete block design as a split-plot with three replications during 2007-08 growing season at the Agricultural Research Station of Ferdowsi University of Mashhad. Three planting dates (18 Oct. (first, 8 Nov. (second and 29 Dec. (third and six cumin ecotypes (Torbat heydarieh, Khaf, Sabzevar, Ghaen, Ghoochan and RZ19 were allocated to main and sub plots, respectively. Results showed that the effects of planting dates, ecotypes and interaction effects of planting dates and cumin ecotypes were significant for yield components (winter survival percentage, number of umbel per plant, number of seeds per umbel and 1000-seed weight and seed yield and biological yield. There was a reduction on yield components (number of umbel per plant, number of seeds per umbel and 1000-seed weight, seed yield and biological yield due to delay planting date from 18 Oct. to 29 Dec. The highest winter survival percentage was achieved on the third planting date. The highest and lowest amount for all of the traits, were achieved in Ghaen and RZ19 ecotypes, respectively. According to the useful results and for the deployment of cumin fall planting in other locations of province, continuation of this study to recommended.

  1. Uptake, Distribution and Accumulation of Copper in Two Ecotypes of Elsholtzia

    Institute of Scientific and Technical Information of China (English)

    JIANG Li-Ying; YANG Xiao-E; YE Zheng-Qian; SHI Wei-Yong

    2003-01-01

    Two ecotypes of Elsholtzia, Elsholtzia splendens and E. Argyi, are dominant plants growing on Cu and Pb-Zn smelters, respectively. Samples of the two ecotypes and the corresponding soils from fields of a copper mining area and a Pb-Zn mining area of Zhejiang Province, China, were analyzed to investigate Cu or Zn tolerance of these two ecotypes. Effects of nine Cu levels (0, 5, 10, 20, 40, 80, 160, 240 and 320 mg Cu L-1 as CuSO4@SH20) on growth and uptake, translocation and accumulation of Cu in these two ecotypes were examined in a solution culture experiment. The experimental results showed that dry weights (DW) of shoots and roots were depressed, and growth of E. Splendens was less depressed tha n that of E. Argyi when treated with ≥ 5 mg Cu L-1. Concentrations of Cu in shoots of E. Splendens and E. Argyi exceeded 1 000 mg kg-1 DW at ≥ 40 mg Cu L-x. The maximum Cu accumulated in the shoots of Gu-treated E. Splendens and E. Argyi reached 101 and 142μg plant-1. Furthermore, analysis of plant samples from the fields showed that these two ecotypes can tolerant excess heavy metals and produced high dry matter, and E. Splendens can accumulate 11.7 mg Cu plant-1 grown on the Cu smelter. Therefore, E. Splendens and E. Argyi could be good plants for phytoremediation.

  2. Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness.

    Science.gov (United States)

    Katyal, Isha; Chaban, Bonnie; Hill, Janet E

    2016-11-01

    Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.

  3. Pb uptake, accumulation, subcellular distribution in a Pb-accumulating ecotype of Sedum alfredii (Hance)

    Institute of Scientific and Technical Information of China (English)

    何冰; 杨肖娥; 倪吾钟; 魏幼璋; 叶海波

    2003-01-01

    Lead concentrations in roots, stems and leaves of accumulating and non-accumulating ecotypes of Sedum alfredii (Hance) were studied through a hydroponic experiment with different Pb concentrations sup-plied as Pb( NO3 )2 .Lead concentrations in leaves and stems of the accumulating ecotype were 4-9 times and 3-5 times those of the non-accumulating ecotype, and Pb-accumulated amounts in stems and leaves of theaccumulating ecotype were 4-9 times and 8-1l times higher than those of the non-accumulating ecotype,respectively. The results indicated that the accumulating ecotype had better ability to transport Pb from roots toshoots. The subeellular distributions of Pb in the root, stem and leaf tissues were studied using sucrose differ-ential centrifugation. Approximately 50% of Pb contents was found to be associated with the cell wall fractionin stems of the accumulating ecotype and the percentage increased to 80% both in roots and leaves, no matter when plants were grown with different levels of Pb. The results indicated that the distribution of Pb on cell walls of the accumulating ecotype could mainly account for the high tolerance to Pb.

  4. Agronomic, metabolomic and lipidomic characterisation of Sicilian Origanum vulgare (L.) ecotypes.

    Science.gov (United States)

    Tuttolomondo, Teresa; Martinelli, Federico; Mariotti, Lorenzo; Leto, Claudio; Maggio, Antonella; La Bella, Salvatore

    2016-01-01

    Although Origanum vulgare (L.) has been deeply analysed at phytochemical level, poor knowledge is available regarding non-volatile compounds such as lipids. The aim of this work was to characterise five wild Sicilian Origanum ecotypes from an agronomic, metabolomic and lipidomic perspective. Serradifalco presented higher dry weight and inflorescences/plant than the others while Favara had a significantly higher number of branches per plant and more extensive flowered stratum. Metabolomic analysis, performed with LC-MS-TOF, allowed a preliminary characterisation of the non-volatile metabolome of the five oregano ecotypes Origanum vulgare ssp. hirtum. Twenty-five metabolites were identified belonging to organic acids, amino acids, lysophosphatidylcholines, carnithines, nucleic bases and lysophosphatidylethanolamines. Lipidomic analysis identified 115 polar plant membrane glycerolipid species. Thirteen of them were differentially present in the two chosen ecotypes. The role of these metabolites in plant physiology from a qualitative and pharmacological point of view was discussed.

  5. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

    DEFF Research Database (Denmark)

    Becraft, Eric D.; Wood, Jason M.; Rusch, Douglas B.;

    2015-01-01

    and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature...

  6. Ultrastructural changes, zinc hyperaccumulation and its relation with antioxidants in two ecotypes of Sedum alfredii Hance.

    Science.gov (United States)

    Jin, Xiao Fen; Yang, Xiao E; Islam, Ejazul; Liu, Dan; Mahmood, Qaisar; Li, Hong; Li, Junying

    2008-11-01

    Zn phytotoxicity and its possible detoxifying responses in two ecotypes of Sedum alfredii Hance, i.e. hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) were investigated. HE grew better with high Zn concentrations of 29.11gkg(-1) DW in shoots when exposed to 500microM Zn2+. Toxicity symptoms caused by Zn in root cells of both ecotypes mainly included plasmolysis, disruption of plasma membranes and increased cell vacuolation. At high supplied Zn concentration, chloroplasts suffered from structural disorganization in both ecotypes. Zn-induced hydrogen peroxide (H2O2) and superoxide radical (O(2)-) productions in leaves were determined by a histochemical method, which revealed that Zn stress may have involved NADPH oxidase, protein phosphatases and intracellular Ca2+ to activate the reactive oxygen species production. Inhibition of glutathione synthesis may have led to increased H2O2 and O(2)- accumulations in leaves of HE. In response to higher Zn concentrations, ascorbic acid significantly increased in both ecotypes and levels of glutathione increased in both leaves and roots of HE and in roots of NHE without any change in the leaves of NHE. The enzymatic activities like those of superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), guaiacol peroxidase (GPX, EC 1.11.1.7), ascorbate peroxidase (APX, EC 1.11.1.11), dehydroascorbate reductase (DHAR, EC 1.8.5.1), and glutathione reductase (GR, EC 1.6.4.2) in leaves of HE were all enhanced at supplied Zn concentration of 500microM, which may account for its better growth.

  7. Phytostabilization potential of two ecotypes of Vetiveria zizanioides in cadmium-contaminated soils: greenhouse and field experiments.

    Science.gov (United States)

    Phusantisampan, Theerawut; Meeinkuirt, Weeradej; Saengwilai, Patompong; Pichtel, John; Chaiyarat, Rattanawat

    2016-10-01

    Soil contamination by cadmium (Cd) poses a serious environmental and public health concern. Phytoremediation, i.e., the use of plants to remove contaminants from soil, has been proposed for treatment of Cd-contaminated ecosystems. In this study, we demonstrated the potential of Vetiveria zizanioides, commonly known as vetiver, to serve as an effective phytoremediation agent. Two ecotypes, i.e., India and Sri Lanka, were grown in greenhouse pots and in the field. Soils were amended with cow manure, pig manure, bat manure, and an organic fertilizer. Among all amendments, pig manure performed best in both greenhouse and field studies in terms of increasing total V. zizanioides biomass production in both ecotypes. In both greenhouse and in the field, tissue of the Sri Lanka ecotype had higher Cd concentrations than did the India ecotype. In the greenhouse, the presence of Cd did not affect total biomass production or root dry weight. The Sri Lanka ecotype had 2.7 times greater adventitious root numbers and 3.6 times greater Cd accumulation in roots than did the India ecotype. In the field study, the Sri Lanka ecotype offers potential as an excluder species, as it accumulated Cd primarily in roots, with translocation factor values 1 for all experiments except for the pig manure amendment. In addition, the highest Cd concentration in the Sri Lanka ecotype root (71.3 mg kg(-1)) was consistent with highest Cd uptake (10.4 mg plant(-1)) in the cow manure treatment. The India ecotype contained lower root Cd concentrations, and Cd accumulation was slightly higher in shoots compared to roots, with translocation factor (TF) values >1. The India ecotype was therefore not considered as an excluder in the Cd-contaminated soil. With the use of excluder species combined with application of organic amendments, soil contamination by Cd may be treated by alternative remediation methods such as phytostabilization.

  8. Cross-cultural and cross-ecotype production of a killer whale `excitement' call suggests universality

    Science.gov (United States)

    Rehn, Nicola; Filatova, Olga A.; Durban, John W.; Foote, Andrew D.

    2011-01-01

    Facial and vocal expressions of emotion have been found in a number of social mammal species and are thought to have evolved to aid social communication. There has been much debate about whether such signals are culturally inherited or are truly biologically innate. Evidence for the innateness of such signals can come from cross-cultural studies. Previous studies have identified a vocalisation (the V4 or `excitement' call) associated with high arousal behaviours in a population of killer whales in British Columbia, Canada. In this study, we compared recordings from three different socially and reproductively isolated ecotypes of killer whales, including five vocal clans of one ecotype, each clan having discrete culturally transmitted vocal traditions. The V4 call was found in recordings of each ecotype and each vocal clan. Nine independent observers reproduced our classification of the V4 call from each population with high inter-observer agreement. Our results suggest the V4 call may be universal in Pacific killer whale populations and that transmission of this call is independent of cultural tradition or ecotype. We argue that such universality is more consistent with an innate vocalisation than one acquired through social learning and may be linked to its apparent function of motivational expression.

  9. Ecotypic differentiation in thermal traits in the tropical to warm-temperate green macrophyte Valonia utricularis

    NARCIS (Netherlands)

    Eggert, A.; Burger, E.M.; Breeman, Arno

    2003-01-01

    Differentiation of thermal traits (i.e. growth, survival and reproduction) was studied in the green macrophyte Valonia utricularis (Roth) C. Agardh, which has a world-wide tropical to warm-temperate distribution. Ecotypic differentiation between northeast Atlantic/Mediterranean and Indo-west Pacific

  10. Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift.

    Science.gov (United States)

    Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

    2014-11-01

    The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift.

  11. Hybrid Sterility over Tens of Meters Between Ecotypes Adapted to Serpentine and Non-Serpentine Soils

    Science.gov (United States)

    Leonie Moyle; Levine Mia; Stanton Maureen; Jessica Wright

    2012-01-01

    The development of hybrid sterility is an important step in the process of speciation, however the role of adaptive evolution in triggering these postzygotic barriers is poorly understood. We show that, in the California endemic plant Collinsia sparsiflora ecotypic adaptation to two distinct soil types is associated with the expression of...

  12. Mixing of porpoise ecotypes in southwestern UK waters revealed by genetic profiling.

    Science.gov (United States)

    Fontaine, Michaël C; Thatcher, Oliver; Ray, Nicolas; Piry, Sylvain; Brownlow, Andrew; Davison, Nicholas J; Jepson, Paul; Deaville, Rob; Goodman, Simon J

    2017-03-01

    Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body sizes compared to those of other UK areas. Southwestern UK porpoises showed admixed ancestry between southern and northern ecotypes with a contact zone extending from the northern Bay of Biscay to the Celtic Sea and Channel. Around the UK, ancestry blends from one genetic group to the other along a southwest--northeast axis, correlating with body size variation, consistent with previously reported morphological differences between the two ecotypes. We also detected isolation by distance among juveniles but not in adults, suggesting that stranded juveniles display reduced intergenerational dispersal. The fine-scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.

  13. Ecotypes as a concept for exploring responses to climate change in fish assemblage

    NARCIS (Netherlands)

    Engelhard, G.H.; Ellis, J.R.; Payne, M.R.; Hofstede, ter R.; Pinnegar, J.K.

    2011-01-01

    How do species-rich fish assemblages respond to climate change or to other anthropogenic or environmental drivers? To explore this, a categorization concept is presented whereby species are assigned with respect to six ecotype classifications, according to biogeography, horizontal and vertical habit

  14. Photosynthetic pigments and stomatal conductance in ecotypes of copoazu (Theobroma grandi orum Willd. Ex. Spreng K. Schum..

    Directory of Open Access Journals (Sweden)

    Juan Carlos Suárez-Salazar

    2016-12-01

    Full Text Available The objective of this work was to evaluate the variability of photosynthetic pigment content and daily stomatal conductance was evaluated in relation to environmental variables in Copoazú (Theobroma grandi orum ecotypes. The ecotypes used were part of the germoplasm bank of the University of the Amazon (Colombia. The study was carried out during the year 2015. Four leaves of the average stratum of four plants were collected for each ecotype, to extract and read at different levels of absorbance and determine the content of photosynthetic pigments. During the hours of 04:00 a.m. to 6:00 p.m., the stomatal conductance (gs was monitored for environmental variables (relative humidity, air temperature, radiation and vapor pressure de cit (VPD. An analysis of variance was made using the Tukey test, correlations and regressions were made between gs and environmental variables. The contents of chlorophyll a, b, total and carotenoids among ecotypes were different (P<0.0001, the ecotype UA-31 presented the highest values, contrasting with the ecotype UA-37. Concerning gs, the interaction ecotype*hour showed signi cant differences (P<0.0001 .The ecotypes that presented the highest values of gs were UA-67 and UA-039, (P<0.0001, radiation (-0.91, P<0.0001 and DPV (-0.94; P<0.0001 0.0001.The results suggest that ecotypes UA-039 and UA-31 were the most suitable in terms of gaseous exchange and content of photosynthetic pigments.

  15. Phenotypic plasticity of sun and shade ecotypes of Stellaria longipes in response to light quality signaling, gibberellins and auxin.

    Science.gov (United States)

    Kurepin, Leonid V; Pharis, Richard P; Neil Emery, R J; Reid, David M; Chinnappa, C C

    2015-09-01

    Stellaria longipes plant communities (ecotypes) occur in several environmentally distinct habitats along the eastern slopes of southern Alberta's Rocky Mountains. One ecotype occurs in a prairie habitat at ∼1000 m elevation where Stellaria plants grow in an environment in which the light is filtered by taller neighbouring vegetation, i.e. sunlight with a low red to far-red (R/FR) ratio. This ecotype exhibits a high degree of phenotypic plasticity by increasing stem elongation in response to the low R/FR ratio light signal. Another Stellaria ecotype occurs nearby at ∼2400 m elevation in a much cooler alpine habitat, one where plants rarely experience low R/FR ratio shade light. Stem elongation of plants is largely regulated by gibberellins (GAs) and auxin, indole-3-acetic acid (IAA). Shoots of the prairie ecotype plants show increased IAA levels under low R/FR ratio light and they also increase their stem growth in response to applied IAA. The alpine ecotype plants show neither response. Plants from both ecotypes produce high levels of growth-active GA1 under low R/FR ratio light, though they differ appreciably in their catabolism of GA1. The alpine ecotype plants exhibit very high levels of GA8, the inactive product of GA1 metabolism, under both normal and low R/FR ratio light. Alpine origin plants may de-activate GA1 by conversion to GA8 via a constitutively high level of expression of the GA2ox gene, thereby maintaining their dwarf phenotype and exhibiting a reduced phenotypic plasticity in terms of shoot elongation. In contrast, prairie plants exhibit a high degree of phenotypic plasticity, using low R/FR ratio light-mediated changes in GA and IAA concentrations to increase shoot elongation, thereby accessing direct sunlight to optimize photosynthesis. There thus appear to be complex adaptation strategies for the two ecotypes, ones which involve modifications in the homeostasis of endogenous hormones.

  16. Adaptive responses reveal contemporary and future ecotypes in a desert shrub.

    Science.gov (United States)

    Richardson, Bryce A; Kitchen, Stanley G; Pendleton, Rosemary L; Pendleton, Burton K; Germino, Matthew J; Rehfeldt, Gerald E; Meyer, Susan E

    2014-03-01

    Interacting threats to ecosystem function, including climate change, wildfire, and invasive species necessitate native plant restoration in desert ecosystems. However, native plant restoration efforts often remain unguided by ecological genetic information. Given that many ecosystems are in flux from climate change, restoration plans need to account for both contemporary and future climates when choosing seed sources. In this study we analyze vegetative responses, including mortality, growth, and carbon isotope ratios in two blackbrush (Coleogyne ramosissima) common gardens that included 26 populations from a range-wide collection. This shrub occupies ecotones between the warm and cold deserts of Mojave and Colorado Plateau ecoregions in western North America. The variation observed in the vegetative responses of blackbrush populations was principally explained by grouping populations by ecoregions and by regression with site-specific climate variables. Aridity weighted by winter minimum temperatures best explained vegetative responses; Colorado Plateau sites were usually colder and drier than Mojave sites. The relationship between climate and vegetative response was mapped within the boundaries of the species-climate space projected for the contemporary climate and for the decade surrounding 2060. The mapped ecological genetic pattern showed that genetic variation could be classified into cool-adapted and warm-adapted ecotypes, with populations often separated by steep dines. These transitions are predicted to occur in both the Mojave Desert and Colorado Plateau ecoregions. While under contemporary conditions the warm-adapted ecotype occupies the majority of climate space, climate projections predict that the cool-adapted ecotype could prevail as the dominant ecotype as the climate space of blackbrush expands into higher elevations and latitudes. This study provides the framework for delineating climate change-responsive seed transfer guidelines, which are needed

  17. Application of otolith shape analysis in identifying different ecotypes of Coilia ectenes in the Yangtze Basin, China

    Digital Repository Service at National Institute of Oceanography (India)

    Radhakrishnan, K.V.; Li, Y.; Jayalakshmy, K.V.; Liu, M.; Murphy, B.R.; Xie, S.

    As the three ecotypes of C. ectenes are prone to intermixing along Yangtze, 84 identifying an efficient methodology for their distinction is imperative. In several cases of 85 recent morphological and genetic studies, controversy arose... 3.2. Shape visualization 190 191 The average shape of the otoliths showed distinct differences among the three 192 ecotypes (Fig. 4). There was a well-developed antirostrum for both the anadromous and 193 the land...

  18. Deep sequencing approach for investigating infectious agents causing fever.

    Science.gov (United States)

    Susilawati, T N; Jex, A R; Cantacessi, C; Pearson, M; Navarro, S; Susianto, A; Loukas, A C; McBride, W J H

    2016-07-01

    Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.

  19. Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study

    Science.gov (United States)

    Boutin, Sébastien; Hagenfeld, Daniel; Zimmermann, Heiko; El Sayed, Nihad; Höpker, Tanja; Greiser, Halina K.; Becher, Heiko; Kim, Ti-Sun; Dalpke, Alexander H.

    2017-01-01

    Periodontitis is characterized by chronic inflammation associated with alteration of the oral microbiota. In contrast to previous microbiome studies focusing a priori on comparison between extreme phenotypes, our study analyzed a random sample of 85 people. The aim of this study was to link microbial differences to disease’s prevalence and severity. Using next generation sequencing of 16S rRNA amplicons and cluster analysis, we observed that the population can be divided into two major ecotypes: One mainly contained periodontal healthy/mild periodontitis individuals whereas the second ecotype showed a heterogeneous microbial distribution and clustered into three distinct sub-ecotypes. Those sub-ecotypes differed with respect to the frequency of diseased patients and displayed a gradual change in distinct subgingival microbiota that goes along with clinical disease symptoms. In ecotype 2, the subgroup with no clinical signs of disease was linked to an increase of F. nucleatum vincentii but also several other species, while only in “end-stage” dysbiosis classical red complex bacteria gained overweight. Therefore, the microbial disease ecotypes observed in our population can lead to an establishment of an early microbial risk profile for clinically healthy patients. PMID:28298910

  20. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    DEFF Research Database (Denmark)

    Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon

    2013-01-01

    BACKGROUND: Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking...... using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p majority of the transcripts (75%) showed ecotype specific expression pattern. By using sequence data...... available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about...

  1. Characterization of starch from two ecotypes of andean achira roots (Canna edulis).

    Science.gov (United States)

    Cisneros, Fausto H; Zevillanos, Roberto; Cisneros-Zevallos, Luis

    2009-08-26

    Starches from two ecotypes of achira roots (Canna edulis Ker-Gawler) were characterized and compared to commercial potato and corn starches. This included scanning electron microscopy (SEM) of starch granules and amylose content determination of starch. Starch solutions or gels were tested by rotational viscometry, Rapid Visco Analyzer (RVA), and texture analysis. Some starch samples were subjected to various treatments: pH reduction, autoclaving at high temperature, and high shear before testing by rotational viscometry. Achira starch showed some unusual properties, such as very large oblong granules (approximately 45-52 microm major axis and approximately 33-34 microm minor axis) and relatively high amylose content (approximately 33-39%). The San Gaban achira ecotype formed high-consistency gels upon cooling, both in RVA study (5% starch) and in texture analysis (8% starch), compared to other starch gels and also exhibited higher thermal resistance to viscosity breakdown.

  2. Ecotypes as a concept for exploring responses to climate change in fish assemblages

    DEFF Research Database (Denmark)

    Engelhard, George H.; Ellis, Jim R.; Payne, Mark;

    2011-01-01

    How do species-rich fish assemblages respond to climate change or to other anthropogenic or environmental drivers? To explore this, a categorization concept is presented whereby species are assigned with respect to six ecotype classifications, according to biogeography, horizontal and vertical...... habitat preference, trophic guild, trophic level, or body size. These classification schemes are termed ecotypology, and the system is applied to fish in the North Sea using International Bottom Trawl Survey data. Over the period 1977–2008, there were changes in the North Sea fish community that can...... or combinations of them. The post-1989 warm biological regime appears to have favoured pelagic species more than demersal species. These community-level patterns agree with the expected responses of ecotypes to climate change and also with anticipated vulnerability to fishing pressure....

  3. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    DEFF Research Database (Denmark)

    Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon;

    2013-01-01

    ontology (GO) categories were identified to delineate natural variation of cold stress regulated differential gene expression in the model plant A. thaliana. The predicted regulatory network model was able to identify new ecotype specific transcription factors and their regulatory interactions, which might...... using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p expression pattern. By using sequence data...

  4. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae.

    Directory of Open Access Journals (Sweden)

    Abigail J Moore

    Full Text Available Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae. We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.

  5. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae).

    Science.gov (United States)

    Moore, Abigail J; Moore, William L; Baldwin, Bruce G

    2014-01-01

    Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.

  6. Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana.

    Science.gov (United States)

    Kissen, R; Hyldbakk, E; Wang, C-W V; Sørmo, C G; Rossiter, J T; Bones, A M

    2012-03-01

    Epithiospecifier protein (ESP) is responsible for diverting glucosinolate hydrolysis from the generation of isothiocyanates to that of epithionitriles or nitriles, and thereby negatively affects the ability of the plant to defend itself against certain insects. Despite this important role of ESP, little is known about its expression in plant tissues and the regulation thereof. We therefore investigated ESP expression by qPCR and Western blot in different organs during the growth cycle of the two Arabidopsis thaliana ecotypes Col-0 and Mt-0. Besides the fact that ESP transcript and protein levels were revealed to be much higher in Mt-0 than in Col-0 in all cases, our qPCR results also indicated that ESP expression is regulated differently in the two A. thaliana ecotypes. No ESP protein was detected by Western blot in any organ or developmental stage for Col-0. During the assays an alternative splice variant of ESP was identified in Col-0, but not Mt-0, leading to a mis-spliced transcript which could explain the low expression levels of ESP in the former ecotype. Analysis of genomic sequences containing the ESP splice sites, of ESP protein level and ESP activity from seven A. thaliana ecotypes showed a positive correlation between the presence of a non-canonical 5' splice site for ESP and the absence of detectable ESP protein levels and ESP activity. When analysing the expression of both transcript variants in Col-0 after treatment with methyl jasmonate, a condition known to "induce ESP", it was indeed the alternative splice variant that was preferentially induced.

  7. Plant response to climate change varies with topography, interactions with neighbors, and ecotype.

    Science.gov (United States)

    Liancourt, Pierre; Spence, Laura A; Song, Daniel S; Lkhagva, Ariuntsetseg; Sharkhuu, Anarmaa; Boldgiv, Bazartseren; Helliker, Brent R; Petraitis, Peter S; Casper, Brenda B

    2013-02-01

    Predicting the future of any given species represents an unprecedented challenge in light of the many environmental and biological factors that affect organismal performance and that also interact with drivers of global change. In a three-year experiment set in the Mongolian steppe, we examined the response of the common grass Festuca lenensis to manipulated temperature and water while controlling for topographic variation, plant-plant interactions, and ecotypic differentiation. Plant survival and growth responses to a warmer, drier climate varied within the landscape. Response to simulated increased precipitation occurred only in the absence of neighbors, demonstrating that plant-plant interactions can supersede the effects of climate change. F. lenensis also showed evidence of local adaptation in populations that were only 300 m apart. Individuals from the steep and dry upper slope showed a higher stress/drought tolerance, whereas those from the more productive lower slope showed a higher biomass production and a greater ability to cope with competition. Moreover, the response of this species to increased precipitation was ecotype specific, with water addition benefiting only the least stress-tolerant ecotype from the lower slope origin. This multifaceted approach illustrates the importance of placing climate change experiments within a realistic ecological and evolutionary framework. Existing sources of variation impacting plant performance may buffer or obscure climate change effects.

  8. Scaling-up permafrost thermal measurements in western Alaska using an ecotype approach

    Science.gov (United States)

    Cable, William L.; Romanovsky, Vladimir E.; Torre Jorgenson, M.

    2016-10-01

    Permafrost temperatures are increasing in Alaska due to climate change and in some cases permafrost is thawing and degrading. In areas where degradation has already occurred the effects can be dramatic, resulting in changing ecosystems, carbon release, and damage to infrastructure. However, in many areas we lack baseline data, such as subsurface temperatures, needed to assess future changes and potential risk areas. Besides climate, the physical properties of the vegetation cover and subsurface material have a major influence on the thermal state of permafrost. These properties are often directly related to the type of ecosystem overlaying permafrost. In this paper we demonstrate that classifying the landscape into general ecotypes is an effective way to scale up permafrost thermal data collected from field monitoring sites. Additionally, we find that within some ecotypes the absence of a moss layer is indicative of the absence of near-surface permafrost. As a proof of concept, we used the ground temperature data collected from the field sites to recode an ecotype land cover map into a map of mean annual ground temperature ranges at 1 m depth based on analysis and clustering of observed thermal regimes. The map should be useful for decision making with respect to land use and understanding how the landscape might change under future climate scenarios.

  9. Diversity of Ralstonia solanacearum in French Guiana expands knowledge of the "emerging ecotype".

    Science.gov (United States)

    Deberdt, P; Guyot, J; Coranson-Beaudu, R; Launay, J; Noreskal, M; Rivière, P; Vigné, F; Laplace, D; Lebreton, L; Wicker, E

    2014-06-01

    Although bacterial wilt remains a major plant disease throughout South America and the Caribbean, the diversity of prevalent Ralstonia solanacearum populations is largely unknown. The genetic and phenotypic diversity of R. solanacearum strains in French Guiana was assessed using diagnostic polymerase chain reactions and sequence-based (egl and mutS) genotyping on a 239-strain collection sampled on the families Solanaceae and Cucurbitaceae, revealing an unexpectedly high diversity. Strains were distributed within phylotypes I (46.9%), IIA (26.8%), and IIB (26.3%), with one new endoglucanase sequence type (egl ST) found within each group. Phylotype IIB strains consisted mostly (97%) of strains with the emerging ecotype (IIB/sequevar 4NPB). Host range of IIB/4NPB strains from French Guiana matched the original emerging reference strain from Martinique. They were virulent on cucumber; virulent and highly aggressive on tomato, including the resistant reference Hawaii 7996; and only controlled by eggplant SM6 and Surya accessions. The emerging ecotype IIB/4NPB is fully established in French Guiana in both cultivated fields and uncultivated forest, rendering the hypothesis of introduction via ornamental or banana cuttings unlikely. Thus, this ecotype may have originated from the Amazonian region and spread throughout the Caribbean region.

  10. Effect of Seawater Stress on Physiological and Biochemical Responses of Five Jerusalem Artichoke Ecotypes

    Institute of Scientific and Technical Information of China (English)

    LONG Xiao-Hua; CHI Jin-He; LIU Ling; LI Qing; LIU Zhao-Pu

    2009-01-01

    Three treatments consisting of 0%,15%,and 30% seawater were investigated to analyse the ecotypic variabilities among five populations of Jerusalem artichoke (Helianthus tuberosus) regarding their responses to seawater stress under a hydroponic culture system.Analyses were done 2,4,and 6 days after treatments.The 15% and 30% seawater treatments reduced the growth rates of roots and shoots of H.tuberosus populations.The activities of superoxide dismutase,peroxidase,and catalase majored in the leaves were stimulated under the seawater stress.The electrolyte leakage and malondialdehyde contents of the leaves were also stimulated owing to seawater stress.The contents of proline and solublesugars in the leaves increased significantly with increasing seawater concentrations.The concentrations of Na+,K+,and Cl-in the aerial parts and roots increased with an increase in the seawater concentration throughout the experimental period.There were ccotypic differences among the five populations of H.tuberosus as evidenced by the analyses of the above items in both aerial parts and roots under seawater treatment.The magnitude of the ecotypic variance components indicated that a substantial proportion of the total variation for these physiological and biochemical responses were owing to ecotype,indicating the possibility of improvement through hybridization and selection.

  11. Evaluating Ecotypes as a means of Scaling-up Permafrost Thermal Measurements in Western Alaska.

    Science.gov (United States)

    Cable, William; Romanovsky, Vladimir

    2015-04-01

    In many regions, permafrost temperatures are increasing due to climate change and in some cases permafrost is thawing and degrading. In areas where degradation has already occurred the effects can be dramatic, resulting in changing ecosystems, carbon release, and damage to infrastructure. Yet in many areas we lack baseline data, such as subsurface temperatures, needed to assess future changes and potential risk areas. Besides climate, the physical properties of the vegetation cover and subsurface material have a major influence on the thermal state of permafrost. These properties are often directly related to the type of ecosystem overlaying permafrost. Thus, classifying the landscape into general ecotypes might be an effective way to scale up permafrost thermal data. To evaluate using ecotypes as a way of scaling-up permafrost thermal data within a region we selected an area in Western Alaska, the Selawik National Wildlife Refuge, which is on the boundary between continuous and discontinuous permafrost. This region was selected because previously an ecological land classification had been conducted and a very high-resolution ecotype map was generated. Using this information we selected 18 spatially distributed sites covering the most abundant ecotypes, where we are collecting low vertical resolution soil temperature data to a depth of 1.5 meters at most sites. At three additional core sites, we are collecting air temperature, snow depth, and high vertical resolution soil temperature to a depth of 3 meters. The sites were installed in the summers of 2011 and 2012; consequently, we have at least two years of data from all sites. Mean monthly and mean annual air temperature and snow depth for all three core sites are similar within the 2012-2014 period. Additionally, the average air temperature and snow depth from our three cores sites compares well with that of a nearby meteorological station for which long-term data is available. During the study period snow depth

  12. Moderate Drought Stress Induces Increased Foliar Dimethylsulphoniopropionate (DMSP Concentration and Isoprene Emission in Two Contrasting Ecotypes of Arundo donax

    Directory of Open Access Journals (Sweden)

    Matthew Haworth

    2017-06-01

    Full Text Available The function of dimethylsulphoniopropionate (DMSP in plants is unclear. It has been proposed as an antioxidant, osmolyte and overflow for excess energy under stress conditions. The formation of DMSP is part of the methionine (MET pathway that is involved in plant stress responses. We used a new analytical approach to accurately quantify the changes in DMSP concentration that occurred in two ecotypes of the biomass crop Arundo donax subject to moderate drought stress under field conditions. The ecotypes of A. donax were from a hot semi-arid habitat in Morocco and a warm-humid environment in Central Italy. The Moroccan ecotype showed more pronounced reductions in photosynthesis, stomatal conductance and photochemical electron transport than the Italian ecotype. An increase in isoprene emission occurred in both ecotypes alongside enhanced foliar concentrations of DMSP, indicative of a protective function of these two metabolites in the amelioration of the deleterious effects of excess energy and oxidative stress. This is consistent with the modification of carbon within the methyl-erythritol and MET pathways responsible for increased synthesis of isoprene and DMSP under moderate drought. The results of this study indicate that DMSP is an important adaptive component of the stress response regulated via the MET pathway in A. donax. DMSP is likely a multifunctional molecule playing a number of roles in the response of A. donax to reduced water availability.

  13. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact.

    Science.gov (United States)

    Le Moan, A; Gagnaire, P-A; Bonhomme, F

    2016-07-01

    Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.

  14. Ecotype variability in growth and secondary metabolite profile in Moringa oleifera: impact of sulfur and water availability.

    Science.gov (United States)

    Förster, Nadja; Ulrichs, Christian; Schreiner, Monika; Arndt, Nick; Schmidt, Reinhard; Mewis, Inga

    2015-03-25

    Moringa oleifera is widely cultivated in plantations in the tropics and subtropics. Previous cultivation studies with M. oleifera focused primarily only on leaf yield. In the present study, the content of potentially health-promoting secondary metabolites (glucosinolates, phenolic acids, and flavonoids) were also investigated. Six different ecotypes were grown under similar environmental conditions to identify phenotypic differences that can be traced back to the genotype. The ecotypes TOT4880 (origin USA) and TOT7267 (origin India) were identified as having the best growth performance and highest secondary metabolite production, making them an ideal health-promoting food crop. Furthermore, optimal cultivation conditions-exemplarily on sulfur fertilization and water availability-for achieving high leaf and secondary metabolite yields were investigated for M. oleifera. In general, plant biomass and height decreased under water deficiency compared to normal cultivation conditions, whereas the glucosinolate content increased. The effects depended to a great extent on the ecotype.

  15. Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii?

    Science.gov (United States)

    Van der Niet, Timotheüs; Pirie, Michael D; Shuttleworth, Adam; Johnson, Steven D; Midgley, Jeremy J

    2014-01-01

    According to the Grant-Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Grant-Stebbins model. Pollinator observations showed that the most common form of E. plukenetii with intermediate corolla length is pollinated by short-billed Orange-breasted sunbirds. Populations at the northern fringe of the distribution are characterized by long corollas, and are mainly pollinated by long-billed Malachite sunbirds. A population with short corollas in the centre of the range was mainly pollinated by insects, particularly short-tongued noctuid moths. Bird exclusion in this population did not have an effect on fruit set, while insect exclusion reduced fruit set. An analysis of floral scent across the range, using coupled gas chromatography-mass spectrometry, showed that the scent bouquets of flowers from moth-pollinated populations are characterized by a larger number of scent compounds and higher emission rates than those in bird-pollinated populations. This was also reflected in clear separation of moth- and bird-pollinated populations in a two-dimensional phenotype space based on non-metric multidimensional scaling analysis of scent data. Phylogenetic analyses of chloroplast and nuclear DNA sequences strongly supported monophyly of E. plukenetii, but not of all the subspecies. Reconstruction of ancestral character states suggests two shifts from traits associated with short

  16. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    DEFF Research Database (Denmark)

    Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon

    2013-01-01

    BACKGROUND: Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking...... using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p ... be crucial for their local geographic adaptation to cold temperature. Additionally, since the approach presented here is general, it could be adapted to study networks regulating biological process in any biological systems....

  17. Ecotypic variability in the metabolic response of seeds to diurnal hydration-dehydration cycles and its relationship to seed vigor.

    Science.gov (United States)

    Bai, Bing; Sikron, Noga; Gendler, Tanya; Kazachkova, Yana; Barak, Simon; Grafi, Gideon; Khozin-Goldberg, Inna; Fait, Aaron

    2012-01-01

    Seeds in the seed bank experience diurnal cycles of imbibition followed by complete dehydration. These conditions pose a challenge to the regulation of germination. The effect of recurring hydration-dehydration (Hy-Dh) cycles were tested on seeds from four Arabidopsis thaliana accessions [Col-0, Cvi, C24 and Ler]. Diurnal Hy-Dh cycles had a detrimental effect on the germination rate and on the final percentage of germination in Col-0, Cvi and C24 ecotypes, but not in the Ler ecotype, which showed improved vigor following the treatments. Membrane permeability measured by ion conductivity was generally increased following each Hy-Dh cycle and was correlated with changes in the redox status represented by the GSSG/GSH (oxidized/reduced glutathione) ratio. Among the ecotypes, Col-0 seeds displayed the highest membrane permeability, whilst Ler was characterized by the greatest increase in electrical conductivity following Hy-Dh cycles. Following Dh 2 and Dh 3, the respiratory activity of Ler seeds significantly increased, in contrast to the other ecotypes, indicative of a dramatic shift in metabolism. These differences were associated with accession-specific content and patterns of change of (i) cell wall-related laminaribiose and mannose; (ii) fatty acid composition, specifically of the unsaturated oleic acid and α-linoleic acid; and (iii) asparagine, ornithine and the related polyamine putrescine. Furthermore, in the Ler ecotype the content of the tricarboxylic acid (TCA) cycle intermediates fumarate, succinate and malate increased in response to dehydration, in contrast to a decrease in the other three ecotypes. These findings provide a link between seed respiration, energy metabolism, fatty acid β-oxidation, nitrogen mobilization and membrane permeability and the improved germination of Ler seeds following Hy-Dh cycles.

  18. Problems with the claim of ecotype and taxon status of the wolf in the Great Lakes region

    Science.gov (United States)

    Cronin, Matthew A.; Mech, L. David

    2009-01-01

    Koblmuller et al. (2009) analysed molecular genetic data of the wolf in the Great Lakes (GL) region of the USA and concluded that the animal was a unique ecotype of grey wolf and that genetic data supported the population as a discrete wolf taxon. However, some of the literature that the researchers used to support their position actually did not, and additional confusion arises from indefinite use of terminology. Herein, we discuss the problems with designation of a wolf population as a taxon or ecotype without proper definition and assessment of criteria.

  19. Establishment of an Indirect Genetic Transformation Method for Arabidopsis thaliana ecotype Bangladesh

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    Bulbul AHMED

    2011-11-01

    Full Text Available Arabidopsis thaliana is a small flowering plant belonging to the Brassicaceae family, which is adopted as a model plant for genetic research. Agrobacterium tumifaciensmediated transformation method for A. thaliana ecotype Bangladesh was established. Leaf discs of A. thaliana were incubated with A. tumefaciens strain LBA4404 containing chimeric nos. nptII. nos and intron-GUS genes. Following inoculation and co-cultivation, leaf discs were cultured on selection medium containing 50 mg/l kanamycin + 50 mg/l cefotaxime + 1.5 mg/l NAA and kanamycin resistant shoots were induced from the leaf discs after two weeks. Shoot regeneration was achieved after transferring the tissues onto fresh medium of the same combination. Finally, the shoots were rooted on MS medium containing 50 mg/l kanamycin. Incorporation and expression of the transgenes were confirmed by PCR analysis. Using this protocol, transgenic A. thaliana plants can be obtained and indicates that genomic transformation in higher plants is possible through insertion of desired gene. Although Agrobacterium mediated genetic transformation is established for A. thaliana, this study was the conducted to transform A. thaliana ecotype Bangladesh.

  20. Ecotype evolution in Glossina palpalis subspecies, major vectors of sleeping sickness.

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    Thierry De Meeûs

    2015-03-01

    Full Text Available BACKGROUND: The role of environmental factors in driving adaptive trajectories of living organisms is still being debated. This is even more important to understand when dealing with important neglected diseases and their vectors. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we analysed genetic divergence, computed from seven microsatellite loci, of 614 tsetse flies (Glossina palpalis gambiensis and Glossina palpalis palpalis, major vectors of animal and human trypanosomes from 28 sites of West and Central Africa. We found that the two subspecies are so divergent that they deserve the species status. Controlling for geographic and time distances that separate these samples, which have a significant effect, we found that G. p. gambiensis from different landscapes (Niayes of Senegal, savannah and coastal environments were significantly genetically different and thus represent different ecotypes or subspecies. We also confirm that G. p. palpalis from Ivory Coast, Cameroon and DRC are strongly divergent. CONCLUSIONS/SIGNIFICANCE: These results provide an opportunity to examine whether new tsetse fly ecotypes might display different behaviour, dispersal patterns, host preferences and vectorial capacities. This work also urges a revision of taxonomic status of Glossina palpalis subspecies and highlights again how fast ecological divergence can be, especially in host-parasite-vector systems.

  1. Identification of Italian ecotypes of Juglans regia L. by molecular, morphological and biochemical markers

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    Pollegioni P

    2006-01-01

    Full Text Available Juglans regia L. is a multipurpose species important for quality wood and fruit production. In order to contrast the erosion and to properly conserve, manage and revaluate the genetic resources of Italian walnut, possible ecotypes, naturally adapted and still present in Italy have been researched. Leaves and fruits have been sampled in Campania region, localities of Montella, Cervinara, Fisciano, and in Abruzzo region, localities of Sulmona, Pescasseroli, Villetta Barrea, and Civitella Alfedena. The sites are located at different altitudes and climatic conditions. Materials have been collected on a total of 276 plants. Molecular, morphological and preliminary biochemical analyses have been carried out on this germplasm and on material belonging to 80 plants of 4 famous Italian walnut varieties (Bleggiana and Feltrina, North Italy; Sorrento and Malizia, Southern Italy, in order to have a comparison model. 134 ISSR, morphological and biochemical data have shown peculiar characters for Montella and Pescasseroli in comparison with the other accessions. Because of the peculiar environmental conditions of their locations, the effect of the temperature on the fruit development and fatty acid contents, it is possible to suppose that Montella and Pescasseroli are ecotypes which could be utilised as essential fat acid source and as material for afforestation of mountain zones.

  2. Evaluation of the defensive behavior of two honeybee ecotypes using a laboratory test

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    Andere Cecilia

    2002-01-01

    Full Text Available Honeybee defensive behavior is a useful selection criterion, especially in areas with Africanized honeybees (Apis mellifera L. In all genetic improvement programs the selected characters must be measured with precision, and because of this we evaluated a metabolic method for testing honeybee defensive behavior in the laboratory for its usefulness in distinguishing between honeybee ecotypes and selecting honeybees based on their level of defensive responses. Ten honeybee colonies were used, five having been produced by feral queens from a subtropical region supposedly colonized by Africanized honeybees and five by queens from a temperate region apparently colonized by European honeybees. We evaluate honeybee defensive behavior using a metabolic test based on oxygen consumption after stimulation with an alarm pheromone, measuring the time to the first response, time to maximum oxygen consumption, duration of activity, oxygen consumption at first response, maximum oxygen consumption and total oxygen consumption, colonies being ranked according to the values obtained for each variable. Significant (p < 0.05 differences were detected between ecotypes for each variable but for all variables the highest rankings were obtained for colonies of subtropical origin, which had faster and more intense responses. All variables were highly associated (p < 0.05. Total oxygen consumption was the best indicator of metabolic activity for defensive behavior because it combined oxygen consumption and the length of the response. This laboratory method may be useful for evaluating the defensive behavior of honey bees in genetic programs designed to select less defensive bees.

  3. Three-Dimensional Evaluation on Ecotypic Diversity of Traditional Chinese Medicine: A Case Study of Artemisia annua L.

    Science.gov (United States)

    Li, Lin; Josef, Brinckmann A; Liu, Bing; Zheng, Sihao; Huang, Linfang; Chen, Shilin

    2017-01-01

    Artemisinin is the first-line drug for anti-malaria recommended by the World Health Organization (WHO). As the sole natural plant source of artemisinin, ecotypes of Artemisia annua L. vary widely in artemisinin content between nations, and China is the main producing area of A. annua. Here we present a three-dimensional evaluation on ecotypic diversity of A. annua from 12 main producing areas in China using high-performance liquid chromatography coupled with evaporative light scattering detection (HPLC-ELSD) method, DNA barcoding and ecological analyses. The results indicated that A. annua exhibited high ecotypic diversity. A. annua grown in the South of the Qinling Mountains-Huaihe River Line had a high artemisinin content, whereas the northern ones were low. Similar pattern was noted in the genetic diversity. The southern A. annua had high intraspecific variation in contrast to the northern A. annua. In terms of ecological analyses, humidity and sunshine time could be the major limiting ecological factors that affect the accumulation of artemisinin. This is the first reported three-dimensional evaluation integrating chemical, molecular and ecological analyses of the ecotypic diversity of A. annua. The work will facilitate exploring the genetic basis of chemical variations and developing strategies for the breeding and cultivation of high quality A. annua.

  4. Flower stalk segments of Arabidopsis thaliana ecotype Columbia lack the capacity to grow in response to exogenously applied auxin.

    Science.gov (United States)

    Soga, K; Wakabayashi, K; Hoson, T; Kamisaka, S

    2000-12-01

    Exogenously applied IAA stimulated cell elongation of segments excised from flower stalks of Arabidopsis thaliana ecotype Landsberg erecta (Ler) by increasing the cell wall extensibility, but it did not affect that of ecotype Columbia (Col). Treatment with a low pH buffer solution (pH 4.0) or fusicoccin (FC), a reagent activating H(+)-ATPases, significantly increased the cell wall extensibility and promoted elongation growth of flower stalk segments of both ecotypes, indicating that the flower stalk segments of Col possess the capacity to grow under acidic pH conditions. IAA promoted the proton excretion in segments of Ler but not of Col. On the other hand, FC increased the proton excretion in segments of Col as much as that of Ler. These results suggest that IAA activates the plasma membrane H(+)-ATPases in the segments of Ler but not those of Col, while FC activates them in both ecotypes. Flower stalks of Col may lack the mechanisms of activation by IAA of the plasma membrane H(+)-ATPases.

  5. Quick divergence but slow convergence during ecotype formation in lake and stream stickleback pairs of variable age.

    Science.gov (United States)

    Lucek, K; Sivasundar, A; Kristjánsson, B K; Skúlason, S; Seehausen, O

    2014-09-01

    When genetic constraints restrict phenotypic evolution, diversification can be predicted to evolve along so-called lines of least resistance. To address the importance of such constraints and their resolution, studies of parallel phenotypic divergence that differ in their age are valuable. Here, we investigate the parapatric evolution of six lake and stream threespine stickleback systems from Iceland and Switzerland, ranging in age from a few decades to several millennia. Using phenotypic data, we test for parallelism in ecotypic divergence between parapatric lake and stream populations and compare the observed patterns to an ancestral-like marine population. We find strong and consistent phenotypic divergence, both among lake and stream populations and between our freshwater populations and the marine population. Interestingly, ecotypic divergence in low-dimensional phenotype space (i.e. single traits) is rapid and seems to be often completed within 100 years. Yet, the dimensionality of ecotypic divergence was highest in our oldest systems and only there parallel evolution of unrelated ecotypes was strong enough to overwrite phylogenetic contingency. Moreover, the dimensionality of divergence in different systems varies between trait complexes, suggesting different constraints and evolutionary pathways to their resolution among freshwater systems.

  6. Disentangling the role of phenotypic plasticity and genetic divergence in contemporary ecotype formation during a biological invasion.

    Science.gov (United States)

    Lucek, Kay; Sivasundar, Arjun; Seehausen, Ole

    2014-09-01

    The occurrence of contemporary ecotype formation through adaptive divergence of populations within the range of an invasive species typically requires standing genetic variation but can be facilitated by phenotypic plasticity. The relative contributions of both of these to adaptive trait differentiation have rarely been simultaneously quantified in recently diverging vertebrate populations. Here we study a case of intraspecific divergence into distinct lake and stream ecotypes of threespine stickleback that evolved in the past 140 years within the invasive range in Switzerland. Using a controlled laboratory experiment with full-sib crosses and treatments mimicking a key feature of ecotypic niche divergence, we test if the phenotypic divergence that we observe in the wild results from phenotypic plasticity or divergent genetic predisposition. Our experimental groups show qualitatively similar phenotypic divergence as those observed among wild adults. The relative contribution of plasticity and divergent genetic predisposition differs among the traits studied, with traits related to the biomechanics of feeding showing a stronger genetic predisposition, whereas traits related to locomotion are mainly plastic. These results implicate that phenotypic plasticity and standing genetic variation interacted during contemporary ecotype formation in this case.

  7. Investigating the Effect of Phosphorus, Potassium and Weed Management on Forage and Seed Yield of Alfalfa Ecotypes (Medicago sativa L.

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    Ali Reza Heidarian

    2012-09-01

    Full Text Available In order to investigate fertilizing and weed management effects on forage and seed yield of alfalfa ecotypes, a field trial was conducted during 2008-2009 growing season at Khorasan Agricultural and Natural Resource Research Center, Mashhad-Iran. Alfalfa ecotypes including (Ghareghozlo, Hoakmabad, Malekkandi, Kozre, Faminin, Galebani, Rahnani, Shorkat, Chaleshtar, Ghareaghaj, Gharoghlogh, Ordobad, Sedighan, Silvana, Sahandava, Ghahavand, Mohajerankaraj and Mashhad were allocated to main plots; sub plots consisted of two levels of none fertilizing and fertilization treatments using simultaneous application of potassium sulphate and phosphate triple at rates of 150 and 350 K/ha, respectively and sub-sub plots were allocated to weeding and none weeding treatments based on a complete randomized block design in a splitsplit- plot scheme with three replicates. Results showed that the effect of ecotype on forage yield was not significant. Gharoghlogh and Silvana produced the highest (18270 kg/ha and the lowest (14630 kg/ha green forage yield, respectively at both cuttings (first and second cuts. The interaction of fertilization and weeding on forage yield was significant (p<0.01. On the other hand, with application of fertilizer, forage yield 11.74% was increased and it was enhanced 26.93% by manual weeding. Furthermore, results revealed that ecotype fertilizer interaction was significant (p<0.05 for weed dry weight. Ecotype weeding interaction was significant (p<0.05 for number of seed per pod and seed weight (p<0.01. In addition, fertilizer weeding interaction was significant (p<0.05 for number of seed per plant. Among the treatments, highest number of seed per plant was produced by fertilizer and weeding treatment (2734 and the lowest one was obtained by non-fertilizer and non-weeding treatment (559.5.

  8. Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs.

    Science.gov (United States)

    Vidal-García, M; Keogh, J S

    2015-12-01

    Animals from different clades but subject to similar environments often evolve similar body shapes and physiological adaptations due to convergent evolution, but this has been rarely tested at the transcontinental level and across entire classes of animal. Australia's biome diversity, isolation and aridification history provide excellent opportunities for comparative analyses on broad-scale macroevolutionary patterns. We collected morphological and environmental data on eighty-four (98%) Australian hylid frog species and categorized them into ecotypes. Using a phylogenetic framework, we tested the hypothesis that frogs from the same ecotype display similar body shape patterns: (i) across all the Australian hylids, and (ii) through comparison with a similar previous study on 127 (97%) Australian myobatrachid species. Body size and shape variation did not follow a strong phylogenetic pattern and was not tightly correlated with environment, but there was a stronger association between morphotype and ecotype. Both arboreal and aquatic frogs had long limbs, whereas limbs of fossorial species were shorter. Other terrestrial species were convergent on the more typical frog body shape. We quantified the strength of morphological convergence at two levels: (i) between fossorial myobatrachid and hylid frogs, and (ii) in each ecomorph within the hylids. We found strong convergence within ecotypes, especially in fossorial species. Ecotypes were also reflected in physiological adaptations: both arboreal and cocooned fossorial frogs tend to have higher rates of evaporative water loss. Our results illustrate how adaptation to different ecological niches plays a crucial role in morphological evolution, boosting phenotypic diversity within a clade. Despite phylogenetic conservatism, morphological adaptation to repeatedly emerging new environments can erase the signature of ancestral morphotypes, resulting in phenotypic diversification and convergence both within and between diverse

  9. Identification of metalliferous ecotypes of Cistus ladanifer L. using RAPD markers.

    Science.gov (United States)

    Quintela-Sabarís, Celestino; Kidd, Petra S; Fraga, María Isabel

    2005-01-01

    The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures.

  10. Identification of metalliferous ecotypes of Cistus ladanifer L. using RAPD markers

    Energy Technology Data Exchange (ETDEWEB)

    Quintela-Sabaris, C.; Fraga, M.I. [Dept. of Botany, Univ. of Santiago de Compostela (Spain); Kidd, P.S. [Dept. of Soil Science and Chemical Agronomy, Univ. of Santiago de Compostela (Spain)

    2005-04-01

    The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures. (orig.)

  11. Ecotype-specific improvement of nitrogen status in European grasses after drought combined with rewetting

    Science.gov (United States)

    Arfin Khan, Mohammed A. S.; Kreyling, Juergen; Beierkuhnlein, Carl; Jentsch, Anke

    2016-11-01

    Drought stress and associated low soil moisture can decrease N status of forage plants by reducing nitrogen (N) uptake. Conversely, rainfall and associated favorable soil moisture can improve plant N status. Yet, it is unclear to which degree drought combined with rewetting can buffer negative effects of drought on N status of forage plants and their populations. Here, we compared shoot N status (N concentration, total N uptake and C/N ratio) of four temperate grass species. Particularly, we investigated ecotypes (populations) grown from seeds from four to six European provenances/species after a drought treatment combined with rewetting (10 day harvest delay) versus continuously watered conditions for control. The experimental combination of drought and rewetting significantly increased shoot N concentration (+96%), N uptake (+31%); and decreased C/N ratio (-46%), biomass production (-29%) and C concentration (-1.4%) compared to control. Shoot N status was found to be different between target grass species and also within their populations under drought combined with rewetting treatment. Presumably drought-adapted populations did not perform better than populations from moist sites indicating no evidence of local adaptation. The drought combined with rewetting event could buffer the negative effects of drought. Shoot N status of grasses after drought and rewetting even exceeded control plants. This surprising finding can potentially be explained by higher N uptake, lack of growth dilution effects or delayed plant maturation. Furthermore, within-species shoot N status responses to drought combined with rewetting event were ecotype-specific, hinting at diverse responses of different population. For rangeland management, we recommend that if a drought event occurs during the growing season, harvesting should be delayed beyond a following rain event.

  12. Defense responses in two ecotypes of Lotus japonicus against non-pathogenic Pseudomonas syringae.

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    Cesar D Bordenave

    Full Text Available Lotus japonicus is a model legume broadly used to study many important processes as nitrogen fixing nodule formation and adaptation to salt stress. However, no studies on the defense responses occurring in this species against invading microorganisms have been carried out at the present. Understanding how this model plant protects itself against pathogens will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important defense mechanisms activated upon bacterial attack, we explored in this work the main responses occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after inoculation with Pseudomonas syringae DC3000 pv. tomato. Our analysis demonstrated that this bacterial strain is unable to cause disease in these accessions, even though the defense mechanisms triggered in these ecotypes might differ. Thus, disease tolerance in MG-20 was characterized by bacterial multiplication, chlorosis and desiccation at the infiltrated tissues. In turn, Gifu B-129 plants did not show any symptom at all and were completely successful in restricting bacterial growth. We performed a microarray based analysis of these responses and determined the regulation of several genes that could play important roles in plant defense. Interestingly, we were also able to identify a set of defense genes with a relative high expression in Gifu B-129 plants under non-stress conditions, what could explain its higher tolerance. The participation of these genes in plant defense is discussed. Our results position the L. japonicus-P. syringae interaction as a interesting model to study defense mechanisms in legume species.

  13. Salares versus coastal ecotypes of quinoa: Salinity responses in Chilean landraces from contrasting habitats.

    Science.gov (United States)

    Ruiz, Karina B; Aloisi, Iris; Del Duca, Stefano; Canelo, Valentina; Torrigiani, Patrizia; Silva, Herman; Biondi, Stefania

    2016-04-01

    Quinoa (Chenopodium quinoa Willd.) is a highly salt-tolerant species subdivided into five ecotypes and exhibiting broad intra-specific differences in tolerance levels. In a greenhouse study, Chilean landraces belonging either to the salares (R49) or coastal lowlands (VI-1, Villarrica) ecotype with contrasting agro-ecological origins were investigated for their responses to high salinity. The effects of two levels of salinity, 100 (T1) and 300 (T2) mM NaCl, on plant growth and on some physiological parameters were measured. Leaf and root Na(+) accumulation differed among landraces. T2 reduced growth and seed yield in all landraces with maximum inhibition relative to controls in R49. Salinity negatively affected chlorophyll and total polyphenol content (TPC) in VI-1 and Villarrica but not R49. Germination on saline or control media of seeds harvested from plants treated or not with NaCl was sometimes different; the best performing landrace was R49 insofar as 45-65% of seeds germinated on 500 mM NaCl-containing medium. In all landraces, average seedling root length declined strongly with increasing NaCl concentration, but roots of R49 were significantly longer than those of VI-1 and Villarrica up to 300 mM NaCl. Salt caused increases in seed TPC relative to controls, but radical scavenging capacity was higher only in seeds from T2 plants of R49. Total SDS-extractable seed proteins were resolved into distinct bands (10-70 kDa) with some evident differences between landraces. Salt-induced changes in protein patterns were landrace-specific. The responses to salinity of the salares landrace are discussed in relation to its better adaptation to an extreme environment.

  14. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA.

    Science.gov (United States)

    Vaistij, Fabián E; Gan, Yinbo; Penfield, Steven; Gilday, Alison D; Dave, Anuja; He, Zhesi; Josse, Eve-Marie; Choi, Giltsu; Halliday, Karen J; Graham, Ian A

    2013-06-25

    Freshly matured seeds exhibit primary dormancy, which prevents germination until environmental conditions are favorable. The establishment of dormancy occurs during seed development and involves both genetic and environmental factors that impact on the ratio of two antagonistic phytohormones: abscisic acid (ABA), which promotes dormancy, and gibberellic acid, which promotes germination. Although our understanding of dormancy breakage in mature seeds is well advanced, relatively little is known about the mechanisms involved in establishing dormancy during seed maturation. We previously showed that the SPATULA (SPT) transcription factor plays a key role in regulating seed germination. Here we investigate its role during seed development and find that, surprisingly, it has opposite roles in setting dormancy in Landsberg erecta and Columbia Arabidopsis ecotypes. We also find that SPT regulates expression of five transcription factor encoding genes: ABA-INSENSITIVE4 (ABI4) and ABI5, which mediate ABA signaling; REPRESSOR-OF-GA (RGA) and RGA-LIKE3 involved in gibberellic acid signaling; and MOTHER-OF-FT-AND-TFL1 (MFT) that we show here promotes Arabidopsis seed dormancy. Although ABI4, RGA, and MFT are repressed by SPT, ABI5 and RGL3 are induced. Furthermore, we show that RGA, MFT, and ABI5 are direct targets of SPT in vivo. We present a model in which SPT drives two antagonistic "dormancy-repressing" and "dormancy-promoting" routes that operate simultaneously in freshly matured seeds. Each of these routes has different impacts and this in turn explains the opposite effect of SPT on seed dormancy of the two ecotypes analyzed here.

  15. Expression and functional analysis of metal transporter genes in two contrasting ecotypes of the hyperaccumulator Thlaspi caerulescens.

    Science.gov (United States)

    Plaza, Sonia; Tearall, Kathryn L; Zhao, Fang-Jie; Buchner, Peter; McGrath, Steve P; Hawkesford, Malcolm J

    2007-01-01

    Zinc (Zn) hyperaccumulation is a constitutive property of Thlaspi caerulescens, whereas cadmium (Cd) hyperaccumulation varies greatly among different ecotypes. The molecular basis of this variation is unknown. Ecotypic differences in the sequences and expression of four representative ZIP family transporter genes were investigated. Genome analysis indicated the presence of at least two closely related copies of the TcIRT1 gene in both Ganges (high Cd accumulating) and Prayon (low Cd accumulating) ecotypes, with different copies being expressed in each, and, furthermore, the two genes potentially encode different length transcripts. The predominant transcript in Prayon was truncated, missing sequence coding for the putative metal-binding site and the five C-terminal transmembrane helices. The two ecotypes were grown hydroponically +/-Fe and Cd, and mRNA abundance determined for four ZIP genes. The four ZIP genes studied (TcIRT1, TcIRT2, TcZNT1, and TcZNT5) were expressed in roots only. TcIRT1 expression (full-length in Ganges, TcIRT1-1G; truncated in Prayon, TcIRT1-2P) was enhanced by Fe deficiency or by exposure to Cd. TcIRT2 expression was induced by Fe deficiency, but was unaffected by Cd exposure. TcZNT5-G showed greater expression in Prayon compared with Ganges. The functions of TcIRT1 from Ganges and Prayon and the Arabidopsis homologue were analysed by heterologous expression in yeast. All three IRT1 genes were able to facilitate growth on low Fe concentrations. Cd sensitivity of yeast was conferred in the order AtIRT1>TcIRT1-1G>TcIRT1-2P (truncated). Cd uptake after 4 h was only detectable following complementation by AtIRT1. The results suggest that although TcIRT1-G may be involved in Cd hyperaccumulation in the Ganges ecotype of T. caerulescens, the transporter expressed in yeast does not have an enhanced ability to transport Cd compared with AtIRT1. Therefore, the unique Cd-accumulating ability of the T. caerulescens Ganges ecotype must be due to the

  16. Habitat Temperature and Precipitation of Arabidopsis thaliana Ecotypes Determine the Response of Foliar Vasculature, Photosynthesis, and Transpiration to Growth Temperature.

    Science.gov (United States)

    Adams, William W; Stewart, Jared J; Cohu, Christopher M; Muller, Onno; Demmig-Adams, Barbara

    2016-01-01

    Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish) were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high) exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 and Swedish ecotypes, of phloem per minor vein in plants grown at the low temperature. In contrast, vein density and minor vein tracheary to sieve element ratio increased with increasing growth temperature - most strongly in Col-0 and least strongly in the Italian ecotype - and transpirational water loss correlated with vein density and number of tracheary elements per minor vein. Plotting of these vascular features as functions of climatic conditions in the habitat of origin suggested that temperatures during the evolutionary history of the ecotypes determined acclimatory responses of the foliar phloem and photosynthesis to temperature in this winter annual that upregulates photosynthesis in response to lower temperature, whereas the precipitation experienced during the evolutionary history of the ecotypes determined adjustment of foliar vein density, xylem, and transpiration to temperature. In particular, whereas photosynthetic capacity, leaf thickness, and foliar minor vein phloem features increased linearly with increasing latitude and decreasing temperature of the habitats of origin in response to experimental growth at low temperature, transpiration rate, foliar vein density, and minor vein tracheary element numbers and cross

  17. Habitat temperature and precipitation of Arabidopsis thaliana ecotypes determine the response of foliar vasculature, photosynthesis, and transpiration to growth temperature

    Directory of Open Access Journals (Sweden)

    William Walter Adams III

    2016-07-01

    Full Text Available Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 and Swedish ecotypes, of phloem per minor vein in plants grown at the low temperature. In contrast, vein density and minor vein tracheary to sieve element ratio increased with increasing growth temperature – most strongly in Col-0 and least strongly in the Italian ecotype – and transpirational water loss correlated with vein density and number of tracheary elements per minor vein. Plotting of these vascular features as functions of climatic conditions in the habitat of origin suggested that temperatures during the evolutionary history of the ecotypes determined acclimatory responses of the foliar phloem and photosynthesis to temperature in this winter annual that upregulates photosynthesis in response to lower temperature, whereas the precipitation experienced during the evolutionary history of the ecotypes determined adjustment of foliar vein density, xylem, and transpiration to temperature. In particular, whereas photosynthetic capacity, leaf thickness, and foliar minor vein phloem features increased linearly with increasing latitude and decreasing temperature of the habitats of origin in response to experimental growth at low temperature, transpiration rate, foliar vein density, and minor vein tracheary element numbers

  18. Association between minor loading vein architecture and light- and CO2-saturated rates of photosynthetic oxygen evolution among Arabidopsis thaliana ecotypes from different latitudes

    Directory of Open Access Journals (Sweden)

    Christopher M Cohu

    2013-07-01

    Full Text Available Through microscopic analysis of veins and assessment of light- and CO2-saturated rates of photosynthetic oxygen evolution, we investigated the relationship between minor loading vein anatomy and photosynthesis of mature leaves in three ecotypes of Arabidopsis thaliana grown under four different combinations of temperature and photon flux density (PFD. All three ecotypes exhibited greater numbers and cross-sectional area of phloem cells as well as higher photosynthesis rates in response to higher PFD and especially lower temperature. The Swedish ecotype exhibited the strongest response to these conditions, the Italian ecotype the weakest response, and the Col-0 ecotype exhibited an intermediate response. Among all three ecotypes, strong linear relationships were found between light- and CO2-saturated rates of photosynthetic oxygen evolution and the number and area of either sieve elements or of companion and phloem parenchyma cells in foliar minor loading veins, with the Swedish ecotype showing the highest number of cells in minor loading veins (and largest minor veins coupled with unprecedented high rates of photosynthesis. Linear, albeit less significant, relationships were also observed between number and cross-sectional area of tracheids per minor loading vein versus light- and CO2-saturated rates of photosynthetic oxygen evolution. We suggest that sugar distribution infrastructure in the phloem is co-regulated with other features that set the upper limit for photosynthesis. The apparent genetic differences among Arabidopsis ecotypes should allow for future identification of the gene(s involved in augmenting sugar-loading and -transporting phloem cells and maximal rates of photosynthesis.

  19. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers.

    Science.gov (United States)

    Andrews, Kimberly R; Perrin, William F; Oremus, Marc; Karczmarski, Leszek; Bowen, Brian W; Puritz, Jonathan B; Toonen, Robert J

    2013-05-01

    The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin (Stenella longirostris) ecotypes. This species contains six known ecotypes (grouped into four subspecies) that exhibit striking differences in morphology, habitat and mating system, despite having adjacent or overlapping ranges and little genetic divergence at previously studied mtDNA and autosomal markers. We examined the phylogeographic structure for all six ecotypes across the species range (n = 261, 17 geographic locations) using DNA sequences from three Y chromosome markers, two maternally inherited mitochondrial (mtDNA) markers, and a biparentally inherited autosomal intron. mtDNA and autosomal analyses revealed low divergence (most Φ(ST) values <0.1) between ecotypes and geographic regions, concordant with previous studies. In contrast, Y intron analyses revealed fixed differences amongst the three most phenotypically divergent groups: S. l. longirostris vs. S. l. roseiventris vs. combined S. l. orientalis/S. l. centroamericana/Tres Marias ecotypes). Another ecotype (whitebelly), previously postulated to be a hybrid between the two phenotypically most divergent ecotypes, had Y haplotypes from both putative parent ecotypes, supporting a hybrid designation. Reduced introgression of the Y chromosome has previously been observed in other organisms ranging from insects to terrestrial mammals, and here we demonstrate this phenomenon in a marine mammal with high dispersal capabilities. These results indicate that reduced introgression of the Y chromosome occurs in a wide taxonomic range of organisms and support the growing body of evidence that rapid evolution of the Y chromosome is important in evolutionary diversification.

  20. Effects of Nano Fertilizer Application and Maternal Corm Weight on Flowering at Some Saffron (Crocus sativus L.) Ecotypes

    OpenAIRE

    AMIRNIA, Reza; Bayat, Mahdi; TAJBAKHSH, Mahdi

    2014-01-01

    To develop saffron planting in Urmia, West Azerbaijan, Iran, a split-split plot experiment based on CRBD was carried out in the Urmia University's research farm for two years . Nanofertilizers (Fe, P, K and nofertilizer (control)) as main plots, saffron ecotypes (Mashhad, Torbat-Heydarieh, Torbat-jam, Gonabad, Ghaen and Birjand) as subplots and maternal corm weight (6, 8, 10 and 12 g) as sub-sub plots were considered. Throughout the two years of the study, results showed significant differenc...

  1. A comparison of the functional traits of common reed (Phragmites australis in northern China: aquatic vs. terrestrial ecotypes.

    Directory of Open Access Journals (Sweden)

    Liping Li

    Full Text Available Common reed (Phragmites australis (Cav. Trin. ex Steud. is distributed widely throughout the world with various ecotypes. This research compares the functional traits and biomass allocation patterns of two contrasting reed ecotypes. Twelve pairs of aquatic and terrestrial reed samples were collected in northern China. Significant differences in functional traits between the two reed ecotypes were observed, while biomass allocation patterns of reed organs did not differ significantly except for at the root. The dry matter content (DMC in the whole of the reed plant, leaf, root, and rhizome was higher; while the specific leaf area (SLA and specific root length (SRL were lower in terrestrial versus aquatic reed. The biomass allocation in organs of the two forms of reed was isometric, only root in the terrestrial habitat increased faster with an increase in the whole plant biomass. It can be affirmed that aquatic and terrestrial reed that adapt to different environments generally has distinct leaf and root functional traits but isometric biomass allocation patterns. This suggests different resource acquisition strategies: (1 aquatic reed grows faster with high SLA and SRL and is more responsive to the environment, while (2 terrestrial reed with high DMC grows slower and is less responsive to the adverse environment (e.g. dry soil conditions.

  2. A comparison of the functional traits of common reed (Phragmites australis) in northern China: aquatic vs. terrestrial ecotypes.

    Science.gov (United States)

    Li, Liping; Han, Wenxuan; Thevs, Niels; Jia, Xiuhong; Ji, Chengjun; Jin, Dongmei; He, Ping; Schmitt, Armin O; Cirella, Giuseppe Tommaso; Zerbe, Stefan

    2014-01-01

    Common reed (Phragmites australis (Cav.) Trin. ex Steud.) is distributed widely throughout the world with various ecotypes. This research compares the functional traits and biomass allocation patterns of two contrasting reed ecotypes. Twelve pairs of aquatic and terrestrial reed samples were collected in northern China. Significant differences in functional traits between the two reed ecotypes were observed, while biomass allocation patterns of reed organs did not differ significantly except for at the root. The dry matter content (DMC) in the whole of the reed plant, leaf, root, and rhizome was higher; while the specific leaf area (SLA) and specific root length (SRL) were lower in terrestrial versus aquatic reed. The biomass allocation in organs of the two forms of reed was isometric, only root in the terrestrial habitat increased faster with an increase in the whole plant biomass. It can be affirmed that aquatic and terrestrial reed that adapt to different environments generally has distinct leaf and root functional traits but isometric biomass allocation patterns. This suggests different resource acquisition strategies: (1) aquatic reed grows faster with high SLA and SRL and is more responsive to the environment, while (2) terrestrial reed with high DMC grows slower and is less responsive to the adverse environment (e.g. dry soil conditions).

  3. Effects of cadmium on ultrastructure and antioxidative defense system in hyperaccumulator and non-hyperaccumulator ecotypes of Sedum alfredii Hance

    Energy Technology Data Exchange (ETDEWEB)

    Jin Xiaofen [Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou 310029 (China); Zhejiang Provincial Key Lab of Subtropical Soil Science and Plant Nutrition, College of Environmental and Natural Resources Science, Zhejiang University, Hangzhou 310029 (China); Yang Xiaoe [Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou 310029 (China); Zhejiang Provincial Key Lab of Subtropical Soil Science and Plant Nutrition, College of Environmental and Natural Resources Science, Zhejiang University, Hangzhou 310029 (China)], E-mail: xyang@zju.edu.cn; Islam, Ejazul [Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou 310029 (China); Zhejiang Provincial Key Lab of Subtropical Soil Science and Plant Nutrition, College of Environmental and Natural Resources Science, Zhejiang University, Hangzhou 310029 (China); Nuclear Institute of Agriculture, Tandojam 48800, Hyderabad (Pakistan); Liu Dan [School of Tourism and Health, Zhejiang Forestry College, 311300 Lin' an (China); Mahmood, Qaisar [Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou 310029 (China); Zhejiang Provincial Key Lab of Subtropical Soil Science and Plant Nutrition, College of Environmental and Natural Resources Science, Zhejiang University, Hangzhou 310029 (China)

    2008-08-15

    Plant growth, ultrastructural and antioxidant adaptations and glutathione biosynthesis in Cd-hyperaccumulating ecotype Sedum alfredii Hance (HE) countering high Cd environment were investigated and compared with its non Cd-hyperaccumulating ecotype (NHE). Cadmium exposure resulted in significant ultrastructural changes in root meristem and leaf mesophyll cells of S. alfredii, but damage was more pronounced in NHE even when Cd concentrations were one-tenth of those applied to HE. Cadmium stress damaged chloroplasts causing imbalanced lamellae formation coupled with early leaf senescence. Histochemical results revealed that glutathione (GSH) biosynthesis inhibition led to overproduction of hydrogen peroxide (H{sub 2}O{sub 2}) and superoxide radical (O{sub 2}{center_dot}{sup -}) in HE but not in NHE. Differences were noted in both HE and NHE for catalase (CAT), guaiacol peroxidase (GPX), ascorbate peroxidase (APX) and glutathione reductase (GR) activities under various Cd stress levels. No relationship was found between antioxidative defense capacity including activities of superoxide dismutase (SOD), CAT, GPX, APX and GR as well as ascorbic acid (AsA) contents and Cd tolerance in the two ecotypes of S. alfredii. The GSH biosynthesis induction in root and shoot exposed to elevated Cd conditions may be involved in Cd tolerance and hyperaccumulation in HE of S. alfredii H.

  4. A study of fluctuating asymmetry in hybrids of dwarf and normal lake whitefish ecotypes (Coregonus clupeaformis) from different glacial races.

    Science.gov (United States)

    Lu, G; Bernatchez, L

    1999-12-01

    Fish ecotypes found in north temperate lakes are increasingly used as model organisms to explore patterns and processes of population divergence that may ultimately cause speciation. Processes involved in their reproductive isolation are, however, still poorly understood. Recent experimental studies on whitefish ecotypes from different glacial races revealed that embryonic mortality of hybrids was 2.4-4.7 times higher than for parental forms. In this study, we compared fluctuating asymmetry (FA) in morphological traits of these same hybrid and pure crosses to test the hypothesis that genetic stress observed in hybrids at embryonic stages is also manifested at later developmental stages. Twelve morphological traits were used to measure asymmetry. Variable degrees of asymmetry were observed depending on traits and crosses, however there was no significant difference in FA among crosses. These results thus provided no evidence in support of the working hypothesis and indicated that genetic stress may differ among life stages. It is more likely that high hybrid embryonic mortality acts together with ecological factors at later stages to increase further the extent of reproductive isolation between sympatric whitefish ecotypes.

  5. Northern ragweed ecotypes flower earlier and longer in response to elevated CO2: what are you sneezing at?

    Science.gov (United States)

    Stinson, Kristina A; Albertine, Jennifer M; Hancock, Laura M S; Seidler, Tristram G; Rogers, Christine A

    2016-10-01

    Significant changes in plant phenology and flower production are predicted over the next century, but we know relatively little about geographic patterns of this response in many species, even those that potentially impact human wellbeing. We tested for variation in flowering responses of the allergenic plant, Ambrosia artemisiifolia (common ragweed). We grew plants originating from three latitudes in the Northeastern USA at experimental levels of CO2 (400, 600, and 800 µL L(-1)). We hypothesized that northern ecotypes adapted to shorter growing seasons would flower earlier than their southern counterparts, and thus disproportionately allocate carbon gains from CO2 to reproduction. As predicted, latitude of origin and carbon dioxide level significantly influenced the timing and magnitude of flowering. Reproductive onset occurred earlier with increasing latitude, with concurrent increases in the number of flowers produced. Elevated carbon dioxide resulted in earlier reproductive onset in all ecotypes, which was significantly more pronounced in the northern populations. We interpret our findings as evidence for ecotypic variation in ragweed flowering time, as well in responses to CO2. Thus, the ecological and human health implications of common ragweed's response to global change are likely to depend on latitude. We conclude that increased flower production, duration, and possibly pollen output, can be expected in Northeastern United States with rising levels of CO2. The effects are likely, however, to be most significant in northern parts of the region.

  6. Identification of ecotype-specific marker genes for categorization of beer-spoiling Lactobacillus brevis.

    Science.gov (United States)

    Behr, Jürgen; Geissler, Andreas J; Preissler, Patrick; Ehrenreich, Armin; Angelov, Angel; Vogel, Rudi F

    2015-10-01

    The tolerance to hop compounds, which is mainly associated with inhibition of bacterial growth in beer, is a multi-factorial trait. Any approaches to predict the physiological differences between beer-spoiling and non-spoiling strains on the basis of a single marker gene are limited. We identified ecotype-specific genes related to the ability to grow in Pilsner beer via comparative genome sequencing. The genome sequences of four different strains of Lactobacillus brevis were compared, including newly established genomes of two highly hop tolerant beer isolates, one strain isolated from faeces and one published genome of a silage isolate. Gene fragments exclusively occurring in beer-spoiling strains as well as sequences only occurring in non-spoiling strains were identified. Comparative genomic arrays were established and hybridized with a set of L. brevis strains, which are characterized by their ability to spoil beer. As result, a set of 33 and 4 oligonucleotide probes could be established specifically detecting beer-spoilers and non-spoilers, respectively. The detection of more than one of these marker sequences according to a genetic barcode enables scoring of L. brevis for their beer-spoiling potential and can thus assist in risk evaluation in brewing industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Induction of cell death by graphene in Arabidopsis thaliana (Columbia ecotype) T87 cell suspensions

    Energy Technology Data Exchange (ETDEWEB)

    Begum, Parvin, E-mail: parvinchy@ees.hokudai.ac.jp; Fugetsu, Bunshi

    2013-09-15

    Highlights: • This study was set up to explore potential influence of graphene on T87 cells. • Fragmented nuclei, membrane damage, mitochondrial dysfunction were observed. • ROS increased, ROS are key mediators in the cell death signaling pathway. • Translocation of graphene into cells and an endocytosis-like structure was observed. • Graphene entering into the cells by endocytosis. -- Abstract: The toxicity of graphene on suspensions of Arabidopsis thaliana (Columbia ecotype) T87 cells was investigated by examining the morphology, mitochondrial dysfunction, reactive oxygen species generation (ROS), and translocation of graphene as the toxicological endpoints. The cells were grown in Jouanneau and Péaud-Lenoel (JPL) media and exposed to graphene at concentrations 0–80 mg/L. Morphological changes were observed by scanning electron microscope and the adverse effects such as fragmented nuclei, membrane damage, mitochondrial dysfunction was observed with fluorescence microscopy by staining with Hoechst 33342/propidium iodide and succinate dehydrogenase (mitochondrial bioenergetic enzyme). Analysis of intracellular ROS by 2′,7′-dichlorofluorescein diacetate demonstrated that graphene induced a 3.3-fold increase in ROS, suggesting that ROS are key mediators in the cell death signaling pathway. Transmission electron microscopy verified the translocation of graphene into cells and an endocytosis-like structure was observed which suggested graphene entering into the cells by endocytosis. In conclusion, our results show that graphene induced cell death in T87 cells through mitochondrial damage mediated by ROS.

  8. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.

    Science.gov (United States)

    Tolonen, Andrew C; Aach, John; Lindell, Debbie; Johnson, Zackary I; Rector, Trent; Steen, Robert; Church, George M; Chisholm, Sallie W

    2006-01-01

    Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, that have different N utilization capabilities and that belong to ecotypes with different depth distributions. An interstrain comparison of how Prochlorococcus responds to changes in ambient nitrogen is thus central to understanding its ecology. We quantified changes in MED4 and MIT9313 global mRNA expression, chlorophyll fluorescence, and photosystem II photochemical efficiency (Fv/Fm) along a time series of increasing N starvation. In addition, the global expression of both strains growing in ammonium-replete medium was compared to expression during growth on alternative N sources. There were interstrain similarities in N regulation such as the activation of a putative NtcA regulon during N stress. There were also important differences between the strains such as in the expression patterns of carbon metabolism genes, suggesting that the two strains integrate N and C metabolism in fundamentally different ways.

  9. Switchgrass Cultivar/Ecotype Selection and Management for Biofuels in the Upper Southeast USA

    Directory of Open Access Journals (Sweden)

    Rocky Lemus

    2014-01-01

    Full Text Available Switchgrass (Panicum virgatum L., a perennial warm-season grass indigenous to the eastern USA, has potential as a biofuels feedstock. The objective of this study was to investigate the performance of upland and lowland switchgrass cultivars under different environments and management treatments. Four cultivars of switchgrass were evaluated from 2000 to 2001 under two management regimes in plots established in 1992 at eight locations in the upper southeastern USA. Two management treatments included 1 a single annual harvest (in late October to early November and a single application of 50 kg N/ha/yr and 2 two annual harvests (in midsummer and November and a split application of 100 kg N/ha/yr. Biomass yields averaged 15 Mg/ha/yr and ranged from 10 to 22 Mg/ha/yr across cultivars, managements, locations, and years. There was no yield advantage in taking two harvests of the lowland cultivars (Alamo and Kanlow. When harvested twice, upland cultivars (Cave-in-Rock and Shelter provided yields equivalent to the lowland ecotypes. Tiller density was 36% lower in stands cutting only once per year, but the stands appeared vigorous after nine years of such management. Lowland cultivars and a one-cutting management (after the tops have senesced using low rates of applied N (50 kg/ha are recommended.

  10. Diversity of thermal ecotypes and potential pathotypes of Bacillus thuringiensis soil isolates.

    Science.gov (United States)

    Swiecicka, Izabela; Bartoszewicz, Marek; Kasulyte-Creasey, Daiva; Drewnowska, Justyna M; Murawska, Emilia; Yernazarova, Aliya; Lukaszuk, Edyta; Mahillon, Jacques

    2013-08-01

    Ecological diversification of Bacillus thuringiensis soil isolates was examined to determine whether bacteria adapted to grow at low temperature and/or potentially pathogenic correspond to genetically distinct lineages. Altogether, nine phylogenetic lineages were found among bacilli originating from North-Eastern Poland (n = 24) and Lithuania (n = 25) using multi-locus sequence typing. This clustering was chiefly confirmed by pulsed-field gel electrophoresis. One third of the bacilli were found to be psychrotolerant, which strongly supports the hypothesis of the existence of thermal ecotypes among B. thuringiensis. PCR screening was also performed to detect potential enterotoxin genes and Bacillus anthracis pXO1- and pXO2-like replicons. The cytK-positive isolates (22%) were significantly associated with two phylogenetic lineages (potential CytK pathotypes), whereas there was no correlation between phylogenetic grouping and the presence of the potential tripartite enterotoxin pathotypes (86% of strains). A statistically significant association between phylogenetic lineages and ecologic properties was found with regard to the cry1-positive Lithuanian isolates, while the cry genes in Polish isolates and the pXO1- and pXO2 replicon-like elements showed scattered distribution across phylogenetic lineages. Our results support the hypothesis that B. thuringiensis comprises strains belonging to different phylogenetic lineages, which exhibit specific ecological properties.

  11. Investigation of the effect of phosphogypsum amendment on two Arabidopsis thaliana ecotype growth and development.

    Science.gov (United States)

    Ayadi, Amal; Chorriba, Amal; Fourati, Amine; Gargouri-Bouzid, Radhia

    2015-01-01

    The production of phosphoric acid from natural phosphate rock leads to an industrial waste called phosphogypsum (PG). About 5 tons of PG are generated per ton of phosphoric acid produced. This acidic waste (pH 2.2) is mostly disposed of by dumping into large stockpiles close to fertilizer production units, where they occupy large land areas that can cause serious environmental damages. Several attempts were made to test PG valorization via soil amendment because of its phosphate, sulphate and calcium content. The aim of the this study was to evaluate the potential use of PG as phosphate amendment in soil using two wild-type Arabidopsis thaliana ecotypes (Wassilewskija and Colombia) as model plants. Plants were grown in a greenhouse for 30 days, on substrates containing various PG concentrations (0%, 15%, 25%, 40% and 50%). The growth rate and physiological parameters (fresh weight, phosphate and chlorophyll content) were determined. The data revealed that 15% PG did not alter plant survival and leaf's dry weight, and the inorganic phosphate (Pi) uptake by plant seemed to be efficient. However, some alterations in Chlorophyll a/Chlorophyll b ratio were noticed. Higher PG concentrations (40 and 50% PG) exhibited an enhanced negative effect on plant growth, survival and Pi uptake. These inhibitory effects of the substrates may be related to the acidity of the medium in addition to its Cd content.

  12. Rapid evolutionary divergence and ecotypic diversification of germination behavior in weedy rice populations.

    Science.gov (United States)

    Xia, Han-Bing; Xia, Hui; Ellstrand, Norman C; Yang, Chao; Lu, Bao-Rong

    2011-09-01

    Feral plants have evolved from well-studied crops, providing good systems for elucidation of how weediness evolves. As yet, they have been largely neglected for this purpose. The evolution of weediness can occur by simple back mutations in domestication genes (domestication in reverse). Whether the evolutionary steps to weediness always occur in reverse remains largely unknown. We examined seed germination behavior in recently evolved weedy rice (Oryza sativa f. spontanea) populations and their coexisting cultivars in eastern and north-eastern China to address whether 'dedomestication' is the simple reverse of domestication. We found that these weedy populations did not diverge from their progenitors by reverting to the pre-domestication trait of seed dormancy. Instead, they have evolved a novel mechanism to avoid growing in inappropriate environments via changes in critical temperature cues for seed germination. Furthermore, we found evidence for subsequent ecotypic divergence of these populations such that the critical temperature for germination correlates with the local habitat temperature at latitudinal gradients. The origins of problematic plant species, weeds and invasives, have already been studied in detail. These plants can thus be used as systems for studying rapid evolution. To determine whether and how that evolution is adaptive, experiments such as those described here can be performed.

  13. Identifying Differences in Abiotic Stress Gene Networks between Lowland and Upland Ecotypes of Switchgrass (DE-SC0008338)

    Energy Technology Data Exchange (ETDEWEB)

    Childs, Kevin [Michigan State Univ., East Lansing, MI (United States); Buell, Robin [Michigan State Univ., East Lansing, MI (United States); Zhao, Bingyu [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Zhang, Xunzhong [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

    2016-11-10

    Switchgrass (Panicum virgatum) is a warm-season C4 grass that is a target lignocellulosic biofuel species for use in the United States due to its local adaption capabilities and high biomass accumulation. Two ecotypes of switchgrass have been described. Members of the lowland ecotype are taller, have narrower leaf blades and generate more biomass compared to individuals from the upland ecotype. Additionally, lowland plants are generally found in the southern United States while upland switchgrass is more typically present in the northern United States. These differences are important as it is envisioned that switchgrass for biofuel production will typically be grown on marginal lands in the northern United States to supplement and diversify farmers' traditional crop incomes. While lowland switchgrass is more productive, it has poor winter survivability in northern latitudes where upland switchgrass is expected to be grown for biofuel use. Abiotic stresses likely to be encountered by switchgrass include drought and salinity. Despite initially being described as preferring wetter environments, members of the lowland ecotype have been characterized as being more drought tolerant than plants of the upland ecotype. Nonetheless, direct trials have indicated that variation for drought tolerance exists in both ecotypes, but prior to this project, only a relatively small number of switchgrass lines had been tested for drought responses. Similarly, switchgrass cultivars have not been widely tested for salt tolerance, but a few studies have shown that even mild salt stress can inhibit growth. The effects of drought and salt stress on plant growth are complex. Both drought and salinity affect the osmotic potential of plant cells and negatively affect plant growth due to reduced water potential and reduced photosynthesis that results from lower stomatal conductance of CO2. Plants respond to drought and salt stress by activating genes that directly attempt to

  14. Comparative assessment on the prevalence of mutations in the Plasmodium falciparum drug-resistant genes in two different ecotypes of Odisha state, India.

    Science.gov (United States)

    Kar, Narayani Prasad; Chauhan, Kshipra; Nanda, Nutan; Kumar, Ashwani; Carlton, Jane M; Das, Aparup

    2016-07-01

    Considering malaria as a local and focal disease, epidemiological understanding of different ecotypes of malaria can help in devising novel control measures. One of the major hurdles in malaria control lies on the evolution and dispersal of the drug-resistant malaria parasite, Plasmodium falciparum. We herewith present data on genetic variation at the Single Nucleotide Polymorphism (SNP) level in four different genes of P. falciparum (Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps) that confer resistance to different antimalarials in two different eco-epidemiological settings, i.e. Hilly-Forest (HF) and Riverine-Plain (RP), in a high malaria endemic district of Odisha state, India. Greater frequency of antimalarial resistance conferring SNPs and haplotypes was observed in all four genes in P. falciparum, and Pfdhps was the most variable gene among the four. No significant genetic differentiation could be observed in isolates from HF and RP ecotypes. Twelve novel, hitherto unreported nucleotide mutations could be observed in the Pfmdr1 and Pfdhps genes. While the Pfdhps gene presented highest haplotype diversity, the Pfcrt gene displayed the highest nucleotide diversity. When the data on all the four genes were complied, the isolates from HF ecotype were found to harbour higher average nucleotide diversity than those coming from RP ecotype. High and positive Tajima's D values were obtained for the Pfcrt and Pfdhfr genes in isolates from both the HF and RP ecotypes, with statistically significant deviation from neutrality in the RP ecotype. Different patterns of Linkage Disequilibrium (LD) among SNPs located in different drug-resistant genes were found in the isolates collected from HF and RP ecotypes. Whereas in the HF ecotype, SNPs in the Pfmdr1 and Pfdhfr were significantly associated, in the RP ecotype, SNPs located in Pfcrt were associated with Pfmdr1, Pfdhfr and Pfdhps. These findings provide a baseline understanding on how different micro eco-epidemiological settings

  15. FLUORESCENCE EMISSION SPECTRA OF MARINE AND BRACKISH-WATER ECOTYPES OF FUCUS VESICULOSUS AND FUCUS RADICANS (PHAEOPHYCEAE) REVEAL DIFFERENCES IN LIGHT-HARVESTING APPARATUS(1).

    Science.gov (United States)

    Maria Gylle, Anna; Rantamäki, Susanne; Ekelund, Nils G A; Tyystjärvi, Esa

    2011-02-01

    The Bothnian Sea in the northerly part of the Baltic Sea is a geologically recent brackish-water environment, and rapid speciation is occurring in the algal community of the Bothnian Sea. We measured low-temperature fluorescence emission spectra from the Bothnian Sea and the Norwegian Sea ecotypes of Fucus vesiculosus L., a marine macroalga widespread in the Bothnian Sea. Powdered, frozen thallus was used to obtain undistorted emission spectra. The spectra were compared with spectra measured from the newly identified species Fucus radicans Bergström et L. Kautsky, which is a close relative of F. vesiculosus and endemic to the Bothnian Sea. The spectrum of variable fluorescence was used to identify fluorescence peaks originating in PSI and PSII in this chl c-containing alga. The spectra revealed much higher PSII emission, compared to PSI emission, in the Bothnian Sea ecotype of F. vesiculosus than in F. radicans or in the Norwegian Sea ecotype of F. vesiculosus. The results suggest that more light-harvesting chl a/c proteins serve PSII in the Bothnian Sea ecotype of F. vesiculosus than in the two other algal strains. Treatment of the Bothnian Sea ecotype of F. vesiculosus in high salinity (10, 20, and 35 practical salinity units) for 1 week did not lead to spectral changes, indicating that the measured features of the Bothnian Sea F. vesiculosus are stable and not simply a direct result of exposure to low salinity.

  16. Genetic differentiation and estimation of effective population size and migration rates in two sympatric ecotypes of the marine snail Littorina saxatilis.

    Science.gov (United States)

    Fernández, J; Galindo, J; Fernández, B; Pérez-Figueroa, A; Caballero, A; Rolán-Alvarez, E

    2005-01-01

    On exposed rocky shores in Galicia (northwest Spain), a striking polymorphism exists between two ecotypes (RB and SU) of Littorina saxatilis that occupy different levels of the intertidal zone and exhibit an incomplete reproductive isolation. The setting has been suggested to represent ongoing sympatric speciation by ecological adaptation of the two ecotypes to their respective habitats. In this article we address whether or not the ecotypes have developed their own population structures in response to the rigors of their corresponding environments and life histories. We analyzed four to five allozymic loci from three surveys of the same sites, spanning a 14-year period. An experimental design including three localities with two transects per locality and three shore levels allowed studying temporal and spatial population structure and estimation of effective population sizes (N(e)), neighborhood sizes (N(n)), and migration rates (m). Genetic differentiation was significantly lower in RB populations (theta(ST) = 0.067) than in SU ones (theta(ST) = 0.124). Mean estimates of N(e), N(n), and m did not differ significantly between ecotypes, but local ecotype differences in migration between the two closest localities (larger migration rates in RB than in SU populations) could explain the pattern in population differentiation.

  17. Deep frying

    NARCIS (Netherlands)

    Koerten, van K.N.

    2016-01-01

    Deep frying is one of the most used methods in the food processing industry. Though practically any food can be fried, French fries are probably the most well-known deep fried products. The popularity of French fries stems from their unique taste and texture, a crispy outside with a mealy soft inter

  18. Deep frying

    NARCIS (Netherlands)

    Koerten, van K.N.

    2016-01-01

    Deep frying is one of the most used methods in the food processing industry. Though practically any food can be fried, French fries are probably the most well-known deep fried products. The popularity of French fries stems from their unique taste and texture, a crispy outside with a mealy soft inter

  19. Deep learning

    CERN Document Server

    Goodfellow, Ian; Courville, Aaron

    2016-01-01

    Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language proces...

  20. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.

    Science.gov (United States)

    Hugoni, Mylène; Taib, Najwa; Debroas, Didier; Domaizon, Isabelle; Jouan Dufournel, Isabelle; Bronner, Gisèle; Salter, Ian; Agogué, Hélène; Mary, Isabelle; Galand, Pierre E

    2013-04-01

    Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.

  1. Salt tolerance of a wild ecotype of vetiver grass (Vetiveria zizanioides L.) in southern China.

    Science.gov (United States)

    Liu, Wan-Gou; Liu, Jin-Xiang; Yao, Mei-Ling; Ma, Qi-Fu

    2016-12-01

    Vetiver grass (Vetiveria zizanioides L.) is widely used in more than 120 countries for land management (e.g. rehabilitation of saline lands). A wild ecotype of vetiver grass was found in southern China in the 1950s, but little is known about its adaptability to saline stress. For the purpose of understanding its tolerance to salinity as well as corresponding tolerance mechanisms, in a greenhouse with natural lighting, seedlings were grown in culture solutions and subjected to a range of NaCl concentrations for 18 days. Compared to no NaCl treatment, 200 mM NaCl significantly reduced leaf water potential, leaf water content, leaf elongation rate, leaf photosynthetic rate and plant relative growth rate and increased leaf malondialdehyde (MDA) content, but the parameters showed only slight reduction at 150 mM NaCl. In addition, salinity caused an increase in the activity of antioxidant enzymes in leaves. Moreover, increasing NaCl levels significantly increased Na(+) but decreased K(+) concentrations in both roots and leaves. The leaves had higher K(+) concentrations at all NaCl levels, but lower Na(+) concentrations compared to the roots, thereby maintaining higher K(+)/Na(+) ratio in leaves. Our results showed that the salinity threshold of this wild vetiver grass is about 100 mM NaCl, i.e. highly tolerant to salt stress. This wild vetiver grass has a high ability to exclude Na(+) and retain K(+) in its leaves, which is a critical strategy for salt tolerance.

  2. Backcasting the decline of a vulnerable Great Plains reproductive ecotype: identifying threats and conservation priorities

    Science.gov (United States)

    Worthington, Thomas A.; Brewer, Shannon K.; Grabowski, Timothy B.; Mueller, Julia

    2014-01-01

    Conservation efforts for threatened or endangered species are challenging because the multi-scale factors that relate to their decline or inhibit their recovery are often unknown. To further exacerbate matters, the perceptions associated with the mechanisms of species decline are often viewed myopically rather than across the entire species range. We used over 80 years of fish presence data collected from the Great Plains and associated ecoregions of the United States, to investigate the relative influence of changing environmental factors on the historic and current truncated distributions of the Arkansas River shiner Notropis girardi. Arkansas River shiner represent a threatened reproductive ecotype considered especially well adapted to the harsh environmental extremes of the Great Plains. Historic (n = 163 records) and current (n = 47 records) species distribution models were constructed using a vector-based approach in MaxEnt by splitting the available data at a time when Arkansas River shiner dramatically declined. Discharge and stream order were significant predictors in both models; however, the shape of the relationship between the predictors and species presence varied between time periods. Drift distance (river fragment length available for ichthyoplankton downstream drift before meeting a barrier) was a more important predictor in the current model and indicated river segments 375–780 km had the highest probability of species presence. Performance for the historic and current models was high (area under the curve; AUC > 0.95); however, forecasting and backcasting to alternative time periods suggested less predictive power. Our results identify fragments that could be considered refuges for endemic plains fish species and we highlight significant environmental factors (e.g., discharge) that could be manipulated to aid recovery.

  3. Backcasting the decline of a vulnerable Great Plains reproductive ecotype: identifying threats and conservation priorities.

    Science.gov (United States)

    Worthington, Thomas A; Brewer, Shannon K; Grabowski, Timothy B; Mueller, Julia

    2014-01-01

    Conservation efforts for threatened or endangered species are challenging because the multi-scale factors that relate to their decline or inhibit their recovery are often unknown. To further exacerbate matters, the perceptions associated with the mechanisms of species decline are often viewed myopically rather than across the entire species range. We used over 80 years of fish presence data collected from the Great Plains and associated ecoregions of the United States, to investigate the relative influence of changing environmental factors on the historic and current truncated distributions of the Arkansas River shiner Notropis girardi. Arkansas River shiner represent a threatened reproductive ecotype considered especially well adapted to the harsh environmental extremes of the Great Plains. Historic (n = 163 records) and current (n = 47 records) species distribution models were constructed using a vector-based approach in MaxEnt by splitting the available data at a time when Arkansas River shiner dramatically declined. Discharge and stream order were significant predictors in both models; however, the shape of the relationship between the predictors and species presence varied between time periods. Drift distance (river fragment length available for ichthyoplankton downstream drift before meeting a barrier) was a more important predictor in the current model and indicated river segments 375-780 km had the highest probability of species presence. Performance for the historic and current models was high (area under the curve; AUC > 0.95); however, forecasting and backcasting to alternative time periods suggested less predictive power. Our results identify fragments that could be considered refuges for endemic plains fish species and we highlight significant environmental factors (e.g., discharge) that could be manipulated to aid recovery. Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

  4. Effects of Elevated CO2 on Biomass and Fungi Associated with Two Ecotypes of Ragweed (Ambrosia artemisiifolia L.

    Directory of Open Access Journals (Sweden)

    G. Brett Runion

    2014-09-01

    Full Text Available Herbicide resistant weed populations have developed due to the repeated application of herbicides. Elevated concentrations of atmospheric CO2 can have positive effects on weed growth, but how rising CO2 might affect herbicide resistant weeds is not known. Ragweed (Ambrosia artemisiifolia L. ecotypes known to be resistant or susceptible to glyphosate herbicide were exposed to either ambient or elevated (ambient + 200 µmol mol-1 concentrations of CO2 in open top chambers. Plants were harvested following 8 weeks of CO2 exposure; at this time, they had begun to exhibit disease symptoms including spots on leaves and stems. Elevated CO2 significantly increased top, root, and total plant biomass. Also, glyphosate resistant plants had significantly greater top, root, and total biomass than plants susceptible to the herbicide. There were no significant CO2 by ecotype interactions. Fungi from 13 genera were associated with ragweed, several of the which can be either pathogens (i.e., Alternaria, Fusarium, Rhizoctonia, aiding the decline in health of the ragweed plants, or saprophytes existing on dead plant tissues. The common foliar disease powdery mildew was significantly higher on susceptible compared with resistant ragweed. Susceptible plants also showed an increased frequency of Rhizoctonia on leaves and Alternaria on stems; however, Fusarium occurred more frequently on resistant ragweed leaves. Fungi were not affected by CO2 concentration or its interaction with ecotype. This study reports the first information on the effects of elevated CO2 on growth of herbicide resistant weeds. This is also the first study examining the impact of herbicide resistance and elevated CO2 on fungi associated with weeds. What effects herbicide resistance might have on plant diseases and how rising atmospheric CO2 might impact these effects needs to be addressed, not only with important weeds but also with crops.

  5. Effects of elevated CO2 on biomass and fungi associated with two ecotypes of ragweed (Ambrosia artemisiifolia L.).

    Science.gov (United States)

    Runion, G Brett; Prior, Stephen A; Price, Andrew J; McElroy, J Scott; Torbert, H Allen

    2014-01-01

    Herbicide resistant weed populations have developed due to the repeated application of herbicides. Elevated concentrations of atmospheric CO2 can have positive effects on weed growth, but how rising CO2 might affect herbicide resistant weeds is not known. Ragweed (Ambrosia artemisiifolia L.) ecotypes known to be resistant or susceptible to glyphosate herbicide were exposed to either ambient or elevated (ambient +200 μ mol mol(-1)) concentrations of CO2 in open top chambers. Plants were harvested following 8 weeks of CO2 exposure; at this time, they had begun to exhibit disease symptoms including spots on leaves and stems. Elevated CO2 significantly increased top, root, and total plant biomass. Also, glyphosate resistant plants had significantly greater top, root, and total biomass than plants susceptible to the herbicide. There were no significant CO2 by ecotype interactions. Fungi from 13 genera were associated with ragweed, several of which can be either pathogens (i.e., Alternaria, Fusarium, Rhizoctonia), aiding the decline in health of the ragweed plants, or saprophytes existing on dead plant tissues. The common foliar disease powdery mildew was significantly higher on susceptible compared with resistant ragweed. Susceptible plants also showed an increased frequency of Rhizoctonia on leaves and Alternaria on stems; however, Fusarium occurred more frequently on resistant ragweed leaves. Fungi were not affected by CO2 concentration or its interaction with ecotype. This study reports the first information on the effects of elevated CO2 on growth of herbicide resistant weeds. This is also the first study examining the impact of herbicide resistance and elevated CO2 on fungi associated with weeds. What effects herbicide resistance might have on plant diseases and how rising atmospheric CO2 might impact these effects needs to be addressed, not only with important weeds but also with crops.

  6. The adaptive significance of differences of root morphology, anatomy and physiology from three ecotypes of reed (Phragmites communis Trin.)

    Institute of Scientific and Technical Information of China (English)

    YuBing Liu; XinRong Li; ZhiShan Zhang; XiaoJun Li; Jin Wang

    2016-01-01

    Reeds are widely distributed in drought and high salt conditions of northwestern China. Leaf epidermal micromorpholo-gy, anatomy, chloroplast ultrastructure and physio-chemical characteristics due to long-term adaptation in the natural habitats of common reed (Phragmites communis Trin.) contrasted considerably among three different ecotypes: dune reed (DR), Gobi salt reed (GSR) and swamp reed (SR). The main objective of the present study is to determine the adapting characteristics of morphology, anatomy and physiological responses of thin roots in DR, GSR and SR. The results show that root length density was higher in SR and few root hairs were observed in DR. Cross-section anatomical features show that each ecotype has an endodermis and exodermis, while cortex thickness and proportion of root cortical aerenchyma and stele in root structure varied among the three ecotypes. The stele and xylem share a larger area in DR compared to GSR and SR. GSR has a large proportion of the cortex with radialized distribution of aerenchyma cells spacing, and the cortex has a peripheral, mechanically stiff ring in the exodermis. SEM and TEM microscope images show that GSR has a scle-renchyma ring with high lignification in the exodermis. The physio-chemical parameters show that GSR had a higher level of stress tolerance than DR. These findings indicate that developed water-absorbing tissues were largely distributed in the root structure of DR, and a main framework with supporting function spacing with aerenchyma was dominant in GSR in the long term adaptation to their natural habitats, respectively.

  7. Root responses and metal accumulation in two contrasting ecotypes of Sedum alfredii Hance under lead and zinc toxic stress.

    Science.gov (United States)

    Li, Ting-Qiang; Yang, Xiao-E; Jin, Xiao-Fen; He, Zhen-Li; Stoffella, Peter-J; Hu, Qing-Hua

    2005-01-01

    Sedum alfredii Hance has been reported to be a Zn-hyperaccumulator plant species. In this study, root morphological and physiological response of the hyperaccumulating ecotype of S. alfredii H. (HE) from the mined area and the non-hyperaccumulating ecotype of S. alfredii H. (NHE) from the agricultural area to supplied levels of Zn and Pb were investigated. The results showed that Zn concentrations in the leaves and the stems of the HE were 34 and 41 times higher, whereas lead concentrations were 1.9 and 2.4 times greater, respectively, than those of the NHE when grown at 1224 microM Zn and/or 200 microM Pb. At combined supply of 1224 microM Zn with 200 microM Pb, however, zinc concentrations in the stems and leaves of the, HE decreased, while lead concentrations in the stems increased significantly, as compared with those of single metal treatment. Lead uptake of the HE was enhanced by Zn addition. Root activity of the HE decreased by Pb treatment in the first two days, but recovered afterward and close to the control at day 10 of the treatment. However, root activity of the NHE decreased by each metal treatment, and was not recovered with the advance of treatment time. Root length, root surface area, and root volumes increased obviously due to Zn and/or Pb/Zn combined treatments for the HE, but significantly decreased due to Pb, Zn, or Pb/Zn combined treatment for the NHE. Zinc and Pb concentrations in both ecotypes of S. alfredii H. were positively correlated with root length, root surface area, and root volumes. Root exudates of the HE, especially treated with Zn, increased the extractability of Pb and Zn from the mined soil. At the Zn supply level of 1224microM, the extractability of root exudates on soil Pb was 3-12 times greater for the HE than for the NHE. These results imply that the tolerance and hyperaccumulation of the hyperaccumulating ecotype of S. alfredii H. to Zn and Pb appear to be closely related to its high adaptation of root growth, morphology

  8. Pomological features, nutritional quality, polyphenol content analysis, and antioxidant properties of domesticated and 3 wild ecotype forms of raspberries (Rubus idaeus L.).

    Science.gov (United States)

    Gülçin, Ilhami; Topal, Fevzi; Çakmakçı, Ramazan; Bilsel, Mine; Gören, Ahmet C; Erdogan, Ummugulsum

    2011-05-01

    The raspberry (Rubus idaeus L.) is an economically important berry crop that contains many phenolic compounds with potential health benefits. In this study, important pomological features, including nutrient content and antioxidant properties, of a domesticated and 3 wild (Yayla, Yavuzlar, and Yedigöl) raspberry fruits were evaluated. Also, the amount of total phenolics and flavonoids in lyophilized aqueous extracts of domesticated and wild ecotypes of raspberry fruits were calculated as gallic acid equivalents (GAEs) and quercetin equivalents (QE). The highest phenolic compounds were found in wild Yayla ecotype (26.66 ± 3.26 GAE/mg extract). Whilst, the highest flavonoids were determined in wild Yedigöl ecotype (6.09 ± 1.21 QA/mg extract). The antioxidant activity of lyophilized aqueous extracts of domesticated and wild ecotypes of raspberry fruits were investigated as trolox equivalents using different in vitro assays including DPPH(•), ABTS(•+), DMPD(•+), and O(•-)(2) radical scavenging activities, H(2)O(2) scavenging activity, ferric (Fe(3+)) and cupric ions (Cu(2+)) reducing abilities, ferrous ions (Fe(2+)) chelating activity. In addition, quantitative amounts of caffeic acid, ferulic acid, syringic acid, ellagic acid, quercetin, α-tocopherol, pyrogallol, p-hydroxybenzoic acid, vanillin, p-coumaric acid, gallic acid, and ascorbic acid in lyophilized aqueous extracts of domesticated and wild ecotypes of raspberry fruits were detected by high-performance liquid chromatography and tandem mass spectrometry (LC-MS-MS). The results clearly show that p-coumaric acid is the main phenolic acid responsible for the antioxidant and radical scavenging activity of lyophilized aqueous extracts of domesticated and wild ecotypes of raspberry fruits.

  9. Evaluation of Effect of Chemical and Organic Fertilizers on Growth Characteristics, Yield and Yield components of three Sesame Ecotypes (Sesamum indicum L.

    Directory of Open Access Journals (Sweden)

    M Goldani

    2014-07-01

    Full Text Available Using organic fertilizers is cause increase soil fertility, improving crop growth and production. For this purpose a greenhouse experiment was carried out in factorial arrangement based on a completely randomized design with three replications during 2011 year. First factor included: three sesame ecotype (MSC3, MSC6, MSC7 and second factor was 6 fertilizer treatments that included: Incorporation manure and chemical fertilizer (216 g manure and 1 gram chemical fertilizer NPK, Chemical fertilizer (2 g NPK, Vermicompost (192 g, Manure ( 228 g, Compost Sulfur granules (192 g per vase and Control (without any manure or fertilizer. Results indicated that different manure treatments had significant effect on morphological and yield components traits, as the most number and length branch per plant was obtained from incorporation manure and chemical fertilizer treatment. Appling incorporation manure and chemical fertilizer treatment had the most biomass in MSC3 ecotype that in comparison of control treatment was increased almost 73 percent. Consuming incorporation manure and chemical fertilizer treatment in MSC3 ecotype was also obtained the most capsule per plant (21.2, number seed per capsule (54.4, 100-seed weight (0.257 g and seed per plant with (1.95 g. The least seed weight per plant with 0.450 g was observed in MSC7 ecotype from application of control treatment. Response of three sesame ecotype (MSC3, MSC6, MSC7 to applied vermin-compost manure was similar; as the amount of seed weight per plant was increased more than 1 g per plant in all these ecotypes and in others fertilizer treatments was not observed this trend. There was significant positive correlation between seed weight per plant and number of capsule per plant (r=0.83**, height (r=0.68** and biomass (r=0.51**. The results showed that incorporation manure and chemical fertilizer was improved on growth and yield characteristics of sesame plant.

  10. Determination ecotypes of Populus caspica Bornm. in plain communities of Caspian forests using morphological markers of leaf and peroxidase isoenzymes

    Directory of Open Access Journals (Sweden)

    Hassan Fallah

    2011-06-01

    Full Text Available In order to determine ecotypes of Persian poplar (Populus caspica in plain communities, 40 tree individuals were selected in provinces of Guilan (Roodbar, Astane Ashrafieh and Mazandaran (Noor, Amol. Samples of two-year branches were taken in similar height and direction of tree crown to assess the quality of peroxidase activity using polyacrilamide gel electrophoresis (PAGE. Also, in numerical taxonomy study of morphology, 13 leaf morphologal traits were measured. Peroxidase banding pattern showed 11 individual bands in two zones of polyacrilamide gel. First zone included 5 polymorphism bands and the second zone represented 6 bands. The results of isoenzyme bands classification and leaf morphological traits showed high isoenzymes and morphological differentiation among populations of these species showing three separated ecotypes including Roodbar, Astaneh Ashrafieh and Noor-Amol. Also, peroxidase band pattern and leaf morphology trait between male and female individuals showed no difference within the population. The results emphasize the used of effective methods of in situ and ex situ to maintain genetic diversity of this species as an endangered and valuable in Hyrcanian forests.

  11. Out of the Pacific and back again: insights into the matrilineal history of Pacific killer whale ecotypes.

    Directory of Open Access Journals (Sweden)

    Andrew D Foote

    Full Text Available Killer whales (Orcinus orca are the most widely distributed marine mammals and have radiated to occupy a range of ecological niches. Disparate sympatric types are found in the North Atlantic, Antarctic and North Pacific oceans, however, little is known about the underlying mechanisms driving divergence. Previous phylogeographic analysis using complete mitogenomes yielded a bifurcating tree of clades corresponding to described ecotypes. However, there was low support at two nodes at which two Pacific and two Atlantic clades diverged. Here we apply further phylogenetic and coalescent analyses to partitioned mitochondrial genome sequences to better resolve the pattern of past radiations in this species. Our phylogenetic reconstructions indicate that in the North Pacific, sympatry between the maternal lineages that make up each ecotype arises from secondary contact. Both the phylogenetic reconstructions and a clinal decrease in diversity suggest a North Pacific to North Atlantic founding event, and the later return of killer whales to the North Pacific. Therefore, ecological divergence could have occurred during the allopatric phase through drift or selection and/or may have either commenced or have been consolidated upon secondary contact due to resource competition. The estimated timing of bidirectional migration between the North Pacific and North Atlantic coincided with the previous inter-glacial when the leakage of fauna from the Indo-Pacific into the Atlantic via the Agulhas current was particularly vigorous.

  12. Identification of the essential oils composition from four ecotypes of Mentha longifolia (L. Huds. growing wild in Isfahan province, Iran

    Directory of Open Access Journals (Sweden)

    REZA ABEDI

    2015-08-01

    Full Text Available Mentha longifolia L., commonly known as wild mint, belongs to family Lamiaceae. The aim of this study was to identify the chemical composition of essential oil extracted from four ecotypes of Mentha longifolia L. grown wild (Shahreza, Chadegan, Isfahan, and Falavarjan in Isfahan province (Central Iran. The essential oil was extracted by a Clevenger approach and analyzed using GC/MS. In the aerial parts of the plant were identified 26, 30, 22 and 25 compounds for Shahreza, Chadegan, Isfahan and Falavarjan ecotypes, respectively. The major constituents of the essential oil from the aerial parts of M. longifolia in Shahreza province were piperitenone oxide (26.71%, 1,8-cineole (20.72%, α-pinene (14.28%, pulegone (7.81%, sabinene (7.06% and trans-caryophyllene (4.23%. The main compositions in Chadegan province were piperitenone oxide (29.13%, 1,8-cineole (28.84%, sabinene (9.05%, pulegone (8.97% and α-pinene (6.31%. The main compositions in Isfahan province were pulegone (44.75%, 1,8-cineole (13.82%, 2-cyclohexen-1-ol, 1-methyl (8.49%, isopulegone (8.07% and menthone (4.37%. In Falavarjan province the constituents were pulegone (33.39%, 1,8-cineole (29.79%, sabinene (11.23% and isopulegone (7.28%.

  13. Stable isotopes reveal ecotypic variation of water uptake patterns in Aleppo pine

    Science.gov (United States)

    Ferrio, Juan Pedro; Lucabaugh, Devon; Chambel, Regina; Voltas, Jordi

    2014-05-01

    Aleppo pine (Pinus halepensis Mill.) has a large natural distribution range that encompasses a multitude of thermal and moisture conditions found in the Mediterranean basin. We hypothesized that due to the recurrent incidences of drought stress and high temperatures that occur at varying degrees along its distribution range, populations of Aleppo pine have undergone ecotypic differentiation in soil water uptake patterns. This study analyzed stable isotopic compositions (δ18O and δ2H) of xylem water to identify adaptive divergence associated to the pattern of soil water consumption by roots of Aleppo pine populations originating from the Mediterranean region. The results from this study show that genetic diversity in the extraction pattern of soil water can be found among populations and ecological regions of Aleppo pine under common garden conditions. However, the ability to detect such differences depended on the period of the year examined. In particular, data collection in full summer (end of July) proved to be the most adequate in revealing genetic divergence among populations, while end of spring and, to a lesser extent, end of summer, were less successful for this purpose. Both water uptake patterns (as estimated by δ18O and δ2H) and above-ground growth, exhibited significant relationships with both climatic and geographical variables. This suggests that the underlying variation among populations can be explained by certain characteristics at origin. In addition, we used a bayesian mixing model (SIAR package for R) that incorporated isotopic signatures from xylem and soil water in order to determine the predominant soil layer of water source consumption at the aforementioned periods of the growing season, where water availably ranged from lowest to highest. This allowed us to gain some understanding of Aleppo pines' differential reaction to drought, at the intraspecific level, across the fluctuating conditions of the growing season by comparing the

  14. The Amazonian Floodplains, an ecotype with challenging questions on volatile organic compound (VOC) emissions

    Science.gov (United States)

    Kesselmeier, J.

    2012-12-01

    based on short-term experiments is risky being transferred to an ecotype which is governed under natural conditions by long term flooding. Furthermore, contrasting such experiments with usually young trees (saplings or a few years old) nothing is known about the emission behavior of adult trees under field conditions.

  15. Deep learning

    Science.gov (United States)

    Lecun, Yann; Bengio, Yoshua; Hinton, Geoffrey

    2015-05-01

    Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

  16. No effect of seed source on multiple aspects of ecosystem functioning during ecological restoration: cultivars compared to local ecotypes of dominant grasses

    Science.gov (United States)

    Baer, Sara G; Gibson, David J; Gustafson, Danny J; Benscoter, Allison M; Reed, Lewis K; Campbell, Ryan E; Klopf, Ryan P; Willand, Jason E; Wodika, Ben R

    2014-01-01

    Genetic principles underlie recommendations to use local seed, but a paucity of information exists on the genetic distinction and ecological consequences of using different seed sources in restorations. We established a field experiment to test whether cultivars and local ecotypes of dominant prairie grasses were genetically distinct and differentially influenced ecosystem functioning. Whole plots were assigned to cultivar and local ecotype grass sources. Three subplots within each whole plot were seeded to unique pools of subordinate species. The cultivar of the increasingly dominant grass, Sorghastrum nutans, was genetically different than the local ecotype, but genetic diversity was similar between the two sources. There were no differences in aboveground net primary production, soil carbon accrual, and net nitrogen mineralization rate in soil between the grass sources. Comparable productivity of the grass sources among the species pools for four years shows functional equivalence in terms of biomass production. Subordinate species comprised over half the aboveground productivity, which may have diluted the potential for documented trait differences between the grass sources to influence ecosystem processes. Regionally developed cultivars may be a suitable alternative to local ecotypes for restoration in fragmented landscapes with limited gene flow between natural and restored prairie and negligible recruitment by seed. PMID:24567751

  17. Characterization of the uranium (VI) complexes formed by the cells of three A. ferrooxidans eco-types using time-resolved laser-induced fluorescence spectroscopy (TRLFS)

    Energy Technology Data Exchange (ETDEWEB)

    Merroun, M.; Geipel, G.; Selenska-Pobell, S.

    2002-05-01

    TRLFS was used to study the properties of the uranium complexes formed by the cells of the three recently described eco-types of A. ferrooxidans /1/. The results demonstrate that the lifetimes of the complexes are type-specific and are increasing in the same order as the capability of the bacterial strains to accumulate uranium. (orig.)

  18. PHYTOTOXICITY AND FIELD EFFICACY OF EXSEROHILUM LONGIROSTRA JC/MIN THE CONTROL OF BARNYARDGRASS ECOTYPES (ECHINOCHLOA CRUS-GALLI VAR. CRUS-GALLI(L. BEAUV

    Directory of Open Access Journals (Sweden)

    SUHAIMI NAPIS

    2005-01-01

    Full Text Available Five selected ecotypes of bamyardgrass (Echinochloa crus-galli var. crus-gatti from several rice growing areas in Malaysia and Indonesia were tested for their susceptibility to the potentia l bioherbicide (Exserohilum longirostratum. Bamyardgrass seedlings at the 2-3-lcaf stage were treated with 2.5xl07 conidia/ml from E. longirostratum at different application frequencies (single, double and triple. In addition, aqueous extract assays were ev aluated for the presence of a phytotoxic compound responsible for the virulence of the bioherbicide. Results of the study showed that disease severity significantly increased 20 days after treatment and resulted in mortality of the seedlin gs. Ecotypes from Perak and Lampung were most susceptible to the bioherbicide upon triple applications. Percentage dry weight reductions were 86.34 and 83.14%, respectively. Other ecotypes (Melaka, Banten and South Sulawesi were observed to have a relatively similar response. Moreover, aqueous extracts of E. longirostratum increased mortality up to 92.50% of bamyardgrass seedlings. These findings suggest that regular (double and triple applications of E. longirostratum at a concentration of 2.5xl07 conidia/ml significantly increased mortality among bamyardgrass ecotypes. Mortality of the seedlings was attributed to the presence of a secondary phytotoxic metabolite.

  19. Deep Fish.

    Science.gov (United States)

    Ishaq, Omer; Sadanandan, Sajith Kecheril; Wählby, Carolina

    2017-01-01

    Zebrafish ( Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.

  20. Root and shoot transcriptome analysis of two ecotypes of Noccaea caerulescens uncovers the role of NcNramp1 in Cd hyperaccumulation.

    Science.gov (United States)

    Milner, Matthew J; Mitani-Ueno, Namiki; Yamaji, Naoki; Yokosho, Kengo; Craft, Eric; Fei, Zhangjun; Ebbs, Stephen; Clemencia Zambrano, M; Ma, Jian Feng; Kochian, Leon V

    2014-05-01

    The Zn/Cd hyperaccumulator, Noccaea caerulescens, has been studied extensively for its ability to accumulate high levels of Zn and Cd in its leaves. Previous studies have indicated that the Zn and Cd hyperaccumulation trait exhibited by this species involves different transport and tolerance mechanisms. It has also been well documented that certain ecotypes of N. caerulescens are much better Cd hyperaccumulators than others. However, there does not seem to be much ecotypic variation for Zn hyperaccumulation in N. caerulescens. In this study we employed a comparative transcriptomics approach to look at root and shoot gene expression in Ganges and Prayon plants in response to Cd stress to identify transporter genes that were more highly expressed in either the roots or shoots of the superior Cd accumulator, Ganges. Comparison of the transcriptomes from the two ecotypes of Noccaea caerulescens identified a number of genes that encoded metal transporters that were more highly expressed in the Ganges ecotype in response to Cd stress. Characterization of one of these transporters, NcNramp1, showed that it is involved in the influx of Cd across the endodermal plasma membrane and thus may play a key role in Cd flux into the stele and root-to-shoot Cd transport. NcNramp1 may be one of the main transporters involved in Cd hyperaccumulation in N. caerulescens and copy number variation appears to be the main reason for high NcNramp1 gene expression underlying the increased Cd accumulation in the Ganges ecotype. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  1. Lead Induced Changes in the Growth and Antioxidant Metabolism of the Lead Accumulating and Non-accumulating Ecotypes of Sedum alfredii

    Institute of Scientific and Technical Information of China (English)

    Dan Liu; Ting-Qiang Li; Xiao-Fen Jin; Xiao-E Yang; Ejazul Islam; Qaisar Mahmood

    2008-01-01

    The phytotoxicity and antioxidative adaptations of lead (Pb) accumulating ecotype (AE) and non-accumulating ecotype (NAE) of Sedum alfredii Hance were investigated under different Pb treatments involving 0, 0.02 mmol/L Pb, 0.1 mmol/L Pb and 0.1 mmol/L Pb/0.1 mmol/L ethylenediaminetetraacetic acid (EDTA) for 6days. With the Increasing Pb level, the Pb concentration in the shoots of AE plants enhanced accordingly, and EDTA supply helped 51% of Pb translocation to shoots of AE compared with those treated with 0.1 mmol/L Pb alone. Moreover, the presence of EDTA alleviated Pb phytotoxicity through changes in plant biomass, root morphology and chlorophyll contents. Lead toxicity Induced hydrogen peroxide (H2O2) accumulation and lipid peroxidation in both ecotypes of S. alfredii. The activities of superoxide dismutase (SOD), guaiacol peroxidase (G-POD), ascorbate peroxidase, and dehydroascorbate reductase elevated in both leaves and roots of AE as well as in leaves of NAE with the increasing Pb levels, but SOD and G-POD declined in roots of NAE. Enhancement in glutathione reductase activity was only detected in roots of NAE while a depression in catalase activity was recorded in the leaves of NAE. A significant enhancement in glutathione and ascorbic acid (AsA) levels occurred In both ecotypes exposed to Pb and Pb/EDTA treatment compared with the control, however, the differences between these two treatments were insignificant. The dehydroascorbate (DHA) contents in roots of both ecotypes were 1.41 to 11.22-fold higher than those in leaves, whereas the ratios of AsA to DHA (1.38 to 6.84) in leaves altering more to the reduced AsA form were much higher than those in roots. These results suggested that antioxidative enzymes and antioxidants play an important role in counteracting Pb stress in S. alfredii.

  2. Different NaCl-Induced Calcium Signatures in the Arabidopsis thaliana Ecotypes Col-0 and C24

    KAUST Repository

    Schmöckel, Sandra M.

    2015-02-27

    A common feature of stress signalling pathways are alterations in the concentration of cytosolic free calcium ([Ca2+]cyt), which allow the specific and rapid transmission of stress signals through a plant after exposure to a stress, such as salinity. Here, we used an aequorin based bioluminescence assay to compare the NaCl-induced changes in [Ca2+]cyt of the Arabidopsis ecotypes Col-0 and C24. We show that C24 lacks the NaCl specific component of the [Ca2+]cyt signature compared to Col-0. This phenotypic variation could be exploited as a screening methodology for the identification of yet unknown components in the early stages of the salt signalling pathway.

  3. Different NaCl-induced calcium signatures in the Arabidopsis thaliana ecotypes Col-0 and C24.

    Science.gov (United States)

    Schmöckel, Sandra M; Garcia, Alexandre F; Berger, Bettina; Tester, Mark; Webb, Alex A R; Roy, Stuart J

    2015-01-01

    A common feature of stress signalling pathways are alterations in the concentration of cytosolic free calcium ([Ca2+]cyt), which allow the specific and rapid transmission of stress signals through a plant after exposure to a stress, such as salinity. Here, we used an aequorin based bioluminescence assay to compare the NaCl-induced changes in [Ca2+]cyt of the Arabidopsis ecotypes Col-0 and C24. We show that C24 lacks the NaCl specific component of the [Ca2+]cyt signature compared to Col-0. This phenotypic variation could be exploited as a screening methodology for the identification of yet unknown components in the early stages of the salt signalling pathway.

  4. A compatible interaction of Alternaria brassicicola with Arabidopsis thaliana ecotype DiG: evidence for a specific transcriptional signature

    Directory of Open Access Journals (Sweden)

    Gepstein Shimon

    2009-03-01

    Full Text Available Abstract Background The interaction of Arabidopsis with Alternaria brassicicola provides a model for disease caused by necrotrophs, but a drawback has been the lack of a compatible pathosystem. Infection of most ecotypes, including the widely-studied line Col-0, with this pathogen generally leads to a lesion that does not expand beyond the inoculated area. This study examines an ecotype, Dijon G (DiG, which is considered sensitive to A. brassicicola. Results We show that the interaction has the characteristics of a compatible one, with expanding rather than limited lesions. To ask whether DiG is merely more sensitive to the pathogen or, rather, interacts in distinct manner, we identified genes whose regulation differs between Col-0 and DiG challenged with A. brassicicola. Suppression subtractive hybridization was used to identify differentially expressed genes, and their expression was verified using semi-quantitative PCR. We also tested a set of known defense-related genes for differential regulation in the two plant-pathogen interactions. Several known pathogenesis-related (PR genes are up-regulated in both interactions. PR1, and a monooxygenase gene identified in this study, MO1, are preferentially up-regulated in the compatible interaction. In contrast, GLIP1, which encodes a secreted lipase, and DIOX1, a pathogen-response related dioxygenase, are preferentially up-regulated in the incompatible interaction. Conclusion The results show that DiG is not only more susceptible, but demonstrate that its interaction with A. brassicicola has a specific transcriptional signature.

  5. Imaging with the fluorogenic dye Basic Fuchsin reveals subcellular patterning and ecotype variation of lignification in Brachypodium distachyon

    Science.gov (United States)

    Kapp, Nikki; Barnes, William J.; Richard, Tom L.; Anderson, Charles T.

    2015-01-01

    Lignin is a complex polyphenolic heteropolymer that is abundant in the secondary cell walls of plants and functions in growth and defence. It is also a major barrier to the deconstruction of plant biomass for bioenergy production, but the spatiotemporal details of how lignin is deposited in actively lignifying tissues and the precise relationships between wall lignification in different cell types and developmental events, such as flowering, are incompletely understood. Here, the lignin-detecting fluorogenic dye, Basic Fuchsin, was adapted to enable comparative fluorescence-based imaging of lignin in the basal internodes of three Brachypodium distachyon ecotypes that display divergent flowering times. It was found that the extent and intensity of Basic Fuchsin fluorescence increase over time in the Bd21-3 ecotype, that Basic Fuchsin staining is more widespread and intense in 4-week-old Bd21-3 and Adi-10 basal internodes than in Bd1-1 internodes, and that Basic Fuchsin staining reveals subcellular patterns of lignin in vascular and interfascicular fibre cell walls. Basic Fuchsin fluorescence did not correlate with lignin quantification by acetyl bromide analysis, indicating that whole-plant and subcellular lignin analyses provide distinct information about the extent and patterns of lignification in B. distachyon. Finally, it was found that flowering time correlated with a transient increase in total lignin, but did not correlate strongly with the patterning of stem lignification, suggesting that additional developmental pathways might regulate secondary wall formation in grasses. This study provides a new comparative tool for imaging lignin in plants and helps inform our views of how lignification proceeds in grasses. PMID:25922482

  6. Deep Vein Thrombosis

    Science.gov (United States)

    Deep vein thrombosis, or DVT, is a blood clot that forms in a vein deep in the body. Most deep vein ... the condition is called thrombophlebitis. A deep vein thrombosis can break loose and cause a serious problem ...

  7. Adaptation to flooding in upland and lowland ecotypes of Cyperus rotundus, a troublesome sedge weed of rice: tuber morphology and carbohydrate metabolism

    Science.gov (United States)

    Peña-Fronteras, Jennifer T.; Villalobos, Mizpah C.; Baltazar, Aurora M.; Merca, Florinia E.; Ismail, Abdelbagi M.; Johnson, David E.

    2009-01-01

    Background and aims In recent years, Cyperus rotundus has become a problem weed in lowland rice (Oryza sativa) grown in rotation with vegetables in the Philippines. As the growth of C. rotundus is commonly suppressed by prolonged flooding, the ability of the weed to grow vigorously in flooded as well as upland conditions suggests that adapted ecotypes occur in these rotations. Studies were conducted to elucidate the mechanisms that permit C. rotundus to tolerate flooded soil conditions. Methods Upland and lowland ecotypes of C. rotundus were compared in terms of growth habit, carbohydrate reserves and metabolism, and activities of enzymes involved in alcoholic fermentation – alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC). Key Results The lowland ecotype has much larger tubers than the upland ecotype. Prior to germination, the amylase activity and total non-structural carbohydrate content in the form of soluble sugars were greater in the tubers of lowland plants than in those of upland C. rotundus. At 24 h after germination in hypoxic conditions, PDC and ADH activities in the lowland plants increased, before decreasing at 48 h following germination. In contrast, ADH and PDC activities in the upland plants increased from 24 to 48 h after germination. Conclusions Tolerance of lowland C. rotundus of flooding may be attributed to large carbohydrate content and amylase activity, and the ability to maintain high levels of soluble sugars in the tubers during germination and early growth. This is coupled with the modulation of ADH and PDC activities during germination, possibly to control the use of carbohydrate reserves and sustain substrate supply in order to avoid starvation and death of seedlings with prolonged flooding. PMID:18515404

  8. Evaluation of Effect of Chemical and Organic Fertilizers on Growth Characteristics, Yield and Yield components of three Sesame Ecotypes (Sesamum indicum L.)

    OpenAIRE

    M Goldani; Fazel Fazeli Kakhki

    2014-01-01

    Using organic fertilizers is cause increase soil fertility, improving crop growth and production. For this purpose a greenhouse experiment was carried out in factorial arrangement based on a completely randomized design with three replications during 2011 year. First factor included: three sesame ecotype (MSC3, MSC6, MSC7) and second factor was 6 fertilizer treatments that included: Incorporation manure and chemical fertilizer (216 g manure and 1 gram chemical fertilizer NPK), Chemical fertil...

  9. PHYTOTOXICITY AND FIELD EFFICACY OF EXSEROHILUM LONGIROSTRA JC/MIN THE CONTROL OF BARNYARDGRASS ECOTYPES (ECHINOCHLOA CRUS-GALLI VAR. CRUS-GALLI(L.) BEAUV)

    OpenAIRE

    SUHAIMI NAPIS; ARIFIN TASRIF; JUGAH KADIR; ABDUL SHUKOR JURAIMI; SOETIKNO SLAMET SASTROUTOMO

    2005-01-01

    Five selected ecotypes of bamyardgrass (Echinochloa crus-galli var. crus-gatti) from several rice growing areas in Malaysia and Indonesia were tested for their susceptibility to the potentia l bioherbicide (Exserohilum longirostratum). Bamyardgrass seedlings at the 2-3-lcaf stage were treated with 2.5xl07 conidia/ml from E. longirostratum at different application frequencies (single, double and triple). In addition, aqueous extract assays were ev aluated for the presence of a phytotoxic c...

  10. Deep blast

    Science.gov (United States)

    From southern New Mexico to the Great Slave Lake of Canada, scientists from the United States and Canada recently detonated 10 underground chemical explosions to generate a clearer picture of the Earth's crust and upper mantle. Called Project Deep Probe, the experiment is designed to see through the crust and into the upper mantle to a depth of 300 miles.In the United States, Earth scientists from Rice University, Purdue University, and the University of Oregon are participating in the project. “Researchers hope to get a picture of the upper mantle beneath the Rocky Mountains and the Colorado Plateau, to understand the role the mantle played in formation and uplift,” says Alan Levander of Rice. To enhance that “picture,” 750 portable seismographs were placed along a roughly north-south line extending from Crownpoint, New Mexico to Edmonton, Alberta. The seismic recordings will be used to enhance weak seismic waves that penetrated the upper mantle.

  11. RAPD-PCR and real-time PCR HRM based genetic variation evaluations of Urtica dioica parts, ecotypes and evaluations of morphotypes in Turkey.

    Science.gov (United States)

    Uzonur, Irem; Akdeniz, Gamze; Katmer, Zeynep; Ersoy, Seyda Karaman

    2013-01-01

    Urtica dioica is an ethnobotanically and medicinally important Complementary and Alternative Medicine (CAM) plant worldwide and in Turkey; 90 % of herbal CAM applications depend on it in Turkey. It has a wide range of habitats in nearly all continents. It is found in all three phytogeographical regions in Turkey (Euro-Siberian, Irano-Turanian, Mediterranean) with high adaptivity to heterogeneous geographies such as climate, soil types and altitudes. This fact in relation to the assessment of chemical constituents of the plant and combining with further genetic and morphological variation data can assist and enhance the works for the utility and reliability of CAM applications in effect and activity of this plant species. In this work we have made some preliminary experiments with novel approaches to reveal the ecotypes and genetic variation of mighty ecotypes of Urtica dioica from different phytogeographical regions of Turkey (Euro-Siberian and Mediterranean). The ecotypes have heterogeneity in both its parts (leaf, stem, root) as revealed by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) using random primers and High-resolution Melt (HRM) analysis using Urtica dioica specific primers and universal chloroplast DNA (cpDNA) primers and morphological traits such as phenolic contents and antioxidant capacities of plants' leaf infusions as used in medicinal applications in Turkey. This work will contribute a lot for the development of molecular markers to detect the genetic variation and heterogeneity of Urtica dioica to further relate with expected phenotypes that are most useful and relevant in CAM applications.

  12. A Comparative Study of Growth Performance and Feed Efficiency in Dominant Black Strain, Fulani Ecotype Chicken and Progeny from their Reciprocal Crosses

    Directory of Open Access Journals (Sweden)

    Sola-Ojo, F. E.

    2012-06-01

    Full Text Available A study of the relative performance of a local chicken (Fulani Ecotype or FExFE, an exotic chicken (Dominant Black or DBxDB, and their reciprocal crosses (DBxFE and FExDB was undertaken. A total of three hundred and thirty (330 chickens comprising 100 DBxDB, 80 DBxFE, 80 FExDB and 70 FExFE were studied. All animals were raised from day old to 21 weeks age contemporaneously under identical housing, feeding and management procedures during which growth parameters were measured. Significant (p DBxFE 1346.80±3.05 > DBxDB 1314.40±3.61 over the 21 week experimental period. FExFE had significantly (p FExFE 67.50±0.02 over the same period. Low mortality (≤ 2% occurred across genotypes with FExFE having the least mortality. The results indicated that reciprocal crossing of pure local Fulani Ecotype with exotic Dominant Black strain produces chickens with indistinguishable Feed Efficiency from the highly improved Dominant Black, and superior to the pure Fulani. Cross breeding of the type reported here may therefore serve as a tool for improving efficiency of Fulani Ecotype local poultry whilst retaining elements of their valued characteristics which include meat value. Further studies will evaluate the hybrids (F1 of FE and DB for retention of desirable characteristics of local breeds.

  13. Seed longevity of red rice ecotypes buried in soil Longevidade de sementes de arroz-vermelho enterradas no solo

    Directory of Open Access Journals (Sweden)

    J.A. Noldin

    2006-12-01

    Full Text Available Red rice is a troublesome weed in irrigated rice production and is spread through contaminated commercial rice seed and machinery. Seed dormancy is a major trait for red rice. Studies were carried out at two locations to determine red rice seed longevity in the soil of several ecotypes from four US states. Five months after burial near Beaumont, Texas only three ecotypes had viable seed (O arroz-vermelho constitui-se na principal planta daninha infestante de lavouras de arroz irrigado e a sua disseminação ocorre, principalmente, pelo uso de sementes comerciais contaminadas e equipamentos agrícolas. A ocorrência de dormência nas sementes é uma das principais características que dificultam o controle do arroz-vermelho em lavouras. O objetivo deste trabalho foi estimar a longevidade no solo de ecótipos de arroz-vermelho provenientes de diferentes áreas de produção de arroz nos Estados Unidos. O estudo foi conduzido em dois locais: Beaumont e College Station, no estado do Texas (TX. Para sementes enterradas a 5 cm de profundidade em Beaumont, apenas três ecótipos apresentaram sementes viáveis (<1%. No entanto, quando as sementes foram enterradas em maior profundidade (25 cm, nove ecótipos tinham sementes viáveis após 2 anos. Trinta e seis meses após o enterrio, cinco ecótipos apresentavam sementes com alguma viabilidade, mas todos inferiores a 1%. Sementes de arroz-vermelho produzidas e enterradas em College Station na profundidade de 12 cm, um dia após a colheita, apresentaram maior longevidade que aquelas mantidas na superfície do solo. Após 17 meses, um dos ecótipos de arroz-preto (TX 4, enterrado a 12 cm, foi o que apresentou maior percentual de viabilidade (2%. Nos dois experimentos, observou-se que os cultivares comerciais, Lemont e Mars, não apresentaram sementes viáveis após cinco meses, independentemente da localização no solo. Os resultados deste estudo sugerem que em áreas com arroz-vermelho deve-se evitar o

  14. Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS

    Science.gov (United States)

    Luo, Qing; Wang, Shiyu; Sun, Li-Na; Wang, Hui

    2017-01-01

    Phytoremediation is an effective method to remediate Pb-contaminated soils and root exudates play an important role in this process. Based on gas chromatography-mass spectrometry (GC-MS) and metabolomics method, this study focuses on the comparative metabolic profiling analysis of root exudates from the Pb-accumulating and non-accumulating ecotypes of Sedum alfredii treated with 0 and 50 μmol/L Pb. The results obtained show that plant type and Pb stress can significantly change the concentrations and species of root exudates, and fifteen compounds were identified and assumed to be potential biomarkers. Leaching experiments showed that l-alanine, l-proline and oxalic acid have a good effect to activate Pb in soil, glyceric acid and 2-hydroxyacetic acid have a general effect to activate Pb in soil. 4-Methylphenol and 2-methoxyphenol might be able to activate Pb in soil, glycerol and diethyleneglycol might be able to stabilize Pb in soil, but these activation effect and stabilization effect were all not obvious.

  15. Non-destructive flavour evaluation of red onion (Allium cepa L.) ecotypes: an electronic-nose-based approach.

    Science.gov (United States)

    Russo, Mariateresa; di Sanzo, Rosa; Cefaly, Vittoria; Carabetta, Sonia; Serra, Demetrio; Fuda, Salvatore

    2013-11-15

    This work reports preliminary results on the potential of a metal oxide sensor (MOS)-based electronic nose, as a non-destructive method to discriminate three "Tropea Red Onion" PGI ecotypes (TrT, TrMC and TrA) from each other and the common red onion (RO), which is usually used to counterfeit. The signals from the sensor array were processed using a canonical discriminant function analysis (DFA) pattern recognition technique. The DFA on onion samples showed a clear separation among the four onion groups with an overall correct classification rate (CR) of 97.5%. Onion flavour is closely linked to pungency and thus to the pyruvic acid content. The e-nose analysis results are in good agreement with pyruvic acid analysis. This work demonstrated that artificial olfactory systems have potential for use as an innovative, rapid and specific non-destructive technique, and may provide a method to protect food products against counterfeiting. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Species Diversity, Abundance, and Host Preferences of Mosquitoes (Diptera: Culicidae) in Two Different Ecotypes of Madagascar With Recent RVFV Transmission.

    Science.gov (United States)

    Jean Jose Nepomichene, Thiery Nirina; Elissa, Nohal; Cardinale, Eric; Boyer, Sebastien

    2015-09-01

    Mosquito diversity and abundance were examined in six Madagascan villages in either arid (Toliary II district) or humid (Mampikony district) ecotypes, each with a history of Rift Valley fever virus transmission. Centers for Disease Control and Prevention light traps without CO2 (LT) placed near ruminant parks and animal-baited net trap (NT) baited with either zebu or sheep/goat were used to sample mosquitoes, on two occasions between March 2011 and October 2011. Culex tritaeniorhynchus (Giles) was the most abundant species, followed by Culex antennatus (Becker) and Anopheles squamosus/cydippis (Theobald/de Meillon). These three species comprised more than half of all mosquitoes collected. The NT captured more mosquitoes in diversity and in abundance than the LT, and also caught more individuals of each species, except for An. squamosus/cydippis. Highest diversity and abundance were observed in the humid and warm district of Mampikony. No host preference was highlighted, except for Cx. tritaeniorhynchus presenting a blood preference for zebu baits. The description of species diversity, abundance, and host preference described herein can inform the development of control measures to reduce the risk of mosquito-borne diseases in Madagascar.

  17. Otolith morphology and hearing abilities in cave- and surface-dwelling ecotypes of the Atlantic molly, Poecilia mexicana (Teleostei: Poeciliidae).

    Science.gov (United States)

    Schulz-Mirbach, Tanja; Ladich, Friedrich; Riesch, Rüdiger; Plath, Martin

    2010-08-01

    Cave fish have rarely been investigated with regard to their inner ear morphology, hearing abilities, and acoustic communication. Based on a previous study that revealed morphological differences in the saccular otolith between a cave and two surface populations of Poecilia mexicana, we checked for additional differences in utricular and lagenar otoliths and tested whether different populations have similar hearing sensitivities. We found pronounced differences in the shape of all three otoliths. Otoliths of the saccule and lagena from cave fish differed from those of surface fish in the features of the face oriented towards the sensory epithelium. In addition, otoliths of the utricle and lagena were significantly heavier in cave fish. Auditory sensitivities were measured between 100 and 1500Hz, utilizing the auditory evoked potential recording technique. We found similar hearing abilities in cave and surface fish, with greatest sensitivity between 200 and 300Hz. An acoustic survey revealed that neither ecotype produced species-specific sounds. Our data indicate that cave dwelling altered the otolith morphology in Atlantic mollies, probably due to metabolic differences. Different otolith morphology, however, did not affect general auditory sensitivity or acoustic behavior.

  18. Comparative proteomics reveals that a saxitoxin-producing and a nontoxic strain of Anabaena circinalis are two different ecotypes.

    Science.gov (United States)

    D'Agostino, Paul M; Song, Xiaomin; Neilan, Brett A; Moffitt, Michelle C

    2014-03-01

    In Australia, saxitoxin production is restricted to the cyanobacterial species Anabaena circinalis and is strain-dependent. We aimed to characterize a saxitoxin-producing and nontoxic strain of A. circinalis at the proteomic level using iTRAQ. Seven proteins putatively involved in saxitoxin biosynthesis were identified within our iTRAQ experiment for the first time. The proteomic profile of the toxic A. circinalis was significantly different from the nontoxic strain, indicating that each is likely to inhabit a unique ecological niche. Under control growth conditions, the saxitoxin-producing A. circinalis displayed a higher abundance of photosynthetic, carbon fixation and nitrogen metabolic proteins. Differential abundance of these proteins suggests a higher intracellular C:N ratio and a higher concentration of intracellular 2-oxoglutarate in our toxic strain compared with the nontoxic strain. This may be a novel site for posttranslational regulation because saxitoxin biosynthesis putatively requires a 2-oxoglutarate-dependent dioxygenase. The nontoxic A. circinalis was more abundant in proteins, indicating cellular stress. Overall, our study has provided the first insight into fundamental differences between a toxic and nontoxic strain of A. circinalis, indicating that they are distinct ecotypes.

  19. DeepPy: Pythonic deep learning

    OpenAIRE

    Larsen, Anders Boesen Lindbo

    2016-01-01

    This technical report introduces DeepPy – a deep learning framework built on top of NumPy with GPU acceleration. DeepPy bridges the gap between highperformance neural networks and the ease of development from Python/NumPy. Users with a background in scientific computing in Python will quickly be able to understand and change the DeepPy codebase as it is mainly implemented using high-level NumPy primitives. Moreover, DeepPy supports complex network architectures by letting the user compose mat...

  20. DeepPy: Pythonic deep learning

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo

    This technical report introduces DeepPy – a deep learning framework built on top of NumPy with GPU acceleration. DeepPy bridges the gap between highperformance neural networks and the ease of development from Python/NumPy. Users with a background in scientific computing in Python will quickly...... be able to understand and change the DeepPy codebase as it is mainly implemented using high-level NumPy primitives. Moreover, DeepPy supports complex network architectures by letting the user compose mathematical expressions as directed graphs. The latest version is available at http...

  1. Cold-acclimation limits low temperature induced photoinhibition by promoting a higher photochemical quantum yield and a more effective PSII restoration in darkness in the Antarctic rather than the Andean ecotype of Colobanthus quitensis Kunt Bartl (Cariophyllaceae

    Directory of Open Access Journals (Sweden)

    Bascuñán-Godoy Luisa

    2012-07-01

    Full Text Available Abstract Background Ecotypes of Colobanthus quitensis Kunt Bartl (Cariophyllaceae from Andes Mountains and Maritime Antarctic grow under contrasting photoinhibitory conditions, reaching differential cold tolerance upon cold acclimation. Photoinhibition depends on the extent of photodamage and recovery capability. We propose that cold acclimation increases resistance to low-temperature-induced photoinhibition, limiting photodamage and promoting recovery under cold. Therefore, the Antarctic ecotype (cold hardiest should be less photoinhibited and have better recovery from low-temperature-induced photoinhibition than the Andean ecotype. Both ecotypes were exposed to cold induced photoinhibitory treatment (PhT. Photoinhibition and recovery of photosystem II (PSII was followed by fluorescence, CO2 exchange, and immunoblotting analyses. Results The same reduction (25% in maximum PSII efficiency (Fv/Fm was observed in both cold-acclimated (CA and non-acclimated (NA plants under PhT. A full recovery was observed in CA plants of both ecotypes under dark conditions, but CA Antarctic plants recover faster than the Andean ecotype. Under PhT, CA plants maintain their quantum yield of PSII, while NA plants reduced it strongly (50% and 73% for Andean and Antarctic plants respectively. Cold acclimation induced the maintenance of PsaA and Cyt b6/f and reduced a 41% the excitation pressure in Antarctic plants, exhibiting the lowest level under PhT. xCold acclimation decreased significantly NPQs in both ecotypes, and reduced chlorophylls and D1 degradation in Andean plants under PhT. NA and CA plants were able to fully restore their normal photosynthesis, while CA Antarctic plants reached 50% higher photosynthetic rates after recovery, which was associated to electron fluxes maintenance under photoinhibitory conditions. Conclusions Cold acclimation has a greater importance on the recovery process than on limiting photodamage. Cold acclimation determined the

  2. Cold-acclimation limits low temperature induced photoinhibition by promoting a higher photochemical quantum yield and a more effective PSII restoration in darkness in the Antarctic rather than the Andean ecotype of Colobanthus quitensis Kunt Bartl (Cariophyllaceae).

    Science.gov (United States)

    Bascuñán-Godoy, Luisa; Sanhueza, Carolina; Cuba, Marely; Zuñiga, Gustavo E; Corcuera, Luis J; Bravo, León A

    2012-07-24

    Ecotypes of Colobanthus quitensis Kunt Bartl (Cariophyllaceae) from Andes Mountains and Maritime Antarctic grow under contrasting photoinhibitory conditions, reaching differential cold tolerance upon cold acclimation. Photoinhibition depends on the extent of photodamage and recovery capability. We propose that cold acclimation increases resistance to low-temperature-induced photoinhibition, limiting photodamage and promoting recovery under cold. Therefore, the Antarctic ecotype (cold hardiest) should be less photoinhibited and have better recovery from low-temperature-induced photoinhibition than the Andean ecotype. Both ecotypes were exposed to cold induced photoinhibitory treatment (PhT). Photoinhibition and recovery of photosystem II (PSII) was followed by fluorescence, CO2 exchange, and immunoblotting analyses. The same reduction (25%) in maximum PSII efficiency (Fv/Fm) was observed in both cold-acclimated (CA) and non-acclimated (NA) plants under PhT. A full recovery was observed in CA plants of both ecotypes under dark conditions, but CA Antarctic plants recover faster than the Andean ecotype.Under PhT, CA plants maintain their quantum yield of PSII, while NA plants reduced it strongly (50% and 73% for Andean and Antarctic plants respectively). Cold acclimation induced the maintenance of PsaA and Cyt b6/f and reduced a 41% the excitation pressure in Antarctic plants, exhibiting the lowest level under PhT. xCold acclimation decreased significantly NPQs in both ecotypes, and reduced chlorophylls and D1 degradation in Andean plants under PhT.NA and CA plants were able to fully restore their normal photosynthesis, while CA Antarctic plants reached 50% higher photosynthetic rates after recovery, which was associated to electron fluxes maintenance under photoinhibitory conditions. Cold acclimation has a greater importance on the recovery process than on limiting photodamage. Cold acclimation determined the kinetic and extent of recovery process under darkness in

  3. The Effect of Irrigation Cut-off in Flowering Stage and Foliar Application of Spermidine on Essential Oil Quantity and Quality of Three Ecotypes of Cumin

    Directory of Open Access Journals (Sweden)

    Sarah Bakhtari

    2017-03-01

    Full Text Available Introduction Cumin (Cuminum cyminum L. is an annual plant that commonly cultivated in arid and semiarid regions of Iran. The crop has a wide range of uses including medicinal, cosmetic and food industry. Cumin occupies about 26% of total area devoted to medicinal plants in Iran. However, cumin is seriously affected by the Fusarium wilt and blight diseases. The diseases usually increase under warm and wet conditions. Control of the diseases incidence is a crucial factor for cumin production. Limited control of the diseases is provided by seed pre-sowing with certain fungicides such as benlate. Soil fumigation with methyle bromide can provide a control measure against the disease but may be limited application value for large scale production systems in the open field. In addition, methyle bromide is considered an ozone-depleting compound and has potential risk on the living environment and human health. Considering the environmental limitations of chemical fungicides, it seems appropriate to search for a supplemental control strategy .It was demonstrated that peak of the diseases incidence is occurred at flowering stage and irrigation cut-off in this time may be reduced the diseases density. Materials and methods This experiment was conducted in a split-split-plot arrangement in randomized complete block design with three replications in research farm of Shahid Bahonar University of Kerman at 2014. The experimental treatments were irrigation (complete irrigation and cut-off the irrigation in flowering stage assigned to main plots, foliar application of spermidine (0, 1 and 2 Mm as subplot and cumin ecotypes (Kerman, Khorasan and Esfahan that was randomized in sub-subplot. The seedbed preparation was made based on common practices at the location. Plots size under the trial was 4 m×3 m so as to get 50 cm inter row spacing in six rows. The ideal density of the crops was considered as 120 plant.m-2. As soon as the seeds were sown, irrigation

  4. Assessment of Qualitative and Quantitative Characters of Two Persian Clover Ecotypes Inoculated by Rhizobium leguminosarum biovartrifoli and Pesudomonas putida Bacteria

    Directory of Open Access Journals (Sweden)

    R Azamei

    2016-02-01

    Full Text Available Introduction Over the past decades, world attitude has changed towards the reduction of environmental pollutants. Harmful effects of synthetic fertilizers on environment have been identified. Bio-fertilizers are not harmful to the environment, but also they have favorable effects on plant growth processes. Soil biotechnology can be defined as the study of soil organisms and their metabolic processes which may have positive effects on plant yields. The main goal of this study is to asess the biotechnology fertilizers beneficial effects on soil organisms and their subsequently to maximize the yield. It is also our desire conside the soil quality, hygiene and environmental protection along this process. Among the strain of nitrogen-fixing bacteria, symbiotic bacteria such as rhizobium bacteria are important and essential in planning the sustainable farming systems. Several studies have shown that crop varieties which inoculated with rhizobium and pseudomonas were superior in yield production and performance. Material and Methods An experiment was designed as factorial performed in randomized complete block design (RCBD with three replications in Agricultural Research Center of Golpayegan (Isfahan during 2010 – 2011. the purpose of this study was to evaluate the effects of inoculation of two ecotypes of Persian clover by various strains of Rhizobium leguminosarum. Biovar trifoli bacteria accompanied with plant growth promoting rhizobacteria (PGPR Pseudomonas putida was employed to find certain qualitative and quantitative characteristics of clover yield, The main plots included two local ecotypes of Persian clover; Arak Haft Chin (V1 and Isfahan Haft Chin (V2, the subplots included inoculation by two strain of Rhizobium; Rb-3, Rb-13 and one strain of Pseudomonas; PS -168.4 cuts were performed during the experiment and 60 kg/ha seed was used for cultivation based on local knowledge. According to recommendations of the Institute of Soil and Water

  5. Ecotypic differentiation between urban and rural populations of the grasshopper Chorthippus brunneus relative to climate and habitat fragmentation.

    Science.gov (United States)

    San Martin Y Gomez, Gilles; Van Dyck, Hans

    2012-05-01

    Urbanization alters environmental conditions in multiple ways and offers an ecological or evolutionary challenge for organisms to cope with. Urban areas typically have a warmer climate and strongly fragmented herbaceous vegetation; the urban landscape matrix is often assumed to be hostile for many organisms. Here, we addressed the issue of evolutionary differentiation between urban and rural populations of an ectotherm insect, the grasshopper Chorthippus brunneus. We compared mobility-related morphology and climate-related life history traits measured on the first generation offspring of grasshoppers from urban and rural populations reared in a common garden laboratory experiment. We predicted (1) the urban phenotype to be more mobile (i.e., lower mass allocation to the abdomen, longer relative femur and wing lengths) than the rural phenotype; (2) the urban phenotype to be more warm adapted (e.g., higher female body mass); and (3) further evidence of local adaptation in the form of significant interaction effects between landscape of origin and breeding temperature. Both males and females of urban origin had significantly longer relative femur and wing lengths and lower mass allocation to the abdomen (i.e., higher investment in thorax and flight muscles) relative to individuals of rural origin. The results were overall significant but small (2-4%). Body mass and larval growth rate were much higher (+10%) in females of urban origin. For the life history traits, we did not find evidence for significant interaction effects between the landscape of origin and the two breeding temperatures. Our results point to ecotypic differentiation with urbanization for mobility-related morphology and climate-related life history traits. We argue that the warmer urban environment has an indirect effect through longer growth season rather than direct effects on the development.

  6. Effect of Drought Stress on Leaf Water Status, Electrolyte Leakage, Photosynthesis Parameters and Chlorophyll Fluorescence of Two Kochia Ecotypes (Kochia scoparia Irrigated With Saline Water

    Directory of Open Access Journals (Sweden)

    A Masoumi

    2012-12-01

    Full Text Available Rainfall deficiency and the development of salinity in Iran are the most important factors for using new salt and drought-resistant plants instead of conventional crops. Kochia species have recently attracted the attention of researchers as a forage and fodder crop in marginal lands worldwide due to its drought and salt tolerant characteristics. This field experiment was performed at the Salinity Research Station of Ferdowsi University of Mashhad, Iran, in a split plot based on randomized complete block design with three replications in 2008. Drought stress, including four levels (control, no irrigation in vegetative stage, no irrigation at reproductive stage and no irrigation at maturity stage for four weeks, and two Kochia ecotypes (Birjand and Borujerd were allocated as main and sub plots, respectively. Relative water content, electrolyte leakage, photosynthesis parameters and chlorophyll fluorescence were assayed every two week from late vegetative stage. Results showed that drought stress decreased significantly measured parameters in plants under stress, in all stages. Plants completely recovered after eliminating stress and rewatering and recovered plants did not show significant difference with control. Electrolyte leaking and chlorophyll fluorescence showed the lowest change among the measured parameters. It can emphasize that resistant to stress conditions in this plant and cell wall is not damaged at this level of stress situation. Birjand ecotype from the arid region, revealed a better response than Borujerd ecotype to drought stress. Probably it returns to initial adaptation of Birjand. In general this plant can recover after severe drought stress well. It is possible to introduce this plant as a new fodder in arid and saline conditions.

  7. Greedy Deep Dictionary Learning

    OpenAIRE

    Tariyal, Snigdha; Majumdar, Angshul; Singh, Richa; Vatsa, Mayank

    2016-01-01

    In this work we propose a new deep learning tool called deep dictionary learning. Multi-level dictionaries are learnt in a greedy fashion, one layer at a time. This requires solving a simple (shallow) dictionary learning problem, the solution to this is well known. We apply the proposed technique on some benchmark deep learning datasets. We compare our results with other deep learning tools like stacked autoencoder and deep belief network; and state of the art supervised dictionary learning t...

  8. Greedy Deep Dictionary Learning

    OpenAIRE

    Tariyal, Snigdha; Majumdar, Angshul; Singh, Richa; Vatsa, Mayank

    2016-01-01

    In this work we propose a new deep learning tool called deep dictionary learning. Multi-level dictionaries are learnt in a greedy fashion, one layer at a time. This requires solving a simple (shallow) dictionary learning problem, the solution to this is well known. We apply the proposed technique on some benchmark deep learning datasets. We compare our results with other deep learning tools like stacked autoencoder and deep belief network; and state of the art supervised dictionary learning t...

  9. To grow or to seed: ecotypic variation in reproductive allocation and cone production by young female Aleppo pine (Pinus halepensis, Pinaceae).

    Science.gov (United States)

    Climent, José; Prada, M Aránzazu; Calama, Rafael; Chambel, M Regina; de Ron, David Sánchez; Alía, Ricardo

    2008-07-01

    Age and size at the first reproduction and the reproductive allocation of plants are linked to different life history strategies. Aleppo pine only reproduces through seed, and, as such, early female reproduction confers high fitness in its infertile highly fire-prone habitats along the Mediterranean coast because life expectancy is short. We investigated the extent of ecotypic differentiation in female reproductive allocation and examined the relation between early female reproduction and vegetative growth. In a common-garden experiment, the threshold age and size at first female reproduction and female reproductive allocation at age seven differed significantly among Aleppo pine provenances of ecologically distinct origin. Significant correlations among reproductive features of the provenances and the ecological traits of origin were found using different analytical tools. In nonlinear models of cone counts vs. stem volume, medium-sized trees (not the largest trees) produced the highest cone yield, confirming that, at the individual level, early female reproduction is incompatible with fast vegetative growth. The contribution of founder effects and adaptation to contrasting fire regimes may be confounding factors. But considering all traits analyzed, the geographical patterns of resource allocation by Aleppo pine suggest ecotypic specialization for either resource-poor (favoring early reproduction) or resource-rich (favoring vegetative growth) habitats.

  10. Lotus japonicus plants of the Gifu B-129 ecotype subjected to alkaline stress improve their Fe(2+) bio-availability through inoculation with Pantoea eucalypti M91.

    Science.gov (United States)

    Campestre, María Paula; Castagno, Luis Nazareno; Estrella, María Julia; Ruiz, Oscar Adolfo

    2016-03-15

    Inoculation assays with Pantoea eucalypti M91 were performed on Lotus japonicus ecotype Gifu. Under alkaline conditions, this ecotype is characterized by the development of interveinal chlorosis of the apical leaves due to low mobilization of Fe(2+). Inoculation with P. eucalypti M91, a plant growth-promoting bacterial strain capable of producing pyoverdine-like and pyochelin-like siderophores under alkaline growth conditions, alters the root, resulting in a herringbone pattern of root branching. Additional features include improvement in Fe(2+) transport to the shoots, acidification of the hydroponic solution of the plant cultures, and an accompanying increase in the efficiency of the PSII parameters. In addition, there was an increase in the expression of the FRO1 and IRT1 genes, accompanied by a significant increase in FRO activity. Results showed that P. eucalypti M91 has a beneficial effect on the Fe acquisition machinery of Strategy I, as described for non-graminaceous monocots and dicots, suggesting its potential as an inoculant for legume crops cultivated in alkaline soils. Copyright © 2016 Elsevier GmbH. All rights reserved.

  11. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated ecotypes in the Mushroom Spring microbial mat

    Directory of Open Access Journals (Sweden)

    Millie T. Olsen

    2015-06-01

    Full Text Available Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2 uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related putative ecotypes have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.

  12. 绿色生态型城市道路评价指标体系%Evaluation index system of green ecotype city road

    Institute of Scientific and Technical Information of China (English)

    李满良; 郑晨; 王朝辉; 曾伟; 狄升贯

    2015-01-01

    In order to evaluate green ecotype city road scientifically and rationally,the concept of green ecotype city road was proposed,and the evaluation index system was set up from 5 aspects, namely,rationality of design,effect of road function,energy-conservation and emission-reduction effect,greening effect and environmental protection effect.5 first grade indexes,14 second grade indexes and 31 third grade indexes were elaborated, and their evaluation standards were determined.The evaluation method of green ecotype city road was established on the basis of Spearman rank correlation coefficient combination determining method and interval approximation method.The green ecotype road of China-Singapore Tianjin Ecotype City was evaluated by using the method and the index system.Evaluation result shows that for the road,21 third grade indexes are excellent and 10 third grade indexes are good.12 second grade indexes are excellent and 2 second grade indexes are good.2 first grade indexes,namely,rationality of design and environmental protection effect are good and the rest are excellent.The distance between the excellent evaluation grade and the evaluation index set of green ecotype city road is 3.82,and is smallest in the distances between the evaluation index set and the evaluation grades,which shows the green ecotype city road is excellent and the evaluation result is consistent with the reality.Therefore,the evaluation index system and the evaluation method are reasonable and reliable.34 tabs,21 refs.%为科学合理地评价绿色生态型城市道路,确立了绿色生态型城市道路概念,从设计合理性、道路功能效果、节能减排效果、绿化效果和环境保护效果五方面提出了绿色生态型城市道路评价指标体系,包括5个一级指标、14个二级指标与31个三级指标,并对各指标进行了阐述,确定了各指标的评价标准,提出了基于 Spearman 等级相关系数组合赋权方法与区间逼近方法

  13. The Effects of Drought Stress on Yield, Yield Components and Anti-oxidant of Two Garlic (Allium sativum L. Ecotypes with Different Planting Densities

    Directory of Open Access Journals (Sweden)

    shiva akbari

    2016-07-01

    Full Text Available Introduction Drought stress reduces plant growth by affecting various physiological and biochemical processes, such as photosynthesis, respiration, translocation, ion uptake, carbohydrates, nutrient metabolism and growth promoters. Garlic (Allium sativum L. is an annual bulb crop that has been cultivated since ancient times and was used as a spice and condiment for many centuries. Garlic is an important plant because of its pharmaceutical properties. The optimum yield of this bulb crop depends on well-managed irrigation, fertilization and cultivation practices. In the final and middle stages of growth, garlic is sensitive to water stress and low irrigation is unsuitable in these stages. This experiment was established to study the influence of drought stress and planting density on yield and its components and the non-enzymatic anti-oxidant content of two different garlic ecotypes. Materials and methods This study was conducted in 2011-2012 in a farmland at the south east of Semnan city. The experimental layout was a split-plot factorial with a randomized complete block design with three replications. The treatments were comprised of three factors: irrigation rates (60%, 80% and 100% of estimated crop evapotranspiration (ETC as the main plot and the factorial combination of three levels of planting density (30, 40 and 50 plants.m-2 and two ecotypes (Tabas and Toroud as the sub-plots. To estimate the crop water requirement, different meteorological parameters were collected from Semnan weather station and were used based on FAO-56 water irrigation calculation instructions. After harvesting, ten garlic plants were sampled randomly in each plot and bulb yield components were measured. To calculate the leaves anti-oxidant content, DPPH method was used. The statistical significances of mean values were assessed by analysis of variance and LSD tests at p≤0.05. All calculations were performed using SAS and Mstat-C softwares. Results and discussion

  14. Effect of Organic and Chemical Fertilizers on Yield and Essential Oil of Two Ecotypes of Savory (Satureja hortensis L. under Normal and Drought Stress Conditions

    Directory of Open Access Journals (Sweden)

    O Akrami nejad

    2016-02-01

    Full Text Available Introduction Savory (Satureja hortensis L. is an annual and aromatic plant from Labiatae family, which has plenty of essential oil and is important in medicinal, food, health and beauty industries (6. In comparison with chemical fertilizers, organic fertilizers especially manure have lots of organic material sources, and can be used as nutrients, especially Nitrogen, Phosphor and Potassium. Organic fertilizers also keeps more water in the soil (14. Water deficit is one of the most important boundaries of production in arid and semi-arid regions. Drought stress reduces water content, limits plant growth and changes some physiological and metabolic activities (31. This experiment was conducted as there is a global interest for production of medicinal plants with sustainable agriculture system, and with low input and shortage of information about Savory reaction to fertilization in drought stress condition. The objective of this research was to compare the effects of chemical fertilizers and different organic fertilizers on quantitative and qualitative characteristics of two ecotypes of savory under drought stress condition. Materials and Methods In order to study the effects of organic and mineral (N, P and K fertilizers on quantitative and qualitative characteristics of savory in drought stress condition, two separate split plot designs with three replications were carried out in 2012-2013 year, at the research field of Shahid Bahonar University of Kerman, Iran. In each design fertilizers including cow manure (30 ton per hectare, poultry manure (10 ton per hectare, chemical fertilizers (used equally with macro elements existing in both poultry and cow manure and control (no fertilizer were used as main factor. Kerman and Khuzestan ecotypes were sub-factor. One of the experiments was irrigated to 100% and the other to 50% of field capacity. Two experiments were analyzed as a combined design. The important characteristics of Savory such as plant

  15. Deep Water Ocean Acoustics

    Science.gov (United States)

    2016-04-30

    OASIS, INC. 1 Report No. QSR-14C0172-Ocean Acoustics-043016 Quarterly Progress Report Technical and Financial Deep Water Ocean Acoustics...understanding of the impact of the ocean and seafloor environmental variability on deep- water (long-range) ocean acoustic propagation and to...improve our understanding. During the past few years, the physics effects studied have been three-dimensional propagation on global scales, deep water

  16. Deep Learning in Bioinformatics

    OpenAIRE

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2016-01-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current res...

  17. Hubble Deep Fields

    Science.gov (United States)

    Ferguson, H.; Murdin, P.

    2000-11-01

    The Hubble Deep Fields are two small areas of the sky that were carefully selected for deep observations by the HUBBLE SPACE TELESCOPE (HST). They represent the deepest optical observations to date and reveal galaxies as faint as V=30, 4 billion times fainter than can be seen with the unaided eye....

  18. Deep Impact Spots Quarry

    Science.gov (United States)

    2005-01-01

    Sixty-nine days before it gets up-close-and-personal with a comet, NASA's Deep Impact spacecraft successfully photographed its quarry, comet Tempel 1, at a distance of 39.7 million miles. The image, taken on April 25, 2005, is the first of many comet portraits Deep Impact will take leading up to its historic comet encounter on July 4.

  19. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2016-07-29

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.

  20. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.

    Science.gov (United States)

    Qin, Qi-Long; Li, Yang; Zhang, Yan-Jiao; Zhou, Zhe-Min; Zhang, Wei-Xin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Wang, Lei; Zhang, Yu-Zhong

    2011-02-01

    Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H(2)O(2) than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.

  1. Auxiliary Deep Generative Models

    DEFF Research Database (Denmark)

    Maaløe, Lars; Sønderby, Casper Kaae; Sønderby, Søren Kaae;

    2016-01-01

    Deep generative models parameterized by neural networks have recently achieved state-of-the-art performance in unsupervised and semi-supervised learning. We extend deep generative models with auxiliary variables which improves the variational approximation. The auxiliary variables leave...... the generative model unchanged but make the variational distribution more expressive. Inspired by the structure of the auxiliary variable we also propose a model with two stochastic layers and skip connections. Our findings suggest that more expressive and properly specified deep generative models converge...

  2. Deep Water Survey Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The deep water biodiversity surveys explore and describe the biodiversity of the bathy- and bentho-pelagic nekton using Midwater and bottom trawls centered in the...

  3. Neurogenesis Deep Learning

    OpenAIRE

    Draelos, Timothy J.; Miner, Nadine E.; Lamb, Christopher C.; Vineyard, Craig M.; Carlson, Kristofor D; James, Conrad D.; Aimone, James B.

    2016-01-01

    Neural machine learning methods, such as deep neural networks (DNN), have achieved remarkable success in a number of complex data processing tasks. These methods have arguably had their strongest impact on tasks such as image and audio processing - data processing domains in which humans have long held clear advantages over conventional algorithms. In contrast to biological neural systems, which are capable of learning continuously, deep artificial networks have a limited ability for incorpor...

  4. Deep Learning in Finance

    OpenAIRE

    Heaton, J. B.; Polson, N. G.; Witte, J. H.

    2016-01-01

    We explore the use of deep learning hierarchical models for problems in financial prediction and classification. Financial prediction problems -- such as those presented in designing and pricing securities, constructing portfolios, and risk management -- often involve large data sets with complex data interactions that currently are difficult or impossible to specify in a full economic model. Applying deep learning methods to these problems can produce more useful results than standard method...

  5. Deep Time Contagion

    Directory of Open Access Journals (Sweden)

    Andy Weir

    2012-11-01

    Full Text Available An artist from London researching the effects of deprioritised subjectivity and contemporary art, Weir presents acoustic recordings made in deep geological repository sites. Repurposing these sites from their typical use as storage space for nuclear waste, Weir addresses the extra-human scale of Deep Time through sonic-fiction. Inhumanly enduring and impinging upon humanity largely imperceptibly, what agency—at what scale—is present?

  6. Auxiliary Deep Generative Models

    OpenAIRE

    Maaløe, Lars; Sønderby, Casper Kaae; Sønderby, Søren Kaae; Winther, Ole

    2016-01-01

    Deep generative models parameterized by neural networks have recently achieved state-of-the-art performance in unsupervised and semi-supervised learning. We extend deep generative models with auxiliary variables which improves the variational approximation. The auxiliary variables leave the generative model unchanged but make the variational distribution more expressive. Inspired by the structure of the auxiliary variable we also propose a model with two stochastic layers and skip connections...

  7. Deep source gas

    Energy Technology Data Exchange (ETDEWEB)

    1985-02-01

    Three separate emplacement concepts could explain the occurrence of gas at extreme depths: abiogenesis (a primordial, nonbiologic origin source); subducted, organic-origin gas (involving the deep, tectonic subduction emplacement of hydrocarbon-generating ocean sediments); and deep sedimentary basin gas (the more conventional emplacement of sedimentary rocks by deep downwarping of the Earth's crust). Of these concepts, Deep Source Gas research focuses on the subducted, organic-origin concept. The purpose of Deep Source Gas research is to verify natural gas arising from depths in excess of 30,000 feet, to relate these occurrences to conceptual models, to define the limits of target areas, to quantify the resource, and to determine the significance of the gas to the nation's reserves. The research emphasizes an Earth science study (geology, geochemistry, and geophysics) of the Cordilleran Geologic Province of western North America. This area is considered a prospective source largely because of known and suspected plate tectonic structures and their youthful emplacement, which increase the likelihood of a timely entrapment of deep-source generated hydrocarbons. Detailed geochemical studies indicate that the deep-source-gas generating capacity of the Aleutian Trench area of southern Alaska is high. Furthermore, geophysical studies show that an apparent fossil subduction zone exists in western Washington. This zone appears to have very thick sedimentary rock units, the existence of which will be evaluated through a more detailed seismic study and possibly through drilling activities. Structural observations made in the northern Brooks Range and central Alaskan Range indicate that overthrusting and compressional features may serve as large-scale target areas for deep source gas generation and occurrence. 12 figures, 2 tables.

  8. Nickel-tolerant ectomycorrhizal Pisolithus albus ultramafic ecotype isolated from nickel mines in New Caledonia strongly enhance growth of the host plant Eucalyptus globulus at toxic nickel concentrations.

    Science.gov (United States)

    Jourand, Philippe; Ducousso, Marc; Reid, Robert; Majorel, Clarisse; Richert, Clément; Riss, Jennifer; Lebrun, Michel

    2010-10-01

    Ectomycorrhizal (ECM) Pisolithus albus (Cooke & Massee), belonging to the ultramafic ecotype isolated in nickel-rich serpentine soils from New Caledonia (a tropical hotspot of biodiversity) and showing in vitro adaptive nickel tolerance, were inoculated to Eucalyptus globulus Labill used as a Myrtaceae plant-host model to study ectomycorrhizal symbiosis. Plants were then exposed to a nickel (Ni) dose-response experiment with increased Ni treatments up to 60 mg kg( - )(1) soil as extractable Ni content in serpentine soils. Results showed that plants inoculated with ultramafic ECM P. albus were able to tolerate high and toxic concentrations of Ni (up to 60 μg g( - )(1)) while uninoculated controls were not. At the highest Ni concentration tested, root growth was more than 20-fold higher and shoot growth more than 30-fold higher in ECM plants compared with control plants. The improved growth in ECM plants was associated with a 2.4-fold reduction in root Ni concentration but a massive 60-fold reduction in transfer of Ni from root to shoots. In vitro, P. albus strains could withstand high Ni concentrations but accumulated very little Ni in its tissue. The lower Ni uptake by mycorrhizal plants could not be explained by increased release of metal-complexing chelates since these were 5- to 12-fold lower in mycorrhizal plants at high Ni concentrations. It is proposed that the fungal sheath covering the plant roots acts as an effective barrier to limit transfer of Ni from soil into the root tissue. The degree of tolerance conferred by the ultramafic P. albus isolates to growth of the host tree species is considerably greater than previously reported for other ECM. The primary mechanisms underlying this improved growth were identified as reduced Ni uptake into the roots and markedly reduced transfer from root to shoot in mycorrhizal plants. The fact that these positive responses were observed at Ni concentrations commonly observed in serpentinic soils suggests that

  9. Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara.

    Science.gov (United States)

    Quaiser, Achim; Zivanovic, Yvan; Moreira, David; López-García, Purificación

    2011-02-01

    To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000  m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii 'surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000  m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles.

  10. Why & When Deep Learning Works: Looking Inside Deep Learnings

    OpenAIRE

    Ronen, Ronny

    2017-01-01

    The Intel Collaborative Research Institute for Computational Intelligence (ICRI-CI) has been heavily supporting Machine Learning and Deep Learning research from its foundation in 2012. We have asked six leading ICRI-CI Deep Learning researchers to address the challenge of "Why & When Deep Learning works", with the goal of looking inside Deep Learning, providing insights on how deep networks function, and uncovering key observations on their expressiveness, limitations, and potential. The outp...

  11. Do Deep Nets Really Need to be Deep?

    OpenAIRE

    Ba, Lei Jimmy; Caruana, Rich

    2013-01-01

    Currently, deep neural networks are the state of the art on problems such as speech recognition and computer vision. In this extended abstract, we show that shallow feed-forward networks can learn the complex functions previously learned by deep nets and achieve accuracies previously only achievable with deep models. Moreover, in some cases the shallow neural nets can learn these deep functions using a total number of parameters similar to the original deep model. We evaluate our method on th...

  12. Phenolic Composition and Antioxidant and Antiproliferative Activities of the Extracts of Twelve Common Bean (Phaseolus vulgaris L. Endemic Ecotypes of Southern Italy before and after Cooking

    Directory of Open Access Journals (Sweden)

    Maria Neve Ombra

    2016-01-01

    Full Text Available Beans are important dietary components with versatile health benefits. We analysed the extracts of twelve ecotypes of Phaseolus vulgaris in order to determine their phenolic profiles, antioxidant activity, and the in vitro antiproliferative activity. Ultra-performance liquid chromatography with diode array detector (UPLC-DAD admitted us to detect and quantify some known polyphenols, such as gallic acid, chlorogenic acid, epicatechin, myricetin, formononetin, caffeic acid, and kaempferol. The antioxidant activity (AA ranged from 1.568 ± 0.041 to 66.572 ± 3.197 mg necessary to inhibit the activity of the 2,2-diphenyl-1-picrylhydrazyl (DPPH radical by 50% (EC50. The extracts, except those obtained from the nonpigmented samples, were capable of inhibiting the proliferation of the human epithelial colorectal adenocarcinoma (Caco-2 cells, human breast cancer cells MCF-7, and A549 NSCLC cell line. Cultivars differed in composition and concentration of polyphenols including anthocyanins; cooking affected the antioxidant activity only marginally. Qualitative and quantitative differences in phenolic composition between the groups of beans influenced the biological activities; on the other hand, we did not find significant differences on the biological activities within the same variety, before and after cooking.

  13. Diversity of Mat-Forming Fungi in Relation to Soil Properties, Disturbance, and Forest Ecotype at Crater Lake National Park, Oregon, USA

    Directory of Open Access Journals (Sweden)

    James M. Trappe

    2012-04-01

    Full Text Available In forest ecosystems, fungal mats are functionally important in nutrient and water uptake in litter and wood decomposition processes, in carbon resource allocation, soil weathering and in cycling of soil resources. Fungal mats can occur abundantly in forests and are widely distributed globally. We sampled ponderosa pine/white fir and mountain hemlock/noble fir communities at Crater Lake National Park for mat-forming soil fungi. Fungus collections were identified by DNA sequencing. Thirty-eight mat-forming genotypes were identified; members of the five most common genera (Gautieria, Lepiota, Piloderma, Ramaria, and Rhizopogon comprised 67% of all collections. The mycorrhizal genera Alpova and Lactarius are newly identified as ectomycorrhizal mat-forming taxa, as are the saprotrophic genera Flavoscypha, Gastropila, Lepiota and Xenasmatella. Twelve typical mat forms are illustrated, representing both ectomycorrhizal and saprotrophic fungi that were found. Abundance of fungal mats was correlated with higher soil carbon to nitrogen ratios, fine woody debris and needle litter mass in both forest ecotypes. Definitions of fungal mats are discussed, along with some of the challenges in defining what comprises a fungal “mat”.

  14. Comparative study of growth traits and haematological parameters of Anak and Nigerian heavy ecotype chickens fed with graded levels of mango seed kernel (Mangifera indica) meal.

    Science.gov (United States)

    Mbunwen, Ndofor-Foleng Harriet; Ngongeh, Lucas Atehmengo; Okolie, Peter Nzeribe; Okoli, Emeka Linus

    2015-08-01

    One hundred fifty Anak and 120 Nigerian heavy local ecotype (NHLE) chickens were used to study the effects of feeding graded levels of mango seed kernel meal (MKM) replacing maize diet on growth traits and haematological parameters. A 2 × 5 factorial arrangement was employed: two breeds and five diets. The birds were randomly allocated to five finisher diets formulated such that MKM replaced maize at 0, 10, 20, 30 and 40% (T1, T2, T3, T4 and T5) inclusion levels, respectively. The effect of breed and dietary treatments on growth performance and blood characteristics were determined. The results showed a significant (P  0.05) when the breeds and treatments were compared. It was concluded that inclusion of dietary MKM below 30% could replace maize in the diets of Anak and NHLE growing chickens without adverse effect on growth performance and blood constituents. This work suggests that genetic differences exist in growth traits of these breeds of chickens. This advantage could be useful in breed improvement programmes and better feeding managements of the NHLE and Anak chickens.

  15. The Development Trend of Modern Ecotype City Park%现代生态型城市公园的发展趋势

    Institute of Scientific and Technical Information of China (English)

    陈宇夫

    2014-01-01

    Along with the country to vigorously promote the process of urbanization, the number of ecotype city park has a significant increase with the city. Establishing the correct dir-ection of ecological city park development, pursuing formal di-versity and integrated into the overal city planning, enhancing the utilization of natural resources, and strengthening the main color, constructing the network management platform, is of gr-eat significance for the sustainable development of ecological city park.%伴随国家大力推进城镇化进程,城市生态公园的数量随城市数量而大量增加。确立正确的城市生态公园发展方向,追求形式多样性的同时融入城市整体规划,加强自然资源的利用,强化主体色彩,建设网络管理平台,对于城市生态公园的可持续发展具有重要意义。

  16. Phenolic Composition and Antioxidant and Antiproliferative Activities of the Extracts of Twelve Common Bean (Phaseolus vulgaris L.) Endemic Ecotypes of Southern Italy before and after Cooking.

    Science.gov (United States)

    Ombra, Maria Neve; d'Acierno, Antonio; Nazzaro, Filomena; Riccardi, Riccardo; Spigno, Patrizia; Zaccardelli, Massimo; Pane, Catello; Maione, Mena; Fratianni, Florinda

    2016-01-01

    Beans are important dietary components with versatile health benefits. We analysed the extracts of twelve ecotypes of Phaseolus vulgaris in order to determine their phenolic profiles, antioxidant activity, and the in vitro antiproliferative activity. Ultra-performance liquid chromatography with diode array detector (UPLC-DAD) admitted us to detect and quantify some known polyphenols, such as gallic acid, chlorogenic acid, epicatechin, myricetin, formononetin, caffeic acid, and kaempferol. The antioxidant activity (AA) ranged from 1.568 ± 0.041 to 66.572 ± 3.197 mg necessary to inhibit the activity of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical by 50% (EC50). The extracts, except those obtained from the nonpigmented samples, were capable of inhibiting the proliferation of the human epithelial colorectal adenocarcinoma (Caco-2) cells, human breast cancer cells MCF-7, and A549 NSCLC cell line. Cultivars differed in composition and concentration of polyphenols including anthocyanins; cooking affected the antioxidant activity only marginally. Qualitative and quantitative differences in phenolic composition between the groups of beans influenced the biological activities; on the other hand, we did not find significant differences on the biological activities within the same variety, before and after cooking.

  17. Alterations in the sugar metabolism and in the vacuolar system of mesophyll cells contribute to the desiccation tolerance of Haberlea rhodopensis ecotypes.

    Science.gov (United States)

    Georgieva, K; Rapparini, F; Bertazza, G; Mihailova, G; Sárvári, É; Solti, Á; Keresztes, Á

    2017-01-01

    Haberlea rhodopensis belongs to the small group of resurrection plants having the unique ability to survive desiccation to air dry state retaining most of its chlorophyll content and then resume normal function upon rehydration. It prefers the shady valleys and northward facing slopes of limestone ridges in mountain zones with high average humidity. Nevertheless, it can be found rarely on rocks directly exposed to the sunlight, without the coverage of the canopy. In the present study, we follow the alterations in the subcellular organization of mesophyll cells and sugar metabolism upon desiccation of shade and sun H. rhodopensis plants. Composition and content of soluble carbohydrates during desiccation and rehydration were different in plants grown below the trees or on the sunny rocks. Sucrose, however, was dominating in both ecotypes. The amount of starch grains in chloroplasts was inversely related to that of sugars. Concomitantly with these changes, the number of vacuoles was multiplied in the cells. This can be explained by the development of small (secondary) vacuoles peripherally in the cytoplasm, rather than by the fragmentation of the single vacuole, proposed earlier in the literature. Accordingly, the centripetal movement of chloroplasts and other organelles may be a result of the dynamic changes in the vacuolar system. Upon rehydration, the inner vacuoles enlarged and the organelles returned to their normal position.

  18. Deep vein thrombosis.

    Science.gov (United States)

    Bandyopadhyay, Gargi; Roy, Subesha Basu; Haldar, Swaraj; Bhattacharya, Rabindra

    2010-12-01

    Occlusive clot formation in the veins causes venous thrombosis, the site most common in the deep veins of leg, called deep vein thrombosis. The clot can block blood flow and when it breaks off, called an embolism which in turn can damage the vital organs. Venous thrombosis occurs via three mechanisms ie, Virchow's triad. The mechanisms are decreased flow rate of blood, damage to the blood vessel wall and an increased tendency of the blood to clot. There are several factors which can increase a person's risk for deep vein thrombosis. The symptoms of deep vein thrombosis in the legs are pain, swelling and redness of the part. One variety of venous thrombosis is phlegmasia alba dolens where the leg becomes pale and cool. Investigations include Doppler ultrasound examination of the limb, D-dimer blood test, plethysmography of the legs, x-rays to show vein in the affected area (venography). Hospitalisation is necessary in some cases with some risk factors. The mainstream of treatment is with anticoagulants, mostly low molecular weight heparin for 6 months. Deep venous thrombosis is a rising problem. Early diagnosis and treatment is associated with a good prognosis.

  19. Deep learning relevance

    DEFF Research Database (Denmark)

    Lioma, Christina; Larsen, Birger; Petersen, Casper

    2016-01-01

    train a Recurrent Neural Network (RNN) on existing relevant information to that query. We then use the RNN to "deep learn" a single, synthetic, and we assume, relevant document for that query. We design a crowdsourcing experiment to assess how relevant the "deep learned" document is, compared......What if Information Retrieval (IR) systems did not just retrieve relevant information that is stored in their indices, but could also "understand" it and synthesise it into a single document? We present a preliminary study that makes a first step towards answering this question. Given a query, we...... to existing relevant documents. Users are shown a query and four wordclouds (of three existing relevant documents and our deep learned synthetic document). The synthetic document is ranked on average most relevant of all....

  20. Auxiliary Deep Generative Models

    DEFF Research Database (Denmark)

    Maaløe, Lars; Sønderby, Casper Kaae; Sønderby, Søren Kaae

    2016-01-01

    Deep generative models parameterized by neural networks have recently achieved state-of-the-art performance in unsupervised and semi-supervised learning. We extend deep generative models with auxiliary variables which improves the variational approximation. The auxiliary variables leave...... the generative model unchanged but make the variational distribution more expressive. Inspired by the structure of the auxiliary variable we also propose a model with two stochastic layers and skip connections. Our findings suggest that more expressive and properly specified deep generative models converge...... faster with better results. We show state-of-the-art performance within semi-supervised learning on MNIST (0.96%), SVHN (16.61%) and NORB (9.40%) datasets....

  1. Auxiliary Deep Generative Models

    DEFF Research Database (Denmark)

    Maaløe, Lars; Sønderby, Casper Kaae; Sønderby, Søren Kaae

    2016-01-01

    Deep generative models parameterized by neural networks have recently achieved state-of-the-art performance in unsupervised and semi-supervised learning. We extend deep generative models with auxiliary variables which improves the variational approximation. The auxiliary variables leave...... the generative model unchanged but make the variational distribution more expressive. Inspired by the structure of the auxiliary variable we also propose a model with two stochastic layers and skip connections. Our findings suggest that more expressive and properly specified deep generative models converge...... faster with better results. We show state-of-the-art performance within semi-supervised learning on MNIST (0.96%), SVHN (16.61%) and NORB (9.40%) datasets....

  2. DEEP UNDERGROUND NEUTRINO EXPERIMENT

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Robert J. [Fermilab

    2016-03-03

    The Deep Underground Neutrino Experiment (DUNE) collaboration will perform an experiment centered on accelerator-based long-baseline neutrino studies along with nucleon decay and topics in neutrino astrophysics. It will consist of a modular 40-kt (fiducial) mass liquid argon TPC detector located deep underground at the Sanford Underground Research Facility in South Dakota and a high-resolution near detector at Fermilab in Illinois. This conguration provides a 1300-km baseline in a megawatt-scale neutrino beam provided by the Fermilab- hosted international Long-Baseline Neutrino Facility.

  3. Deep boreholes; Tiefe Bohrloecher

    Energy Technology Data Exchange (ETDEWEB)

    Bracke, Guido [Gesellschaft fuer Anlagen- und Reaktorsicherheit gGmbH Koeln (Germany); Charlier, Frank [NSE international nuclear safety engineering gmbh, Aachen (Germany); Geckeis, Horst [Karlsruher Institut fuer Technologie (Germany). Inst. fuer Nukleare Entsorgung; and others

    2016-02-15

    The report on deep boreholes covers the following subject areas: methods for safe enclosure of radioactive wastes, requirements concerning the geological conditions of possible boreholes, reversibility of decisions and retrievability, status of drilling technology. The introduction covers national and international activities. Further chapters deal with the following issues: basic concept of the storage in deep bore holes, status of the drilling technology, safe enclosure, geomechanics and stability, reversibility of decisions, risk scenarios, compliancy with safe4ty requirements and site selection criteria, research and development demand.

  4. Deep Vein Thrombosis

    Centers for Disease Control (CDC) Podcasts

    2012-04-05

    This podcast discusses the risk for deep vein thrombosis in long-distance travelers and ways to minimize that risk.  Created: 4/5/2012 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 4/5/2012.

  5. Deep Vein Thrombosis

    African Journals Online (AJOL)

    OWNER

    Il s'agissait de la main et les recherches en ligne. Des termes ..... Cerrato D, Ariano G, and Fiacchino F : Deep vein ... Surg 1988; 75: 1053–7. 19. Salzman ... Alikhan R, Cohen AT, Combe S, Samama .... Kakkar AK, Williamson RCN. Thrombo.

  6. Teaching for Deep Learning

    Science.gov (United States)

    Smith, Tracy Wilson; Colby, Susan A.

    2007-01-01

    The authors have been engaged in research focused on students' depth of learning as well as teachers' efforts to foster deep learning. Findings from a study examining the teaching practices and student learning outcomes of sixty-four teachers in seventeen different states (Smith et al. 2005) indicated that most of the learning in these classrooms…

  7. Teaching for Deep Learning

    Science.gov (United States)

    Smith, Tracy Wilson; Colby, Susan A.

    2007-01-01

    The authors have been engaged in research focused on students' depth of learning as well as teachers' efforts to foster deep learning. Findings from a study examining the teaching practices and student learning outcomes of sixty-four teachers in seventeen different states (Smith et al. 2005) indicated that most of the learning in these classrooms…

  8. Deep Stochastic Radar Models

    OpenAIRE

    Wheeler, Tim Allan; Holder, Martin; Winner, Hermann; Kochenderfer, Mykel

    2017-01-01

    Accurate simulation and validation of advanced driver assistance systems requires accurate sensor models. Modeling automotive radar is complicated by effects such as multipath reflections, interference, reflective surfaces, discrete cells, and attenuation. Detailed radar simulations based on physical principles exist but are computationally intractable for realistic automotive scenes. This paper describes a methodology for the construction of stochastic automotive radar models based on deep l...

  9. Deep-sea fungi

    Digital Repository Service at National Institute of Oceanography (India)

    Raghukumar, C.; Damare, S.

    The deep-sea environment, despite being rich in mineral nutrients and near-saturation levels of oxygen, because of its darkness is not conducive to photosynthesis, the process that sustains life on earth. If a liigh abundance and diversity of life...

  10. Leaf cuticular lipids on the Shandong and Yukon ecotypes of saltwater cress, Eutrema salsugineum, and their response to water deficiency and impact on cuticle permeability.

    Science.gov (United States)

    Xu, Xiaojing; Feng, Jinchao; Lü, Shiyou; Lohrey, Greg T; An, Huiling; Zhou, Yijun; Jenks, Matthew A

    2014-08-01

    The impact of water-deficit stress on leaf cuticular waxes and cutin monomers, and traits associated with cuticle permeability were examined in Shandong and Yukon ecotypes of Eutrema salsugineum (syn. Thellungiella salsuginea). Although Shandong exhibits glaucous leaves, and Yukon is non-glaucous, wax amounts on non-stressed Yukon leaves were 4.6-fold higher than on Shandong, due mainly to Yukon's eightfold higher wax fatty acids, especially the C22 and C24 acid homologues. Water deficit caused a 26.9% increase in total waxes on Shandong leaves, due mainly to increased C22 and C24 acids; and caused 10.2% more wax on Yukon, due mainly to an increase in wax alkanes. Total cutin monomers on non-stressed leaves of Yukon were 58.3% higher than on Shandong. Water deficit caused a 28.2% increase in total cutin monomers on Shandong, whereas total cutin monomers were not induced on Yukon. With or without stress, more abundant cuticle lipids were generally associated with lower water loss rates, lower chlorophyll efflux rates and an extended time before water deficit-induced wilting. In response to water deficit, Shandong showed elevated transcription of genes encoding elongase subunits, consistent with the higher stress induction of acids by Shandong. Yukon's higher induction of CER1 and CER3 transcripts may explain why alkanes increased most on Yukon after water deficit. Eutrema, with its diverse cuticle lipids and responsiveness, provides a valuable genetic resource for identifying new genes and alleles effecting cuticle metabolism, and lays groundwork for studies of the cuticle's role in extreme stress tolerance.

  11. Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

    KAUST Repository

    Jimenez Infante, Francy M.

    2015-12-11

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

  12. Ecological speciation in an island snail: evidence for the parallel evolution of a novel ecotype and maintenance by ecologically dependent postzygotic isolation.

    Science.gov (United States)

    Stankowski, Sean

    2013-05-01

    Speciation is the process by which reproductive isolation evolves between populations. Two general models of speciation have been proposed: ecological speciation, where reproductive barriers evolve due to ecologically based divergent selection, and mutation-order speciation, where populations fix different mutations as they adapt to similar selection pressures. I evaluate these alternative models and determine the progress of speciation in a diverse group of land snails, genus Rhagada, inhabiting Rosemary Island. A recently derived keeled-flat morphotype occupies two isolated rocky hills, while globose-shelled snails inhabit the surrounding plains. The study of one hill reveals that they are separated by a narrow hybrid zone. As predicted by ecological speciation theory, there are local and landscape level associations between shell shape and habitat, and the morphological transition coincides with a narrow ecotone between the two distinct environments. Microsatellite DNA revealed a cline of hybrid index scores much wider than the morphological cline, further supporting the ecological maintenance of the morphotypes. The hybrid zone does not run through an area of low population density, as is expected for mutation-order hybrid zones, and there is a unimodal distribution of phenotypes at the centre, suggesting that there is little or no prezygotic isolation. Instead, these data suggest that the ecotypes are maintained by ecologically dependent postzygotic isolation (i.e. ecological selection against hybrids). Mitochondrial and Microsatellite DNA indicate that the keeled-flat form evolved recently, and without major historical disruptions to gene flow. The data also suggest that the two keeled-flat populations, inhabiting similar rocky hills, have evolved in parallel. These snails provide a complex example of ecological speciation in its early stages.

  13. Selection and Validation of Reference Genes for Real-Time Quantitative PCR in Hyperaccumulating Ecotype of Sedum alfredii under Different Heavy Metals Stresses

    Science.gov (United States)

    Liu, Mingying; Qiao, Guirong; Jiang, Jing; Zhuo, Renying

    2013-01-01

    Real-time Quantitative PCR (RT-qPCR) has become an effective method for accurate analysis of gene expression in several biological systems as well as under different experimental conditions. Although with high sensitivity, specificity and broad dynamic range, this method requires suitable reference genes for transcript normalization in order to guarantee reproducible and meaningful results. In the present study, we evaluated five traditional housekeeping genes and five novel reference genes in Hyperaccumulating ecotype of Sedum alfredii, a well known hyperaccumulator for heavy metals phytoremediation, under Cd, Pb, Zn and Cu stresses of seven different durations. The expression stability of these ten candidates were determined with three programs - geNorm, NormFinder and BestKeeper. The results showed that all the selected reference genes except for SAND could be used for RT-qPCR normalization. Among them UBC9 and TUB were ranked as the most stable candidates across all samples by three programs together. For the least stable reference genes, however, BestKeeper produced different results compared with geNorm and NormFinder. Meanwhile, the expression profiles of PCS under Cd, Pb, Zn and Cu stresses were assessed using UBC9 and TUB respectively, and similar trends were obtained from the results of the two groups. The distinct expression patterns of PCS indicated that various strategies could be taken by plants in adaption to different heavy metals stresses. This study will provide appropriate reference genes for further gene expression quantification using RT-qPCR in Hyperaccumulator S. alfredii. PMID:24340067

  14. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    Science.gov (United States)

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  15. Deep gluteal syndrome.

    Science.gov (United States)

    Martin, Hal David; Reddy, Manoj; Gómez-Hoyos, Juan

    2015-07-01

    Deep gluteal syndrome describes the presence of pain in the buttock caused from non-discogenic and extrapelvic entrapment of the sciatic nerve. Several structures can be involved in sciatic nerve entrapment within the gluteal space. A comprehensive history and physical examination can orientate the specific site where the sciatic nerve is entrapped, as well as several radiological signs that support the suspected diagnosis. Failure to identify the cause of pain in a timely manner can increase pain perception, and affect mental control, patient hope and consequently quality of life. This review presents a comprehensive approach to the patient with deep gluteal syndrome in order to improve the understanding of posterior hip anatomy, nerve kinematics, clinical manifestations, imaging findings, differential diagnosis and treatment considerations.

  16. The Deep Lens Survey

    CERN Document Server

    Wittman, D; Dell'Antonio, I P; Becker, A C; Margoniner, V E; Cohen, J; Norman, D; Loomba, D; Squires, G; Wilson, G; Stubbs, C; Hennawi, J F; Spergel, D N; Boeshaar, P C; Clocchiatti, A; Hamuy, M; Bernstein, G; González, A; Guhathakurta, R; Hu, W; Seljak, U; Zaritsky, D

    2002-01-01

    The Deep Lens Survey (DLS) is a deep BVRz' imaging survey of seven 2x2 degree fields, with all data to be made public. The primary scientific driver is weak gravitational lensing, but the survey is also designed to enable a wide array of other astrophysical investigations. A unique feature of this survey is the search for transient phenomena. We subtract multiple exposures of a field, detect differences, classify, and release transients on the Web within about an hour of observation. Here we summarize the scientific goals of the DLS, field and filter selection, observing techniques and current status, data reduction, data products and release, and transient detections. Finally, we discuss some lessons which might apply to future large surveys such as LSST.

  17. Research on the effects of winter protection for grape with ecotype arch-tile units%酿酒葡萄园生态型弓瓦防寒效果研究

    Institute of Scientific and Technical Information of China (English)

    李映龙; 单守明; 平吉成; 张军翔

    2011-01-01

    Based on testing new type units of winter protection for wine grape, instead of burying earth soft which is traditional measure for cold prevention in winter, we studied influence of soil temperature on grape roots (Cabernet Sauvignon) by ecotype arch-tile units. Result showed that soil temperatures dealing with ecotype arch-tile units were higher than those with burying earth soil treatment, but not significant. In the spring, mortality of branches and tendrils with arch-tile units was slightly higher than that with burying earth soil treatment; Differences did not reach a significant level, but fracture rate of new shoots with arch-tile units is significantly lower than that with burying earth soil treatment. Therefore, under the experimental conditions, the effects of winter protection by ecotype arch-tile units equal to that of burying earth soil, ecotype arch-tile units were able to make over-wintering Cabernet grapes live safely.%为了探索能替代葡萄冬季埋土防寒措施的新型防寒装置,本试验以赤霞珠葡萄为材料,研究生态型弓瓦防寒装置对葡萄根系土层温度的影响,结果表明,弓瓦防寒装置处理的各土层温度高于埋土处理,但是差异不显著.在春季,弓瓦处理的枝蔓死亡率略高于埋土处理;差异没有达到显著水平,但是新梢折断率显著低于埋土处理,因此,在试验条件下,生态型弓瓦防寒装置的防寒效果和埋土防寒措施相当,可以使赤霞珠葡萄安全越冬.

  18. Sinorhizobium meliloti-induced chitinase gene expression in Medicago truncatula ecotype R108-1: a comparison between symbiosis-specific class V and defence-related class IV chitinases.

    Science.gov (United States)

    Salzer, Peter; Feddermann, Nadja; Wiemken, Andres; Boller, Thomas; Staehelin, Christian

    2004-08-01

    The Medicago truncatula (Gaertn.) ecotypes Jemalong A17 and R108-1 differ in Sinorhizobium meliloti-induced chitinase gene expression. The pathogen-inducible class IV chitinase gene, Mtchit 4, was strongly induced during nodule formation of the ecotype Jemalong A17 with the S. meliloti wild-type strain 1021. In the ecotype R108-1, the S. meliloti wild types Sm1021 and Sm41 did not induce Mtchit 4 expression. On the other hand, expression of the putative class V chitinase gene, Mtchit 5, was found in roots of M. truncatula cv. R108-1 nodulated with either of the rhizobial strains. Mtchit 5 expression was specific for interactions with rhizobia. It was not induced in response to fungal pathogen attack, and not induced in roots colonized with arbuscular mycorrhizal (AM) fungi. Elevated Mtchit 5 gene expression was first detectable in roots forming nodule primordia. In contrast to Mtchit 4, expression of Mtchit 5 was stimulated by purified Nod factors. Conversely, Mtchit 4 expression was strongly elevated in nodules formed with the K-antigen-deficient mutant PP699. Expression levels of Mtchit 5 were similarly increased in nodules formed with PP699 and its parental wild-type strain Sm41. Phylogenetic analysis of the deduced amino acid sequences of Mtchit 5 (calculated molecular weight = 41,810 Da, isoelectric point pH 7.7) and Mtchit 4 (calculated molecular weight 30,527 Da, isoelectric point pH 4.9) revealed that the putative Mtchit 5 chitinase forms a separate clade within class V chitinases of plants, whereas the Mtchit 4 chitinase clusters with pathogen-induced class IV chitinases from other plants. These findings demonstrate that: (i) Rhizobium-induced chitinase gene expression in M. truncatula occurs in a plant ecotype-specific manner, (ii) Mtchit 5 is a putative chitinase gene that is specifically induced by rhizobia, and (iii) rhizobia-specific and defence-related chitinase genes are differentially influenced by rhizobial Nod factors and K antigens.

  19. Deep Blind Compressed Sensing

    OpenAIRE

    Singh, Shikha; Singhal, Vanika; Majumdar, Angshul

    2016-01-01

    This work addresses the problem of extracting deeply learned features directly from compressive measurements. There has been no work in this area. Existing deep learning tools only give good results when applied on the full signal, that too usually after preprocessing. These techniques require the signal to be reconstructed first. In this work we show that by learning directly from the compressed domain, considerably better results can be obtained. This work extends the recently proposed fram...

  20. Deep gluteal syndrome

    OpenAIRE

    Martin, Hal David; Reddy, Manoj; Gómez-Hoyos, Juan

    2015-01-01

    Deep gluteal syndrome describes the presence of pain in the buttock caused from non-discogenic and extrapelvic entrapment of the sciatic nerve. Several structures can be involved in sciatic nerve entrapment within the gluteal space. A comprehensive history and physical examination can orientate the specific site where the sciatic nerve is entrapped, as well as several radiological signs that support the suspected diagnosis. Failure to identify the cause of pain in a timely manner can increase...

  1. Deep Water Ocean Acoustics

    Science.gov (United States)

    2015-10-19

    PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/ MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) 11. SPONSOR/MONITOR’S REPORT...understanding. During the past few years, the physics effects studied have been three-dimensional propagation on global scales, deep water ambient ...of 19000 km. This is an incredible data set as the source shot times and locations were recorded as were the source levels using a monitor

  2. Deep Water Ocean Acoustics

    Science.gov (United States)

    2015-07-17

    understanding. During the past few years, the physics effects studied have been three-dimensional propagation on global scales, deep water ambient noise ...and Climate of the Ocean, Phase II (ECCO2): High-Resolution Global-Ocean and Sea-Ice Data Synthesis) model re- analysis for the years 1992 and 1993...the Massachusetts Institute of Technology general circulation model (MITgcm) to the available satellite and in-situ data5. The ECCO2 product is the

  3. The deep subterranean biosphere

    Science.gov (United States)

    Pedersen, Karsten

    1993-08-01

    The main purpose with this review is to summarise present research on the microbiology of deep subterranean environments, deeper than 50-100 m. Included are mainly studies where drilling, excavation, core sampling and ground water sampling have been made for research. Studies done in environments penetrated for commercial purposes, such as water wells, mining, oil recovery etc., have been dismissed because of the obvious risk for contamination during the penetration. Different measures that can be applied to reduce the risk of microbial contamination of sampled specimens by the access operations are discussed. The requirement for reliable estimations of the present microbial biomass, its activity and diversity in subterranean ecosystems, is fundamental. An array of different methods to achieve this goal are presented. The depth limit for subterranean life is suggested to be set by temperature, provided there is energy available for microbial life. If so, it should be possible to enrich thermophilic bacteria from deep hot ground waters which also has been done. There are only a few sites where the subterranean microbiology has been studied in multidisiplinary programs including chemistry and geology. The two most extensively published sites are the sediments of the Atlantic coastal plain of South Carolina, USA, studied in a subsurface program, initiated and sponsored by the U.S. Department of Energy, and crystalline bed-rock in Sweden studied in a program concerning the safety of future underground repositories for nuclear waste. This review presents an array of independent reports suggesting that microbial life is widespread at depth in the crust of earth—the deep subterranean biosphere. The obvious consequences is that microbes may be involved in many subterranean geochemical processes, such as diagenesis, weathering, precipitation, and in oxidation or reduction reactions of metals, carbon, nitrogen and sulfur—just as they are in most terranean environments.

  4. Deep Red (Profondo Rosso)

    CERN Document Server

    Cine Club

    2015-01-01

    Wednesday 29 April 2015 at 20:00 CERN Council Chamber    Deep Red (Profondo Rosso) Directed by Dario Argento (Italy, 1975) 126 minutes A psychic who can read minds picks up the thoughts of a murderer in the audience and soon becomes a victim. An English pianist gets involved in solving the murders, but finds many of his avenues of inquiry cut off by new murders, and he begins to wonder how the murderer can track his movements so closely. Original version Italian; English subtitles

  5. Ecotypic and allozyme variation of Capsella bursa-pastoris and C. rubella (Brassicaceae along latitude and altitude gradients on the Iberian Peninsula

    Directory of Open Access Journals (Sweden)

    Hoffrogge, Raimund

    1999-12-01

    Full Text Available Life-history traits (onset of flowering, leaf number, rosette diameter, plant height, branching number, fruit dimensions, seed number of Capsella species from the Iberian Península associated with colotúzing ability were compared in a random block field experiment. Data were evaluated by a principal component analysis. Allozymes (AAT, LAP, GDH and leaf types were recorded. C. bursa-pastoris plants originating from low and high elevations of the summer dry Mediterranean climatic zone (Sierra Nevada were early flowering, whereas those originating from the Pyrenees with an alpine climate were late. In C. bursa-pastoris the "rhomboidea" leaf type was very frequent, whereas in C. rubella it was the "heteris" leaf type. There was a change of leaf type frequencies along geographical clines which is explained by adaptive components of the leaf shape. The allozymes displayed a geographical distribuüon pattem and in C. bursa-pastoris a certain multilocus genotype appeared to be a molecular marker for an early flowering ecotype(inicio de la floración, número de hojas, diámetro de la roseta, altura de la planta, número de ramas, dimensiones del fruto y número de semillas de plantas de Capsella procedentes de la Península Ibérica mediante un experimento de bloques aleatorios en el campo. Los datos se evaluaron con un análisis de componentes principales. También se registraron el tipo de hojas y el perfil aloenzimático de las plantas. Las plantas de Capsella bursa-pastoris procedentes de altitudes altas y bajas de la zona climática Mediterránea de verano seco (Sierra Nevada mostraron ser de floración temprana, mientras que las plantas de los Pirineos, con un clima alpino, presentaron una floración tardía. En C. bursa-pastoris el tipo de hoja "rhomboidea" resultó ser el más frecuente, en tanto que en C. rubella lo fue el tipo "heteris". Se observó un cambio en las frecuencias de los tipos de hojas a lo largo de una clina geográfica, lo

  6. Deep Reinforcement Learning: An Overview

    OpenAIRE

    Li, Yuxi

    2017-01-01

    We give an overview of recent exciting achievements of deep reinforcement learning (RL). We start with background of deep learning and reinforcement learning, as well as introduction of testbeds. Next we discuss Deep Q-Network (DQN) and its extensions, asynchronous methods, policy optimization, reward, and planning. After that, we talk about attention and memory, unsupervised learning, and learning to learn. Then we discuss various applications of RL, including games, in particular, AlphaGo, ...

  7. Deep 6-DOF Tracking.

    Science.gov (United States)

    Garon, Mathieu; Lalonde, Jean-Francois

    2017-08-10

    We present a temporal 6-DOF tracking method which leverages deep learning to achieve state-of-the-art performance on challenging datasets of real world capture. Our method is both more accurate and more robust to occlusions than the existing best performing approaches while maintaining real-time performance. To assess its efficacy, we evaluate our approach on several challenging RGBD sequences of real objects in a variety of conditions. Notably, we systematically evaluate robustness to occlusions through a series of sequences where the object to be tracked is increasingly occluded. Finally, our approach is purely data-driven and does not require any hand-designed features: robust tracking is automatically learned from data.

  8. Context and Deep Learning Design

    Science.gov (United States)

    Boyle, Tom; Ravenscroft, Andrew

    2012-01-01

    Conceptual clarification is essential if we are to establish a stable and deep discipline of technology enhanced learning. The technology is alluring; this can distract from deep design in a surface rush to exploit the affordances of the new technology. We need a basis for design, and a conceptual unit of organization, that are applicable across…

  9. Context and Deep Learning Design

    Science.gov (United States)

    Boyle, Tom; Ravenscroft, Andrew

    2012-01-01

    Conceptual clarification is essential if we are to establish a stable and deep discipline of technology enhanced learning. The technology is alluring; this can distract from deep design in a surface rush to exploit the affordances of the new technology. We need a basis for design, and a conceptual unit of organization, that are applicable across…

  10. A SURVEY OF DEEP SPACE COMMUNICATIONS

    Institute of Scientific and Technical Information of China (English)

    Zhang Gengxin; Xie Zhidong; Bian Dongming; Sun Qian

    2011-01-01

    Deep space communications has played an important role in deep space exploration.Compared with common satellite and terrestrial communications,deep space communications faces more challenging environment.The paper investigated the unique features of deep space communications in detail,discussed the key technologies and its development trends for deep space communica- tions.

  11. Deep Learning the Universe

    Science.gov (United States)

    Singh, Shiwangi; Bard, Deborah

    2017-01-01

    Weak gravitational lensing is an effective tool to map the structure of matter in the universe, and has been used for more than ten years as a probe of the nature of dark energy. Beyond the well-established two-point summary statistics, attention is now turning to methods that use the full statistical information available in the lensing observables, through analysis of the reconstructed shear field. This offers an opportunity to take advantage of powerful deep learning methods for image analysis. We present two early studies that demonstrate that deep learning can be used to characterise features in weak lensing convergence maps, and to identify the underlying cosmological model that produced them.We developed an unsupervised Denoising Convolutional Autoencoder model in order to learn an abstract representation directly from our data. This model uses a convolution-deconvolution architecture, which is fed with input data (corrupted with binomial noise to prevent over-fitting). Our model effectively trains itself to minimize the mean-squared error between the input and the output using gradient descent, resulting in a model which, theoretically, is broad enough to tackle other similarly structured problems. Using this model we were able to successfully reconstruct simulated convergence maps and identify the structures in them. We also determined which structures had the highest “importance” - i.e. which structures were most typical of the data. We note that the structures that had the highest importance in our reconstruction were around high mass concentrations, but were highly non-Gaussian.We also developed a supervised Convolutional Neural Network (CNN) for classification of weak lensing convergence maps from two different simulated theoretical models. The CNN uses a softmax classifier which minimizes a binary cross-entropy loss between the estimated distribution and true distribution. In other words, given an unseen convergence map the trained CNN determines

  12. Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade.

    Directory of Open Access Journals (Sweden)

    Yann Blouin

    Full Text Available Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR analysis (MLVA 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by

  13. Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade.

    Science.gov (United States)

    Blouin, Yann; Hauck, Yolande; Soler, Charles; Fabre, Michel; Vong, Rithy; Dehan, Céline; Cazajous, Géraldine; Massoure, Pierre-Laurent; Kraemer, Philippe; Jenkins, Akinbowale; Garnotel, Eric; Pourcel, Christine; Vergnaud, Gilles

    2012-01-01

    Molecular and phylogeographic studies have led to the definition within the Mycobacterium tuberculosis complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major M. tuberculosis lineages were identified, with only two M. africanum and one M. bovis isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of

  14. Deep cervical infection?

    Directory of Open Access Journals (Sweden)

    Bernardo T

    2012-06-01

    Full Text Available Introduction: Inflammatory cervical swelling may have several causes. The jugular vein thrombosis is a rare entity, often forgotten. Most frequently arises due to a cervical sepsis by the use of a central venous catheter or intravenous drug abuse (drug addicts. Rarely, is secondary to a hypercoagulability state associated with a visceral carcinoma (Trousseau Syndrome. Material and Methods: The authors present the case of a 65 years old male, who used the ENT Emergency Service due to a painful left cervical swelling with local and systemic inflammatory signs of 3 days duration. Results: An cervical ultrasound suggested a neck abscess. CT was performed and confirmed the ultrasound results. Because of its location in the path of the internal jugular vein, we requested re-evaluation by CT with intravenous contrast and doppler ultrasound, obtaining the diagnosis of thrombosis of the internal jugular vein. Further studies were conduct to clarify the hypercoagulability state, since the patient had no known predisposing factor. Finally the diagnosis of unresectable gastric carcinoma was made. Discussion and Conclusion: The ENT must be aware and be able to understand any cervical imagiologic studies. A deep knowledge of the anatomical imagiología is important for the diagnosis of jugular thrombosis. When we have a case of spontaneous jugular thrombosis, we must look for possible visceral carcinoma.

  15. Deep space telescopes

    CERN Document Server

    CERN. Geneva

    2006-01-01

    The short series of seminars will address results and aims of current and future space astrophysics as the cultural framework for the development of deep space telescopes. It will then present such new tools, as they are currently available to, or imagined by, the scientific community, in the context of the science plans of ESA and of all major world space agencies. Ground-based astronomy, in the 400 years since Galileo’s telescope, has given us a profound phenomenological comprehension of our Universe, but has traditionally been limited to the narrow band(s) to which our terrestrial atmosphere is transparent. Celestial objects, however, do not care about our limitations, and distribute most of the information about their physics throughout the complete electromagnetic spectrum. Such information is there for the taking, from millimiter wavelengths to gamma rays. Forty years astronomy from space, covering now most of the e.m. spectrum, have thus given us a better understanding of our physical Universe then t...

  16. Deep Mapping and Spatial Anthropology

    Directory of Open Access Journals (Sweden)

    Les Roberts

    2016-01-01

    Full Text Available This paper provides an introduction to the Humanities Special Issue on “Deep Mapping”. It sets out the rationale for the collection and explores the broad-ranging nature of perspectives and practices that fall within the “undisciplined” interdisciplinary domain of spatial humanities. Sketching a cross-current of ideas that have begun to coalesce around the concept of “deep mapping”, the paper argues that rather than attempting to outline a set of defining characteristics and “deep” cartographic features, a more instructive approach is to pay closer attention to the multivalent ways deep mapping is performatively put to work. Casting a critical and reflexive gaze over the developing discourse of deep mapping, it is argued that what deep mapping “is” cannot be reduced to the otherwise a-spatial and a-temporal fixity of the “deep map”. In this respect, as an undisciplined survey of this increasing expansive field of study and practice, the paper explores the ways in which deep mapping can engage broader discussion around questions of spatial anthropology.

  17. Deep learning for computational chemistry.

    Science.gov (United States)

    Goh, Garrett B; Hodas, Nathan O; Vishnu, Abhinav

    2017-06-15

    The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the last few years, we have seen the transformative impact of deep learning in many domains, particularly in speech recognition and computer vision, to the extent that the majority of expert practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. In this review, we provide an introductory overview into the theory of deep neural networks and their unique properties that distinguish them from traditional machine learning algorithms used in cheminformatics. By providing an overview of the variety of emerging applications of deep neural networks, we highlight its ubiquity and broad applicability to a wide range of challenges in the field, including quantitative structure activity relationship, virtual screening, protein structure prediction, quantum chemistry, materials design, and property prediction. In reviewing the performance of deep neural networks, we observed a consistent outperformance against non-neural networks state-of-the-art models across disparate research topics, and deep neural network-based models often exceeded the "glass ceiling" expectations of their respective tasks. Coupled with the maturity of GPU-accelerated computing for training deep neural networks and the exponential growth of chemical data on which to train these networks on, we anticipate that deep learning algorithms will be a valuable tool for computational chemistry. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light

    Directory of Open Access Journals (Sweden)

    Shane eNowack

    2015-06-01

    Full Text Available Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP. These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted putative ecotype that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.

  19. A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta

    Directory of Open Access Journals (Sweden)

    Coupland George

    2005-08-01

    Full Text Available Abstract Background Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have not been tested for simultaneous RNA isolation for RT-PCR applications. In addition, traditional map-based cloning technologies often use ill-proportioned marker regions even when working with the model plant Arabidopsis thaliana, where the availability of the full genome sequence can now be exploited for the creation of a high-density marker systems. Results We designed a high-density polymorphic marker set between two frequently used ecotypes. This new polymorphic marker set allows size separation of PCR products on agarose gels and provides an initial resolution of 10 cM in linkage mapping experiments, facilitated by a rapid plant nucleic acid extraction protocol using minimal amounts of A. thaliana tissue. Using this extraction protocol, we have also characterized segregating T-DNA insertion mutations. In addition, we have shown that our rapid nucleic acid extraction protocol can also be used for monitoring transcript levels by RT-PCR amplification. Finally we have demonstrated that our nucleic acid isolation method is also suitable for other plant species, such as tobacco and barley. Conclusion To facilitate high-throughput linkage mapping and other genomic applications, our nucleic acid isolation protocol yields sufficient quality of DNA and RNA templates for PCR and RT-PCR reactions, respectively. This new technique requires considerably less time compared to other purification methods, and in combination with a new polymorphic PCR marker set dramatically reduces the workload required for linkage mapping of mutations in A. thaliana utilizing crosses between Col-0 and Landsberg erecta (Ler ecotypes.

  20. Deep Learning in Drug Discovery.

    Science.gov (United States)

    Gawehn, Erik; Hiss, Jan A; Schneider, Gisbert

    2016-01-01

    Artificial neural networks had their first heyday in molecular informatics and drug discovery approximately two decades ago. Currently, we are witnessing renewed interest in adapting advanced neural network architectures for pharmaceutical research by borrowing from the field of "deep learning". Compared with some of the other life sciences, their application in drug discovery is still limited. Here, we provide an overview of this emerging field of molecular informatics, present the basic concepts of prominent deep learning methods and offer motivation to explore these techniques for their usefulness in computer-assisted drug discovery and design. We specifically emphasize deep neural networks, restricted Boltzmann machine networks and convolutional networks.

  1. DeepSurveyCam—A Deep Ocean Optical Mapping System

    OpenAIRE

    Tom Kwasnitschka; Kevin Köser; Jan Sticklus; Marcel Rothenbeck; Tim Weiß; Emanuel Wenzlaff; Timm Schoening; Lars Triebe; Anja Steinführer; Colin Devey; Jens Greinert

    2016-01-01

    Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor), and the limitations of localization technologies (no GPS). The absence of natural light complicates energy budget considerations for deep ...

  2. Deep Brain Stimulation for Parkinson's Disease

    Science.gov (United States)

    ... You are here Home » Disorders » All Disorders Deep Brain Stimulation for Parkinson's Disease Information Page Deep Brain Stimulation for Parkinson's Disease Information Page Search Disorders ...

  3. Deep Drilling Technology of China

    Institute of Scientific and Technical Information of China (English)

    Ni Rongfu

    1995-01-01

    @@ Since the drilling of well Songji-6 by the drilling crew No. 32139 in Daqing in 1963,there havebeen some 1600 over 4 000 m deep wells completed till 1993, among which two are above 7 000 m in depth.

  4. Deep Space Climate Observatory (DSCOVR)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Deep Space Climate ObserVatoRy (DSCOVR) satellite is a NOAA operated asset located at the first Lagrange point (L1). This places it approximately 1% of the...

  5. Lunar Probe Reaches Deep Space

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ China's second lunar probe, Chang'e-2, has reached an orbit 1.5 million kilometers from Earth for an additional mission of deep space exploration, the State Administration for Science, Technology and Industry for National Defense announced.

  6. Deep Learning for Computational Chemistry

    OpenAIRE

    Goh, Garrett B.; Hodas, Nathan O.; Vishnu, Abhinav

    2017-01-01

    The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the last few years, we have seen the transformative impact of deep learning in many domains, particularly in speech recognition and computer vision, to the extent that the majority of...

  7. Hot, deep origin of petroleum: deep basin evidence and application

    Science.gov (United States)

    Price, Leigh C.

    1978-01-01

    Use of the model of a hot deep origin of oil places rigid constraints on the migration and entrapment of crude oil. Specifically, oil originating from depth migrates vertically up faults and is emplaced in traps at shallower depths. Review of petroleum-producing basins worldwide shows oil occurrence in these basins conforms to the restraints of and therefore supports the hypothesis. Most of the world's oil is found in the very deepest sedimentary basins, and production over or adjacent to the deep basin is cut by or directly updip from faults dipping into the basin deep. Generally the greater the fault throw the greater the reserves. Fault-block highs next to deep sedimentary troughs are the best target areas by the present concept. Traps along major basin-forming faults are quite prospective. The structural style of a basin governs the distribution, types, and amounts of hydrocarbons expected and hence the exploration strategy. Production in delta depocenters (Niger) is in structures cut by or updip from major growth faults, and structures not associated with such faults are barren. Production in block fault basins is on horsts next to deep sedimentary troughs (Sirte, North Sea). In basins whose sediment thickness, structure and geologic history are known to a moderate degree, the main oil occurrences can be specifically predicted by analysis of fault systems and possible hydrocarbon migration routes. Use of the concept permits the identification of significant targets which have either been downgraded or ignored in the past, such as production in or just updip from thrust belts, stratigraphic traps over the deep basin associated with major faulting, production over the basin deep, and regional stratigraphic trapping updip from established production along major fault zones.

  8. Taking a deep breath

    Directory of Open Access Journals (Sweden)

    Carlos Renato Zacharias

    2012-12-01

    be paid to language revision and reference citation. Together with its authors and readers, IJHDR contributes to the development of a kind of knowledge close to the borders of science. Therefore, to establish a valid scientific background, the articles must be clearly written, and based on sound assumptions. High-visibility for articles is a fundamental aspect desired by all authors. As an open and free access journal, IJHDR meets that condition, and we are planning to make our influence and visibility even wider. Inclusion in the major databases has paramount importance in the academic milieu, however, it should be considered as a consequence, rather than a goal. In 2013, IJHDR will chair a collaborative project with several research institutions aiming to deliver information everywhere, increasing the visibility of the published articles. Thus, now it is the time to take a deep breath, relax, and prepare you for the forthcoming work! See you in 2013!

  9. A Deep ALMA Image of the Hubble Ultra Deep Field

    Science.gov (United States)

    Dunlop, J. S.

    2016-12-01

    Although primarily designed as a high-resolution imaging spectrometer at submillimetre/millimetre wavelengths, the Atacama Large Millimeter/submillimeter Array (ALMA) has a vital role to play in producing the key deep, unconfused, submillimetre/millimetre continuum surveys required to bridge the current gap in our understanding of visible and dust-obscured star formation in the young Universe. The first such survey has now been completed, comprising a mosaic of 45 ALMA pointings at a wavelength of 1.3 mm, covering the Hubble Ultra Deep Field (HUDF). This deep, homogeneous ALMA survey, combined with the wealth of existing data in the HUDF, has already provided new clarity on the nature of dusty star-forming galaxies, and the relative evolution of dust-obscured and unobscured star formation over cosmic time.

  10. Accelerating Deep Learning with Shrinkage and Recall

    OpenAIRE

    Zheng, Shuai; Vishnu, Abhinav; Ding, Chris

    2016-01-01

    Deep Learning is a very powerful machine learning model. Deep Learning trains a large number of parameters for multiple layers and is very slow when data is in large scale and the architecture size is large. Inspired from the shrinking technique used in accelerating computation of Support Vector Machines (SVM) algorithm and screening technique used in LASSO, we propose a shrinking Deep Learning with recall (sDLr) approach to speed up deep learning computation. We experiment shrinking Deep Lea...

  11. Deep Learning and Bayesian Methods

    Science.gov (United States)

    Prosper, Harrison B.

    2017-03-01

    A revolution is underway in which deep neural networks are routinely used to solve diffcult problems such as face recognition and natural language understanding. Particle physicists have taken notice and have started to deploy these methods, achieving results that suggest a potentially significant shift in how data might be analyzed in the not too distant future. We discuss a few recent developments in the application of deep neural networks and then indulge in speculation about how such methods might be used to automate certain aspects of data analysis in particle physics. Next, the connection to Bayesian methods is discussed and the paper ends with thoughts on a significant practical issue, namely, how, from a Bayesian perspective, one might optimize the construction of deep neural networks.

  12. Deep Learning and Bayesian Methods

    Directory of Open Access Journals (Sweden)

    Prosper Harrison B.

    2017-01-01

    Full Text Available A revolution is underway in which deep neural networks are routinely used to solve diffcult problems such as face recognition and natural language understanding. Particle physicists have taken notice and have started to deploy these methods, achieving results that suggest a potentially significant shift in how data might be analyzed in the not too distant future. We discuss a few recent developments in the application of deep neural networks and then indulge in speculation about how such methods might be used to automate certain aspects of data analysis in particle physics. Next, the connection to Bayesian methods is discussed and the paper ends with thoughts on a significant practical issue, namely, how, from a Bayesian perspective, one might optimize the construction of deep neural networks.

  13. Mapping the deep sea floor

    DEFF Research Database (Denmark)

    Nielsen, Kristian Hvidtfelt

    By the early 20th century, oceanographers intensified their efforts to map the deep sea. The great depth of the Philippine Trench was first observed by the German Planet Expedition in 1912. During World War II, the US naval vessel Cape Johnson used directional echo-sounding to obtain a depth of 10......,497 m. In 1951, the Danish Galathea Deep Sea Expedition from 1950 to 1952 verified the result of the Cape Johnson sounding. Today, the greatest depth in the Philippine Trench is the Galathea Depth of 10,540 m. The Galathea Expedition produced several echograms of the deepest parts of the Philippine...... Trench in order to map its bathymetric features. The resulting maps are presented in this poster. Unlike many other contemporary developments in deep sea topography and cartography that were shaped by the Cold War, the Galathea maps of the Philippine Trench were intimately connected with the expedition...

  14. Antioxidant system in two ecotypes of reed (Phragmites communis) leaves from different habitats%不同生境两种生态型芦苇的抗氧化系统

    Institute of Scientific and Technical Information of China (English)

    宫海军; 陈坤明; 高永生; 赵志光; 王锁民; 张承烈

    2004-01-01

    以分布于甘肃临泽平川乡的两种芦苇生态型--水生芦苇(水芦)和重度盐化草甸芦苇(盐芦)叶片为材料,研究了其抗氧化系统的特征.结果表明,与水芦相比,盐芦中未出现活性氧和MDA(丙二醛)的积累,抗氧化酶SOD(超氧化物歧化酶)、CAT(过氧化氢酶)、POD(过氧化物酶)和APX(抗坏血酸过氧化物酶)的活性显著升高.总抗坏血酸和类胡萝卜素含量在两种生态型芦苇中没有差异,但还原型抗坏血酸和总谷胱甘肽含量在盐芦中显著升高.而且,盐芦的LOX(脂氧合酶)活性比水芦低.这些结果表明,盐芦中有效的抗氧化防御系统对抵抗盐渍胁迫起着重要的作用.此外,盐芦中高活性的Ca2+- 和 Mg2+-ATPase对细胞中过多离子的转运以及避免离子毒害起着重要的作用.%Using plants possessing stable genetic tolerance/resistance under natural environmental conditions to study the mechanism of plants' adaptation to environmental stress are very significant. However, relevant work is very limited. In this work, two ecotypes of reed (Phragmites communis Trin.), referred to as "swamp reed (SR)" and "heavy salt meadow reed (HSMR)" according to their habitats, growing in Pingchuan Town, Linze County, Gansu Province (China) were investigated for the antioxidant system in their leaves. The results showed that compared with the SR, there were no accumulations of reactive oxygen species and MDA (malondialdehyde) in the HSMR. The activities of SOD (superoxide dismutase), CAT (catalase), POD (peroxidase) and APX (ascorbate peroxidase) were significantly higher in the HSMR than those in the SR. There were no differences in the contents of total ascorbic acid and carotenoids between the two ecotypes, while the contents of reduced ascorbic acid and total glutathione were higher in the HSMR than that in the SR. Moreover, the LOX (lipoxygenase) in the HSMR showed a decreased activity compared with the SR. These results suggested that more

  15. The ANDES Deep Underground Laboratory

    CERN Document Server

    Bertou, X

    2013-01-01

    ANDES (Agua Negra Deep Experiment Site) is a unique opportunity to build a deep underground laboratory in the southern hemisphere. It will be built in the Agua Negra tunnel planned between Argentina and Chile, and operated by the CLES, a Latin American consortium. With 1750m of rock overburden, and no close- by nuclear power plant, it will provide an extremely radiation quiet environment for neutrino and dark matter experiments. In particular, its location in the southern hemisphere should play a major role in understanding dark matter modulation signals.

  16. Bonaire Deep Reef Expedition I

    OpenAIRE

    Becking, L.E.; Meesters, H.W.G.

    2014-01-01

    From 30 May – 1 June 2013 the deep reef of Bonaire, Caribbean Netherlands, was explored with the aid of the “Curasub” submarine of Substation Curaçao. The shallow reefs of the Caribbean are considered a biodiversity-hotspot, an area with exceptional diversity of plants, animals and ecosystems yet surprisingly little is known about the flora and fauna of the deeper reefs. Particularly the deep reefs of Bonaire, St. Eustatius and Saba have hardly been explored. This represents a critical knowle...

  17. Deep space infections of neck.

    Science.gov (United States)

    Kaluskar, S; Bajaj, P; Bane, P

    2007-03-01

    A retrospective study was performed on fourteen cases of deep cervical space infections in the neck admitted for diagnosis and treatment to the ENT Department, during a period of seven years from 1989-1997. Of the fourteen, four patients had Ludwig's angina and of the fourteen, one had a very serious complication resulting in death. Early diagnosis and adequate treatment were of paramount importance. The role of tracheostomy and management of airway in deep cervical space infections of the neck is discussed to gether with bacteriology, antibiotic treatment and surgical management.

  18. Stimulation Technologies for Deep Well Completions

    Energy Technology Data Exchange (ETDEWEB)

    None

    2003-09-30

    The Department of Energy (DOE) is sponsoring the Deep Trek Program targeted at improving the economics of drilling and completing deep gas wells. Under the DOE program, Pinnacle Technologies is conducting a study to evaluate the stimulation of deep wells. The objective of the project is to assess U.S. deep well drilling & stimulation activity, review rock mechanics & fracture growth in deep, high pressure/temperature wells and evaluate stimulation technology in several key deep plays. An assessment of historical deep gas well drilling activity and forecast of future trends was completed during the first six months of the project; this segment of the project was covered in Technical Project Report No. 1. The second progress report covers the next six months of the project during which efforts were primarily split between summarizing rock mechanics and fracture growth in deep reservoirs and contacting operators about case studies of deep gas well stimulation.

  19. STIMULATION TECHNOLOGIES FOR DEEP WELL COMPLETIONS

    Energy Technology Data Exchange (ETDEWEB)

    Stephen Wolhart

    2003-06-01

    The Department of Energy (DOE) is sponsoring a Deep Trek Program targeted at improving the economics of drilling and completing deep gas wells. Under the DOE program, Pinnacle Technologies is conducting a project to evaluate the stimulation of deep wells. The objective of the project is to assess U.S. deep well drilling & stimulation activity, review rock mechanics & fracture growth in deep, high pressure/temperature wells and evaluate stimulation technology in several key deep plays. Phase 1 was recently completed and consisted of assessing deep gas well drilling activity (1995-2007) and an industry survey on deep gas well stimulation practices by region. Of the 29,000 oil, gas and dry holes drilled in 2002, about 300 were drilled in the deep well; 25% were dry, 50% were high temperature/high pressure completions and 25% were simply deep completions. South Texas has about 30% of these wells, Oklahoma 20%, Gulf of Mexico Shelf 15% and the Gulf Coast about 15%. The Rockies represent only 2% of deep drilling. Of the 60 operators who drill deep and HTHP wells, the top 20 drill almost 80% of the wells. Six operators drill half the U.S. deep wells. Deep drilling peaked at 425 wells in 1998 and fell to 250 in 1999. Drilling is expected to rise through 2004 after which drilling should cycle down as overall drilling declines.

  20. Bonaire Deep Reef Expedition I

    NARCIS (Netherlands)

    Becking, L.E.; Meesters, H.W.G.

    2014-01-01

    From 30 May – 1 June 2013 the deep reef of Bonaire, Caribbean Netherlands, was explored with the aid of the “Curasub” submarine of Substation Curaçao. The shallow reefs of the Caribbean are considered a biodiversity-hotspot, an area with exceptional diversity of plants, animals and ecosystems yet

  1. Digging Deeper: The Deep Web.

    Science.gov (United States)

    Turner, Laura

    2001-01-01

    Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

  2. Bonaire Deep Reef Expedition I

    NARCIS (Netherlands)

    Becking, L.E.; Meesters, H.W.G.

    2014-01-01

    From 30 May – 1 June 2013 the deep reef of Bonaire, Caribbean Netherlands, was explored with the aid of the “Curasub” submarine of Substation Curaçao. The shallow reefs of the Caribbean are considered a biodiversity-hotspot, an area with exceptional diversity of plants, animals and ecosystems yet su

  3. Digging Deeper: The Deep Web.

    Science.gov (United States)

    Turner, Laura

    2001-01-01

    Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

  4. Keeping It Simple and Deep.

    Science.gov (United States)

    Strong, Richard; Silver, Harvey; Perini, Matthew

    1999-01-01

    Like today's educators, Japanese haiku poets were caught between standards (like courtly love) and everyday realities. From this tension, they created a remarkable poetic form. Three examples from teachers' professional development work apply simple-and-deep principles to listening tasks, an assessment "deal," and curricular-standards…

  5. Deep-Sky Video Astronomy

    CERN Document Server

    Massey, Steve

    2009-01-01

    A guide to using modern integrating video cameras for deep-sky viewing and imaging with the kinds of modest telescopes available commercially to amateur astronomers. It includes an introduction and a brief history of the technology and camera types. It examines the pros and cons of this unrefrigerated yet highly efficient technology

  6. Deep-water sediment bypass

    NARCIS (Netherlands)

    Stevenson, Christopher J.; Jackson, Christopher A L; Hodgson, David M.; Hubbard, Stephen M.; Eggenhuisen, Joris T.

    2015-01-01

    Submarine gravity flows are a key process for transporting large volumes of sediment from the continents to the deep sea. The location, volume, and character of the sediment bypassed by these flows dictates the areal extent and thickness of the associated deposits. Despite its importance, sediment b

  7. Stimulation Technologies for Deep Well Completions

    Energy Technology Data Exchange (ETDEWEB)

    Stephen Wolhart

    2005-06-30

    The Department of Energy (DOE) is sponsoring the Deep Trek Program targeted at improving the economics of drilling and completing deep gas wells. Under the DOE program, Pinnacle Technologies conducted a study to evaluate the stimulation of deep wells. The objective of the project was to review U.S. deep well drilling and stimulation activity, review rock mechanics and fracture growth in deep, high-pressure/temperature wells and evaluate stimulation technology in several key deep plays. This report documents results from this project.

  8. DeepSurveyCam—A Deep Ocean Optical Mapping System

    Directory of Open Access Journals (Sweden)

    Tom Kwasnitschka

    2016-01-01

    Full Text Available Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor, and the limitations of localization technologies (no GPS. The absence of natural light complicates energy budget considerations for deep diving flash-equipped drones. Refraction effects influence geometric image formation considerations with respect to field of view and focus, while attenuation and scattering degrade the radiometric image quality and limit the effective visibility. As an improvement on the stated issues, we present an AUV-based optical system intended for autonomous visual mapping of large areas of the seafloor (square kilometers in up to 6000 m water depth. We compare it to existing systems and discuss tradeoffs such as resolution vs. mapped area and show results from a recent deployment with 90,000 mapped square meters of deep ocean floor.

  9. DeepSurveyCam--A Deep Ocean Optical Mapping System.

    Science.gov (United States)

    Kwasnitschka, Tom; Köser, Kevin; Sticklus, Jan; Rothenbeck, Marcel; Weiß, Tim; Wenzlaff, Emanuel; Schoening, Timm; Triebe, Lars; Steinführer, Anja; Devey, Colin; Greinert, Jens

    2016-01-28

    Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor), and the limitations of localization technologies (no GPS). The absence of natural light complicates energy budget considerations for deep diving flash-equipped drones. Refraction effects influence geometric image formation considerations with respect to field of view and focus, while attenuation and scattering degrade the radiometric image quality and limit the effective visibility. As an improvement on the stated issues, we present an AUV-based optical system intended for autonomous visual mapping of large areas of the seafloor (square kilometers) in up to 6000 m water depth. We compare it to existing systems and discuss tradeoffs such as resolution vs. mapped area and show results from a recent deployment with 90,000 mapped square meters of deep ocean floor.

  10. DeepSurveyCam—A Deep Ocean Optical Mapping System

    Science.gov (United States)

    Kwasnitschka, Tom; Köser, Kevin; Sticklus, Jan; Rothenbeck, Marcel; Weiß, Tim; Wenzlaff, Emanuel; Schoening, Timm; Triebe, Lars; Steinführer, Anja; Devey, Colin; Greinert, Jens

    2016-01-01

    Underwater photogrammetry and in particular systematic visual surveys of the deep sea are by far less developed than similar techniques on land or in space. The main challenges are the rough conditions with extremely high pressure, the accessibility of target areas (container and ship deployment of robust sensors, then diving for hours to the ocean floor), and the limitations of localization technologies (no GPS). The absence of natural light complicates energy budget considerations for deep diving flash-equipped drones. Refraction effects influence geometric image formation considerations with respect to field of view and focus, while attenuation and scattering degrade the radiometric image quality and limit the effective visibility. As an improvement on the stated issues, we present an AUV-based optical system intended for autonomous visual mapping of large areas of the seafloor (square kilometers) in up to 6000 m water depth. We compare it to existing systems and discuss tradeoffs such as resolution vs. mapped area and show results from a recent deployment with 90,000 mapped square meters of deep ocean floor. PMID:26828495

  11. A deep ALMA image of the Hubble Ultra Deep Field

    CERN Document Server

    Dunlop, J S; Biggs, A D; Geach, J E; Michalowski, M J; Ivison, R J; Rujopakarn, W; van Kampen, E; Kirkpatrick, A; Pope, A; Scott, D; Swinbank, A M; Targett, T A; Aretxaga, I; Austermann, J E; Best, P N; Bruce, V A; Chapin, E L; Charlot, S; Cirasuolo, M; Coppin, K E K; Ellis, R S; Finkelstein, S L; Hayward, C C; Hughes, D H; Ibar, E; Khochfar, S; Koprowski, M P; Narayanan, D; Papovich, C; Peacock, J A; Robertson, B; Vernstrom, T; van der Werf, P P; Wilson, G W; Yun, M

    2016-01-01

    We present the results of the first, deep ALMA imaging covering the full 4.5 sq arcmin of the Hubble Ultra Deep Field (HUDF) as previously imaged with WFC3/IR on HST. Using a mosaic of 45 pointings, we have obtained a homogeneous 1.3mm image of the HUDF, achieving an rms sensitivity of 35 microJy, at a resolution of 0.7 arcsec. From an initial list of ~50 >3.5sigma peaks, a rigorous analysis confirms 16 sources with flux densities S(1.3) > 120 microJy. All of these have secure galaxy counterparts with robust redshifts ( = 2.15), and 12 are also detected at 6GHz in new deep JVLA imaging. Due to the wealth of supporting data in this unique field, the physical properties of the ALMA sources are well constrained, including their stellar masses (M*) and UV+FIR star-formation rates (SFR). Our results show that stellar mass is the best predictor of SFR in the high-z Universe; indeed at z > 2 our ALMA sample contains 7 of the 9 galaxies in the HUDF with M* > 2 x 10^10 Msun and we detect only one galaxy at z > 3.5, re...

  12. China's first deep manned submersible,JIAOLONG

    Institute of Scientific and Technical Information of China (English)

    LIU Feng; CUI WeiCheng; LI XiangYang

    2010-01-01

    @@ A deep manned submersible is indispensable to deep ocean exploration.No other equipment can bring scientists to extreme sea floor depths to do research in situ.Marine geology, seafloor geophysics, marine biology, and oceanic chemistry are the fields that scientists are particularly eager to study [1-6].Chinese scientists have long dreamed of using their own submersible to probe the deep sea.China's recent fast development of a deep manned submersible has realized that dream.

  13. Deep Image: Scaling up Image Recognition

    OpenAIRE

    Wu, Ren; Yan, Shengen; Shan, Yi; Dang, Qingqing; Sun, Gang

    2015-01-01

    We present a state-of-the-art image recognition system, Deep Image, developed using end-to-end deep learning. The key components are a custom-built supercomputer dedicated to deep learning, a highly optimized parallel algorithm using new strategies for data partitioning and communication, larger deep neural network models, novel data augmentation approaches, and usage of multi-scale high-resolution images. Our method achieves excellent results on multiple challenging computer vision benchmarks.

  14. Hybrid mask for deep etching

    KAUST Repository

    Ghoneim, Mohamed T.

    2017-08-10

    Deep reactive ion etching is essential for creating high aspect ratio micro-structures for microelectromechanical systems, sensors and actuators, and emerging flexible electronics. A novel hybrid dual soft/hard mask bilayer may be deposited during semiconductor manufacturing for deep reactive etches. Such a manufacturing process may include depositing a first mask material on a substrate; depositing a second mask material on the first mask material; depositing a third mask material on the second mask material; patterning the third mask material with a pattern corresponding to one or more trenches for transfer to the substrate; transferring the pattern from the third mask material to the second mask material; transferring the pattern from the second mask material to the first mask material; and/or transferring the pattern from the first mask material to the substrate.

  15. Deep learning for computational biology.

    Science.gov (United States)

    Angermueller, Christof; Pärnamaa, Tanel; Parts, Leopold; Stegle, Oliver

    2016-07-29

    Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.

  16. Density functionals from deep learning

    CERN Document Server

    McMahon, Jeffrey M

    2016-01-01

    Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep learning is developed to approximate this functional. Deep learning allows computational models that are capable of naturally discovering intricate structure in large and/or high-dimensional data sets, with multiple levels of abstraction. As no assumptions are made as to the form of this structure, this approach is much more powerful and flexible than traditional approaches. As an example application, the model is shown to perform well on approximating the kinetic-energy density functional for noninteracting electrons. The model is analyzed in detail, and its advantages over conventional machine learning are discussed.

  17. DeepFlavour in CMS

    CERN Document Server

    CERN. Geneva

    2017-01-01

    Flavour-tagging of jets is an important task in collider based high energy physics and a field where machine learning tools are applied by all major experiments. A new tagger (DeepFlavour) was developed and commissioned in CMS that is based on an advanced machine learning procedure. A deep neural network is used to do multi-classification of jets that origin from a b-quark, two b-quarks, a c-quark, two c-quarks or light colored particles (u, d, s-quark or gluon). The performance was measured in both, data and simulation. The talk will also include the measured performance of all taggers in CMS. The different taggers and results will be discussed and compared with some focus on details of the newest tagger.

  18. Consolidated Deep Actor Critic Networks (DRAFT)

    NARCIS (Netherlands)

    Van der Laan, T.A.

    2015-01-01

    The works [Volodymyr et al. Playing atari with deep reinforcement learning. arXiv preprint arXiv:1312.5602, 2013.] and [Volodymyr et al. Human-level control through deep reinforcement learning. Nature, 518(7540):529–533, 2015.] have demonstrated the power of combining deep neural networks with Watki

  19. TOPIC MODELING: CLUSTERING OF DEEP WEBPAGES

    OpenAIRE

    Muhunthaadithya C; Rohit J.V; Sadhana Kesavan; Sivasankar, E.

    2015-01-01

    The internet is comprised of massive amount of information in the form of zillions of web pages.This information can be categorized into the surface web and the deep web. The existing search engines can effectively make use of surface web information.But the deep web remains unexploited yet. Machine learning techniques have been commonly employed to access deep web content.

  20. Consolidated Deep Actor Critic Networks (DRAFT)

    NARCIS (Netherlands)

    Van der Laan, T.A.

    2015-01-01

    The works [Volodymyr et al. Playing atari with deep reinforcement learning. arXiv preprint arXiv:1312.5602, 2013.] and [Volodymyr et al. Human-level control through deep reinforcement learning. Nature, 518(7540):529–533, 2015.] have demonstrated the power of combining deep neural networks with Watki

  1. TOPIC MODELING: CLUSTERING OF DEEP WEBPAGES

    OpenAIRE

    Muhunthaadithya C; Rohit J.V; Sadhana Kesavan; E. Sivasankar

    2015-01-01

    The internet is comprised of massive amount of information in the form of zillions of web pages.This information can be categorized into the surface web and the deep web. The existing search engines can effectively make use of surface web information.But the deep web remains unexploited yet. Machine learning techniques have been commonly employed to access deep web content.

  2. Is Multitask Deep Learning Practical for Pharma?

    Science.gov (United States)

    Ramsundar, Bharath; Liu, Bowen; Wu, Zhenqin; Verras, Andreas; Tudor, Matthew; Sheridan, Robert P; Pande, Vijay

    2017-08-28

    Multitask deep learning has emerged as a powerful tool for computational drug discovery. However, despite a number of preliminary studies, multitask deep networks have yet to be widely deployed in the pharmaceutical and biotech industries. This lack of acceptance stems from both software difficulties and lack of understanding of the robustness of multitask deep networks. Our work aims to resolve both of these barriers to adoption. We introduce a high-quality open-source implementation of multitask deep networks as part of the DeepChem open-source platform. Our implementation enables simple python scripts to construct, fit, and evaluate sophisticated deep models. We use our implementation to analyze the performance of multitask deep networks and related deep models on four collections of pharmaceutical data (three of which have not previously been analyzed in the literature). We split these data sets into train/valid/test using time and neighbor splits to test multitask deep learning performance under challenging conditions. Our results demonstrate that multitask deep networks are surprisingly robust and can offer strong improvement over random forests. Our analysis and open-source implementation in DeepChem provide an argument that multitask deep networks are ready for widespread use in commercial drug discovery.

  3. Consolidated Deep Actor Critic Networks (DRAFT)

    NARCIS (Netherlands)

    Van der Laan, T.A.

    2015-01-01

    The works [Volodymyr et al. Playing atari with deep reinforcement learning. arXiv preprint arXiv:1312.5602, 2013.] and [Volodymyr et al. Human-level control through deep reinforcement learning. Nature, 518(7540):529–533, 2015.] have demonstrated the power of combining deep neural networks with

  4. Deep Learning on Imaging Calorimetry

    OpenAIRE

    Mahapatra, Jayesh; Pierini, Maurizio; Vlimant, Jean-Roch; Spiropulu, Maria

    2016-01-01

    Abstract Particle reconstruction is a significant task in analysis of CMS data. Currently physics based algorithms in conjunction with CMS readouts are used. In this project we explored deep learning as a technique for photon identification and reconstruction on the public LCD CaloImage dataset. Several network architectures were tested for performing classification (photon vs pion discrimination) and regression analysis of energy of particle hits. The performance of the topologies were p...

  5. Implementing Deep Inference in Tom

    OpenAIRE

    Kahramanogullari, Ozan; Moreau, Pierre-Etienne; Reilles, Antoine

    2005-01-01

    ISSN 1430-211X; The calculus of structures is a proof theoretical formalism which generalizes sequent calculus with the feature of deep inference: in contrast to sequent calculus, the calculus of structures does not rely on the notion of main connective and, like in term rewriting, it permits the application of the inference rules at any depth inside a formula. Tom is a pattern matching processor that integrates term rewriting facilities into imperative languages. In this paper, relying on th...

  6. Deep Learning for Health Informatics.

    Science.gov (United States)

    Ravi, Daniele; Wong, Charence; Deligianni, Fani; Berthelot, Melissa; Andreu-Perez, Javier; Lo, Benny; Yang, Guang-Zhong

    2017-01-01

    With a massive influx of multimodality data, the role of data analytics in health informatics has grown rapidly in the last decade. This has also prompted increasing interests in the generation of analytical, data driven models based on machine learning in health informatics. Deep learning, a technique with its foundation in artificial neural networks, is emerging in recent years as a powerful tool for machine learning, promising to reshape the future of artificial intelligence. Rapid improvements in computational power, fast data storage, and parallelization have also contributed to the rapid uptake of the technology in addition to its predictive power and ability to generate automatically optimized high-level features and semantic interpretation from the input data. This article presents a comprehensive up-to-date review of research employing deep learning in health informatics, providing a critical analysis of the relative merit, and potential pitfalls of the technique as well as its future outlook. The paper mainly focuses on key applications of deep learning in the fields of translational bioinformatics, medical imaging, pervasive sensing, medical informatics, and public health.

  7. Deep Corals, Deep Learning: Moving the Deep Net Towards Real-Time Image Annotation

    OpenAIRE

    Henry, Lea-Anne; Mukherjee, Sankha S.; Robertson, Neil M.; De Clippele, Laurence; Roberts, J Murray

    2016-01-01

    The mismatch between human capacity and the acquisition of Big Data such as Earth imagery undermines commitments to Convention on Biological Diversity (CBD) and Aichi targets. Artificial intelligence (AI) solutions to Big Data issues are urgently needed as these could prove to be faster, more accurate, and cheaper. Reducing costs of managing protected areas in remote deep waters and in the High Seas is of great importance, and this is a realm where autonomous technology will be transformative.

  8. Deep Learning and Music Adversaries

    DEFF Research Database (Denmark)

    Kereliuk, Corey Mose; Sturm, Bob L.; Larsen, Jan

    2015-01-01

    the minimal perturbation of the input image such that the system misclassifies it with high confidence. We adapt this approach to construct and deploy an adversary of deep learning systems applied to music content analysis. In our case, however, the system inputs are magnitude spectral frames, which require...... compared to systems based on a majority vote over individually classified audio frames. Furthermore, we experiment with a new system that integrates an adversary into the training loop, but do not find that this improves the resilience of the system to new adversaries....

  9. Andrew Ng 谈 Deep Learning

    Institute of Scientific and Technical Information of China (English)

    卢鸫翔

    2014-01-01

    Andrew Ng是Deep Learning领域最富盛名的科学家之一,他也是斯坦福人工智能实验室主任,在线教育平台Coursera的创始人之一。2014年5月,他加入百度,负责“百度大脑”计划,并担任百度首席科学家。目前,他接受了《程序员》的专访。

  10. Autonomous robotics and deep learning

    CERN Document Server

    Nath, Vishnu

    2014-01-01

    This Springer Brief examines the combination of computer vision techniques and machine learning algorithms necessary for humanoid robots to develop "true consciousness." It illustrates the critical first step towards reaching "deep learning," long considered the holy grail for machine learning scientists worldwide. Using the example of the iCub, a humanoid robot which learns to solve 3D mazes, the book explores the challenges to create a robot that can perceive its own surroundings. Rather than relying solely on human programming, the robot uses physical touch to develop a neural map of its en

  11. Deep endometriosis of the colon.

    Science.gov (United States)

    Ropacka-Lesiak, Mariola; Świder-Musielak, Joanna; Wójcicka, Małgorzata; Łyczywek, Anna; Skrzypek, Maciej; Waliszewski, Wojciech

    2013-01-01

    The article presents a case of deep intestinal endometriosis in a 27-year-old woman who complained of dysmenorrhea and infertility. The diagnostic process included ultrasonography as well as colonoscopy, barium enema and CT imaging. Because of the presence of two distant changes which involved nearly the full thickness of the rectal wall and the major part of its circumference, the decision to perform an anterior rectal resection with a simultaneous retroperitoneal colorectostomy was made. The Knight technique was implemented. The surgery involved the anterior rectal resection, the transverse rectal stump closure by use of a stapling device (TA50), and the creation of colorectal circular anastomosis with the CEEA 31 stapler.

  12. BIOCHEMICAL AND MOLECULAR CHARACTERIZATION OF RED RICE ECOTYPES FROM THE RIO GRANDE DO SUL STATE, BRAZIL CARACTERIZAÇÃO BIOQUÍMICA E MOLECULAR DE ACESSOS DE ARROZ VERMELHO COLETADOS NO ESTADO DO RIO GRANDE DO SUL

    Directory of Open Access Journals (Sweden)

    Gaspar Malone

    2007-09-01

    Full Text Available

    Red rice is one of the most important weeds of cultivated rice in Brazil. On the other hand, red rice constitutes a collection of genes lost during the cultivated rice domestication process and has a fundamental importance for recovery of promising genic constitutions. This study had the objective to analyze the genetic variability of a colletion of red rice (Oryza sativa L. ecotypes from Rio Grande do Sul State, Brazil, through isoenzimatic and microsatellite markers. Thirty four accesses from the Seed and Biotechnology Laboratory germplasm bank, at Federal University of Pelotas, were analyzed using six isoenzimatic systems and nineteen microsatellite markers. Twenty-three biochemical and 54 molecular alleles were identified and used to estimate the polymorphism (PIC and genetic similarity indexes. The analyzed red rice population presents large genetic variability, evidencing the potentiality to map characteristics of interest to seed physiology. Biochemical markers of the isoenzime type and molecular markers of the microsatellite type are efficient to estimate the genetic variability in red rice ecotypes.

    KEY-WORDS: Oryza sativa; biochemical markers; microsatellite markers; genetic variability.

    O arroz vermelho é uma das principais espécies daninhas para cultivo de arroz no Brasil. Por outro lado, constitui-se num acervo de genes perdidos durante a domesticação do arroz cultivado, que poderá ser importante para a recuperação de constituições gênicas promissoras. O objetivo desde trabalho foi analisar a variabilidade genética de uma coleção de acessos de arroz vermelho (Oryza sativa L. coletados no Estado de Rio Grande do Sul, Brasil, através de marcadores bioquímicos do tipo isoenzimas, e marcadores moleculares do tipo microssatélites. Trinta e quatro acessos

  13. 定向转育卵圆生态型大白菜雄性不育系的研究%Directional Breeding of An Oval-ecotype Male Sterile Line of Chinese Cabbage(Brassica campestris L. ssp. pekinensis)

    Institute of Scientific and Technical Information of China (English)

    谭翀; 郭瑛琪; 岳艳玲

    2014-01-01

    [目的]探究大白菜定向转育卵圆生态型雄性不育系的方法。[方法]以大白菜核不育"复等位基因遗传假说"为理论依据,以甲型两用系‘AB12’为不育供体品系,以卵圆生态型可育品系‘06048’为待转育品系,采用杂交、回交、兄妹交和测交的方法,按照定向转育方案将核不育基因定向转育。[结果]各世代育性分离比率与理论相一致,成功育成了一种不育株率100%的具有‘06048’园艺性状的新核不育系,实现了核不育基因和园艺特性的同时转育。[结论]该研究成果验证此定向转育方案是可行的,进一步为基因型为 msms的其他园艺性状的大白菜定向转育提供理论基础,也可以推广应用到整个芸薹属其它经济作物中,极大的拓宽了优良核不育基因的实际应用范围。%Objective] The study aimed to explore the method for directional breeding of a male-sterile line in oval-ecotype Chinese cabbage. [Method] Based on "Multiple Al ele Hypothesis of Genic Male Sterile Chinese Cabbage", an inbred line ‘06048’ of oval ecotype was used as the receptor, and male fertile plant of ‘AB12’ was used as the donor line. Crossing, backcross, selfing, testcross and sibling were ap-plied to transfer the multiple al eles under the directional genetic model. [Result] Segregation ratio of every generation was consistent with theoretical value. A new male sterile line with 100% male sterility and ‘06048’ horticultural traits was ob-tained successful y, which accomplished the transfer of male sterile multiple al ele and horticultural characters of receptor line at the same time. [Conclusion] The re-search verifies that the model of directional transfer is feasible, provides a theoreti-cal basis for the directional transfer of Chinese cabbage with other horticultural traits whose genotype is msms. The model can also be applied to other Brassica crops, to generate genetic male sterile lines

  14. The NTT Susi Deep Field

    CERN Document Server

    Arnouts, S; Cristiani, S; Zaggia, S R; Fontana, A; Giallongo, E

    1999-01-01

    We present a deep BVrI multicolor catalog of galaxies in a 5.62 sq.arcmin field 80 arcsec south of the high redshift (z=4.7) quasar BR 1202-0725, derived from observations with the direct CCD camera SUSI at the ESO NTT. The formal 5$\\sigma$ magnitude limits (in 2 x FWHM apertures) are 26.9, 26.5, 25.9 and 25.3 in B, V, r and I respectively. Counts, colors for the star and galaxy samples are discussed and a comparison with a deep HST image in the I band is presented. The percentage of merged or blended galaxies in the SUSI data to this magnitude limit is estimated to be not higher than 1%. At the same galactic latitude of the HDF but pointing toward the galactic center, the star density in this field is found to be ~3 times higher, with ~20% of the objects with V-I > 3.0. Reliable colors have been measured for galaxies selected down to r = 26. The choice of the optical filters has been optimized to define a robust multicolor selection of galaxies at 3.8 <= z <= 4.4. Within this interval the surface densi...

  15. Exploring life's limits: Deep geobiochemistry

    Science.gov (United States)

    Cox, A. D.

    2014-12-01

    N-dimensional chemical space on Earth and beyond produces diverse habitats for microbial activity. Hydrothermal environments cover a wide range of habitable space up to and including life's known limits and provide a window into deep geological, geochemical, and biological processes. Hydrothermal water compositions, as sampled from and measured in terrestrial hot springs on Earth's surface, vary in chemical constituent speciation and concentrations over orders of magnitude in a plethora of geochemical parameters with biological significance, including hydronium ion, sulfide, iron, zinc, magnesium, manganese, and molybdenum. Proteins provide a link between geochemistry and microbial activity by catalyzing chemical reactions. Proteins extracted and identified by tandem mass spectrometry from 13 hot spring sediments and biofilms - covering pH values from 2-9 and diverse geochemical compositions - function as efflux transporters, permeases, electron transporters, and others, suggesting that these processes were present in the environment and occurring at the time of sampling. Metalloenzymes have been identified, including the iron protein rubrerythrin, thought to be involved in oxidative stress protection in anaerobic bacteria and archaea, as well as proteins involved in macronutrient processing (carbon, phosphorus, nitrogen, and sulfur). The melding of biochemistry with geochemistry shows potential for quantifying microbial activity in deep environments by demonstrating the presence - and as techniques improve, relative abundances - of reaction-catalyzing enzymes. Moreover, using hot spring sources and their outflow channels as chemical and biological models of geologic time helps decipher the origin and co-evolution of life and geochemistry.

  16. Academic Training: Deep Space Telescopes

    CERN Multimedia

    Françoise Benz

    2006-01-01

    2005-2006 ACADEMIC TRAINING PROGRAMME LECTURE SERIES 20, 21, 22, 23, 24 February from 11:00 to 12:00 - Council Chamber on 20, 21, 23, 24 February, TH Auditorium, bldg 4 - 3-006, on 22 February Deep Space Telescopes G. BIGNAMI / CNRS, Toulouse, F & Univ. di Pavia, I The short series of seminars will address results and aims of current and future space astrophysics as the cultural framework for the development of deep space telescopes. It will then present such new tools, as they are currently available to, or imagined by, the scientific community, in the context of the science plans of ESA and of all major world space agencies. Ground-based astronomy, in the 400 years since Galileo's telescope, has given us a profound phenomenological comprehension of our Universe, but has traditionally been limited to the narrow band(s) to which our terrestrial atmosphere is transparent. Celestial objects, however, do not care about our limitations, and distribute most of the information about their physics thro...

  17. Pathogens spectrum of deep human mycosis

    Directory of Open Access Journals (Sweden)

    A. B. Kulko

    2012-01-01

    Full Text Available The article describes characteristics of two different etiology groups of deep human mycosis — extremely dangerous endemic deep mycoses (histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, penicilliosis due to Penicillium marneffei and opportunistic deep mycosis (candidiasis, cryptococcosis, aspergillosis, mucormycosis. Information on fungal pathogens and antifungal agents is presented. The own results of cultural studies obtained during pneumomycosis diagnosis in patients with tuberculosis are shown.

  18. TOPIC MODELING: CLUSTERING OF DEEP WEBPAGES

    Directory of Open Access Journals (Sweden)

    Muhunthaadithya C

    2015-07-01

    Full Text Available The internet is comprised of massive amount of information in the form of zillions of web pages.This information can be categorized into the surface web and the deep web. The existing search engines can effectively make use of surface web information.But the deep web remains unexploited yet. Machine learning techniques have been commonly employed to access deep web content.

  19. Pathogens spectrum of deep human mycosis

    Directory of Open Access Journals (Sweden)

    A. B. Kulko

    2014-07-01

    Full Text Available The article describes characteristics of two different etiology groups of deep human mycosis — extremely dangerous endemic deep mycoses (histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, penicilliosis due to Penicillium marneffei and opportunistic deep mycosis (candidiasis, cryptococcosis, aspergillosis, mucormycosis. Information on fungal pathogens and antifungal agents is presented. The own results of cultural studies obtained during pneumomycosis diagnosis in patients with tuberculosis are shown.

  20. Learning Multiple Tasks with Deep Relationship Networks

    OpenAIRE

    Long, Mingsheng; Wang, Jianmin

    2015-01-01

    Deep neural networks trained on large-scale dataset can learn transferable features that promote learning multiple tasks for inductive transfer and labeling mitigation. As deep features eventually transition from general to specific along the network, a fundamental problem is how to exploit the relationship structure across different tasks while accounting for the feature transferability in the task-specific layers. In this work, we propose a novel Deep Relationship Network (DRN) architecture...

  1. Switchgrass cultivars alter microbial contribution to deep soil C in Nebraska

    Science.gov (United States)

    Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland) and cultivars, there has been little focus on the impact of plant belowgro...

  2. The cyanide gasp and spontaneous deep breaths.

    Science.gov (United States)

    Glogowska, M; Richardson, P S

    1973-01-01

    Stimulation of the carotid body chemoreceptors with cyanide in anaesthetized rabbits usually causes a deep breath or gasp, but only if the vagus nerves are intact. This gasp has several similarities with spontaneous deep breaths in eupnoea. In paralysed rabbits, artificially ventilated, chemoreceptor stimulation induces an augmented discharge in the phrenic nerve equivalent to a gasp. In spontaneously breathing rabbits spontaneous deep breaths are more frequent with hypoxia than with normoxia. The results are interpreted in relation to (i) positive feedback from the lungs and (ii) summation of chemoreceptor and tonic vagal drive causing augmented deep breaths.

  3. Deep-sea fungi: Occurrence and adaptations

    Digital Repository Service at National Institute of Oceanography (India)

    Damare, S.

    in it being the least understood environments on the earth. The understanding of deep sea will unravel a lot of exciting information about the history of life existing on earth. The deep sea was thought to be a very difficult environment for life forms.... Danovaro R, Fabiano M, Della Croce N (1995) Labile organic matter and microbial biomasses in deep-sea sediments (Eastern Mediterranean Sea). Deep-Sea Research I, 40: 953-65. DasSarma S, Arora P (2001) Halophiles. Encyclopedia of Life Sciences. Macmillan...

  4. Deep learning in neural networks: an overview.

    Science.gov (United States)

    Schmidhuber, Jürgen

    2015-01-01

    In recent years, deep artificial neural networks (including recurrent ones) have won numerous contests in pattern recognition and machine learning. This historical survey compactly summarizes relevant work, much of it from the previous millennium. Shallow and Deep Learners are distinguished by the depth of their credit assignment paths, which are chains of possibly learnable, causal links between actions and effects. I review deep supervised learning (also recapitulating the history of backpropagation), unsupervised learning, reinforcement learning & evolutionary computation, and indirect search for short programs encoding deep and large networks.

  5. Deep subspace mapping in hyperspectral imaging

    Science.gov (United States)

    Wadströmer, Niclas; Gustafsson, David; Perersson, Henrik; Bergström, David

    2016-10-01

    We propose a novel Deep learning approach using autoencoders to map spectral bands to a space of lower dimensionality while preserving the information that makes it possible to discriminate different materials. Deep learning is a relatively new pattern recognition approach which has given promising result in many applications. In Deep learning a hierarchical representation of increasing level of abstraction of the features is learned. Autoencoder is an important unsupervised technique frequently used in Deep learning for extracting important properties of the data. The learned latent representation is a non-linear mapping of the original data which potentially preserve the discrimination capacity.

  6. The deep ocean under climate change

    Science.gov (United States)

    Levin, Lisa A.; Le Bris, Nadine

    2015-11-01

    The deep ocean absorbs vast amounts of heat and carbon dioxide, providing a critical buffer to climate change but exposing vulnerable ecosystems to combined stresses of warming, ocean acidification, deoxygenation, and altered food inputs. Resulting changes may threaten biodiversity and compromise key ocean services that maintain a healthy planet and human livelihoods. There exist large gaps in understanding of the physical and ecological feedbacks that will occur. Explicit recognition of deep-ocean climate mitigation and inclusion in adaptation planning by the United Nations Framework Convention on Climate Change (UNFCCC) could help to expand deep-ocean research and observation and to protect the integrity and functions of deep-ocean ecosystems.

  7. Automatic speech recognition a deep learning approach

    CERN Document Server

    Yu, Dong

    2015-01-01

    This book summarizes the recent advancement in the field of automatic speech recognition with a focus on discriminative and hierarchical models. This will be the first automatic speech recognition book to include a comprehensive coverage of recent developments such as conditional random field and deep learning techniques. It presents insights and theoretical foundation of a series of recent models such as conditional random field, semi-Markov and hidden conditional random field, deep neural network, deep belief network, and deep stacking models for sequential learning. It also discusses practical considerations of using these models in both acoustic and language modeling for continuous speech recognition.

  8. Deep Circulation in the South China Sea

    Science.gov (United States)

    Zhao, Xiaolong; Zhao, Wei; Xu, Xiaobiao; Tian, Jiwei; Zhou, Chun

    2016-04-01

    The South China Sea (SCS) is the largest marginal sea of the northwest Pacific. The deep circulation in the SCS is investigated on the basis of the Hybrid Coordinate Ocean Model (HYCOM). All the experiments show reasonable agreement with observation from mooring arrays. Analysis of these results provides a detailed spatial structure and temporal variability of the deep circulation in the SCS. The major features of the SCS deep circulation are basin-scale cyclonic gyre and concentrated deep western boundary current (DWBC). The transport of the DWBC is ~2 Sv at 16.5°N with a width of ~53 km. As flowing southwestward, the DWBC becomes weaker with a wider range. Deep upwelling in the SCS is estimated of 0.19 to 1.15 m d-1 with the strongest area around the DWBC. The model results reveal the existence of 80 to 120 days oscillation in the deep northeastern circulation and the DWBC, which are also the areas with large eddy kinetic energy. This seasonal oscillation is northwestward with a velocity amplitude of ~1.0~1.5 cm s-1. The distribution of mixing parameters in the deep SCS plays a role in both spatial structure and volume transport of the deep circulation. Compared with the north shelf of the SCS with the Luzon Strait, deep circulation in the SCS is more sensitive to the large vertical mixing parameters of the Zhongsha Island Chain area.

  9. The deep ocean under climate change.

    Science.gov (United States)

    Levin, Lisa A; Le Bris, Nadine

    2015-11-13

    The deep ocean absorbs vast amounts of heat and carbon dioxide, providing a critical buffer to climate change but exposing vulnerable ecosystems to combined stresses of warming, ocean acidification, deoxygenation, and altered food inputs. Resulting changes may threaten biodiversity and compromise key ocean services that maintain a healthy planet and human livelihoods. There exist large gaps in understanding of the physical and ecological feedbacks that will occur. Explicit recognition of deep-ocean climate mitigation and inclusion in adaptation planning by the United Nations Framework Convention on Climate Change (UNFCCC) could help to expand deep-ocean research and observation and to protect the integrity and functions of deep-ocean ecosystems.

  10. DEEP after 15 years: lessons for GTC

    Directory of Open Access Journals (Sweden)

    David C. Koo

    2007-01-01

    Full Text Available DEEP2 es la mayor exploración espectroscópica del nuevo Keck de aproximadamente 35,000 galaxias de campo cuyo fin es el de proporcionar el censo y mapa detallados del cosmos en el corrimiento al rojo z 1. Presentamos revisión general de DEEP2 y de su predecesor, DEEP1. Varios resultados científicos y las ventajas de DEEP2 aseguran que el GTC será científicamente poderoso a pesar de su llegada tardía entre los telescopios de clase de 8-10 m.

  11. LUNA: Nuclear Astrophysics Deep Underground

    CERN Document Server

    Broggini, Carlo; Guglielmetti, Alessandra; Menegazzo, Roberto

    2010-01-01

    Nuclear astrophysics strives for a comprehensive picture of the nuclear reactions responsible for synthesizing the chemical elements and for powering the stellar evolution engine. Deep underground in the Gran Sasso laboratory the cross sections of the key reactions of the proton-proton chain and of the Carbon-Nitrogen-Oxygen (CNO) cycle have been measured right down to the energies of astrophysical interest. The salient features of underground nuclear astrophysics are summarized here. The main results obtained by LUNA in the last twenty years are reviewed, and their influence on the comprehension of the properties of the neutrino, of the Sun and of the Universe itself are discussed. Future directions of underground nuclear astrophysics towards the study of helium and carbon burning and of stellar neutron sources in stars are pointed out.

  12. Deep vein thrombosis in pregnancy.

    Science.gov (United States)

    Colman-Brochu, Stephanie

    2004-01-01

    This article provides a review of the incidence, pathophysiology, and treatment of deep vein thrombosis (DVT) in pregnancy, a rare but serious complication of pregnancy. The incidence of DVT in pregnancy varies widely, but it is a leading cause of maternal morbidity in both the United States and the United Kingdom. Risk factors during pregnancy include prolonged bed rest or immobility, pelvic or leg trauma, and obesity. Additional risk factors are preeclampsia, Cesarean section, instrument-assisted delivery, hemorrhage, multiparity, varicose veins, a previous history of a thromboembolic event, and hereditary or acquired thrombophilias such as Factor V Leiden. Heparin is the anticoagulant of choice to treat active thromboembolic disease or to administer for thromboprophylaxis, but low molecular-weight heparin is being used with increasing frequency in the pregnant woman. Perinatal nurses should be aware of the symptoms, diagnostic tools, and treatment options available to manage active thrombosis during pregnancy and in the intrapartum and postpartum periods.

  13. NESTOR Deep Sea Neutrino Telescope

    Science.gov (United States)

    NESTOR Collaboration; Aggouras, G.; Anassontzis, E. G.; Ball, A. E.; Bourlis, G.; Chinowsky, W.; Fahrun, E.; Grammatikakis, G.; Green, C.; Grieder, P.; Katrivanos, P.; Koske, P.; Leisos, A.; Markopoulos, E.; Minkowsky, P.; Nygren, D.; Papageorgiou, K.; Przybylski, G.; Resvanis, L. K.; Siotis, I.; Sopher, J.; Staveris-Polikalas, A.; Tsagli, V.; Tsirigotis, A.; Tzamarias, S.; Zhukov, V. A.

    2006-01-01

    One module of NESTOR, the Mediterranean deep-sea neutrino telescope, was deployed at a depth of 4000m, 14km off the Sapienza Island, off the South West coast of Greece. The deployment site provides excellent environmental characteristics. The deployed NESTOR module is constructed as a hexagonal star like latticed titanium star with 12 Optical Modules and an one-meter diameter titanium sphere which houses the electronics. Power and data were transferred through a 30km electro-optical cable to the shore laboratory. In this report we describe briefly the detector and the detector electronics and discuss the first physics data acquired and give the zenith angular distribution of the reconstructed muons.

  14. Deep Borehole Disposal Safety Analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Freeze, Geoffrey A. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Stein, Emily [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Price, Laura L. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); MacKinnon, Robert J. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Tillman, Jack Bruce [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2016-10-01

    This report presents a preliminary safety analysis for the deep borehole disposal (DBD) concept, using a safety case framework. A safety case is an integrated collection of qualitative and quantitative arguments, evidence, and analyses that substantiate the safety, and the level of confidence in the safety, of a geologic repository. This safety case framework for DBD follows the outline of the elements of a safety case, and identifies the types of information that will be required to satisfy these elements. At this very preliminary phase of development, the DBD safety case focuses on the generic feasibility of the DBD concept. It is based on potential system designs, waste forms, engineering, and geologic conditions; however, no specific site or regulatory framework exists. It will progress to a site-specific safety case as the DBD concept advances into a site-specific phase, progressing through consent-based site selection and site investigation and characterization.

  15. Deep brain stimulation: postoperative issues.

    Science.gov (United States)

    Deuschl, Günther; Herzog, Jan; Kleiner-Fisman, Galit; Kubu, Cynthia; Lozano, Andres M; Lyons, Kelly E; Rodriguez-Oroz, Maria C; Tamma, Filippo; Tröster, Alexander I; Vitek, Jerrold L; Volkmann, Jens; Voon, Valerie

    2006-06-01

    Numerous factors need to be taken into account when managing a patient with Parkinson's disease (PD) after deep brain stimulation (DBS). Questions such as when to begin programming, how to conduct a programming screen, how to assess the effects of programming, and how to titrate stimulation and medication for each of the targeted sites need to be addressed. Follow-up care should be determined, including patient adjustments of stimulation, timing of follow-up visits and telephone contact with the patient, and stimulation and medication conditions during the follow-up assessments. A management plan for problems that can arise after DBS such as weight gain, dyskinesia, axial symptoms, speech dysfunction, muscle contractions, paresthesia, eyelid, ocular and visual disturbances, and behavioral and cognitive problems should be developed. Long-term complications such as infection or erosion, loss of effect, intermittent stimulation, tolerance, and pain or discomfort can develop and need to be managed. Other factors that need consideration are social and job-related factors, development of dementia, general medical issues, and lifestyle changes. This report from the Consensus on Deep Brain Stimulation for Parkinson's Disease, a project commissioned by the Congress of Neurological Surgeons and the Movement Disorder Society, outlines answers to a series of questions developed to address all aspects of DBS postoperative management and decision-making with a systematic overview of the literature (until mid-2004) and by the expert opinion of the authors. The report has been endorsed by the Scientific Issues Committee of the Movement Disorder Society and the American Society of Stereotactic and Functional Neurosurgery.

  16. De novo peptide sequencing by deep learning.

    Science.gov (United States)

    Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

    2017-07-18

    De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7-22.9% higher accuracy at the amino acid level and 38.1-64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5-100% coverage and 97.2-99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming.

  17. Deep web search: an overview and roadmap

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien; Trieschnigg, Rudolf Berend; Hiemstra, Djoerd

    2011-01-01

    We review the state-of-the-art in deep web search and propose a novel classification scheme to better compare deep web search systems. The current binary classification (surfacing versus virtual integration) hides a number of implicit decisions that must be made by a developer. We make these

  18. Research Proposal for Distributed Deep Web Search

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien

    2010-01-01

    This proposal identifies two main problems related to deep web search, and proposes a step by step solution for each of them. The first problem is about searching deep web content by means of a simple free-text interface (with just one input field, instead of a complex interface with many input

  19. Temperature Impacts on Deep-Sea Biodiversity

    Science.gov (United States)

    Yasuhara, M.; Danovaro, R.

    2015-12-01

    Temperature is considered to be a fundamental factor controlling biodiversity in marine ecosystems, but precisely what role temperature plays in modulating diversity is still not clear. The deep ocean, lacking light and in situ photosynthetic primary production, is an ideal model system to test the effects of temperature changes on biodiversity. Here we synthesize current knowledge on temperature-diversity relationships in the deep sea. Our results from both present and past deep-sea assemblages suggest that, when a wide range of deep-sea bottom-water temperatures is considered, a unimodal relationship exists between temperature and diversity (that may be right skewed). It is possible that temperature is important only when at relatively high and low levels but does not play a major role in the intermediate temperature range. Possible mechanisms explaining the temperature-biodiversity relationship include the physiological-tolerance hypothesis, the metabolic hypothesis, island biogeography theory, or some combination of these. The possible unimodal relationship discussed here may allow us to identify tipping points at which on-going global change and deep-water warming may increase or decrease deep-sea biodiversity. Predicted changes in deep-sea temperatures due to human-induced climate change may have more adverse consequences than expected considering the sensitivity of deep-sea ecosystems to temperature changes.

  20. Research Proposal for Distributed Deep Web Search

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien-Tsoi T.E.

    2010-01-01

    This proposal identifies two main problems related to deep web search, and proposes a step by step solution for each of them. The first problem is about searching deep web content by means of a simple free-text interface (with just one input field, instead of a complex interface with many input fiel

  1. Deep web search: an overview and roadmap

    NARCIS (Netherlands)

    Tjin-Kam-Jet, K.; Trieschnigg, D.; Hiemstra, D.

    2011-01-01

    We review the state-of-the-art in deep web search and propose a novel classification scheme to better compare deep web search systems. The current binary classification (surfacing versus virtual integration) hides a number of implicit decisions that must be made by a developer. We make these decisio

  2. Research Proposal for Distributed Deep Web Search

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien

    2010-01-01

    This proposal identifies two main problems related to deep web search, and proposes a step by step solution for each of them. The first problem is about searching deep web content by means of a simple free-text interface (with just one input field, instead of a complex interface with many input fiel

  3. Deep web search: an overview and roadmap

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien; Trieschnigg, Rudolf Berend; Hiemstra, Djoerd

    2011-01-01

    We review the state-of-the-art in deep web search and propose a novel classification scheme to better compare deep web search systems. The current binary classification (surfacing versus virtual integration) hides a number of implicit decisions that must be made by a developer. We make these decisio

  4. [MRI compatibility of deep brain stimulator].

    Science.gov (United States)

    Zhang, Yujing

    2013-07-01

    Deep brain stimulation (DBS) therapy develops rapidly in clinical application. The structures of deep brain stimulator and magnetic resonance imaging (MRI) equipment are introduced, the interactions are analyzed, and the two compatible problems of radio frequency (RF) heating and imaging artifact are summarized in this paper.

  5. Temperature impacts on deep-sea biodiversity.

    Science.gov (United States)

    Yasuhara, Moriaki; Danovaro, Roberto

    2016-05-01

    Temperature is considered to be a fundamental factor controlling biodiversity in marine ecosystems, but precisely what role temperature plays in modulating diversity is still not clear. The deep ocean, lacking light and in situ photosynthetic primary production, is an ideal model system to test the effects of temperature changes on biodiversity. Here we synthesize current knowledge on temperature-diversity relationships in the deep sea. Our results from both present and past deep-sea assemblages suggest that, when a wide range of deep-sea bottom-water temperatures is considered, a unimodal relationship exists between temperature and diversity (that may be right skewed). It is possible that temperature is important only when at relatively high and low levels but does not play a major role in the intermediate temperature range. Possible mechanisms explaining the temperature-biodiversity relationship include the physiological-tolerance hypothesis, the metabolic hypothesis, island biogeography theory, or some combination of these. The possible unimodal relationship discussed here may allow us to identify tipping points at which on-going global change and deep-water warming may increase or decrease deep-sea biodiversity. Predicted changes in deep-sea temperatures due to human-induced climate change may have more adverse consequences than expected considering the sensitivity of deep-sea ecosystems to temperature changes.

  6. Deep learning for neuroimaging: a validation study.

    Science.gov (United States)

    Plis, Sergey M; Hjelm, Devon R; Salakhutdinov, Ruslan; Allen, Elena A; Bockholt, Henry J; Long, Jeffrey D; Johnson, Hans J; Paulsen, Jane S; Turner, Jessica A; Calhoun, Vince D

    2014-01-01

    Deep learning methods have recently made notable advances in the tasks of classification and representation learning. These tasks are important for brain imaging and neuroscience discovery, making the methods attractive for porting to a neuroimager's toolbox. Success of these methods is, in part, explained by the flexibility of deep learning models. However, this flexibility makes the process of porting to new areas a difficult parameter optimization problem. In this work we demonstrate our results (and feasible parameter ranges) in application of deep learning methods to structural and functional brain imaging data. These methods include deep belief networks and their building block the restricted Boltzmann machine. We also describe a novel constraint-based approach to visualizing high dimensional data. We use it to analyze the effect of parameter choices on data transformations. Our results show that deep learning methods are able to learn physiologically important representations and detect latent relations in neuroimaging data.

  7. Evaluation of the DeepWind concept

    DEFF Research Database (Denmark)

    Schmidt Paulsen, Uwe; Borg, Michael; Gonzales Seabra, Luis Alberto

    , as well as the technical and scientific recommendations are performed. The work is a result of the contributions within the DeepWind project which is supported by the European Commission, Grant 256769 FP7 Energy 2010 - Future emerging technologies, and by the DeepWind beneficiaries: DTU(DK), AAU......The report describes the DeepWind 5 MW conceptual design as a baseline for results obtained in the scientific and technical work packages of the DeepWind project. A comparison of DeepWi nd with existing VAWTs and paper projects are carried out and the evaluation of the concept in terms of cost......(DK), TUDELFT(NL), TUTRENTO(I), DHI(DK), SINTEF(N), MARINTEK(N), MARIN(NL), NREL(USA), STATOIL(N), VESTAS(D K) and NENUPHAR(F)....

  8. Microplastic pollution in deep-sea sediments.

    Science.gov (United States)

    Van Cauwenberghe, Lisbeth; Vanreusel, Ann; Mees, Jan; Janssen, Colin R

    2013-11-01

    Microplastics are small plastic particles (microplastics have been accumulating in the marine environment for decades and have been detected throughout the water column and in sublittoral and beach sediments worldwide. However, up to now, it has never been established whether microplastic presence in sediments is limited to accumulation hot spots such as the continental shelf, or whether they are also present in deep-sea sediments. Here we show, for the first time ever, that microplastics have indeed reached the most remote of marine environments: the deep sea. We found plastic particles sized in the micrometre range in deep-sea sediments collected at four locations representing different deep-sea habitats ranging in depth from 1100 to 5000 m. Our results demonstrate that microplastic pollution has spread throughout the world's seas and oceans, into the remote and largely unknown deep sea.

  9. Study on Community Structure of Arthropod in Different Ecotypes of Maize Fields%不同生态型夏玉米田节肢动物群落特征的研究

    Institute of Scientific and Technical Information of China (English)

    辛肇军; 李照会; 叶保华

    2012-01-01

    The composition of arthropod communities in different ecotypes of maize fields were investigated, and the arthropod community characteristics and the relative abundance of each group were analyzed in this paper. The individual numbers, richness, diversity index and evenness index in maize - vegetable and maize - fruit fields were higher than those in maize fields, but the ecological dominance was lower. The number of predacious and parasitic natural enemies in maize fields was less than that in maize - vegetable and maize -fruit fields. The species richness changed obviously in different time series in summer maize fields, which increased rapidly from the middle of July and reached the largest as 61 kinds at August 13, and then decreased gradually until to the lowest point on September 29.%分析了泰安市3种不同生态型夏玉米田节肢动物群落结构组成及相关特征指数、优势种群和优势度,并研究了不同生态型夏玉米田节肢动物群落中各类群的相对多度.结果表明,粮菜区和粮果区节肢动物丰富度、个体总数、多样性指数和均匀度指数均明显高于纯粮区,而生态优势度均明显低于纯粮区,纯粮区捕食性和寄生性天敌种群数量少于粮菜区和粮果区.夏玉米田物种丰富度在不同时间序列上差异明显,自7月中旬开始物种丰富度呈急剧增大趋势,8月13日物种丰富度达最大值61种,此后物种丰富度逐渐波动减少,9月29日达最低点.

  10. Deep Carbon Cycling in the Deep Hydrosphere: Abiotic Organic Synthesis and Biogeochemical Cycling

    Science.gov (United States)

    Sherwood Lollar, B.; Sutcliffe, C. N.; Ballentine, C. J.; Warr, O.; Li, L.; Ono, S.; Wang, D. T.

    2014-12-01

    Research into the deep carbon cycle has expanded our understanding of the depth and extent of abiotic organic synthesis in the deep Earth beyond the hydrothermal vents of the deep ocean floor, and of the role of reduced gases in supporting deep subsurface microbial communities. Most recently, this research has expanded our understanding not only of the deep biosphere but the deep hydrosphere - identifying for the first time the extreme antiquity (millions to billions of years residence time) of deep saline fracture waters in the world's oldest rocks. Energy-rich saline fracture waters in the Precambrian crust that makes up more than 70% of the Earth's continental lithosphereprovide important constraints on our understanding of the extent of the crust that is habitable, on the time scales of hydrogeologic isolation (and conversely mixing) of fluids relevant to the deep carbon cycle, and on the geochemistry of substrates that sustain both abiotic organic synthesis and biogeochemical cycles driven by microbial communities. Ultimately the chemistry and hydrogeology of the deep hydrosphere will help define the limits for life in the subsurface and the boundary between the biotic-abiotic fringe. Using a variety of novel techniques including noble gas analysis, clumped isotopologues of methane, and compound specific isotope analysis of CHNOS, this research is addressing questions about the distribution of deep saline fluids in Precambrian rocks worldwide, the degree of interconnectedness of these potential biomes, the habitability of these fluids, and the biogeographic diversity of this new realm of the deep hydrosphere.

  11. Comparison Between Six Ecotypes of Vetiver Grasses in Photosynthetic Light Response and Diurnal Variation of Photosynthetic Parameters%6种生态型香根草光合光响应特征及光合参数日变化的比较

    Institute of Scientific and Technical Information of China (English)

    周强; 胡淑宝; 王青青; 李贵生; 唐丽; 於丙军

    2015-01-01

    A study was carried out in order to investigate differences between six ecotypes of vetiver grasses ( Karnataka, Sunshine, Huffman, Kandy, Monto and Veriveria nermorlis) in photosynthetic physiology and rules of diurnal variation of photosynthetic parameters. Results show that the six ecotypes of vetiver grasses varied sharply in light saturation point (LSP), light compensation point (LCP), maximum net photosynthetic rate (Pn,max), dark respiration rate (Rd) and di⁃urnal variation of net photosynthetic rates ( Pn ) . Among the six ecotypes, Karnataka and Veriveria nermorlis were higher in LSP, LCP and Pn,max; Sunshine and Kandy, lower in LSP; Sunshine and Huffman, lowest in LCP;Monto, lowest in Pn,max;Karnataka, higher in Rd;and Huffman, lower in Rd . Furthermore, the diurnal variations of Pn of Karnataka and Veriveria nermorlis both could be depicted as two single⁃peak curves with Pn,max appearing at 12:00, while the diurnal var⁃iations of Pn of the other four ecotypes, as double⁃peak curves with an obvious midday depression appearing at 12:00. Re⁃lationships of Pn with ecological factors, such as air temperature ( Ta ) , air CO2 concentration ( Ca ) , relative air humidity (HR) and photosynthetically active radiation (PAR), were analyzed by correlation, path and decision coefficients, re⁃spectively, indicating that PAR is the primary determining factor for Pn of the six ecotypes of vetiver grasses, HR , the main limiting factor for Pn of Karnataka, Huffman, Monto and Veriveria nermorlis, and Ta the main limiting factor for Pn of Sun⁃shine and Kandy.%为了研究不同生态型香根草( Vetiveria zizanioides)的光合生理差异,比较了Karnataka、Sunshine、Huffman、Kandy、Monto和Veriveria nermorlis这6种生态型香根草的光合光响应特征和光合参数日变化规律。结果表明,除表观量子效率(AQY)外,6种生态型香根草的光饱和点(LSP)、光补偿点(LCP)、最大

  12. 不同生态型小飞蓬对酸樱桃镉积累及土壤酶活性的影响%Effects of Different Ecotypes of Conyza canadensis on Cd Accumulation of Sour Cherry and Soil Enzyme Activity

    Institute of Scientific and Technical Information of China (English)

    程籍; 廖明安; 林立金; 刘娟; 汤福义; 罗丽; 梅洛银; 刘雨

    2013-01-01

    为研究镉污染下,不同生态型小飞蓬对酸樱桃镉积累及土壤酶活性的影响,通过盆栽试验研究了2类生态型(矿山生态型和非矿山生态型)小飞蓬与酸樱桃混种对2类植物生物量、镉含量及土壤酶活性的影响。结果表明,与矿山生态型和非矿山生态型小飞蓬混种的酸樱桃地上部生物量分别较单种降低了31.92%和34.62%,根系生物量较单种分别降低了42.47%和33.33%;地上部镉含量分别比单种下降35.42%和44.44%,根系的镉含量分别比单种下降17.01%和28.70%。2种混种方式均使土壤有效镉含量、土壤过氧化氢酶活性、土壤脲酶活性较各自单种有所增加,土壤蔗糖酶活性有所下降。因此,2种不同生态型小飞蓬混种酸樱桃,虽然使酸樱桃生长受到一定抑制,但对土壤微生物环境有一定改善效果,且能有效降低酸樱桃对镉的吸收,其中以混种矿山生态型小飞蓬的效果更好。%To study the effects of different ecotypes of Conyza canadensis on cadmium ( Cd ) accumulation of sour cherry and soil enzyme activity ,the pot experiment was adopted to study the effects of intercropping two eco-types(Mining and non-mining ecotype) of Conyza canadensis and sour cherry on their biomass,Cd content and soil enzyme activity .The results showed that , sour cherry intercropping with mining or non-mining ecotype of Conyza canadensis,the shoot biomass were respectively decreased by 31.92%and 34.62%than the monoculture,the root biomass were respectively decreased by 42 .47%and 33 .33%than the monoculture;the Cd content in shoot were respectively decreased by 35 .42%and 44 .44%than the monoculture ,the Cd content in root respectively decreased 17 .01%and 28 .70%than the monoculture .The soil available Cd content ,soil catalase activity ,soil urease activity were respectively increased than the monoculture in both two kinds of intercropping methods

  13. Overview of deep learning in medical imaging.

    Science.gov (United States)

    Suzuki, Kenji

    2017-07-08

    The use of machine learning (ML) has been increasing rapidly in the medical imaging field, including computer-aided diagnosis (CAD), radiomics, and medical image analysis. Recently, an ML area called deep learning emerged in the computer vision field and became very popular in many fields. It started from an event in late 2012, when a deep-learning approach based on a convolutional neural network (CNN) won an overwhelming victory in the best-known worldwide computer vision competition, ImageNet Classification. Since then, researchers in virtually all fields, including medical imaging, have started actively participating in the explosively growing field of deep learning. In this paper, the area of deep learning in medical imaging is overviewed, including (1) what was changed in machine learning before and after the introduction of deep learning, (2) what is the source of the power of deep learning, (3) two major deep-learning models: a massive-training artificial neural network (MTANN) and a convolutional neural network (CNN), (4) similarities and differences between the two models, and (5) their applications to medical imaging. This review shows that ML with feature input (or feature-based ML) was dominant before the introduction of deep learning, and that the major and essential difference between ML before and after deep learning is the learning of image data directly without object segmentation or feature extraction; thus, it is the source of the power of deep learning, although the depth of the model is an important attribute. The class of ML with image input (or image-based ML) including deep learning has a long history, but recently gained popularity due to the use of the new terminology, deep learning. There are two major models in this class of ML in medical imaging, MTANN and CNN, which have similarities as well as several differences. In our experience, MTANNs were substantially more efficient in their development, had a higher performance, and required a

  14. The Hubble Ultra Deep Field

    CERN Document Server

    Beckwith, S V W; Koekemoer, A M; Caldwell, J A R; Ferguson, H C; Hook, R; Lucas, R A; Bergeron, L E; Corbin, M; Jogee, S; Panagia, N; Robberto, M; Royle, P; Somerville, R S; Sosey, M; Beckwith, Steven V. W.; Stiavelli, Massimo; Koekemoer, Anton M.; Caldwell, John A. R.; Ferguson, Henry C.; Hook, Richard; Lucas, Ray A.; Bergeron, Louis E.; Corbin, Michael; Jogee, Shardha; Panagia, Nino; Robberto, Massimo; Royle, Patricia; Somerville, Rachel S.; Sosey, Megan

    2006-01-01

    This paper presents the Hubble Ultra Deep Field (HUDF), a one million second exposure of an 11 square minute-of-arc region in the southern sky with the Hubble Space Telescope. The exposure time was divided among four filters, F435W (B435), F606W (V606), F775W (i775), and F850LP (z850), to give approximately uniform limiting magnitudes mAB~29 for point sources. The image contains at least 10,000 objects presented here as a catalog. Few if any galaxies at redshifts greater than ~4 resemble present day spiral or elliptical galaxies. Using the Lyman break dropout method, we find 504 B-dropouts, 204 V-dropouts, and 54 i-dropouts. Using these samples that are at different redshifts but derived from the same data, we find no evidence for a change in the characteristic luminosity of galaxies but some evidence for a decrease in their number densities between redshifts of 4 and 7. The ultraviolet luminosity density of these samples is dominated by galaxies fainter than the characteristic luminosity, and the HUDF reveal...

  15. Ice Nucleation in Deep Convection

    Science.gov (United States)

    Jensen, Eric; Ackerman, Andrew; Stevens, David; Gore, Warren J. (Technical Monitor)

    2001-01-01

    The processes controlling production of ice crystals in deep, rapidly ascending convective columns are poorly understood due to the difficulties involved with either modeling or in situ sampling of these violent clouds. A large number of ice crystals are no doubt generated when droplets freeze at about -40 C. However, at higher levels, these crystals are likely depleted due to precipitation and detrainment. As the ice surface area decreases, the relative humidity can increase well above ice saturation, resulting in bursts of ice nucleation. We will present simulations of these processes using a large-eddy simulation model with detailed microphysics. Size bins are included for aerosols, liquid droplets, ice crystals, and mixed-phase (ice/liquid) hydrometers. Microphysical processes simulated include droplet activation, freezing, melting, homogeneous freezing of sulfate aerosols, and heterogeneous ice nucleation. We are focusing on the importance of ice nucleation events in the upper part of the cloud at temperatures below -40 C. We will show that the ultimate evolution of the cloud in this region (and the anvil produced by the convection) is sensitive to these ice nucleation events, and hence to the composition of upper tropospheric aerosols that get entrained into the convective column.

  16. Looking Deep with Infrared Eyes

    Science.gov (United States)

    2006-07-01

    Today, British astronomers are releasing the first data from the largest and most sensitive survey of the heavens in infrared light to the ESO user community. The UKIRT Infrared Deep Sky Survey (UKIDSS) has completed the first of seven years of data collection, studying objects that are too faint to see at visible wavelengths, such as very distant or very cool objects. New data on young galaxies is already challenging current thinking on galaxy formation, revealing galaxies that are massive at a much earlier stage of development than expected. These first science results already show how powerful the full survey will be at finding rare objects that hold vital clues to how stars and galaxies in our Universe formed. UKIDSS will make an atlas of large areas of the sky in the infrared. The data become available to the entire ESO user community immediately after they are entered into the archive [2]. Release to the world follows 18 months after each release to ESO. "Astronomers across Europe will jump on these exciting new data. We are moving into new territory - our survey is both wide and deep, so we are mapping huge volumes of space. That's how we will locate rare objects - the very nearest and smallest stars, and young galaxies at the edge of the universe," said Andy Lawrence from the University of Edinburgh, UKIDSS Principal Investigator. The UKIDSS data are collected by the United Kingdom Infrared Telescope [3] situated near the summit of Mauna Kea in Hawaii using the Wide Field Camera (WFCAM) built by the United Kingdom Astronomy Technology Centre (UKATC) in Edinburgh. WFCAM is the most powerful infrared imager in the world, generating enormous amounts of data - 150 gigabytes per night (equivalent to more than 200 CDs) - and approximately 10.5 Terabytes in total so far (or 15,000 CDs). Mark Casali, now at ESO, was the Project Scientist in charge of the WFCAM instrument construction at the UKATC. "WFCAM was a bold technological undertaking," said Mark Casali

  17. [Deep brain stimulation and neuroethics].

    Science.gov (United States)

    Katayama, Yoichi; Fukaya, Chikashi

    2009-01-01

    The use of deep brain stimulation (DBS) for mental disorders has been discussed in Japan from the viewpoint of ethical problems. Trials of experimental therapies require a basis of sound scientific rationale. New standard therapy emerges from such trials through detailed analysis of the outcome and side effects. Long-suffering patients with intractable symptoms may desperately seek an experimental therapy even though it has not yet been accepted as standard therapy. The ethical committee of each institution evaluates the level of scientific rationale and the expected level of benefits on the bias of the reported data, and decides whether the patients can receive the experimental therapy. However, the use of DBS for mental disorders is not based on sound scientific rational, since the disease mechanisms involved are far from understood. The data reported from the previous trials are insufficient for assuring the satisfactory results for mental disoder patients. Most institutions in Japan do not accept such levels of scientific rationale and expected benefits. Furthermore, from the cultural perspective, strong skepticism exists in Japan with regard to surgical interventions for mental disorders. Such an attitude is unexpectedly in harmony with many of the subjects currently discussed in the field of neuroethics. For example, who has the right to control DBS? How does someone decide the level of control of mental function by DBS? These questions are related to the discussion on how human society is formed and how the ethics are decided by considering both scientific rationale and human society.

  18. Orientation selective deep brain stimulation

    Science.gov (United States)

    Lehto, Lauri J.; Slopsema, Julia P.; Johnson, Matthew D.; Shatillo, Artem; Teplitzky, Benjamin A.; Utecht, Lynn; Adriany, Gregor; Mangia, Silvia; Sierra, Alejandra; Low, Walter C.; Gröhn, Olli; Michaeli, Shalom

    2017-02-01

    Objective. Target selectivity of deep brain stimulation (DBS) therapy is critical, as the precise locus and pattern of the stimulation dictates the degree to which desired treatment responses are achieved and adverse side effects are avoided. There is a clear clinical need to improve DBS technology beyond currently available stimulation steering and shaping approaches. We introduce orientation selective neural stimulation as a concept to increase the specificity of target selection in DBS. Approach. This concept, which involves orienting the electric field along an axonal pathway, was tested in the corpus callosum of the rat brain by freely controlling the direction of the electric field on a plane using a three-electrode bundle, and monitoring the response of the neurons using functional magnetic resonance imaging (fMRI). Computational models were developed to further analyze axonal excitability for varied electric field orientation. Main results. Our results demonstrated that the strongest fMRI response was observed when the electric field was oriented parallel to the axons, while almost no response was detected with the perpendicular orientation of the electric field relative to the primary fiber tract. These results were confirmed by computational models of the experimental paradigm quantifying the activation of radially distributed axons while varying the primary direction of the electric field. Significance. The described strategies identify a new course for selective neuromodulation paradigms in DBS based on axonal fiber orientation.

  19. Biodiversity Science In The Deep Sea: The ESF EuroDEEP Programme

    Science.gov (United States)

    Jonckheere, I. G.

    2007-12-01

    What little we know of deep-sea ecosystems indicates that they host one of the highest biodiversities on the planet as well as important mineral and biological resources, which are increasingly being exploited. Understanding deep-sea biodiversity and ecosystem functioning, from viruses to megafauna, is essential to assess the impact of natural and anthropogenic factors and provide management options. The aim of the multidisciplinary ESF EUROCORES Programme EuroDEEP, Ecosystem Functioning and Biodiversity in Deep Sea, is to further explore and identify the different deep-sea habitats, assessing both the abiotic and biotic processes that sustain and maintain deep-sea communities. The scope is to interpret variations of biodiversity within and between deep-sea habitats, and the interactions of the biota with the ecosystems in which they live. The resulting scientific data are a prerequisite for the sustainable use and the development of management and conservation options aiming at the sustainable use of marine resources that will benefit society as a whole. The Programme aims at providing the necessary framework and funding for the development of top-quality deep- sea research at the European level in a global context (Census of Marine Life and SCOR/IGBP). In particular, it builds on sharing of national large-scale resources, which are essential for deep-sea research (i.e. ships, ROVs, submersibles, AUVs, deep-towed vehicles, deep-sea sampling equipment, new sensors, etc.) as well as the coordination of efforts amongst scientists and laboratories from the countries involved and links with ongoing projects. EuroDEEP will participate in the development of new technologies as well as data management, analysis and modelling. Most of all, EuroDEEP will catalyse excellent research on what biodiversity exists in the deep sea, how it is generated and maintained by abiotic and biotic processes, and what the role of the deep-sea is in the biogeochemical processes affecting the

  20. The physiology of deep-water running.

    Science.gov (United States)

    Reilly, Thomas; Dowzer, Clare N; Cable, N T

    2003-12-01

    Deep-water running is performed in the deep end of a swimming pool, normally with the aid of a flotation vest. The method is used for purposes of preventing injury and promoting recovery from strenuous exercise and as a form of supplementary training for cardiovascular fitness. Both stroke volume and cardiac output increase during water immersion: an increase in blood volume largely offsets the cardiac decelerating reflex at rest. At submaximal exercise intensities, blood lactate responses to exercise during deep-water running are elevated in comparison to treadmill running at a given oxygen uptake (VO2). While VO2, minute ventilation and heart rate are decreased under maximal exercise conditions in the water, deep-water running nevertheless can be justified as providing an adequate stimulus for cardiovascular training. Responses to training programmes have confirmed the efficacy of deep-water running, although positive responses are most evident when measured in a water-based test. Aerobic performance is maintained with deep-water running for up to 6 weeks in trained endurance athletes; sedentary individuals benefit more than athletes in improving maximal oxygen uptake. There is some limited evidence of improvement in anaerobic measures and in upper body strength in individuals engaging in deep-water running. A reduction in spinal loading constitutes a role for deep-water running in the prevention of injury, while an alleviation of muscle soreness confirms its value in recovery training. Further research into the applications of deep-water running to exercise therapy and athletes' training is recommended.

  1. Deep Webpage Classification and Extraction (DWCE

    Directory of Open Access Journals (Sweden)

    Supriya

    2013-04-01

    Full Text Available As the Deep web (or Hidden web information is hidden behind the search query forms, this information can only be accessed by interacting with these forms. Therefore, development of automated system that interacts with the search forms and extracts the hidden web pages would be of great value to human users. To accomplishthis task stated above, this paper proposes a novel method “Deep Webpage Classification and Extraction” which classifies the websites into appropriate domain, extracts their query interfaces and retrieves all result pages of deep websites using query building system.

  2. Zooplankton at deep Red Sea brine pools

    KAUST Repository

    Kaartvedt, Stein

    2016-03-02

    The deep-sea anoxic brines of the Red Sea comprise unique, complex and extreme habitats. These environments are too harsh for metazoans, while the brine–seawater interface harbors dense microbial populations. We investigated the adjacent pelagic fauna at two brine pools using net tows, video records from a remotely operated vehicle and submerged echosounders. Waters just above the brine pool of Atlantis II Deep (2000 m depth) appeared depleted of macrofauna. In contrast, the fauna appeared to be enriched at the Kebrit Deep brine–seawater interface (1466 m).

  3. Harnessing the Deep Web: Present and Future

    OpenAIRE

    J. Madhavan; Afanasiev, L.; Antova, L.; Halevy, A

    2009-01-01

    Over the past few years, we have built a system that has exposed large volumes of Deep-Web content to Google.com users. The content that our system exposes contributes to more than 1000 search queries per-second and spans over 50 languages and hundreds of domains. The Deep Web has long been acknowledged to be a major source of structured data on the web, and hence accessing Deep-Web content has long been a problem of interest in the data management community. In this paper, we report on where...

  4. Earthquakes induced by deep penetrating bombing?

    Institute of Scientific and Technical Information of China (English)

    Serguei Yu. Balassanian

    2005-01-01

    The data of M≥5 earthquakes occurred in one year before and after 4 deep penetrating bombs in the region within 500 km and 1 000 km from the shooting site are presented. The 4 bombs are those happened in 1999 Kosovo of Yugoslavia, the 1991 Baghdad of Iraq, the 2001 Tora Bora of Afghanistan, and the 2003 Kirkuk of Iraq, respectively. The data indicate that the deep penetrating bombs may have remotely triggered some earthquakes. The deep penetrating bombs in seismically active regions should be forbidden.

  5. Nonaxisymmetric Variations Deep in the Convection Zone

    Science.gov (United States)

    Duvall, Thomas

    2002-01-01

    Using a deep-focusing time-distance technique and the MDI medium-1 data, a preliminary study of nonaxisymmetric variability deep in the convection zone has been performed. The purpose of the present study is to see what signals might be present in raw travel times indicating variation. To this end, noise levels will be examined. Correlations with point separations in the range 40-50 deg. have been measured for the entire medium-1 dataset over a significant fraction of the solar disk. Both flows and mean-time variations have been examined. Separation of near-surface signals from deep signals will also be examined.

  6. Harnessing the Deep Web: present and future

    OpenAIRE

    Madhavan, J; Afanasiev, L.; Antova, L.; Halevy, A.

    2009-01-01

    Over the past few years, we have built a system that has exposed large volumes of Deep-Web content to Google.com users. The content that our system exposes contributes to more than 1000 search queries per-second and spans over 50 languages and hundreds of domains. The Deep Web has long been acknowledged to be a major source of structured data on the web, and hence accessing Deep-Web content has long been a problem of interest in the data management community. In this paper, we report on where...

  7. Anisotropy in the deep Earth

    Science.gov (United States)

    Romanowicz, Barbara; Wenk, Hans-Rudolf

    2017-08-01

    Seismic anisotropy has been found in many regions of the Earth's interior. Its presence in the Earth's crust has been known since the 19th century, and is due in part to the alignment of anisotropic crystals in rocks, and in part to patterns in the distribution of fractures and pores. In the upper mantle, seismic anisotropy was discovered 50 years ago, and can be attributed for the most part, to the alignment of intrinsically anisotropic olivine crystals during large scale deformation associated with convection. There is some indication for anisotropy in the transition zone, particularly in the vicinity of subducted slabs. Here we focus on the deep Earth - the lower mantle and core, where anisotropy is not yet mapped in detail, nor is there consensus on its origin. Most of the lower mantle appears largely isotropic, except in the last 200-300 km, in the D″ region, where evidence for seismic anisotropy has been accumulating since the late 1980s, mostly from shear wave splitting measurements. Recently, a picture has been emerging, where strong anisotropy is associated with high shear velocities at the edges of the large low shear velocity provinces (LLSVPs) in the central Pacific and under Africa. These observations are consistent with being due to the presence of highly anisotropic MgSiO3 post-perovskite crystals, aligned during the deformation of slabs impinging on the core-mantle boundary, and upwelling flow within the LLSVPs. We also discuss mineral physics aspects such as ultrahigh pressure deformation experiments, first principles calculations to obtain information about elastic properties, and derivation of dislocation activity based on bonding characteristics. Polycrystal plasticity simulations can predict anisotropy but models are still highly idealized and neglect the complex microstructure of polyphase aggregates with strong and weak components. A promising direction for future progress in understanding the origin of seismic anisotropy in the deep mantle

  8. NATURAL GAS RESOURCES IN DEEP SEDIMENTARY BASINS

    Energy Technology Data Exchange (ETDEWEB)

    Thaddeus S. Dyman; Troy Cook; Robert A. Crovelli; Allison A. Henry; Timothy C. Hester; Ronald C. Johnson; Michael D. Lewan; Vito F. Nuccio; James W. Schmoker; Dennis B. Riggin; Christopher J. Schenk

    2002-02-05

    From a geological perspective, deep natural gas resources are generally defined as resources occurring in reservoirs at or below 15,000 feet, whereas ultra-deep gas occurs below 25,000 feet. From an operational point of view, ''deep'' is often thought of in a relative sense based on the geologic and engineering knowledge of gas (and oil) resources in a particular area. Deep gas can be found in either conventionally-trapped or unconventional basin-center accumulations that are essentially large single fields having spatial dimensions often exceeding those of conventional fields. Exploration for deep conventional and unconventional basin-center natural gas resources deserves special attention because these resources are widespread and occur in diverse geologic environments. In 1995, the U.S. Geological Survey estimated that 939 TCF of technically recoverable natural gas remained to be discovered or was part of reserve appreciation from known fields in the onshore areas and State waters of the United. Of this USGS resource, nearly 114 trillion cubic feet (Tcf) of technically-recoverable gas remains to be discovered from deep sedimentary basins. Worldwide estimates of deep gas are also high. The U.S. Geological Survey World Petroleum Assessment 2000 Project recently estimated a world mean undiscovered conventional gas resource outside the U.S. of 844 Tcf below 4.5 km (about 15,000 feet). Less is known about the origins of deep gas than about the origins of gas at shallower depths because fewer wells have been drilled into the deeper portions of many basins. Some of the many factors contributing to the origin of deep gas include the thermal stability of methane, the role of water and non-hydrocarbon gases in natural gas generation, porosity loss with increasing thermal maturity, the kinetics of deep gas generation, thermal cracking of oil to gas, and source rock potential based on thermal maturity and kerogen type. Recent experimental simulations

  9. Deep Ultraviolet Macroporous Silicon Filters Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I proposal describes a novel method to make deep and far UV optical filters from macroporous silicon. This type of filter consists of an array of...

  10. Semantic Antinomies and Deep Structure Analysis

    Science.gov (United States)

    Zuber, Ryszard

    1975-01-01

    This article discusses constructions known as semantic antinomies, that is, the paradoxical results of false presuppositions, and how they can be dealt with by means of deep structure analysis. See FL 508 186 for availability. (CLK)

  11. Absolute photoacoustic thermometry in deep tissue.

    Science.gov (United States)

    Yao, Junjie; Ke, Haixin; Tai, Stephen; Zhou, Yong; Wang, Lihong V

    2013-12-15

    Photoacoustic thermography is a promising tool for temperature measurement in deep tissue. Here we propose an absolute temperature measurement method based on the dual temperature dependences of the Grüneisen parameter and the speed of sound in tissue. By taking ratiometric measurements at two adjacent temperatures, we can eliminate the factors that are temperature irrelevant but difficult to correct for in deep tissue. To validate our method, absolute temperatures of blood-filled tubes embedded ~9 mm deep in chicken tissue were measured in a biologically relevant range from 28°C to 46°C. The temperature measurement accuracy was ~0.6°C. The results suggest that our method can be potentially used for absolute temperature monitoring in deep tissue during thermotherapy.

  12. Deep Sea Actinomycetes and Their Secondary Metabolites

    Directory of Open Access Journals (Sweden)

    Kui Hong

    2017-05-01

    Full Text Available Deep sea is a unique and extreme environment. It is a hot spot for hunting marine actinomycetes resources and secondary metabolites. The novel deep sea actinomycete species reported from 2006 to 2016 including 21 species under 13 genera with the maximum number from Microbacterium, followed by Dermacoccus, Streptomyces and Verrucosispora, and one novel species for the other 9 genera. Eight genera of actinomycetes were reported to produce secondary metabolites, among which Streptomyces is the richest producer. Most of the compounds produced by the deep sea actinomycetes presented antimicrobial and anti-cancer cell activities. Gene clusters related to biosynthesis of desotamide, heronamide, and lobophorin have been identified from the deep sea derived Streptomyces.

  13. Turbopump Design for Deep Throttling Capability Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will demonstrate the benefits of a partial emission pump coupled with a zero net positive suction pressure inducer design to achieve robust, deep...

  14. Deep Space Optical Communication (DSOC) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop key technologies that enable operational deep space optical communications.Spacecraft disturbance isolation platform for sub-microradian pointing with...

  15. Applications of Deep Learning in Biomedicine.

    Science.gov (United States)

    Mamoshina, Polina; Vieira, Armando; Putin, Evgeny; Zhavoronkov, Alex

    2016-05-02

    Increases in throughput and installed base of biomedical research equipment led to a massive accumulation of -omics data known to be highly variable, high-dimensional, and sourced from multiple often incompatible data platforms. While this data may be useful for biomarker identification and drug discovery, the bulk of it remains underutilized. Deep neural networks (DNNs) are efficient algorithms based on the use of compositional layers of neurons, with advantages well matched to the challenges -omics data presents. While achieving state-of-the-art results and even surpassing human accuracy in many challenging tasks, the adoption of deep learning in biomedicine has been comparatively slow. Here, we discuss key features of deep learning that may give this approach an edge over other machine learning methods. We then consider limitations and review a number of applications of deep learning in biomedical studies demonstrating proof of concept and practical utility.

  16. Deep venous thrombosis of the upper extremity

    DEFF Research Database (Denmark)

    Klitfod, Lotte; Broholm, R; Baekgaard, N

    2013-01-01

    to the condition. Malignancy and therapeutic interventions are major risk factors for the secondary deep vein thrombosis in combination with the patient's characteristics, comorbidities and prior history of deep vein thrombosis. Complications: recurrent deep venous thrombosis, pulmonary embolism and Post......Upper extremity deep venous thrombosis (UEDVT) occurs either spontaneously, as a consequence of strenuous upper limb activity (also known as the Paget-Schroetter syndrome) or secondary to an underlying cause. Primary and secondary UEDVT differs in long-term sequelae and mortality. This review...... will focus on the clinical presentation, risk factors, diagnosis, and treatment strategies of UEDVT. In the period from January to October 2012 an electronic literature search was performed in the PubMed/MEDLINE database, and 27 publications were included. Clinical presentation: swelling, pain and functional...

  17. MWD tool for deep, small diameter boreholes

    Energy Technology Data Exchange (ETDEWEB)

    Buytaert, J.P.R.; Duckworth, A.

    1992-03-17

    This patent describes an apparatus for measuring a drilling parameters while drilling a borehole in an earth formation, wherein the borehole includes a small diameter deep borehole portion and a large diameter upper borehole portion. It includes small diameter drillstring means for drilling the deep borehole portion; sensor means, disposed within the small diameter drillstring means, for measuring a drilling parameter characteristic of the deep portion of the borehole while drilling the deep portion of the borehole and for providing sensor output signals indicative of the measured parameter; an upper drillstring portion extending between the surface of the formation and the small diameter drillstring means, the upper drillstring portion including a large diameter drillstring portion; data transmission means disposed within the large diameter drillstring portion and responsive to the sensor output.

  18. Methods in mooring deep sea sediment traps

    Digital Repository Service at National Institute of Oceanography (India)

    Venkatesan, R.; Fernando, V.; Rajaraman, V.S.; Janakiraman, G.

    The experience gained during the process of deployment and retrieval of nearly 39 sets of deep sea sediment trap moorings on various ships like FS Sonne, ORV Sagarkanya and DSV Nand Rachit are outlined. The various problems encountered...

  19. DEEP NECK INFECTION AFTER THIRD MOLAR EXTRACTION*

    Directory of Open Access Journals (Sweden)

    Seda YILMAZ

    2015-04-01

    Full Text Available Odontogenic and oropharyngeal infections are relatively common in the cervicofacial region. In rare cases, odontogenic or peritonsillar abscesses may spread through the deep fascial cervical spaces and cause life-threatening complications. Odontogenic infection is the most common cause of deep neck infections and it accounts for 43% of the cases. Early diagnosis, immediate antibiotic treatment, and surgical drainage are the basis of therapeutic success. Deep neck infections are potentially life threatening complications if they are not diagnosed in time and treated quickly. This case report presents clinical, radiological features and treatment of the spread of abscesses through cervical spaces of an unusual case of deep neck infection that was caused by the secondary infection of the root remnants after extraction.

  20. Deep Water Horizon (HB1006, EK60)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Monitor and measure the biological, chemical, and physical environment in the area of the oil spill from the deep water horizon oil rig in the Gulf of Mexico. A wide...

  1. Ethical issues in deep brain stimulation

    NARCIS (Netherlands)

    M.H.N. Schermer (Maartje)

    2011-01-01

    textabstractDeep brain stimulation (DBS) is currently used to treat neurological disorders like Parkinson's disease, essential tremor, and dystonia, and is explored as an experimental treatment for psychiatric disorders like major depression and obsessive compulsive disorder. This mini review

  2. Semantic Antinomies and Deep Structure Analysis

    Science.gov (United States)

    Zuber, Ryszard

    1975-01-01

    This article discusses constructions known as semantic antinomies, that is, the paradoxical results of false presuppositions, and how they can be dealt with by means of deep structure analysis. See FL 508 186 for availability. (CLK)

  3. Toolkits and Libraries for Deep Learning.

    Science.gov (United States)

    Erickson, Bradley J; Korfiatis, Panagiotis; Akkus, Zeynettin; Kline, Timothy; Philbrick, Kenneth

    2017-08-01

    Deep learning is an important new area of machine learning which encompasses a wide range of neural network architectures designed to complete various tasks. In the medical imaging domain, example tasks include organ segmentation, lesion detection, and tumor classification. The most popular network architecture for deep learning for images is the convolutional neural network (CNN). Whereas traditional machine learning requires determination and calculation of features from which the algorithm learns, deep learning approaches learn the important features as well as the proper weighting of those features to make predictions for new data. In this paper, we will describe some of the libraries and tools that are available to aid in the construction and efficient execution of deep learning as applied to medical images.

  4. Science and Exploration Deep Space Gateway Workshop

    Science.gov (United States)

    Spann, James F.

    2017-01-01

    We propose a workshop whose outcome is a publically disseminated product that articulates SMD investigations and HEOMD Life Science research, including international collaborations, that are made possible by the new opportunities in space that result from the Deep Space Gateway.

  5. Deep gold mine fracture zone behaviour

    CSIR Research Space (South Africa)

    Napier, JAL

    1998-12-01

    Full Text Available The investigation of the behaviour of the fracture zone surrounding deep level gold mine stopes is detailed in three main sections of this report. Section 2 outlines the ongoing study of fundamental fracture process and their numerical...

  6. LEGACY - EOP Temperature data for deep corals

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Thermographs were deployed opportunistically in patches of deep coral at depths greater than 300 m. Sites included the Makapuu precious coral bed, the Cross Seamount...

  7. Deep Webpage Classification and Extraction (DWCE)

    OpenAIRE

    Supriya; Meenakshi Sharma

    2013-01-01

    As the Deep web (or Hidden web) information is hidden behind the search query forms, this information can only be accessed by interacting with these forms. Therefore, development of automated system that interacts with the search forms and extracts the hidden web pages would be of great value to human users. To accomplishthis task stated above, this paper proposes a novel method “Deep Webpage Classification and Extraction” which classifies the websites into appropriate domain, extracts their ...

  8. Life Support for Deep Space and Mars

    Science.gov (United States)

    Jones, Harry W.; Hodgson, Edward W.; Kliss, Mark H.

    2014-01-01

    How should life support for deep space be developed? The International Space Station (ISS) life support system is the operational result of many decades of research and development. Long duration deep space missions such as Mars have been expected to use matured and upgraded versions of ISS life support. Deep space life support must use the knowledge base incorporated in ISS but it must also meet much more difficult requirements. The primary new requirement is that life support in deep space must be considerably more reliable than on ISS or anywhere in the Earth-Moon system, where emergency resupply and a quick return are possible. Due to the great distance from Earth and the long duration of deep space missions, if life support systems fail, the traditional approaches for emergency supply of oxygen and water, emergency supply of parts, and crew return to Earth or escape to a safe haven are likely infeasible. The Orbital Replacement Unit (ORU) maintenance approach used by ISS is unsuitable for deep space with ORU's as large and complex as those originally provided in ISS designs because it minimizes opportunities for commonality of spares, requires replacement of many functional parts with each failure, and results in substantial launch mass and volume penalties. It has become impractical even for ISS after the shuttle era, resulting in the need for ad hoc repair activity at lower assembly levels with consequent crew time penalties and extended repair timelines. Less complex, more robust technical approaches may be needed to meet the difficult deep space requirements for reliability, maintainability, and reparability. Developing an entirely new life support system would neglect what has been achieved. The suggested approach is use the ISS life support technologies as a platform to build on and to continue to improve ISS subsystems while also developing new subsystems where needed to meet deep space requirements.

  9. Bootstrapping Deep Lexical Resources: Resources for Courses

    CERN Document Server

    Baldwin, Timothy

    2007-01-01

    We propose a range of deep lexical acquisition methods which make use of morphological, syntactic and ontological language resources to model word similarity and bootstrap from a seed lexicon. The different methods are deployed in learning lexical items for a precision grammar, and shown to each have strengths and weaknesses over different word classes. A particular focus of this paper is the relative accessibility of different language resource types, and predicted ``bang for the buck'' associated with each in deep lexical acquisition applications.

  10. Deep-Plane Lipoabdominoplasty in East Asians

    OpenAIRE

    Kim, June-kyu; Jang, Jun-Young; Hong, Yoon Gi; Sim, Hyung Bo; Sun, Sang Hoon

    2016-01-01

    Background The objective of this study was to develop a new surgical technique by combining traditional abdominoplasty with liposuction. This combination of operations permits simpler and more accurate management of various abdominal deformities. In lipoabdominoplasty, the combination of techniques is of paramount concern. Herein, we introduce a new combination of liposuction and abdominoplasty using deep-plane flap sliding to maximize the benefits of both techniques. Methods Deep-plane lipoa...

  11. Unconstrained Face Verification using Deep CNN Features

    OpenAIRE

    Chen, Jun-Cheng; Patel, Vishal M.; Chellappa, Rama

    2015-01-01

    In this paper, we present an algorithm for unconstrained face verification based on deep convolutional features and evaluate it on the newly released IARPA Janus Benchmark A (IJB-A) dataset. The IJB-A dataset includes real-world unconstrained faces from 500 subjects with full pose and illumination variations which are much harder than the traditional Labeled Face in the Wild (LFW) and Youtube Face (YTF) datasets. The deep convolutional neural network (DCNN) is trained using the CASIA-WebFace ...

  12. A Generative Model for Deep Convolutional Learning

    OpenAIRE

    Pu, Yunchen; Yuan, Xin; Carin, Lawrence

    2015-01-01

    A generative model is developed for deep (multi-layered) convolutional dictionary learning. A novel probabilistic pooling operation is integrated into the deep model, yielding efficient bottom-up (pretraining) and top-down (refinement) probabilistic learning. Experimental results demonstrate powerful capabilities of the model to learn multi-layer features from images, and excellent classification results are obtained on the MNIST and Caltech 101 datasets.

  13. Microbial life in the deep terrestrial subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B. [E.I. DuPont de Nemours and Co., Aiken, SC (United States). Savannah River Lab.; Balkwill, D.L. [Florida State Univ., Tallahassee, FL (United States); Beeman, R.E. [Univ. of Oklahoma, Norman, OK (United States)] [and others

    1988-12-31

    The distribution and function of microorganisms is a vital issue in microbial ecology. The US Department of Energy`s Program, ``Microbiology of the Deep Subsurface,`` concentrates on establishing fundamental scientific information about organisms at depth, and the use of these organisms for remediation of contaminants in deep vadose zone and groundwater environments. This investigation effectively extends the Biosphere hundreds of meters into the Geosphere and has implications to a variety of subsurface activities.

  14. Contemporary deep recurrent learning for recognition

    Science.gov (United States)

    Iftekharuddin, K. M.; Alam, M.; Vidyaratne, L.

    2017-05-01

    Large-scale feed-forward neural networks have seen intense application in many computer vision problems. However, these networks can get hefty and computationally intensive with increasing complexity of the task. Our work, for the first time in literature, introduces a Cellular Simultaneous Recurrent Network (CSRN) based hierarchical neural network for object detection. CSRN has shown to be more effective to solving complex tasks such as maze traversal and image processing when compared to generic feed forward networks. While deep neural networks (DNN) have exhibited excellent performance in object detection and recognition, such hierarchical structure has largely been absent in neural networks with recurrency. Further, our work introduces deep hierarchy in SRN for object recognition. The simultaneous recurrency results in an unfolding effect of the SRN through time, potentially enabling the design of an arbitrarily deep network. This paper shows experiments using face, facial expression and character recognition tasks using novel deep recurrent model and compares recognition performance with that of generic deep feed forward model. Finally, we demonstrate the flexibility of incorporating our proposed deep SRN based recognition framework in a humanoid robotic platform called NAO.

  15. Diabetic retinopathy screening using deep neural network.

    Science.gov (United States)

    Ramachandran, Nishanthan; Chiong, Hong Sheng; Sime, Mary Jane; Wilson, Graham A

    2017-09-07

    Importance There is a burgeoning interest in the use of deep neural network in diabetic retinal screening. To determine whether a deep neural network could satisfactorily detect diabetic retinopathy that requires referral to an ophthalmologist from a local diabetic retinal screening programme and an international database. Design Retrospective audit Samples Diabetic retinal photos from Otago database photographed during October 2016 (485 photos); and 1200 photos from Messidor international database. Receiver operating characteristic curve to illustrate the ability of a deep neural network to identify referable diabetic retinopathy (moderate or worse diabetic retinopathy or exudates within one disc diameter of the fovea). Main Outcome Measures Area under the receiver operating characteristic curve, sensitivity and specificity RESULTS: For detecting referable diabetic retinopathy, the deep neural network had an area under receiver operating characteristic curve of 0.901 (95% CI, 0.807-0.995) with 84.6% sensitivity and 79.7% specificity for Otago and 0.980 (95% CI, 0.973-0.986) with 96.0% sensitivity and 90.0% specificity for Messidor. Conclusions and Relevance This study has shown that a deep neural network can detect referable diabetic retinopathy with sensitivities and specificities close to or better than 80% from both an international and a domestic (New Zealand) database. We believe that deep neural networks can be integrated into community screening once they can successfully detect both diabetic retinopathy and diabetic macular oedema. This article is protected by copyright. All rights reserved.

  16. Cellular recurrent deep network for image registration

    Science.gov (United States)

    Alam, M.; Vidyaratne, L.; Iftekharuddin, Khan M.

    2015-09-01

    Image registration using Artificial Neural Network (ANN) remains a challenging learning task. Registration can be posed as a two-step problem: parameter estimation and actual alignment/transformation using the estimated parameters. To date ANN based image registration techniques only perform the parameter estimation, while affine equations are used to perform the actual transformation. In this paper, we propose a novel deep ANN based image rigid registration that combines parameter estimation and transformation as a simultaneous learning task. Our previous work shows that a complex universal approximator known as Cellular Simultaneous Recurrent Network (CSRN) can successfully approximate affine transformations with known transformation parameters. This study introduces a deep ANN that combines a feed forward network with a CSRN to perform full rigid registration. Layer wise training is used to pre-train feed forward network for parameter estimation and followed by a CSRN for image transformation respectively. The deep network is then fine-tuned to perform the final registration task. Our result shows that the proposed deep ANN architecture achieves comparable registration accuracy to that of image affine transformation using CSRN with known parameters. We also demonstrate the efficacy of our novel deep architecture by a performance comparison with a deep clustered MLP.

  17. Deep plane facelifting for facial rejuvenation.

    Science.gov (United States)

    Gordon, Neil; Adam, Stewart

    2014-08-01

    The purpose of this article is to provide the facial plastic surgeon with anatomical and embryologic evidence to support the use of the deep plane technique for optimal treatment of facial aging. A detailed description of the procedure is provided to allow safe and consistent performance. Insights into anatomical landmarks, technical nuances, and alternative approaches for facial variations are presented. The following points will be further elucidated in the article. The platysma muscle/submuscular aponeurotic system/galea are the continuous superficial cervical fascia encompassing the majority of facial fat, and this superficial soft tissue envelope is poorly anchored to the face. The deep cervical fascia binds the structural aspects of the face and covers the facial nerve and buccal fat pad. Facial aging is mainly due to gravity's long-term effects on the superficial soft tissue envelope, with more subtle effects on the deeper structural compartments. The deep plane is the embryologic cleavage plane between these fascial layers, and is the logical place for facial dissection. The deep plane allows access to the buccal fat pad for treatment of jowling. Soft tissue mobilization is maximized in deep plane dissections and requires careful hairline planning. Flap advancement creates tension only at the fascia level allowing natural, tension-free skin closure, and long-lasting outcomes. The deep plane advancement flap is well vascularized and resistant to complications.

  18. DeepInfer: open-source deep learning deployment toolkit for image-guided therapy

    Science.gov (United States)

    Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A.; Kapur, Tina; Wells, William M.; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

    2017-03-01

    Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research work ows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

  19. DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy.

    Science.gov (United States)

    Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A; Kapur, Tina; Wells, William M; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

    2017-02-11

    Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

  20. Nutritional Aspects of Six Quinoa (Chenopodium quinoa Willd. Ecotypes from three Geographical Areas of Chile Aspectos Nutricionales de Seis Ecotipos de Quínoa (Chenopodium quinoa Willd. de Tres Zonas Geográficas de Chile

    Directory of Open Access Journals (Sweden)

    Margarita Miranda

    2012-06-01

    Full Text Available This study explored the diversity of the quinoa crop in Chile from a nutritional perspective. Nutritional properties, minerals, vitamins, and saponin content were assessed in seeds of six Chilean quinoa (Chenopodium quinoa Willd. ecotypes grown in three main production areas with distinctive climatic and edaphic conditions: Ancovinto and Cancosa in the North-Altiplano or High Plateau, Cáhuil and Faro in the central coastal area, and Regalona and Villarrica in the south of the country. There were significant differences (P La diversidad en el cultivo de la quinoa (Chenopodium quinoa Willd. de Chile fue explorada desde una perspectiva nutricional. En este contexto las propiedades nutricionales como también los contenidos de minerales, vitaminas y saponina fueron evaluados en las semillas de seis ecotipos chilenos de quínoa, cultivados en las tres principales zonas de producción con condiciones edafoclimáticas distintas: Ancovinto y Cancosa del altiplano del norte, Cáhuil y Faro de la zona costera central y, Regalona y Villarrica en el sur del país. Hubo diferencias significativas (P < 0.05 en todas las propiedades nutricionales de las semillas de todas las zonas. El ecotipo Villarrica tenia el mayor contenido de proteína (16.10 g 100 g-1 MS y de vitamina E y C (4.644 ± 0.240 y 23.065 ± 1.119 mg 100 g-1 MS, respectivamente. El mayor contenido de vitamina B1 (0.648 ± 0.006 mg 100 g-1 MS y B3 (1.569 ± 0.026 mg 100 g-1 MS fue encontrado en el ecotipo Regalona, y el mayor contenido de vitamina B2 (0.081 ± 0.002 mg 100 g-1 MS en el ecotipo Ancovinto. El K fue el mineral más abundante con un valor de 2325.56 mg 100 g-1 MS en el ecotipo Cancosa. El contenido de saponina fluctuó entre 0.84 g 100 g-1 MS en el ecotipo Villarrica y 3.91 g 100 g-1 MS en el ecotipo Cáhuil. Hubo diferencias significativas entre los ecotipos chilenos de quínoa cultivados bajo diferentes condiciones climáticas. No obstante, las semillas de quinoa de cualquier

  1. Deep-sea pollen research in China

    Institute of Scientific and Technical Information of China (English)

    SUN Xiangjun; LUO Yunli; CHEN Huaicheng

    2003-01-01

    This paper briefly presents the progress of deep-sea pollen research in China since the beginning ofninetieths of the last Century. All the deep-sea pollen contri-butions mainly come from the South China Sea (SCS) andthe East China Sea (ECS). The German-Chinese joint cruise(Sonne 95) and ODP 184 cruise initiated by Chinese scientistsin the SCS provided excellent material for the deep-sea pol-len research. So far a number of pollen results of 20-30 kaand million years from the SCS have been published. A couple of deep-sea pollen records from Okinawa Through of the ECS also came out. The high resolution pollen records obtained from the continuous deposits with high sedimentation rates and reliable age control of the deep-sea sediments provided a high time resolution history (hundred to millennial scales) of vegetation, environment and monsoon evolution of the pollen source areas (southern China and Japan). Spectral analysis of deep-sea pollen records from the SCS discovered orbital (100, 41, 23, 10 ka) and suborbital cyclicities (Heinrich and Dansgaard/Oscheger-O/D events) in the vege-tation changes. Moreover, cross spectral analysis showed that the trend of vegetation changes in northern SCS was regulated mainly by changes of the ice volume in the Northern Hemisphere. The pollen record of the last 20 ka from the Okinawa Through of the ECS indicates that the marine environmental change lagged that on the terrestrail by about 1000 year. The asynchronous environmental changes between land and sea were probably caused by the time difference in thermohaline circulation. This study underscored the role of the deep-sea plant fossils as a bridge across the land and sea.

  2. Ultra Deep Wave Equation Imaging and Illumination

    Energy Technology Data Exchange (ETDEWEB)

    Alexander M. Popovici; Sergey Fomel; Paul Sava; Sean Crawley; Yining Li; Cristian Lupascu

    2006-09-30

    In this project we developed and tested a novel technology, designed to enhance seismic resolution and imaging of ultra-deep complex geologic structures by using state-of-the-art wave-equation depth migration and wave-equation velocity model building technology for deeper data penetration and recovery, steeper dip and ultra-deep structure imaging, accurate velocity estimation for imaging and pore pressure prediction and accurate illumination and amplitude processing for extending the AVO prediction window. Ultra-deep wave-equation imaging provides greater resolution and accuracy under complex geologic structures where energy multipathing occurs, than what can be accomplished today with standard imaging technology. The objective of the research effort was to examine the feasibility of imaging ultra-deep structures onshore and offshore, by using (1) wave-equation migration, (2) angle-gathers velocity model building, and (3) wave-equation illumination and amplitude compensation. The effort consisted of answering critical technical questions that determine the feasibility of the proposed methodology, testing the theory on synthetic data, and finally applying the technology for imaging ultra-deep real data. Some of the questions answered by this research addressed: (1) the handling of true amplitudes in the downward continuation and imaging algorithm and the preservation of the amplitude with offset or amplitude with angle information required for AVO studies, (2) the effect of several imaging conditions on amplitudes, (3) non-elastic attenuation and approaches for recovering the amplitude and frequency, (4) the effect of aperture and illumination on imaging steep dips and on discriminating the velocities in the ultra-deep structures. All these effects were incorporated in the final imaging step of a real data set acquired specifically to address ultra-deep imaging issues, with large offsets (12,500 m) and long recording time (20 s).

  3. Deep Web表单标签提取探究

    Institute of Scientific and Technical Information of China (English)

    邵崇洁; 陈丽君; 徐贝; 丁特战

    2012-01-01

    随着Internet的不断发展,DeepWeb已经成为Web上重要的信息资源,DeepWeb表单标签提取是访问DeepWeb资源的前提与基础。该文提出了倒推算法来处理DeepWeb表单标签。

  4. 47 CFR 32.2424 - Submarine & deep sea cable.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Submarine & deep sea cable. 32.2424 Section 32... Submarine & deep sea cable. (a) This account shall include the original cost of submarine cable and deep sea... defined below, are to be maintained for nonmetallic submarine and deep sea cable and metallic...

  5. Development of deep eutectic solvents applied in extraction and separation.

    Science.gov (United States)

    Li, Xiaoxia; Row, Kyung Ho

    2016-09-01

    Deep eutectic solvents, as an alternative to ionic liquids, have greener credentials than ionic liquids, and have attracted considerable attention in related chemical research. Deep eutectic solvents have attracted increasing attention in chemistry for the extraction and separation of various target compounds from natural products. This review highlights the preparation of deep eutectic solvents, unique properties of deep eutectic solvents, and synthesis of deep-eutectic-solvent-based materials. On the other hand, application in the extraction and separation of deep eutectic solvents is also included in this report. In this paper, the available data and references in this field are reviewed to summarize the applications and developments of deep eutectic solvents. Based on the development of deep eutectic solvents, an exploitation of new deep eutectic solvents and deep eutectic solvents-based materials is expected to diversify into extraction and separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 生态型辅导员团队建设初探--以湖南电气职业技术学院为个案研究%Preliminary Studies on Political Instructor Ecotype Team Building:A Case Study of Hunan Electrical College of Technology

    Institute of Scientific and Technical Information of China (English)

    匡翠芳; 刘鑫

    2015-01-01

    在高校生态环境中,辅导员的实际生态位受到挤压。本文从生态型辅导员团队建设模式架构、团队精神凝练、团队成长平台搭建、高效服务平台构建四个方面探索生态型辅导员团队建设路径。%The niche of political instructor is being oppressed. This paper aims to explore building an ecotype team through four aspects, namely, the forming of ecological framework model, the imbuing of team spirit, the establishing of teammenber growth platform and the constructing of efficient service platform.

  7. Study on Deep Web Search Interface%Deep Web查询接口研究

    Institute of Scientific and Technical Information of China (English)

    钱程; 阳小兰

    2012-01-01

    Deep Web查询接口是Web数据库的接口,其对于Deep Web数据库集成至关重要.本文根据网页表单的结构特征定义查询接口;针对非提交查询法,给出界定Deep Web查询接口的一些规则;提出提交查询法,根据链接属性的特点进行判断,找到包含查询接口的页面;采用决策树C4.5算法进行分类,并用Java语言实现Deep Web查询接口系统.%Deep Web search interface is the interface of Web database. It is essential for the integration of Deep Web databases. According to the structural characteristics of the Web form, search interface is defined. For non-submission query method, some of the rules as defined in the Deep Web search interface are given. The submission query method is proposed, which finds out the page containing the search interface with the features of the link properties. The Web pages are classified with the C4. S decision tree algorithm, and the Deep Web search interface system is realized by using Java.

  8. The Deep Space Network: A Radio Communications Instrument for Deep Space Exploration

    Science.gov (United States)

    Renzetti, N. A.; Stelzried, C. T.; Noreen, G. K.; Slobin, S. D.; Petty, S. M.; Trowbridge, D. L.; Donnelly, H.; Kinman, P. W.; Armstrong, J. W.; Burow, N. A.

    1983-01-01

    The primary purpose of the Deep Space Network (DSN) is to serve as a communications instrument for deep space exploration, providing communications between the spacecraft and the ground facilities. The uplink communications channel provides instructions or commands to the spacecraft. The downlink communications channel provides command verification and spacecraft engineering and science instrument payload data.

  9. Harnessing the Deep Web: Present and Future

    CERN Document Server

    Madhavan, Jayant; Antova, Lyublena; Halevy, Alon

    2009-01-01

    Over the past few years, we have built a system that has exposed large volumes of Deep-Web content to Google.com users. The content that our system exposes contributes to more than 1000 search queries per-second and spans over 50 languages and hundreds of domains. The Deep Web has long been acknowledged to be a major source of structured data on the web, and hence accessing Deep-Web content has long been a problem of interest in the data management community. In this paper, we report on where we believe the Deep Web provides value and where it does not. We contrast two very different approaches to exposing Deep-Web content -- the surfacing approach that we used, and the virtual integration approach that has often been pursued in the data management literature. We emphasize where the values of each of the two approaches lie and caution against potential pitfalls. We outline important areas of future research and, in particular, emphasize the value that can be derived from analyzing large collections of potenti...

  10. Deep-Plane Lipoabdominoplasty in East Asians

    Directory of Open Access Journals (Sweden)

    June-Kyu Kim

    2016-07-01

    Full Text Available BackgroundThe objective of this study was to develop a new surgical technique by combining traditional abdominoplasty with liposuction. This combination of operations permits simpler and more accurate management of various abdominal deformities. In lipoabdominoplasty, the combination of techniques is of paramount concern. Herein, we introduce a new combination of liposuction and abdominoplasty using deep-plane flap sliding to maximize the benefits of both techniques.MethodsDeep-plane lipoabdominoplasty was performed in 143 patients between January 2007 and May 2014. We applied extensive liposuction on the entire abdomen followed by a sliding flap through the deep plane after repairing the diastasis recti. The abdominal wound closure was completed with repair of Scarpa's fascia.ResultsThe average amount of liposuction aspirate was 1,400 mL (700–3,100 mL, and the size of the average excised skin ellipse was 21.78×12.81 cm (from 15×10 to 25×15 cm. There were no major complications such as deep-vein thrombosis or pulmonary embolism. We encountered 22 cases of minor complications: one wound infection, one case of skin necrosis, two cases of undercorrection, nine hypertrophic scars, and nine seromas. These complications were solved by conservative management or simple revision.ConclusionsThe use of deep-plane lipoabdominoplasty can correct abdominal deformities more effectively and with fewer complications than traditional abdominoplasty.

  11. Training Deep Spiking Neural Networks Using Backpropagation.

    Science.gov (United States)

    Lee, Jun Haeng; Delbruck, Tobi; Pfeiffer, Michael

    2016-01-01

    Deep spiking neural networks (SNNs) hold the potential for improving the latency and energy efficiency of deep neural networks through data-driven event-based computation. However, training such networks is difficult due to the non-differentiable nature of spike events. In this paper, we introduce a novel technique, which treats the membrane potentials of spiking neurons as differentiable signals, where discontinuities at spike times are considered as noise. This enables an error backpropagation mechanism for deep SNNs that follows the same principles as in conventional deep networks, but works directly on spike signals and membrane potentials. Compared with previous methods relying on indirect training and conversion, our technique has the potential to capture the statistics of spikes more precisely. We evaluate the proposed framework on artificially generated events from the original MNIST handwritten digit benchmark, and also on the N-MNIST benchmark recorded with an event-based dynamic vision sensor, in which the proposed method reduces the error rate by a factor of more than three compared to the best previous SNN, and also achieves a higher accuracy than a conventional convolutional neural network (CNN) trained and tested on the same data. We demonstrate in the context of the MNIST task that thanks to their event-driven operation, deep SNNs (both fully connected and convolutional) trained with our method achieve accuracy equivalent with conventional neural networks. In the N-MNIST example, equivalent accuracy is achieved with about five times fewer computational operations.

  12. Training Deep Spiking Neural Networks using Backpropagation

    Directory of Open Access Journals (Sweden)

    Jun Haeng Lee

    2016-11-01

    Full Text Available Deep spiking neural networks (SNNs hold the potential for improving the latency and energy efficiency of deep neural networks through data-driven event-based computation. However, training such networks is difficult due to the non-differentiable nature of spike events. In this paper, we introduce a novel technique, which treats the membrane potentials of spiking neurons as differentiable signals, where discontinuities at spike times are considered as noise. This enables an error backpropagation mechanism for deep SNNs that follows the same principles as in conventional deep networks, but works directly on spike signals and membrane potentials. Compared with previous methods relying on indirect training and conversion, our technique has the potential to capture the statistics of spikes more precisely. We evaluate the proposed framework on artificially generated events from the original MNIST handwritten digit benchmark, and also on the N-MNIST benchmark recorded with an event-based dynamic vision sensor, in which the proposed method reduces the error rate by a factor of more than three compared to the best previous SNN, and also achieves a higher accuracy than a conventional convolutional neural network (CNN trained and tested on the same data. We demonstrate in the context of the MNIST task that thanks to their event-driven operation, deep SNNs (both fully connected and convolutional trained with our method achieve accuracy equivalent with conventional neural networks. In the N-MNIST example, equivalent accuracy is achieved with about five times fewer computational operations.

  13. Deep-Plane Lipoabdominoplasty in East Asians

    Science.gov (United States)

    Jang, Jun-Young; Hong, Yoon Gi; Sim, Hyung Bo; Sun, Sang Hoon

    2016-01-01

    Background The objective of this study was to develop a new surgical technique by combining traditional abdominoplasty with liposuction. This combination of operations permits simpler and more accurate management of various abdominal deformities. In lipoabdominoplasty, the combination of techniques is of paramount concern. Herein, we introduce a new combination of liposuction and abdominoplasty using deep-plane flap sliding to maximize the benefits of both techniques. Methods Deep-plane lipoabdominoplasty was performed in 143 patients between January 2007 and May 2014. We applied extensive liposuction on the entire abdomen followed by a sliding flap through the deep plane after repairing the diastasis recti. The abdominal wound closure was completed with repair of Scarpa's fascia. Results The average amount of liposuction aspirate was 1,400 mL (700–3,100 mL), and the size of the average excised skin ellipse was 21.78×12.81 cm (from 15×10 to 25×15 cm). There were no major complications such as deep-vein thrombosis or pulmonary embolism. We encountered 22 cases of minor complications: one wound infection, one case of skin necrosis, two cases of undercorrection, nine hypertrophic scars, and nine seromas. These complications were solved by conservative management or simple revision. Conclusions The use of deep-plane lipoabdominoplasty can correct abdominal deformities more effectively and with fewer complications than traditional abdominoplasty. PMID:27462568

  14. Biodiversity of deep-sea microorganisms

    Directory of Open Access Journals (Sweden)

    Fengping Wang

    2013-07-01

    Full Text Available The oceans, with an average depth of 3,800 meters and an average pressure about 38 MPa, cover about 70% of the surface of the Earth. Geological structures under the seawater, such as marine sediments, oceanic crust, hydrothermal vents, and the cold seeps, vary significantly with regard to physical and chemical properties. In combination, these diverse environments contain the largest microbial ecosystem in the world. In deep seawater, the major microorganism groups are Alpha-& Gammaproteobacteria, and Marine Group I. In deep-sea sediments, the abundance of microbes is related to the content of organic matter and distance from land. Methane Oxidizing Archaea (ANME and sulfate reducing bacteria (Deltaproteobacteria are common in deep-sea cold seep environments; while in hydrothermal vents, the richness and dynamics of chemical substances have led to highly diversified archaeal and bacterial groups. In contrast, the oceanic crust is mainly composed of basic and ultrabasic rocks rich in minerals, and as a result houses microorganisms that are mainly autotrophic, utilizing iron, manganese and sulfur. Because more than 99% of deep-sea microorganisms cannot be cultured, an understanding of their diversity, physiological features, and biogeochemical roles remains to be fully achieved. In this article, we review and summarize what is known about the distribution and diversity of deep-sea microorganisms in diverse habitats. It is emphasized that there is much to learn about these microbes.

  15. Deep Panuke : uniquely positioned for future success

    Energy Technology Data Exchange (ETDEWEB)

    LeBlanc, L. [PanCanadian Petroleum Ltd., Calgary, AB (Canada)

    2001-07-01

    An overview of PanCanadian's involvement in east coast activities and the Deep Panuke Project was presented with focus on regional developments. A map depicting oil and gas fields in eastern Canada's offshore was included. PanCanadian holds 100 per cent interest in the Deep Panuke gas field which is located in the Scotian Basin and is expected to produce 400 MMcf/d by 2005. The master schedule for the Deep Panuke for 2000 to 2004 was presented. A map depicting PanCanadian land holdings interests in the Scotian Shelf was also included. Different types of gravity based structures and their installations were presented along with the construction status of the Eirik Raude deep water drilling rig. Maps depicting drilling location and coal bed methane zones were also included and means by which acid gas (H2S) will be disposed were illustrated. The Deep Panuke project has obtained approvals from the Canada-Nova Scotia Offshore Petroleum Board, the National Energy Board, the Nova Scotia Utility and Review Board, Fisheries and Oceans Canada, Environment Canada and Industry Canada. The next step in the development process is to present a front-end engineering design and to show development plans for environmental assessment, socio-economic assessments and a Nova Scotia benefits plan. tabs., figs.

  16. Study of Deep Web Form-tag Extraction%Deep Web表单标签提取探究

    Institute of Scientific and Technical Information of China (English)

    邵崇洁; 陈丽君; 徐贝; 丁特战

    2012-01-01

    随着Internet的不断发展,Deep Web已经成为Web上重要的信息资源,Deep Web表单标签提取是访问Deep Web资源的前提与基础.该文提出了倒推算法来处理Deep Web表单标签.

  17. INVESTIGATION OF PERFORMANCE CURVES OF THREE STAGE DEEP WELL PUMPS

    OpenAIRE

    Gölcü, Mustafa

    2002-01-01

    In literature, pumps which are known as vertical turbine pump (VTP) have been designed to work vertically. Today, they are known as deep well pumps. These pumps are especially used in narrow and very deep wells where the surface sources are insufficient. Therefore, it is necessary to select suitable stage number to benefit from deep well pumps efficiently. In this study, a new deep well pump has been designed and the performances of three stage deep well pumps have been investigated experimen...

  18. Deep Extreme Learning Machine and Its Application in EEG Classification

    OpenAIRE

    Shifei Ding; Nan Zhang; Xinzheng Xu; Lili Guo; Jian Zhang

    2015-01-01

    Recently, deep learning has aroused wide interest in machine learning fields. Deep learning is a multilayer perceptron artificial neural network algorithm. Deep learning has the advantage of approximating the complicated function and alleviating the optimization difficulty associated with deep models. Multilayer extreme learning machine (MLELM) is a learning algorithm of an artificial neural network which takes advantages of deep learning and extreme learning machine. Not only does MLELM appr...

  19. Deep Extreme Learning Machine and Its Application in EEG Classification

    OpenAIRE

    2015-01-01

    Recently, deep learning has aroused wide interest in machine learning fields. Deep learning is a multilayer perceptron artificial neural network algorithm. Deep learning has the advantage of approximating the complicated function and alleviating the optimization difficulty associated with deep models. Multilayer extreme learning machine (MLELM) is a learning algorithm of an artificial neural network which takes advantages of deep learning and extreme learning machine. Not only does MLELM appr...

  20. Deep learning in TMVA Benchmarking Benchmarking TMVA DNN Integration of a Deep Autoencoder

    CERN Document Server

    Huwiler, Marc

    2017-01-01

    The TMVA library in ROOT is dedicated to multivariate analysis, and in partic- ular oers numerous machine learning algorithms in a standardized framework. It is widely used in High Energy Physics for data analysis, mainly to perform regression and classication. To keep up to date with the state of the art in deep learning, a new deep learning module was being developed this summer, oering deep neural net- work, convolutional neural network, and autoencoder. TMVA did not have yet any autoencoder method, and the present project consists in implementing the TMVA autoencoder class based on the deep learning module. It also includes some bench- marking performed on the actual deep neural network implementation, in comparison to the Keras framework with Tensorflow and Theano backend.

  1. Advances in Deep Web classification%Deep Web站点分类研究进展

    Institute of Scientific and Technical Information of China (English)

    陆余良; 房珊瑶; 刘金红; 施凡

    2010-01-01

    如何高效、准确地组织和检索Deep Web蕴含的高质量信息已经成为未来Web挖掘和数据库领域面临的一项崭新课题和挑战,而Deep Web分类则是Deep Web信息检索的基础.该论文综合论述了Deep Web信息集成的研究概况,重点分析了结构化Deep Web分类的主要方法和存在的主要问题,并且讨论了解决这些问题的可能方法;最后对未来工作进行展望.

  2. Deep South Atlantic carbonate chemistry and increased interocean deep water exchange during last deglaciation

    Science.gov (United States)

    Yu, Jimin; Anderson, Robert F.; Jin, Zhangdong; Menviel, Laurie; Zhang, Fei; Ryerson, Fredrick J.; Rohling, Eelco J.

    2014-04-01

    Carbon release from the deep ocean at glacial terminations is a critical component of past climate change, but the underlying mechanisms remain poorly understood. We present a 28,000-year high-resolution record of carbonate ion concentration, a key parameter of the global carbon cycle, at 5-km water depth in the South Atlantic. We observe similar carbonate ion concentrations between the Last Glacial Maximum and the late Holocene, despite elevated concentrations in the glacial surface ocean. This strongly supports the importance of respiratory carbon accumulation in a stratified deep ocean for atmospheric CO2 reduction during the last ice age. After ˜9 μmol/kg decline during Heinrich Stadial 1, deep South Atlantic carbonate ion concentration rose by ˜24 μmol/kg from the onset of Bølling to Pre-boreal, likely caused by strengthening North Atlantic Deep Water formation (Bølling) or increased ventilation in the Southern Ocean (Younger Drays) or both (Pre-boreal). The ˜15 μmol/kg decline in deep water carbonate ion since ˜10 ka is consistent with extraction of alkalinity from seawater by deep-sea CaCO3 compensation and coral reef growth on continental shelves during the Holocene. Between 16,600 and 15,000 years ago, deep South Atlantic carbonate ion values converged with those at 3.4-km water depth in the western equatorial Pacific, as did carbon isotope and radiocarbon values. These observations suggest a period of enhanced lateral exchange of carbon between the deep South Atlantic and Pacific Oceans, probably due to an increased transfer of momentum from southern westerlies to the Southern Ocean. By spreading carbon-rich deep Pacific waters around Antarctica for upwelling, invigorated interocean deep water exchange would lead to more efficient CO2 degassing from the Southern Ocean, and thus to an atmospheric CO2 rise, during the early deglaciation.

  3. NGS-based deep bisulfite sequencing.

    Science.gov (United States)

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  4. The South China Sea Deep: Introduction

    Science.gov (United States)

    Wang, Pinxian; Li, Qianyu; Dai, Minhan

    2015-12-01

    The South China Sea (SCS) has increasingly become a global focus in ocean research and hydrocarbon explorations. Over the last two decades, at least 17 international cruises including two ODP/IODP expeditions were conducted in the SCS, and more than 2000 exploratory wells were drilled (Wang et al., 2014a). While its sedimentary basins on the continental shelf and slope are explored for offshore resources, the deep basin below 3500 m in depth that overlies the basaltic oceanic crust preserves the key to understanding their formation and development. In order to better understand the life history and functional system of the marginal sea, a major research program "Deep Sea Processes and Evolution of the South China Sea", or "The South China Sea Deep" for short, was launched in January 2011 by the National Natural Science Foundation (NSFC) of China. This venture represents the first ever large-scale basic-research program in ocean science in the country (Wang, 2012).

  5. From DeepCore to PINGU

    Directory of Open Access Journals (Sweden)

    Yáñez J.P.

    2016-01-01

    Full Text Available Very large volume neutrino telescopes (VLVNTs observe atmospheric neutrinos over a wide energy range (GeV to TeV, after they travel distances as large as the Earth's diameter. DeepCore, the low energy extension of IceCube, has started making meaningful measurements of the neutrino oscillation parameters θ23 and | Δm232| by analyzing the atmospheric flux at energies above 10 GeV. PINGU, a proposed project to lower DeepCore's energy threshold, aims to use the same flux to further increase the precision with which these parameters are known, and eventually determine the sign of Δm232. The latest results from DeepCore, and the planned transition to PINGU, are discussed here.

  6. Deep Learning in Medical Image Analysis.

    Science.gov (United States)

    Shen, Dinggang; Wu, Guorong; Suk, Heung-Il

    2017-03-09

    This review covers computer-assisted analysis of images in the field of medical imaging. Recent advances in machine learning, especially with regard to deep learning, are helping to identify, classify, and quantify patterns in medical images. At the core of these advances is the ability to exploit hierarchical feature representations learned solely from data, instead of features designed by hand according to domain-specific knowledge. Deep learning is rapidly becoming the state of the art, leading to enhanced performance in various medical applications. We introduce the fundamentals of deep learning methods and review their successes in image registration, detection of anatomical and cellular structures, tissue segmentation, computer-aided disease diagnosis and prognosis, and so on. We conclude by discussing research issues and suggesting future directions for further improvement. Expected final online publication date for the Annual Review of Biomedical Engineering Volume 19 is June 4, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  7. Strategic Technologies for Deep Space Transport

    Science.gov (United States)

    Litchford, Ronald J.

    2016-01-01

    Deep space transportation capability for science and exploration is fundamentally limited by available propulsion technologies. Traditional chemical systems are performance plateaued and require enormous Initial Mass in Low Earth Orbit (IMLEO) whereas solar electric propulsion systems are power limited and unable to execute rapid transits. Nuclear based propulsion and alternative energetic methods, on the other hand, represent potential avenues, perhaps the only viable avenues, to high specific power space transport evincing reduced trip time, reduced IMLEO, and expanded deep space reach. Here, key deep space transport mission capability objectives are reviewed in relation to STMD technology portfolio needs, and the advanced propulsion technology solution landscape is examined including open questions, technical challenges, and developmental prospects. Options for potential future investment across the full compliment of STMD programs are presented based on an informed awareness of complimentary activities in industry, academia, OGAs, and NASA mission directorates.

  8. Microbial survival in deep space environment.

    Science.gov (United States)

    Silverman, G. J.

    1971-01-01

    Review of the knowledge available on the extent to which microorganisms (mainly microbial spores, vegetative cells, and fungi) are capable of surviving the environment of deep space, based on recent simulation experiments of deep space. A description of the experimental procedures used is followed by a discussion of deep space ecology, the behavior of microorganisms in ultrahigh vacuum, and factors influencing microbial survival. It is concluded that, so far, simulation experiments have proved far less lethal to microorganisms than to other forms of life. There are, however, wide gaps in the knowledge available, and no accurate predictions can as yet be made on the degree of lethality that might be incurred by a microbial population on a given mission. Therefore, sterilization of spacecraft surfaces is deemed necessary if induced panspermia (i.e., interplanetary life propagation) is to be avoided.

  9. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    This chapter presents research on deep learning in a digital learning environment and raises the question if digital instructional designs can catalyze deeper learning than traditional classroom teaching. As a theoretical point of departure the notion of ‘situated learning’ is utilized...... and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, unistructural, multistructural or relational learning. The research concludes that ‘The Open Source Learning Stream’ can catalyze deep learning and that there are four types of ‘Open Source Learning streams’; individual/ asynchronous, individual/synchronous, shared/asynchronous and shared...

  10. Deep Learning in Medical Imaging: General Overview

    Science.gov (United States)

    Lee, June-Goo; Jun, Sanghoon; Cho, Young-Won; Lee, Hyunna; Kim, Guk Bae

    2017-01-01

    The artificial neural network (ANN)–a machine learning technique inspired by the human neuronal synapse system–was introduced in the 1950s. However, the ANN was previously limited in its ability to solve actual problems, due to the vanishing gradient and overfitting problems with training of deep architecture, lack of computing power, and primarily the absence of sufficient data to train the computer system. Interest in this concept has lately resurfaced, due to the availability of big data, enhanced computing power with the current graphics processing units, and novel algorithms to train the deep neural network. Recent studies on this technology suggest its potentially to perform better than humans in some visual and auditory recognition tasks, which may portend its applications in medicine and healthcare, especially in medical imaging, in the foreseeable future. This review article offers perspectives on the history, development, and applications of deep learning technology, particularly regarding its applications in medical imaging. PMID:28670152

  11. NASA Deep Space Network Operations Scheduling

    Science.gov (United States)

    Enari, D. M.

    The functioning of the Deep Space Network Operations Scheduling, Jet Propulsion Laboratory, CA is reviewed. The primary objectives of the Operations Scheduling are: to schedule the worldwide global allocation of ground communications, tracking facilities, and equipment; and to provide deep space telecommunications for command, tracking, telemetry, and control in support of flight mission operations and tests. Elements of the earth set are Deep Space Stations (DSS) which provide the telecommunications link between the earth and spacecraft; NASA Communications Network; Network Data Processing Area; Network Operations Control Area which provides operational direction to the DSS; Mission Control and Computing systems; and Mission Support areas which provide flight control of the spacecraft. Elements of the space set include mission priorities and requirements which determine the spacecraft queue for allocating network resources. Scheduling is discussed in terms of long-range (3 years), mid-range (8 weeks), and short-range (2 weeks).

  12. Deep Learning in Medical Imaging: General Overview.

    Science.gov (United States)

    Lee, June-Goo; Jun, Sanghoon; Cho, Young-Won; Lee, Hyunna; Kim, Guk Bae; Seo, Joon Beom; Kim, Namkug

    2017-01-01

    The artificial neural network (ANN)-a machine learning technique inspired by the human neuronal synapse system-was introduced in the 1950s. However, the ANN was previously limited in its ability to solve actual problems, due to the vanishing gradient and overfitting problems with training of deep architecture, lack of computing power, and primarily the absence of sufficient data to train the computer system. Interest in this concept has lately resurfaced, due to the availability of big data, enhanced computing power with the current graphics processing units, and novel algorithms to train the deep neural network. Recent studies on this technology suggest its potentially to perform better than humans in some visual and auditory recognition tasks, which may portend its applications in medicine and healthcare, especially in medical imaging, in the foreseeable future. This review article offers perspectives on the history, development, and applications of deep learning technology, particularly regarding its applications in medical imaging.

  13. Serre-type equations in deep water

    CERN Document Server

    Dutykh, Denys; Chhay, Marx

    2016-01-01

    This manuscript is devoted to the modelling of water waves in the deep water regime with some emphasis on the underlying variational structures. The present article should be considered as a review of some existing models and modelling approaches even if new results are presented as well. Namely, we derive the deep water analogue of the celebrated Serre-Green-Naghdi equations which have become the standard model in shallow water environments. The relation to existing models is discussed. Moreover, the multi-symplectic structure of these equations is reported as well. The results of this work can be used to develop various types of robust structure-preserving variational integrators in deep water. The methodology of constructing approximate models presented in this study can be naturally extrapolated to other physical flow regimes as well.

  14. Deep learning in medical imaging: General overview

    Energy Technology Data Exchange (ETDEWEB)

    Lee, June Goo; Jun, Sang Hoon; Cho, Young Won; Lee, Hyun Na; KIm, Guk Bae; Seo, Joon Beom; Kim, Nam Kug [University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

    2017-08-01

    The artificial neural network (ANN)–a machine learning technique inspired by the human neuronal synapse system–was introduced in the 1950s. However, the ANN was previously limited in its ability to solve actual problems, due to the vanishing gradient and overfitting problems with training of deep architecture, lack of computing power, and primarily the absence of sufficient data to train the computer system. Interest in this concept has lately resurfaced, due to the availability of big data, enhanced computing power with the current graphics processing units, and novel algorithms to train the deep neural network. Recent studies on this technology suggest its potentially to perform better than humans in some visual and auditory recognition tasks, which may portend its applications in medicine and health care, especially in medical imaging, in the foreseeable future. This review article offers perspectives on the history, development, and applications of deep learning technology, particularly regarding its applications in medical imaging.

  15. Deep Change Discovering the Leader Within

    CERN Document Server

    Quinn, Robert E

    1996-01-01

    Don't let your company kill you!. Open this book at your own risk. It contains ideas that may lead to a profound self-awakening. An introspective journey for those in the trenches of today's modern organizations, Deep Change is a survival manual for finding our own internal leadership power. By helping us learn new ways of thinking and behaving, it shows how we can transform ourselves from victims to powerful agents of change. And for anyone who yearns to be an internally driven leader, to motivate the people around them, and return to a satisfying work life, Deep Change holds the key.

  16. Silicon Deep Etching Techniques for MEMS Devices

    Institute of Scientific and Technical Information of China (English)

    WU Ying; OU Yi-hong; JIANG Yong-qing; LI Bin

    2003-01-01

    Silicon deep etching technique is the key fabrication step in the development of MEMS. The mask selectivity and the lateral etching control are the two primary factors that decide the result of deep etching process. These two factors are studied in this paper. The experimental results show that the higher selectivity can be gotten when F- gas is used as etching gas and Al is introduced as mask layer. The lateral etching problems can be solved by adjusting the etching condition, such as increasing the RF power, changing the gas composition and flow volume of etching machine.

  17. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, unistructural, multistructural or relational learning. The research concludes that ‘The Open Source Learning Stream’ can catalyze deep learning and that there are four types of ‘Open Source Learning streams’; individual/ asynchronous, individual/synchronous, shared/asynchronous and shared...

  18. Keyword search in the Deep Web

    OpenAIRE

    Calì, Andrea; Martinenghi, D.; Torlone, R.

    2015-01-01

    The Deep Web is constituted by data accessible through Web\\ud pages, but not readily indexable by search engines, as they are returned\\ud in dynamic pages. In this paper we propose a framework for accessing\\ud Deep Web sources, represented as relational tables with so-called ac-\\ud cess limitations, with keyword-based queries. We formalize the notion\\ud of optimal answer and investigate methods for query processing. To our\\ud knowledge, this problem has never been studied in a systematic way.

  19. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    Science.gov (United States)

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.

  20. DeepCAD: A Computer-Aided Diagnosis System for Mammographic Masses Using Deep Invariant Features

    Directory of Open Access Journals (Sweden)

    Qaisar Abbas

    2016-10-01

    Full Text Available The development of a computer-aided diagnosis (CAD system for differentiation between benign and malignant mammographic masses is a challenging task due to the use of extensive pre- and post-processing steps and ineffective features set. In this paper, a novel CAD system is proposed called DeepCAD, which uses four phases to overcome these problems. The speed-up robust features (SURF and local binary pattern variance (LBPV descriptors are extracted from each mass. These descriptors are then transformed into invariant features. Afterwards, the deep invariant features (DIFs are constructed in supervised and unsupervised fashion through multilayer deep-learning architecture. A fine-tuning step is integrated to determine the features, and the final decision is performed via softmax linear classifier. To evaluate this DeepCAD system, a dataset of 600 region-of-interest (ROI masses including 300 benign and 300 malignant masses was obtained from two publicly available data sources. The performance of DeepCAD system is compared with the state-of-the-art methods in terms of area under the receiver operating characteristics (AUC curve. The difference between AUC of DeepCAD and other methods is statistically significant, as it demonstrates a sensitivity (SN of 92%, specificity (SP of 84.2%, accuracy (ACC of 91.5% and AUC of 0.91. The experimental results indicate that the proposed DeepCAD system is reliable for providing aid to radiologists without the need for explicit design.

  1. DeepBipolar: Identifying genomic mutations for bipolar disorder via deep learning.

    Science.gov (United States)

    Laksshman, Sundaram; Bhat, Rajendra Rana; Viswanath, Vivek; Li, Xiaolin

    2017-09-01

    Bipolar disorder, also known as manic depression, is a brain disorder that affects the brain structure of a patient. It results in extreme mood swings, severe states of depression, and overexcitement simultaneously. It is estimated that roughly 3% of the population of the United States (about 5.3 million adults) suffers from bipolar disorder. Recent research efforts like the Twin studies have demonstrated a high heritability factor for the disorder, making genomics a viable alternative for detecting and treating bipolar disorder, in addition to the conventional lengthy and costly postsymptom clinical diagnosis. Motivated by this study, leveraging several emerging deep learning algorithms, we design an end-to-end deep learning architecture (called DeepBipolar) to predict bipolar disorder based on limited genomic data. DeepBipolar adopts the Deep Convolutional Neural Network (DCNN) architecture that automatically extracts features from genotype information to predict the bipolar phenotype. We participated in the Critical Assessment of Genome Interpretation (CAGI) bipolar disorder challenge and DeepBipolar was considered the most successful by the independent assessor. In this work, we thoroughly evaluate the performance of DeepBipolar and analyze the type of signals we believe could have affected the classifier in distinguishing the case samples from the control set. © 2017 Wiley Periodicals, Inc.

  2. Upper-extremity deep venous thrombosis: a review.

    Science.gov (United States)

    Mai, Cuc; Hunt, Daniel

    2011-05-01

    Upper-extremity deep venous thrombosis is less common than lower-extremity deep venous thrombosis. However, upper-extremity deep venous thrombosis is associated with similar adverse consequences and is becoming more common in patients with complex medical conditions requiring central venous catheters or wires. Although guidelines suggest that this disorder be managed using approaches similar to those for lower-extremity deep venous thrombosis, studies are refining the prognosis and management of upper-extremity deep venous thrombosis. Physicians should be familiar with the diagnostic and treatment considerations for this disease. This review will differentiate between primary and secondary upper-extremity deep venous thromboses; assess the risk factors and clinical sequelae associated with upper-extremity deep venous thrombosis, comparing these with lower-extremity deep venous thrombosis; and describe an approach to treatment and prevention of secondary upper-extremity deep venous thrombosis based on clinical evidence.

  3. Deep inelastic scattering near the Coulomb barrier

    Energy Technology Data Exchange (ETDEWEB)

    Gehring, J.; Back, B.; Chan, K. [and others

    1995-08-01

    Deep inelastic scattering was recently observed in heavy ion reactions at incident energies near and below the Coulomb barrier. Traditional models of this process are based on frictional forces and are designed to predict the features of deep inelastic processes at energies above the barrier. They cannot be applied at energies below the barrier where the nuclear overlap is small and friction is negligible. The presence of deep inelastic scattering at these energies requires a different explanation. The first observation of deep inelastic scattering near the barrier was in the systems {sup 124,112}Sn + {sup 58,64}Ni by Wolfs et al. We previously extended these measurements to the system {sup 136}Xe + {sup 64}Ni and currently measured the system {sup 124}Xe + {sup 58}Ni. We obtained better statistics, better mass and energy resolution, and more complete angular coverage in the Xe + Ni measurements. The cross sections and angular distributions are similar in all of the Sn + Ni and Xe + Ni systems. The data are currently being analyzed and compared with new theoretical calculations. They will be part of the thesis of J. Gehring.

  4. A quantitative lubricant test for deep drawing

    DEFF Research Database (Denmark)

    Olsson, David Dam; Bay, Niels; Andreasen, Jan L.

    2010-01-01

    A tribological test for deep drawing has been developed by which the performance of lubricants may be evaluated quantitatively measuring the maximum backstroke force on the punch owing to friction between tool and workpiece surface. The forming force is found not to give useful information...

  5. Ethical issues in deep brain stimulation

    NARCIS (Netherlands)

    M.H.N. Schermer (Maartje)

    2011-01-01

    textabstractDeep brain stimulation (DBS) is currently used to treat neurological disorders like Parkinson's disease, essential tremor, and dystonia, and is explored as an experimental treatment for psychiatric disorders like major depression and obsessive compulsive disorder. This mini review discus

  6. Pathways to deep decarbonization in India

    DEFF Research Database (Denmark)

    Shukla, P.; Dhar, Subash; Pathak, Minal

    This report is a part of the global Deep Decarbonisation Pathways (DDP) Project. The analysis consider two development scenarios for India and assess alternate roadmaps for transiting to a low carbon economy consistent with the globally agreed 2°C stabilization target. The report does not consider...

  7. Progress in deep-UV photoresists

    Indian Academy of Sciences (India)

    P B Sahoo; R Vyas; M Wadhwa; S Verma

    2002-11-01

    Higher resolution can be achieved in lithography by decreasing the wavelength of the exposure source. However, resist material and their processing are also important when we move to a shorter wavelength lithography technology. This paper reviews the recent development and challenges of deep-UV photoresists and their processing technology.

  8. Research and Teaching About the Deep Earth

    Science.gov (United States)

    Williams, Michael L.; Mogk, David W.; McDaris, John

    2010-08-01

    Understanding the Deep Earth: Slabs, Drips, Plumes and More; Virtual Workshop, 17-19 February and 24-26 February 2010; Images and models of active faults, subducting plates, mantle drips, and rising plumes are spurring new excitement about deep-Earth processes and connections between Earth's internal systems and plate tectonics. The new results and the steady progress of Earthscope's USArray across the country are also providing a special opportunity to reach students and the general public. The pace of discoveries about the deep Earth is accelerating due to advances in experimental, modeling, and sensing technologies; new data processing capabilities; and installation of new networks, especially the EarthScope facility. EarthScope is an interdisciplinary program that combines geology and geophysics to study the structure and evolution of the North American continent. To explore the current state of deep-Earth science and ways in which it can be brought into the undergraduate classroom, 40 professors attended a virtual workshop given by On the Cutting Edge, a program that strives to improve undergraduate geoscience education through an integrated cooperative series of workshops and Web-based resources. The 6-day two-part workshop consisted of plenary talks, large and small group discussions, and development and review of new classroom and laboratory activities.

  9. Deep learning for studies of galaxy morphology

    Science.gov (United States)

    Tuccillo, D.; Huertas-Company, M.; Decencière, E.; Velasco-Forero, S.

    2017-06-01

    Establishing accurate morphological measurements of galaxies in a reasonable amount of time for future big-data surveys such as EUCLID, the Large Synoptic Survey Telescope or the Wide Field Infrared Survey Telescope is a challenge. Because of its high level of abstraction with little human intervention, deep learning appears to be a promising approach. Deep learning is a rapidly growing discipline that models high-level patterns in data as complex multilayered networks. In this work we test the ability of deep convolutional networks to provide parametric properties of Hubble Space Telescope like galaxies (half-light radii, Sérsic indices, total flux etc..). We simulate a set of galaxies including point spread function and realistic noise from the CANDELS survey and try to recover the main galaxy parameters using deep-learning. We compare the results with the ones obtained with the commonly used profile fitting based software GALFIT. This way showing that with our method we obtain results at least equally good as the ones obtained with GALFIT but, once trained, with a factor 5 hundred time faster.

  10. Nonlinear Deep Kernel Learning for Image Annotation.

    Science.gov (United States)

    Jiu, Mingyuan; Sahbi, Hichem

    2017-02-08

    Multiple kernel learning (MKL) is a widely used technique for kernel design. Its principle consists in learning, for a given support vector classifier, the most suitable convex (or sparse) linear combination of standard elementary kernels. However, these combinations are shallow and often powerless to capture the actual similarity between highly semantic data, especially for challenging classification tasks such as image annotation. In this paper, we redefine multiple kernels using deep multi-layer networks. In this new contribution, a deep multiple kernel is recursively defined as a multi-layered combination of nonlinear activation functions, each one involves a combination of several elementary or intermediate kernels, and results into a positive semi-definite deep kernel. We propose four different frameworks in order to learn the weights of these networks: supervised, unsupervised, kernel-based semisupervised and Laplacian-based semi-supervised. When plugged into support vector machines (SVMs), the resulting deep kernel networks show clear gain, compared to several shallow kernels for the task of image annotation. Extensive experiments and analysis on the challenging ImageCLEF photo annotation benchmark, the COREL5k database and the Banana dataset validate the effectiveness of the proposed method.

  11. Lorentz violation and deep inelastic scattering

    Directory of Open Access Journals (Sweden)

    V. Alan Kostelecký

    2017-06-01

    Full Text Available The effects of quark-sector Lorentz violation on deep inelastic electron–proton scattering are studied. We show that existing data can be used to establish first constraints on numerous coefficients for Lorentz violation in the quark sector at an estimated sensitivity of parts in a million.

  12. Lorentz violation and deep inelastic scattering

    Science.gov (United States)

    Kostelecký, V. Alan; Lunghi, E.; Vieira, A. R.

    2017-06-01

    The effects of quark-sector Lorentz violation on deep inelastic electron-proton scattering are studied. We show that existing data can be used to establish first constraints on numerous coefficients for Lorentz violation in the quark sector at an estimated sensitivity of parts in a million.

  13. Top Tagging by Deep Learning Algorithm

    CERN Document Server

    Akil, Ali

    2015-01-01

    In this report I will show the application of a deep learning algorithm on a Monte Carlo simulation sample to test its performance in tagging hadronic decays of boosted top quarks and compare what we get with the results of the application of some other algorithms.

  14. Lorentz violation and deep inelastic scattering

    CERN Document Server

    Kostelecky, Alan; Vieira, A R

    2016-01-01

    The effects of quark-sector Lorentz violation on deep inelastic electron-proton scattering are studied. We show that existing data can be used to establish first constraints on numerous coefficients for Lorentz violation in the quark sector at an estimated sensitivity of parts in a million.

  15. Stimulating Deep Learning Using Active Learning Techniques

    Science.gov (United States)

    Yew, Tee Meng; Dawood, Fauziah K. P.; a/p S. Narayansany, Kannaki; a/p Palaniappa Manickam, M. Kamala; Jen, Leong Siok; Hoay, Kuan Chin

    2016-01-01

    When students and teachers behave in ways that reinforce learning as a spectator sport, the result can often be a classroom and overall learning environment that is mostly limited to transmission of information and rote learning rather than deep approaches towards meaningful construction and application of knowledge. A group of college instructors…

  16. Using Cooperative Structures to Promote Deep Learning

    Science.gov (United States)

    Millis, Barbara J.

    2014-01-01

    The author explores concrete ways to help students learn more and have fun doing it while they support each other's learning. The article specifically shows the relationships between cooperative learning and deep learning. Readers will become familiar with the tenets of cooperative learning and its power to enhance learning--even more so when…

  17. Deep Support Vector Machines for Regression Problems

    NARCIS (Netherlands)

    Wiering, Marco; Schutten, Marten; Millea, Adrian; Meijster, Arnold; Schomaker, Lambertus

    2013-01-01

    In this paper we describe a novel extension of the support vector machine, called the deep support vector machine (DSVM). The original SVM has a single layer with kernel functions and is therefore a shallow model. The DSVM can use an arbitrary number of layers, in which lower-level layers contain su

  18. Processes and consequences of deep subduction

    NARCIS (Netherlands)

    Rubie, David C.; Hilst, R.D. van der

    2001-01-01

    Subduction of slabs of oceanic lithosphere into the deep mantle involves a wide range of geophysical and geochemical processes and is of major importance for the physical and chemical evolution of the Earth. For example, subduction and subduction-related volcanism are major processes through

  19. Fingerprint Minutiae Extraction using Deep Learning

    CSIR Research Space (South Africa)

    Darlow, Luke Nicholas

    2017-10-01

    Full Text Available components, such as image enhancement. We pose minutiae extraction as a machine learning problem and propose a deep neural network – MENet, for Minutiae Extraction Network – to learn a data-driven representation of minutiae points. By using the existing...

  20. Deep Belief Nets for Topic Modeling

    DEFF Research Database (Denmark)

    Maaløe, Lars; Arngren, Morten; Winther, Ole

    2015-01-01

    . Efficient retrieval can be carried out in the latent representation. We work both on public benchmarks and digital media content provided by Issuu, an on-line publishing platform. This article also comes with a newly developed deep belief nets toolbox for topic modeling tailored towards performance...

  1. Deep Mantle Seismic Modeling and Imaging

    Science.gov (United States)

    Lay, Thorne; Garnero, Edward J.

    2011-05-01

    Detailed seismic modeling and imaging of Earth's deep interior is providing key information about lower-mantle structures and processes, including heat flow across the core-mantle boundary, the configuration of mantle upwellings and downwellings, phase equilibria and transport properties of deep mantle materials, and mechanisms of core-mantle coupling. Multichannel seismic wave analysis methods that provide the highest-resolution deep mantle structural information include network waveform modeling and stacking, array processing, and 3D migrations of P- and S-wave seismograms. These methods detect and identify weak signals from structures that cannot be resolved by global seismic tomography. Some methods are adapted from oil exploration seismology, but all are constrained by the source and receiver distributions, long travel paths, and strong attenuation experienced by seismic waves that penetrate to the deep mantle. Large- and small-scale structures, with velocity variations ranging from a fraction of a percent to tens of percent, have been detected and are guiding geophysicists to new perspectives of thermochemical mantle convection and evolution.

  2. Diagnosing deep venous thrombosis in primary care

    NARCIS (Netherlands)

    Oudega, Rudolphus

    2005-01-01

    In patients suspected of deep venous thrombosis (DVT) in primary care, it is a challenge to discriminate the patients with DVT from those without DVT. The risk of missing the diagnosis and the risk of unnecessary referral and treatment with a potential harmful therapy has to be balanced by the prima

  3. Gene Variants Associated With Deep Vein Thrombosis

    NARCIS (Netherlands)

    Bezemer, Irene D.; Bare, Lance A.; Doggen, Carine J.M.; Arellano, Andre R.; Tong, Carmen; Rowland, Charles M.; Catanese, Joseph; Young, Bradford A.; Reitsma, Pieter H.; Devlin, James J.; Rosendaal, Frits R.

    2008-01-01

    Context The genetic causes of deep vein thrombosis (DVT) are not fully understood. Objective To identify single-nucleotide polymorphisms (SNPs) associated with DVT. Design, Setting, and Patients We used 3 case-control studies of first DVT. A total of 19 682 gene-centric SNPs were genotyped in 44

  4. Integrated piezoelectric actuators in deep drawing tools

    Science.gov (United States)

    Neugebauer, R.; Mainda, P.; Drossel, W.-G.; Kerschner, M.; Wolf, K.

    2011-04-01

    The production of car body panels are defective in succession of process fluctuations. Thus the produced car body panel can be precise or damaged. To reduce the error rate, an intelligent deep drawing tool was developed at the Fraunhofer Institute for Machine Tools and Forming Technology IWU in cooperation with Audi and Volkswagen. Mechatronic components in a closed-loop control is the main differentiating factor between an intelligent and a conventional deep drawing tool. In correlation with sensors for process monitoring, the intelligent tool consists of piezoelectric actuators to actuate the deep drawing process. By enabling the usage of sensors and actuators at the die, the forming tool transform to a smart structure. The interface between sensors and actuators will be realized with a closed-loop control. The content of this research will present the experimental results with the piezoelectric actuator. For the analysis a production-oriented forming tool with all automotive requirements were used. The disposed actuators are monolithic multilayer actuators of the piezo injector system. In order to achieve required force, the actuators are combined in a cluster. The cluster is redundant and economical. In addition to the detailed assembly structures, this research will highlight intensive analysis with the intelligent deep drawing tool.

  5. Discovery of Deep Structure from Unlabeled Data

    Science.gov (United States)

    2014-11-01

    classification performance. A central theme emerging repeatedly from this work is the ultimate similarity of different unsupervised learning algorithms...34 representations from unlabeled data. The major goal was to innovate new unsupervised deep learning algorithms capable of learning important semantic...tasks, and have had impact on both academia and industry. 15. SUBJECT TERMS unsupervised learning, reduced boltzman machine, recursive neural

  6. Deep Water Coral (HB1402, EK60)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The cruise will survey and collect samples of deep-sea corals and related marine life in the canyons in the northern Gulf of Maine in U.S. and Canadian waters. The...

  7. Parity violation in deep inelastic scattering

    Energy Technology Data Exchange (ETDEWEB)

    Souder, P. [Syracuse Univ., NY (United States)

    1994-04-01

    AA beam of polarized electrons at CEBAF with an energy of 8 GeV or more will be useful for performing precision measurements of parity violation in deep inelastic scattering. Possible applications include precision tests of the Standard Model, model-independent measurements of parton distribution functions, and studies of quark correlations.

  8. Study on Deep Structure of Humor

    Institute of Scientific and Technical Information of China (English)

    闫林琼

    2007-01-01

    Humor is the common favorite of people in all walks of life and at all ages. Studying the deep structure of humor, that is, the psychological and cognitive foundation in producing and comprehending humor, is quite practical in helping people first to recognize, understand and appreciate others' humor and then to apply their own humor to their daily communication.

  9. Using Cooperative Structures to Promote Deep Learning

    Science.gov (United States)

    Millis, Barbara J.

    2014-01-01

    The author explores concrete ways to help students learn more and have fun doing it while they support each other's learning. The article specifically shows the relationships between cooperative learning and deep learning. Readers will become familiar with the tenets of cooperative learning and its power to enhance learning--even more so when…

  10. Geometric Deep Learning: Going beyond Euclidean data

    Science.gov (United States)

    Bronstein, Michael M.; Bruna, Joan; LeCun, Yann; Szlam, Arthur; Vandergheynst, Pierre

    2017-07-01

    Many scientific fields study data with an underlying structure that is a non-Euclidean space. Some examples include social networks in computational social sciences, sensor networks in communications, functional networks in brain imaging, regulatory networks in genetics, and meshed surfaces in computer graphics. In many applications, such geometric data are large and complex (in the case of social networks, on the scale of billions), and are natural targets for machine learning techniques. In particular, we would like to use deep neural networks, which have recently proven to be powerful tools for a broad range of problems from computer vision, natural language processing, and audio analysis. However, these tools have been most successful on data with an underlying Euclidean or grid-like structure, and in cases where the invariances of these structures are built into networks used to model them. Geometric deep learning is an umbrella term for emerging techniques attempting to generalize (structured) deep neural models to non-Euclidean domains such as graphs and manifolds. The purpose of this paper is to overview different examples of geometric deep learning problems and present available solutions, key difficulties, applications, and future research directions in this nascent field.

  11. Deep Friendship Between Vietnam And China

    Institute of Scientific and Technical Information of China (English)

    Vu; Xuan; Hong

    2014-01-01

    <正>Vietnam and China are neighbors joined by rivers and mountains.Geographical location and history ensure close friendship.This is especially true since they both endured a long revolutionary struggle to achieve national liberation,forging what Chairman Ho Chi Minh once praised as"deep friendship between comrades and brothers".The history of the past 60 years

  12. Deep Belief Networks for dimensionality reduction

    NARCIS (Netherlands)

    Noulas, A.K.; Kröse, B.J.A.

    2008-01-01

    Deep Belief Networks are probabilistic generative models which are composed by multiple layers of latent stochastic variables. The top two layers have symmetric undirected connections, while the lower layers receive directed top-down connections from the layer above. The current state-of-the-art tra

  13. Deep Support Vector Machines for Regression Problems

    NARCIS (Netherlands)

    Wiering, Marco; Schutten, Marten; Millea, Adrian; Meijster, Arnold; Schomaker, Lambertus

    2013-01-01

    In this paper we describe a novel extension of the support vector machine, called the deep support vector machine (DSVM). The original SVM has a single layer with kernel functions and is therefore a shallow model. The DSVM can use an arbitrary number of layers, in which lower-level layers contain

  14. A Study of Detrainment from Deep Convection

    Science.gov (United States)

    Glenn, I. B.; Krueger, S. K.

    2014-12-01

    Uncertainty in the results of Global Climate Model simulations has been attributed to errors and simplifications in how parameterizations of convection coarsely represent the processes of entrainment, detrainment, and mixing between convective clouds and their environment. Using simulations of convection we studied these processes at a resolution high enough to explicitly resolve them. Two of several recently developed analysis techniques that allow insight into these processes at their appropriate scale are an Eulerian method of directly measuring entrainment and detrainment, and a Lagrangian method that uses particle trajectories to map convective mass flux over height and a cloud variable of interest. The authors of the Eulerian technique used it to show that the dynamics of shells of cold, humid air that surround shallow convective updrafts have important effects on the properties of air entrained and detrained from the updrafts. There is some evidence for the existence of such shells around deep convective updrafts as well, and that detrainment is more important than entrainment in determining the ultimate effect of the deep convection on the large scale environment. We present results from analyzing a simulation of deep convection through the Eulerian method as well as using Lagrangian particle trajectories to illustrate the role of the shell in the process of detrainment and mixing between deep convection and its environment.

  15. 25 years of continental deep subduction

    Institute of Scientific and Technical Information of China (English)

    ZHENG YongFei

    2009-01-01

    @@ This year marks the 25th anniversary of the discovery of coesite in metamorphic rocks of supracrustal origin.This initiated a revolution of the plate tectonics theory due to intensive studies of ultrahigh pressure metamorphism and continental deep subduction.The occurrence of coesite was first reported in 1984 by two French scientists,C.Chopin and D.C.Smith,respectively.

  16. Launching a Projectile into Deep Space

    Science.gov (United States)

    Maruszewski, Richard F., Jr.

    2004-01-01

    As part of the discussion about Newton's work in a history of mathematics course, one of the presentations calculated the amount of energy necessary to send a projectile into deep space. Afterwards, the students asked for a recalculation with two changes: First the launch under study consisted of a single stage, but the students desired to…

  17. Deep community detection in topologically incomplete networks

    Science.gov (United States)

    Xin, Xin; Wang, Chaokun; Ying, Xiang; Wang, Boyang

    2017-03-01

    In this paper, we consider the problem of detecting communities in topologically incomplete networks (TIN), which are usually observed from real-world networks and where some edges are missing. Existing approaches to community detection always consider the input network as connected. However, more or less, even nearly all, edges are missing in real-world applications, e.g. the protein-protein interaction networks. Clearly, it is a big challenge to effectively detect communities in these observed TIN. At first, we bring forward a simple but useful method to address the problem. Then, we design a structured deep convolutional neural network (CNN) model to better detect communities in TIN. By gradually removing edges of the real-world networks, we show the effectiveness and robustness of our structured deep model on a variety of real-world networks. Moreover, we find that the appropriate choice of hop counts can improve the performance of our deep model in some degree. Finally, experimental results conducted on synthetic data sets also show the good performance of our proposed deep CNN model.

  18. Deep Brain Stimulation - the challenges ahead

    NARCIS (Netherlands)

    Heida, T.; Holsheimer, J.; Geelen, J.A.G.; Veltink, P.H.

    2005-01-01

    Parkinson’s disease (PD) is characterized by progressive loss of dopamine neurons in the pars compacta of the substantia nigra, which results in reduced activity in the thalamus. Clinically effective deep brain stimulation (DBS) has been achieved with electrode contacts in the anterior- dorsal subth

  19. Climate Change Affects Deep Sea Life

    Institute of Scientific and Technical Information of China (English)

    Emma Marris; 秦春雨

    2004-01-01

    @@ The remote and lightless deep-sea floor has long been thought to be protected from events on the surface, such as global warming. But it now seems that climate change impinges on the rhythm of life on the seabed after all.

  20. Deep neck abscesses: the Singapore experience.

    Science.gov (United States)

    Lee, Yan Qing; Kanagalingam, Jeevendra

    2011-04-01

    This study aims to review our experience with deep neck abscesses, identify key trends, and improve the management of this condition. This is a retrospective chart review of patients diagnosed with deep neck abscesses in the Department of ENT (Otorhinolaryngology) at Tan Tock Seng Hospital, Singapore between 2004 and 2009. Patient demographics, etiology, bacteriology, systemic disease, radiology, treatment, complications, duration of hospitalization, and outcomes were reviewed. 131 patients were included (64.9% male, 35.1% female) with a median age of 51.0 years. 54 (41.2%) patients had diabetes mellitus. The parapharyngeal space (23.7%) was the most commonly involved space. Odontogenic and upper airway infections were the leading causes of deep neck abscesses (28.0% each). Klebsiella pneumoniae (27.1%) was the most commonly cultured organism in this study and among the diabetic patients (50.0%). 108 (82.4%) patients underwent surgical drainage. 42 patients suffered complications. All 19 patients, who had upper airway obstruction, had either a tracheostomy or intubation. Patients with multi-space abscesses, diabetes mellitus, and complications had prolonged hospitalizations. Old age and diabetes are risk factors for developing deep neck abscesses and their sequelae. The empiric choice of antibiotics should recognize that a dental source is likely, and that Klebsiella is most common in diabetics. Surgical drainage and adequate antibiotic coverage remains the cornerstone of treatment of deep neck abscesses. Therapeutic needle aspiration may successfully replace surgical drainage, if the abscesses are small and no complications are imminent. Airway obstruction should be anticipated in multi-space and floor of mouth abscesses.

  1. Spectral Tuning of Deep Red Cone Pigments†

    Science.gov (United States)

    Amora, Tabitha L.; Ramos, Lavoisier S.; Galan, Jhenny F.; Birge, Robert R.

    2008-01-01

    Visual pigments are G-protein-coupled receptors that provide a critical interface between organisms and their external environment. Natural selection has generated vertebrate pigments that absorb light from the far-UV (360 nm) to the deep red (630 nm) while using a single chromophore, in either the A1 (11-cis-retinal) or A2 (11-cis-3,4-dehydroretinal) form. The fact that a single chromophore can be manipulated to have an absorption maximum across such an extended spectral region is remarkable. The mechanisms of wavelength regulation remain to be fully revealed, and one of the least well-understood mechanisms is that associated with the deep red pigments. We investigate theoretically the hypothesis that deep red cone pigments select a 6-s-trans conformation of the retinal chromophore ring geometry. This conformation is in contrast to the 6-s-cis ring geometry observed in rhodopsin and, through model chromophore studies, the vast majority of visual pigments. Nomographic spectral analysis of 294 A1 and A2 cone pigment literature absorption maxima indicates that the selection of a 6-s-trans geometry red shifts M/LWS A1 pigments by ~1500 cm−1 (~50 nm) and A2 pigments by ~2700 cm−1 (~100 nm). The homology models of seven cone pigments indicate that the deep red cone pigments select 6-s-trans chromophore conformations primarily via electrostatic steering. Our results reveal that the generation of a 6-s-trans conformation not only achieves a significant red shift but also provides enhanced stability of the chromophore within the deep red cone pigment binding sites. PMID:18370404

  2. Spectral tuning of deep red cone pigments.

    Science.gov (United States)

    Amora, Tabitha L; Ramos, Lavoisier S; Galan, Jhenny F; Birge, Robert R

    2008-04-22

    Visual pigments are G-protein-coupled receptors that provide a critical interface between organisms and their external environment. Natural selection has generated vertebrate pigments that absorb light from the far-UV (360 nm) to the deep red (630 nm) while using a single chromophore, in either the A1 (11- cis-retinal) or A2 (11- cis-3,4-dehydroretinal) form. The fact that a single chromophore can be manipulated to have an absorption maximum across such an extended spectral region is remarkable. The mechanisms of wavelength regulation remain to be fully revealed, and one of the least well-understood mechanisms is that associated with the deep red pigments. We investigate theoretically the hypothesis that deep red cone pigments select a 6- s- trans conformation of the retinal chromophore ring geometry. This conformation is in contrast to the 6- s- cis ring geometry observed in rhodopsin and, through model chromophore studies, the vast majority of visual pigments. Nomographic spectral analysis of 294 A1 and A2 cone pigment literature absorption maxima indicates that the selection of a 6- s- trans geometry red shifts M/LWS A1 pigments by approximately 1500 cm (-1) ( approximately 50 nm) and A2 pigments by approximately 2700 cm (-1) ( approximately 100 nm). The homology models of seven cone pigments indicate that the deep red cone pigments select 6- s- trans chromophore conformations primarily via electrostatic steering. Our results reveal that the generation of a 6- s- trans conformation not only achieves a significant red shift but also provides enhanced stability of the chromophore within the deep red cone pigment binding sites.

  3. Dining in the Deep: The Feeding Ecology of Deep-Sea Fishes

    Science.gov (United States)

    Drazen, Jeffrey C.; Sutton, Tracey T.

    2017-01-01

    Deep-sea fishes inhabit ˜75% of the biosphere and are a critical part of deep-sea food webs. Diet analysis and more recent trophic biomarker approaches, such as stable isotopes and fatty-acid profiles, have enabled the description of feeding guilds and an increased recognition of the vertical connectivity in food webs in a whole-water-column sense, including benthic-pelagic coupling. Ecosystem modeling requires data on feeding rates; the available estimates indicate that deep-sea fishes have lower per-individual feeding rates than coastal and epipelagic fishes, but the overall predation impact may be high. A limited number of studies have measured the vertical flux of carbon by mesopelagic fishes, which appears to be substantial. Anthropogenic activities are altering deep-sea ecosystems and their services, which are mediated by trophic interactions. We also summarize outstanding data gaps.

  4. Automatic classification of Deep Web sources%Deep Web数据源自动分类

    Institute of Scientific and Technical Information of China (English)

    金灵芝; 王小玲; 朱守中

    2009-01-01

    随着World Wide Web(WWW)的飞速发展,Deep Web中蕴含了海量的可供访问的信息,并且还在迅速地增长.其中大部分的Deep Web是结构化的,把这些结构化的Deep Web按其领域进行分类,是Deep Web集成查询接口生成的一个非常重要的步骤.文中提出了一种利用朴素贝叶斯分类的方法,并通过实验证明了其有效性.

  5. Dining in the Deep: The Feeding Ecology of Deep-Sea Fishes.

    Science.gov (United States)

    Drazen, Jeffrey C; Sutton, Tracey T

    2017-01-03

    Deep-sea fishes inhabit ∼75% of the biosphere and are a critical part of deep-sea food webs. Diet analysis and more recent trophic biomarker approaches, such as stable isotopes and fatty-acid profiles, have enabled the description of feeding guilds and an increased recognition of the vertical connectivity in food webs in a whole-water-column sense, including benthic-pelagic coupling. Ecosystem modeling requires data on feeding rates; the available estimates indicate that deep-sea fishes have lower per-individual feeding rates than coastal and epipelagic fishes, but the overall predation impact may be high. A limited number of studies have measured the vertical flux of carbon by mesopelagic fishes, which appears to be substantial. Anthropogenic activities are altering deep-sea ecosystems and their services, which are mediated by trophic interactions. We also summarize outstanding data gaps.

  6. Study on Deep Well Dewatering Optimization Design in Deep Foundation Pit and Engineering Application

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on analyses of the theories of groundwater unsteady flow in deep well dewatering in the deep foundation pit, Theis equations are chosen to calculate and analyze the relationship between water level drawdown of confined aquifer and dewatering duration. In order to reduce engineering cost and diminish detrimental effect on ambient surrounding, optimization design target function based on the control of confined water drawdown and four restriction requisitions based on the control of safe water level, resistance to throwing up from the bottom of foundation pit, avoiding excessively great subsidence and unequal surface subsidence are proposed. A deep well dewatering project in the deep foundation pit is optimally designed. The calculated results including confined water level drawdown and surface subsidence are in close agreement with the measured results, and the optimization design can effectively control both surface subsidence outside foundation pit and unequal subsidence as a result of dewatering.

  7. Testing time for deep water[Deep water test facility in Rotterdam, NL

    Energy Technology Data Exchange (ETDEWEB)

    Snieckus, Darius

    2000-06-01

    A new deep water test facility in Rotterdam in the Netherlands is described. The construction is a basin measuring 45m by 36m and some 10.5m deep: it can accommodate large scale model tests at depths equivalent to 1000m by using a hydraulic 'moveable' floor buoyed by syntactic foam. For simulation of depths of 3000m it opens its 'deep pit' - a well 5m diameter and 20m deep. The facility can also simulate the winds, waves and currents met offshore in places such as the Shetlands, West Africa and the Gulf of Mexico. The article includes pictures and diagrams of the facility.

  8. Crop response to deep tillage - a meta-analysis

    Science.gov (United States)

    Schneider, Florian; Don, Axel; Hennings, Inga; Schmittmann, Oliver; Seidel, Sabine J.

    2017-04-01

    Subsoil, i.e. the soil layer below the topsoil, stores tremendous stocks of nutrients and can keep water even under drought conditions. Deep tillage may be a method to enhance the plant-availability of subsoil resources. However, in field trials, deep tillage effects on crop yields were inconsistent. Therefore, we conducted a meta-analysis of crop yield response to subsoiling, deep ploughing and deep mixing of soil profiles. Our search resulted in 1530 yield comparisons following deep and conventional control tillage on 67 experimental cropping sites. The vast majority of the data derived from temperate latitudes, from trials conducted in the USA (679 observations) and Germany (630 observations). On average, crop yield response to deep tillage was slightly positive (6% increase). However, individual deep tillage effects were highly scattered including about 40% yield depressions after deep tillage. Deep tillage on soils with root restrictive layers increased crop yields about 20%, while soils containing >70% silt increased the risk of yield depressions following deep tillage. Generally, deep tillage effects increased with drought intensity indicating deep tillage as climate adaptation measure at certain sites. Our results suggest that deep tillage can facilitate the plant-availability of subsoil nutrients, which increases crop yields if (i) nutrients in the topsoil are growth limiting, and (ii) deep tillage does not come at the cost of impairing topsoil fertility. On sites with root restrictive soil layers, deep tillage can be an effective measure to mitigate drought stress and improve the resilience of crops. However, deep tillage should only be performed on soils with a stable structure, i.e. <70% silt content. We will discuss the contribution of deep tillage options to enhance the sustainability of agricultural production by facilitating the uptake of nutrients and water from the subsoil.

  9. New optimized drill pipe size for deep-water, extended reach and ultra-deep drilling

    Energy Technology Data Exchange (ETDEWEB)

    Jellison, Michael J.; Delgado, Ivanni [Grant Prideco, Inc., Hoston, TX (United States); Falcao, Jose Luiz; Sato, Ademar Takashi [PETROBRAS, Rio de Janeiro, RJ (Brazil); Moura, Carlos Amsler [Comercial Perfuradora Delba Baiana Ltda., Rio de Janeiro, RJ (Brazil)

    2004-07-01

    A new drill pipe size, 5-7/8 in. OD, represents enabling technology for Extended Reach Drilling (ERD), deep water and other deep well applications. Most world-class ERD and deep water wells have traditionally been drilled with 5-1/2 in. drill pipe or a combination of 6-5/8 in. and 5-1/2 in. drill pipe. The hydraulic performance of 5-1/2 in. drill pipe can be a major limitation in substantial ERD and deep water wells resulting in poor cuttings removal, slower penetration rates, diminished control over well trajectory and more tendency for drill pipe sticking. The 5-7/8 in. drill pipe provides a significant improvement in hydraulic efficiency compared to 5-1/2 in. drill pipe and does not suffer from the disadvantages associated with use of 6-5/8 in. drill pipe. It represents a drill pipe assembly that is optimized dimensionally and on a performance basis for casing and bit programs that are commonly used for ERD, deep water and ultra-deep wells. The paper discusses the engineering philosophy behind 5-7/8 in. drill pipe, the design challenges associated with development of the product and reviews the features and capabilities of the second-generation double-shoulder connection. The paper provides drilling case history information on significant projects where the pipe has been used and details results achieved with the pipe. (author)

  10. The development of deep learning in synthetic aperture radar imagery

    CSIR Research Space (South Africa)

    Schwegmann, Colin P

    2017-05-01

    Full Text Available sensing techniques but comes at the price of additional complexities. To adequately cope with these, researchers have begun to employ advanced machine learning techniques known as deep learning to Synthetic Aperture Radar data. Deep learning represents...

  11. Medical Mysteries: "We Feel Deep Compassion for Patients..."

    Science.gov (United States)

    ... Javascript on. Feature: Medical Mysteries “We feel deep compassion for patients...” Past Issues / Spring 2011 Table of ... maybe even relief. As doctors, we feel deep compassion for patients who have been without hope because ...

  12. Stratification-Based Outlier Detection over the Deep Web

    National Research Council Canada - National Science Library

    Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

    2016-01-01

    .... Introduction As a result of the rapid development of e-commerce, the deep web has been increasingly valued by data mining researchers in recent years. The deep web, which is termed to make a contr...

  13. Extreme Longevity in Proteinaceous Deep-Sea Corals

    Energy Technology Data Exchange (ETDEWEB)

    Roark, E B; Guilderson, T P; Dunbar, R B; Fallon, S J; Mucciarone, D A

    2009-02-09

    Deep-sea corals are found on hard substrates on seamounts and continental margins world-wide at depths of 300 to {approx}3000 meters. Deep-sea coral communities are hotspots of deep ocean biomass and biodiversity, providing critical habitat for fish and invertebrates. Newly applied radiocarbon age date from the deep water proteinaceous corals Gerardia sp. and Leiopathes glaberrima show that radial growth rates are as low as 4 to 35 {micro}m yr{sup -1} and that individual colony longevities are on the order of thousands of years. The management and conservation of deep sea coral communities is challenged by their commercial harvest for the jewelry trade and damage caused by deep water fishing practices. In light of their unusual longevity, a better understanding of deep sea coral ecology and their interrelationships with associated benthic communities is needed to inform coherent international conservation strategies for these important deep-sea ecosystems.

  14. Learning approaches in accounting education: Towards deep learning

    Directory of Open Access Journals (Sweden)

    Yeng Wai Lau

    2015-09-01

    Full Text Available Deep learning facilitates development of generic skills pertinent to prepare graduates for employment. Accounting education with syllabuses burdened with accounting standards to be memorized and regurgitated in examinations does little to promote deep learning. This study conducted a questionnaire survey to examine the extent to which accounting undergraduates at a public university in Malaysia adopt deep learning. This study demonstrates that deep learning is not readily attainable. Surface learning, which promotes rote memorization, constitutes a stepping stone towards deep learning. Having a preference or thirst for meanings is also pertinent to motivate undergraduates to move from rote memorization to seek meanings and thus deep learning. Female undergraduates have been found to be more inclined to adopt deep learning. Much is still to be learned on how best to promote deep learning as learning is a life-long process where everyday life experiences, both on and off-campus, facilitate learning and development.

  15. Deep Soil: Quantifying and Modeling Subsurface Carbon

    Science.gov (United States)

    James, J. N.; Devine, W.; Harrison, R. B.

    2014-12-01

    Some soil carbon datasets that are spatially rich, such as the USDA Forest Service Inventory and Analysis National Program dataset, sample soil to only 20 cm (8 inches), despite evidence that substantial stores of soil C can be found deeper in the soil profile. The maximum extent of tree rooting is typically many meters deep and provides: direct exchange with the soil solution; redistribution of water from deep horizons toward the surface during times of drought; resources for active microbial communities in deep soil around root channels; and direct carbon inputs through exudates and root turnover. This study examined soil carbon to a depth of 2.5 meters across 22 soils in Pacific Northwest Douglas-fir forests. Excavations at 20 additional sites took place in summer 2014, greatly expanding the spatial coverage and extent of the data set. Forest floor and mineral soil bulk density samples were collected at depths of 0.1, 0.5, 1.0, 1.5, 2.0 and 2.5 meters. Pool estimates from systematic sampling depths shallower than 1.5 m yielded significantly smaller estimates than the total soil stock to 2.5 meters (P<0.01). On average, only 5% of soil C was found in the litter layer, 35% was found below 0.5 meter, and 21% was found below 1.0 meter. Due to the difficulty of excavating and measuring deep soil carbon, a series of nonlinear mixed effect models were fit to the data to predict deep soil carbon stocks given sampling to 1.0 meter. A model using an inverse polynomial function predicted soil carbon to 2.5 meters with -5.6% mean error. The largest errors occurred in Andisols with non-crystalline minerals, which can adsorb large quantities of carbon on mineral surfaces and preserve it from decomposition. An accurate spatial dataset of soil depth to bedrock would be extremely useful to constrain models of the vertical distribution of soil carbon. Efforts to represent carbon in spatial models would benefit from considering the vertical distribution of carbon in soil. Sampling

  16. Morphology and Tectonic Evolution of Endeavor Deep

    Science.gov (United States)

    Pockalny, R. A.; Larson, R. L.; Popham, C. T.; Natland, J. H.; Abrams, L. J.; Sonder, L. J.

    2004-12-01

    Endeavor Deep is located on the Nazca/Juan Fernandez plate boundary near the triple junction of the Pacific, Nazca and Antarctic plates. The deep is the tip of the northward propagating East Ridge, which defines the eastern side of the microplate and is presently exposing ~3 Myr old oceanic crust created at the ultra-fast spreading (~150 km/myr) East Pacific Rise. Recently collected high-resolution EM300 bathymetry, deep-tow DSL120 sidescan, surface-towed magnetics, and near-bottom JASON II observations provide important details about the tectonic character and origin of Endeavor Deep. These data define a 70 km-long, 40 km-wide, and 3 km-deep rift which shoals and narrows toward the rift tip to the NW and is deeper and wider away from the rift tip toward the SE. The southern wall of the rift is uplifted and has a characteristic flexural profile. The northern wall is also uplifted, however, the classic flexural profile is complicated by the presence of a large EW-trending massif, which appears to be a rift-truncated compressional ridge emplaced during a phase of NS-oriented compression. Along both rift walls, a series of terraces suggest a series of down-dropped blocks associated with ongoing extension. Along the rift floor, a relatively flat, featureless bottom in the NW evolves into hummocky terrane in the central part of the basin that is characterized by volcanic features reminiscent of 1-2 km diameter pancakes in plan-view. Farther to the SE, tectonic lineations and pillow ridges oriented parallel to the trend of the rift valley dominate the basin floor. Magnetic profiles across this portion of the survey area indicate a well-formed central magnetic anomaly with a width equivalent to a spreading rate of 20 km/Myr, which is predicted by tectonic reconstructions of the plate boundary. Overall, these observations define a four-phase evolution of Endeavor Deep: 1) initial crustal formation at the ultra-fast spreading East Pacific Rise ~3 Ma, 2) regional compression

  17. Protein secondary structure prediction using deep convolutional neural fields

    OpenAIRE

    Sheng Wang; Jian Peng; Jianzhu Ma; Jinbo Xu

    2015-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF)...

  18. Right hemisphere reading in a case of developmental deep dyslexia

    OpenAIRE

    Funnell, Elaine; Pitchford, Nicola; de Haan, Bianca; Morgan, Paul

    2007-01-01

    The right hemisphere hypothesis of deep dyslexia has received support from functional imaging studies of acquired deep dyslexia following damage to the left cerebral hemisphere, but no imaging studies of cases of developmental deep dyslexia, in which brain damage is not suspected, have been reported. In this paper, we report the first evidence of right hyperactivation in an adult case of developmental deep dyslexia. Hyperactivation was observed in the right inferior frontal cortex during fMRI...

  19. China’s first deep manned submersible,JIAOLONG

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A deep manned submersible is indispensable to deep ocean exploration. No other equipment can bring scientists to ex-treme sea floor depths to do research in situ. Marine geology, seafloor geophysics,marine biology,and oceanic chemistry are the fields that scientists are particularly eager to study [1-6]. Chinese scientists have long dreamed of using their own submersible to probe the deep sea. China’s recent fast development of a deep manned submersible has realized that dream.

  20. Learning approaches in accounting education: Towards deep learning

    OpenAIRE

    Yeng Wai Lau; Shi Yee Lim

    2015-01-01

    Deep learning facilitates development of generic skills pertinent to prepare graduates for employment. Accounting education with syllabuses burdened with accounting standards to be memorized and regurgitated in examinations does little to promote deep learning. This study conducted a questionnaire survey to examine the extent to which accounting undergraduates at a public university in Malaysia adopt deep learning. This study demonstrates that deep learning is not readily attainable. Surface ...