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Sample records for amber

  1. Jurassic Amber in Lebanon

    Institute of Scientific and Technical Information of China (English)

    Dany AZAR; Raymond G(E)ZE; Antoine EL-SAMRANI; Jacqueline MAALOULY; André NEL

    2010-01-01

    Reports of amber predating the Lower Cretaceous are unusual and scarce; they mostly refer to amber pieces of millimetric dimension.In the present study,we report the discovery of 10 new outcrops of Jurassic amber in Lebanon.Some of these had large centimetric-sized pieces of amber.The new localities are described,amber is characterized,and its infrared spectra given.Although the new Jurassic amber yielded to date no more than fungal inclusions,this material is significant and promising.The discovery of several Jurassic outcrops provides crucial information on the prevailing paleoenvironment of that time.

  2. Amber : Een revolutie in Radar

    NARCIS (Netherlands)

    Huizing, A.G.

    2011-01-01

    Eind dit jaar verwachtTNO versie 4.0 op te leveren van zijn betaalbare digitale multibeamradar Amber. Het systeem is oorcpronkelijk ontwikkeld voor kleine toestellen die vliegen zonder hulp van de verkeersleiding. lnmiddels kijken de TN0'ers naar veel meer toepassingen, van havenbewaking tot zorg op

  3. Provenance studies of amber by PIXE

    Energy Technology Data Exchange (ETDEWEB)

    Lowe, L.; Ruvalcaba S, J.L. [Centro de Estudios Mayas, Instituto de Investigaciones Filologicas, UNAM C.P. 04510 Mexico D.F. (Mexico)

    1999-07-01

    Analyses by Infrared Spectroscopy and {sup 13} C Nuclear Magnetic Resonance are suitable to determine the paleobotanic source of amber, but cannot differentiate between beds of the same paleobotanic source. Particle Induced X-ray Emission (PIXE) using an external set-up is presented as a new and non-destructive semiquantitative method for provenance studies of amber. PIXE analysis is focused at inorganic contents of amber, considering that the composition of microscopic inclusions depends on the sedimentation environment and it can be used to determine similarities and differences between amber samples and correlate them with amber beds. Results of analyses on amber samples from several world regions and a group of archaeological samples from Chiapas, Mexico, are presented. Amber from different regions have specific inorganic elemental contents; archaeological samples can be associated with beds, even if they have the same paleobotanic origin. (Author)

  4. The molecular composition of ambers

    Science.gov (United States)

    Grimalt, J.O.; Simoneit, B.R.T.; Hatcher, P.G.; Nissenbaum, A.

    1988-01-01

    Bulk (elemental composition, IR, CP/MAS 13C NMR) and molecular (GC-MS) analyses have been performed on a series of ambers and resins derived from different locations (Dominican Republic, Philippines, Canada, Israel, New Zealand, Chile) having diverse botanical affinities (Araucariaceae, Hymenaea) and variable age (from Holocene to Early Cretaceous). No major differences have been observed from the elemental composition and the spectroscopic data; however, the molecular analyses of the solvent extractable fraction show that a specific mixture of components is present in each sample. These are mainly diterpenoid products that in general are also found abundantly in the higher plants from which the ambers and resins originate. Nevertheless, a direct relationship between major terpenoid constituents in fossil resins and precursor plant materials can only be established for the younger samples. Irrespective of the geographical or botanical origin of the ambers and resins, several common age-dependent molecular transformation trends can be recognized: (1) progressive loss of olefinic bonds (especially those located in exocyclic positions), (2) decrease of functionalized products, and (3) increasing proportion of aromatized components. However, even in the samples of older age (Cretaceous) the degree of aromatization is very low when compared with that of other higher-plant related materials such as fossilized woods or low rank coals. This indicates that maturation must involve essentially olefin polymerization processes instead of extensive aromatization. ?? 1988.

  5. Comparing amber fossil assemblages across the Cenozoic.

    Science.gov (United States)

    Penney, David; Langan, A Mark

    2006-06-22

    To justify faunistic comparisons of ambers that differ botanically, geographically and by age, we need to determine that resins sampled uniformly. Our pluralistic approach, analysing size distributions of 671 fossilized spider species from different behavioural guilds, demonstrates that ecological information about the communities of two well-studied ambers is retained. Several lines of evidence show that greater structural complexity of Baltic compared to Dominican amber trees explains the presence of larger web-spinners. No size differences occur in active hunters. Consequently, we demonstrate for the first time that resins were trapping organisms uniformly and that comparisons of amber palaeoecosystem structure across deep time are possible.

  6. The identity of Romanian amber (rumanite) with Baltic amber (succinite).

    Energy Technology Data Exchange (ETDEWEB)

    Stout, E. C.; Beck, C. W.; Anderson, K. B.; Chemistry; Vassar Coll.

    2000-11-01

    Romanian amber (rumanite) has been considered to be a separate species of fossil resin for more than a century. While earlier investigators held it to be very similar to succinite (Baltic amber), modern scholars have assigned it a distinctly different botanical origin. We have found that almost all of the constituents of the ether-soluble fractions of 13 specimens of authentic rumanite identified by gas chromatography-mass spectrometry have previously been reported in the soluble fraction of succinite, including succinic acid and its monoterpene esters. Additionally and significantly, the soluble fraction of rumanite contains a number defunctionalized compounds that do not preexist in succinite, but that are produced by pyrolysis of whole succinite or of its insoluble polymeric fraction. Simultaneous methylation pyrolysis-gas chromatography-mass spectrometry of the polymeric fraction of seven of the rumanite specimens yielded further copious amounts of dimethyl succinate, a number of diterpene resin acid methyl esters, and additional defunctionalized compounds known to be pyrolysis products of succinite. The evidence shows conclusively that the botanical origin of rumanite is not distinct from that of succinite. Rather, rumanite is a succinite that has suffered partial thermal degradation in the course of the folding of the Oligocene Kliwa sandstone formation in which it is most commonly found.

  7. Technology for melting amber chips to produce a solid block

    Science.gov (United States)

    Vikhareva, A. S.; Melnikov, A. G.; Utyev, O. M.

    2016-04-01

    This research is relevant, because the bulk of the mined amber comes in amber chips. Therefore, we have decided to review the current ways of melting amber chips to develop the most technologically efficient algorithm and to use it further for producing decorative items. The purpose of the work is to perfect the technology of obtaining whole-piece amber from amber chips and to explore the usability of the obtained material in decorative items and jewelry.

  8. NEW POSSIBILITY FOR THE USE OF PLASMA DISCHARGES TO IDENTIFY AMBER AND CHANGES IN AMBER STRUCTURE

    Directory of Open Access Journals (Sweden)

    Sebastian Gnapowski

    2012-12-01

    Full Text Available Pulsed power discharge applied in air to the amber surface was found to cause improvement in its appearance and color changes such as to red, a color not natural to amber but attractive for jewelry. Needle and plate electrodes were used during experiments. Pulsed power discharges in air particularly turned amber red at the edges and around the needle electrode. Discharges in water did not change amber structure because discharge occurring on the surface does not cross the amber structure. Discharges in silicone oil had a different effect, with most discharge passing through the amber structure, causing fine cracks. Unfortunately, the absence of a consistent amber structure causes difficulty in selecting the correct discharge (shock wave power. Using new technology, we have changed the appearance a very old material-amber (about 40 – 60 million years old – to make it more attractive for customers; this technology is also useful for detecting artificial amber (costume jewellery without causing damage to the product.

  9. Fossil harvestmen (Arachnida, Opiliones from Bitterfeld amber

    Directory of Open Access Journals (Sweden)

    Jason Dunlop

    2009-07-01

    Full Text Available Fossil harvestmen (Arachnida: Opiliones: Dyspnoi and Eupnoi are described from Bitterfeld amber, Sachsen-Anhalt, Germany deposited in the Museum für Naturkunde, Berlin. The exact age of this amber has been in dispute, but recent work suggests it is youngest Palaeogene (Oligocene: Chattian. Histricostoma tuberculatum (Koch & Berendt, 1854, Caddo dentipalpus (Koch & Berendt, 1854, Dicranopalpus ramiger (Koch & Berendt, 1854 and Leiobunum longipes Menge, 1854 – all of which are also known from Eocene Baltic amber – are reported from Bitterfeld amber for the first time. They support the idea that both ambers sampled a similar terrestrial arthropod fauna: irrespective of any difference in age. Mitostoma gruberi sp. n. and Amilenus deltshevi sp. n. are described as new. One fossil is, in our opinion, morphologically indistinguishable from the extant species Lacinius erinaceus Staręga, 1966 from the Caucuses, and is tentatively assigned to this taxon. The Bitterfeld material thus includes the first fossil record of the extant genera Amilenus Martens, 1969 and Lacinius Thorell, 1876 respectively.

  10. Miocene amber inclusions from the Bitterfeld area. [German Democratic Republic

    Energy Technology Data Exchange (ETDEWEB)

    Barthel, M.; Hetzer, H.

    1982-07-01

    This paper presents color and black and white photographs enlarged from 1:10 to 1:100 of insect inclusions in amber from a new amber field located in a sandy-silty layer between two brown coal seams, the main Bitterfeld brown coal seam and the Breitenfeld brown coal seam. The amber is 22 million years old, which is 12 million years younger than Baltic amber. The brown coal seams are Miocene formations. The origin of the amber is resin from the Mesozoic conifer Cupressospermum saxonicum Mai. Insect inclusions are well preserved, 55 photographs are provided, showing samples of mosquitoes, spiders, beetles, flies and other insects, from insect groups Arachnida, Myriapoda, and Hexapoda. Each insect sample from the inclusions is described in detail by scientists from the Museum of Natural History in Berlin. Infrared spectrograms of different amber pieces are also analyzed and aspects of amber genesis in the Bitterfeld area are discussed.

  11. Putative ancient microorganisms from amber nuggets.

    Science.gov (United States)

    Veiga-Crespo, Patricia; Blasco, Lucía; Poza, Margarita; Villa, Tomás G

    2007-06-01

    Evolutionary microbiology studies based on the isolation of ancient DNA and/or microbial samples are scarce due to the difficulty of finding well preserved biological specimens. However, amber is a fossil resin with natural preserving properties for microbial cells and DNA. The visualization by transmission electron microscopy of different microorganism-like specimens found in amber nuggets from both the Miocene and the Cretaceous periods was accompanied by studies of ancient DNA obtained from the nuggets. After the design of specific primers based on the present sequences of both genes in Saccharomyces cerevisiae, the ancestral AGP2 sequence from the Miocene, as well as the 18S rRNA from the Cretaceous, were amplified.

  12. Penis morphology in a Burmese amber harvestman

    Science.gov (United States)

    Dunlop, Jason A.; Selden, Paul A.; Giribet, Gonzalo

    2016-02-01

    A unique specimen of the fossil harvestman Halitherses grimaldii Giribet and Dunlop, 2005 (Arachnida: Opiliones) from the Cretaceous (ca. 99 Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in H. grimaldii appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which H. grimaldii was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that H. grimaldii represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.

  13. Evidence concerning oxidation as a surface reaction in Baltic amber

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2012-01-01

    The aim of this study was to provide evidence about oxidation as a surface reaction during degradation of Baltic amber. A clear understanding of the amber-oxygen interaction modalities is essential to develop conservation techniques for museum collections of amber objects. Pellet-shaped samples......, obtained from pressed amber powder, were subjected to accelerated thermal ageing. Cross-sections of the pellets were analyzed by infrared micro-spectroscopy, in order to identify and quantify changes in chemical properties. The experimental results showed strong oxidation exclusively at the exterior part...

  14. OHANA, the AMBER/VLTI Snapshot Survey

    Science.gov (United States)

    Rivinius, T.; de Wit, W.; Demers, Z.; Quirrenbach, A.; VLTI Science Operations Team

    2016-11-01

    We report on the OHANA interferometric snapshot survey, carried out by the VLTI group at the Paranal observatory. It makes use of observing time not useful for any other scheduled scientific or technical tasks in the sense of a backup programme, to characterize the mass-loss for early-type stars. The survey employs the combination of AMBER's high spectral and spatial resolution. The spatially unresolved central object provides a reference frame for the fringe properties observed in the light of the continuum.

  15. OHANA, the AMBER/VLTI Snapshot Survey

    CERN Document Server

    Rivinius, Th; Demers, Z; Quirrenbach, A

    2016-01-01

    We report on the OHANA interferometric snapshot survey, carried out by the VLTI group at the Paranal observatory. It makes use of observing time not useful for any other scheduled scientific or technical tasks in the sense of a backup programme, to characterize the mass-loss for early-type stars. The survey employs the combination of AMBER's high spectral and spatial resolution. The spatially unresolved central object provides a reference frame for the fringe properties observed in the light of the continuum.

  16. AMBER: Uma linguagem para o desenvolvimento de sistemas distribuidos

    NARCIS (Netherlands)

    Ferreira Pires, L.; Guareis de Farias, C.R.; Farines, J.M.; Westphall, C.

    2001-01-01

    This paper presents the architectural model AMBER for the design of distributed systems developed at the University of Twente. This model allows the specification of distributed systems in terms of structures of functional entities and their corresponding behaviour. AMBER was originally developed to

  17. Characterization of an amber suppressor in Pneumococcus.

    Science.gov (United States)

    Gasc, A M; Vacher, J; Buckingham, R; Sicard, A M

    1979-01-01

    Partial revertant has been isolated, with resistance to aminopterin intermediate between wild type and mutant. This phenotype is the result of a mutation at a gene unlinked to the amiA locus. This suppressor mutation (su+) has no phenotypic characteristics by itself except a slow growth. 9 amiA mutants (belonging to 6 sites) are affected by su+ out of the 30 investigated mutants (i.e. 22 sites). The efficiency of suppression is site dependent. Two sites out of 14 mutants belonging to the thymidylate synthetase gene are suppressible. Thymidylate synthetase activity is partially restored by su+. Optochin mutants can also be suppressed. Thus su+ is not gene specific but site specific. Moreover when the str-41 allele conferring resistance to streptomycin is introduced by transformation, the suppression effect is restricted. All these properties are characteristic of an informational suppressor. The t-RNA extracted from the suppressor strain su+ but not the wild type restored the synthesis of coat protein coded by RNA from an amber mutant of bacteriophage f2. Attempts to detect ochre suppression activity gave negative results. It is suggested that the su+ gene is amber specific. Thus su+ can provide insight into the nature of suppressible mutations which should be point mutations. Both low efficiency and high efficiency mutants are affected by su+; this is additional evidence that both categories contain point mutations.

  18. Tropical and Holarctic Ants in Late Eocene Ambers

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2016-04-01

    Full Text Available Based on representative collections, the ratio of tropical and Holarctic ant species in Priabonian (Late Eocene Baltic, Bitterfeld (Saxonian, Danish and Rovno ambers is analyzed for the first time. In surveyed representative collections of Baltic amber, the ratios of Holarctic and tropical ant species are from 1.1 to 1.5; with 10 Holarctic and 9 tropical species (out of 31 in the PIN-964 collection, and 9 and 5 species (out of 29 in the Giecewicz collection; the ratio in the representative collection of Saxonian amber is 0.9, 11 Holarctic species vs. 12 tropical species (out of 55; in the representative collection of Rovno amber it is 0.65, 15 vs. 23 species (out of 79; and in the representative collection of Danish amber it is 0.64, 7 vs. 11 species (out of 36. Hence, in representative collections of Baltic amber, Holarctic species clearly prevail not just in terms of the share of their specimens (by 9.8 to 19.6 times, but also by the number of species. In Bitterfeld amber, Holarctic species are somewhat less numerous than tropical ones, but their specimens are 6 times greater. In representative collections of Rovno and Danish ambers, the number of Holarctic species is 1.5 to 1.7 times smaller than that of tropical species, but the number of their specimens is 4.9 to 6.9 times greater. The numbers of tropical and Holarctic species represented by more than one specimen is similar in Priabonian ambers, 25 versus 22, but Holarctic species include four dominants or subdominants. The abundance of temperate elements in the Priabonian amber ant fauna along with the relatively small number of tropical elements greatly distinguishes it from the Middle European Lutetian ant faunas of Messel and Eckfeld in shale, which do not have temperate elements at all. Formica phaethusa Wheeler, Glaphyromyrmex oligocenicus Wheeler, Plagiolepis squamifera Mayr, Proceratium eocenicum Dlussky, Hypoponera atavia (Mayr, Ponera lobulifera Dlussky, Aphaenogaster mersa

  19. An enigmatic spiny harvestman from Baltic amber

    Directory of Open Access Journals (Sweden)

    J. A. Dunlop

    2012-08-01

    Full Text Available A new harvestman (Arachnida: Opiliones from Baltic amber (Palaeogene: Eocene; ca. 44–49 Ma is described as Piankhi steineri n. gen., n. sp. This enigmatic fossil expresses long, slender pedipalps without a tarsal claw, which is characteristic for the suborder Dyspnoi. The chelicerae are notably enlarged and the dorsal body surface is formed from a carapace with a separate prosomatic tergite (metapeltidium, plus a large opisthosomal scute (or scutum parvum. However these characters, combined with the distinctly spiny limbs and further rows of spines across the fossil's opisthosoma, have no parallel among the modern dyspnoid harvestmen that we are aware of. The fossil resolves features reminiscent of modern members of the dyspnoid families Ceratolasmatidae, Nipponopsalididae, Ischyropsalididae and Sabaconidae, but does not show unequivocal apomorphies of any one particular family. We must entertain the possibility that this is an extinct body plan from the Eocene of north-central Europe, and we tentatively refer the fossil to a new genus in an unresolved position among the Ischyropsalidoidea (Dyspnoi. An amorphous triangular structure behind the anal region is assumed to be faecal matter, rather than part of the original anatomy. doi:10.1002/mmng.201200007

  20. Identification of rumanite (Romanian amber) as thermally altered succinite (Baltic amber)

    Science.gov (United States)

    Stout, E. C.; Beck, C. W.; Anderson, K. B.

    Romanian amber (rumanite) has been considered to be a separate species of fossil resin for more than a century. While earlier investigators held it to be very similar to succinite (Baltic amber), modern scholars have assigned it a distinctly different botanical origin. We have found that almost all of the constituents of the ether-soluble fractions of 13 specimens of authentic rumanite identified by gas chromatography-mass spectrometry have previously been reported in the soluble fraction of succinite, including succinic acid and its monoterpene esters. Additionally and significantly, the soluble fraction of rumanite contains a number defunctionalized compounds that do not preexist in succinite, but that are produced by pyrolysis of whole succinite or of its insoluble polymeric fraction. Simultaneous methylation pyrolysis-gas chromatography-mass spectrometry of the polymeric fraction of seven of the rumanite specimens yielded further copious amounts of dimethyl succinate, a number of diterpene resin acid methyl esters, and additional defunctionalized compounds known to be pyrolysis products of succinite. The evidence shows conclusively that the botanical origin of rumanite is not distinct from that of succinite. Rather, rumanite is a succinite that has suffered partial thermal degradation in the course of the folding of the Oligocene Kliwa sandstone formation in which it is most commonly found.

  1. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber

    Science.gov (United States)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan C.; Alonso, Jesús; Ascaso, Carmen

    2009-05-01

    Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.

  2. First Psocodean (Psocodea,Empheriidae) from the Cretaceous Amber of New Jersey

    Institute of Scientific and Technical Information of China (English)

    Dany AZAR; André NEL; Julian F.PETRULEVI(C)IUS

    2010-01-01

    Representatives of the extinct psocid family Empheriidae are known from Eocene Baltic amber,Lowermost Eocene French amber (Oise),and Lower Cretaceous Spanish amber (Alava).We report herein the first discovery of an empheriid psocid from the Cretaceous amber of New Jersey as Jerseyempheria grimaldii gen.et sp.nov.The fossil is figured and described.The new species is distinguished from related taxa.A discussion and checklist of Empheriidae are provided.

  3. Optical configuration and analysis of the AMBER/VLTI instrument

    CERN Document Server

    Robbe-Dubois, S; Petrov, R G; Lisi, F; Beckmann, U; Antonelli, P; Bresson, Y; Martinot-Lagarde, G; Roussel, A; Salinari, P; Vannier, M; Chelli, A; Dugué, M; Duvert, G; Gennari, S; Gluck, L; Kern, P; LeCoarer, E; Malbet, F; Millour, F; Perraut, K; Puget, P; Rantakyro, F; Tatulli, E; Weigelt, G; Zins, G

    2008-01-01

    This paper describes the design goals and engineering efforts that led to the realization of AMBER (Astronomical Multi BEam combineR) and to the achievement of its present performance. On the basis of the general instrumental concept, AMBER was decomposed into modules whose functions and detailed characteristics are given. Emphasis is put on the spatial filtering system, a key element of the instrument. We established a budget for transmission and contrast degradation through the different modules, and made the detailed optical design. The latter confirmed the overall performance of the instrument and defined the exact implementation of the AMBER optics. The performance was assessed with laboratory measurements and commissionings at the VLTI, in terms of spectral coverage and resolution, instrumental contrast higher than 0.80, minimum magnitude of 11 in K, absolute visibility accuracy of 1%, and differential phase stability of 1E-3 rad over one minute.

  4. IOT Overview: Calibrations of the VLTI Instruments (MIDI and AMBER)

    Science.gov (United States)

    Morel, S.; Rantakyrö, F.; Rivinius, T.; Stefl, S.; Hummel, C.; Brillant, S.; Schöller, M.; Percheron, I.; Wittkowski, M.; Richichi, A.; Ballester, P.

    We present here a short review of the calibration processes that are currently applied to the instruments AMBER and MIDI of the VLTI (Very Large Telescope Interferometer) at Paranal. We first introduce the general principles to calibrate the raw data (the "visibilities") that have been measured by long-baseline optical interferometry. Then, we focus on the specific case of the scientific operation of the VLTI instruments. We explain the criteria that have been used to select calibrator stars for the observations with the VLTI instruments, as well as the routine internal calibration techniques. Among these techniques, the "P2VM" (Pixel-to-Visibility Matrix) in the case of AMBER is explained. Also, the daily monitoring of AMBER and MIDI, that has recently been implemented, is shortly introduced.

  5. Amber Trust on ostmas Tallinna Külmhoone emafirmat / Liis Kängsepp

    Index Scriptorium Estoniae

    Kängsepp, Liis, 1981-

    2005-01-01

    Skandinaavia-USA investeerimisfond Amber Trust loodab enne aasta lõppu allkirjastada Tallinna Külmhoone emafirma Kauno Pieno Centras ostulepingu. Diagramm: Tallinna Külmhoone majandusnäitajad. Vt. samas: Amber Trust tahab investeerida üle 2 miljardi krooni; Amber laiendas tegevust Vetteli kaudu Soome

  6. Identification of Carboniferous (320 million years old) class Ic amber.

    Science.gov (United States)

    Bray, P Sargent; Anderson, Ken B

    2009-10-02

    The presence of amber, the fossil form of the resins produced by many types of higher plants, has been reported from many localities in Mesozoic and Cenozoic rocks. We have found Class I (polylabdanoid) amber in Carboniferous sediments dating to approximately 320 million years ago. This result demonstrates that preconifer gymnosperms evolved the biosynthetic mechanisms to produce complex polyterpenoid resins earlier than previously believed and that the biosynthetic pathways leading to the types of polylabdanoid resins that are now typically found in conifers and those now typically found in angiosperms had already diverged by the Carboniferous.

  7. Chemotaxonomical aspects of lower Cretaceous amber from Reconcavo Basin, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Ricardo; Azevedo, Debora A., E-mail: ricardopereira@iq.ufrj.b, E-mail: debora@iq.ufrj.b [Universidade Federal do Rio de Janeiro (IQ/UFRJ), RJ (Brazil). Inst. de Quimica; Carvalho, Ismar S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Geociencias; Fernandes, Antonio Carlos S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Museu Nacional. Dept. de Geologia e Paleontologia

    2011-07-01

    The chemical composition of Lower Cretaceous amber samples from Reconcavo Basin (Salvador, Bahia) was performed by GC-MS to characterize possible botanical sources. The compounds identified were hydrocarbonic and polar diterpenoids, such as abietane, dehydroabietane, tetrahydroretene, dehydroabietol, dehydroabietic acid, ferruginol and sugiol. Other diterpenoid classes were not detected as well as triterpenoids. The composition of the extracts and chemosystematic data allows relating the samples to conifers of Podocarpaceae or Cheirolepidiaceae families due to detection of ferruginol, a specific biomarker to these families. The data concerning Cretaceous amber in the Reconcavo Basin provided information concerning the presence of a resinous flora in the Maracangalha Formation sediments during the Lower Cretaceous. (author)

  8. Community Structure in the Amber Forest: Study of the Arthropod Syninclusia in the Rovno Amber(Late Eocene of Ukraine)

    Institute of Scientific and Technical Information of China (English)

    Evgeny E.PERKOVSKY; Alexandr P.RASNITSYN; Anatoly P.VLASKIN; Sergej P.RASNITSYN

    2010-01-01

    Arthropodan syninclusions in the Late Eocene Rovno amber were examined using x2 to reveal correlation of the component groups(some taxa of Diptera,ants,aphids,and mites)supposedly indicative of the biocoenotic relationships in the ancient amber forest.Three tightly correlated groups were identified,representing a putative aerial plankton guild(Chironomidae+Ceratopogonidae)and two tree-trunk guilds,one of which(Dolichopodidae+Germaraphis)is possibly connected to more open or/and more hygrophilous habitats than the other(Sciara zone Diptera+"Acarus"rhombeus).The ants were not linked with any of the above components.

  9. Structural changes in amber due to uranium mineralization.

    Science.gov (United States)

    Havelcová, Martina; Machovič, Vladimír; Mizera, Jiří; Sýkorová, Ivana; René, Miloš; Borecká, Lenka; Lapčák, Ladislav; Bičáková, Olga; Janeček, Oldřich; Dvořák, Zdeněk

    2016-07-01

    The presence of uranium, with a bulk mass fraction of about 1.5 wt% and radiolytic alterations are a feature of Cenomanian amber from Křižany, at the northeastern edge of the North Bohemian Cretaceous uranium ore district. Pores and microcracks in the amber were filled with a mineral admixture, mainly in the form of Zr-Y-REE enriched uraninite. As a result of radiolytic alterations due to the presence of uranium, structural changes were observed in the Křižany amber in comparison with a reference amber from Nové Strašecí in central Bohemia; this was of similar age and botanical origin but did not contain elevated levels of uranium. Structural changes involved an increase in aromaticity due to dehydroaromatization of aliphatic cyclic hydrocarbons, loss of oxygen functional groups, an increase in the degree of polymerization, crosslinking of CC bonds, formation of a three-dimensional hydrocarbon network in the bulk organic matrix, and carbonization of the organic matrix around the uraninite infill.

  10. Review of the El Soplao Amber Outcrop,Early Cretaceous of Cantabria,Spain

    Institute of Scientific and Technical Information of China (English)

    María NAJARRO; Francisco VELASCO; Fernando TORNOS; Véronique DAVIERO-GOMEZ; Bernard GOMEZ; Xavier DELCL(O)S; Enrique PE(N)ALVER; Ricardo P(E)REZ-DE LA FUENTE; Jaime ORTEGA-BLANCO; Cesar MENOR-SALV(A)N; Eduardo BARR(O)N; Carmen SORIANO; Idoia ROSALES; Rafael L(O)PEZ DEL VALLE

    2010-01-01

    El Soplao outcrop,an Early Cretaceous amber deposit recently discovered in northern Spain(Cantabria),has been shown to be the largest site of amber with arthropod inclusions that has been found in Spain so far.Relevant data provided herein for biogeochemistry of the amber,palynology,taphonomy and arthropod bioinclusious complement those previously published.This set of data suggests at least two botanical sources for the amber of El Soplao deposit.The first(type A amber)strongly supports a source related to Cheirolepidiaceae,and the second(type B amber)shows non-specific conifer biomarkers.Comparison of molecular composition of type A amber with Frenelopsis leaves(Cheicolepidiaceae)strongly suggests a biochemical affinity and a common botanical origin.A preliminary palynologlcal study indicates a regional high taxonomical diversity,mainly of pteridophyte spores and gymnosperm pollen grains.According to the preliminary palynological data,the region was inhabited by conifer forests adapted to a dry season under a subtropical climate.The abundant charcoalified wood associated with the amber in the same beds is evidence of paleofires that most likely promoted both the resin production and an intensive erosion of the litter,and subsequent great accumulation of amber plus plant cuticles.In addition,for the first time in the fossil record,charcoalified plant fibers as bioinclusious in amber are reported.Other relevant taphonomic data are the exceptional presence of serpulids and bryozoans on the surfaces of some amber pieces indicating both a long exposure on marine or brackish-water and a mixed assemblage of amber.Lastly,new findings of insect bioinclusions,some of them uncommon in the fossil record or showing remarkable adaptations,are reported.In conclusion,a documented scenario for the origin of the El Soplao amber outcrop is provided.

  11. Webspinners in Early Eocene amber from western India (Insecta, Embiodea

    Directory of Open Access Journals (Sweden)

    Michael Engel

    2011-11-01

    Full Text Available The family Scelembiidae (Neoembiodea: Embiomorpha: Archembioidea is recorded from Asia for the first time, based on two individuals preserved in Early Eocene amber from the Cambay Basin, western India. Kumarembia hurleyi Engel & Grimaldi, gen. n. et sp. n., is described, figured, and distinguished from other archembioid genera. The genus shares male genitalic features with scelembiids, otherwise known from South America and Africa.

  12. Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber

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    Alonso Jesús

    2009-02-01

    Full Text Available Abstract Background Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Pyritization is the most important and extensive mode of preservation of animals and especially of plants. Entrapping in amber, a fossilized resin, is considered an alternative mode of biological preservation. For the first time, the internal organization of 114-million-year-old microfossils entrapped in Lower Cretaceous amber is described and analyzed, using adapted scanning electron microscopy in backscattered electron mode in association with energy dispersive X-ray spectroscopy microanalysis. Double fossilization of several protists included in diverse taxonomical groups and some vegetal debris is described and analyzed. Results In protists without an exoskeleton or shell (ciliates, naked amoebae, flagellates, determinate structures, including the nuclei, surface envelopes (cortex or cytoplasmic membrane and hyaloplasm are the main sites of pyritization. In protists with a biomineralized skeleton (diatoms, silicon was replaced by pyrite. Permineralization was the main mode of pyritization. Framboidal, subhedral and microcrystalline are the predominant pyrite textures detected in the cells. Abundant pyritized vegetal debris have also been found inside the amber nuggets and the surrounding sediments. This vegetal debris usually contained numerous pyrite framboids and very densely packed polycrystalline pyrite formations infilled with different elements of the secondary xylem. Conclusion Embedding in amber and pyritization are not always alternative modes of biological preservation during geological times, but double fossilization is possible under certain environmental conditions. Pyritization in protists shows a quite different pattern with regard to plants, due to the different composition and cellular architecture in these microorganisms and organisms. Anaerobic sulphate

  13. Seeking carotenoid pigments in amber-preserved fossil feathers

    Science.gov (United States)

    Thomas, Daniel B.; Nascimbene, Paul C.; Dove, Carla J.; Grimaldi, David A.; James, Helen F.

    2014-06-01

    Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

  14. UPPER TRIASSIC AMBER FROM THE DOLOMITES (NORTHERN ITALY.A PALEOCLIMATIC INDICATOR?

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    PIERO GIANOLLA

    1998-11-01

    Full Text Available Amber in Triassic deposits in the Dolomites is demonstrated for the first time. The amber-bearing deposits belong to the middle part of the Dürrenstein Formation, referred to uppermost Julian (Lower Carnian, about 225 My. Chemico-physical features of amber, which occurs as small yellow to reddish droplets, have been determined. Infrared (IR spectroscopy shows typical bands of fossil resins; the "fingerprint" region of the spectrum presents a unique pattern that cannot be referred to any other known fossil resin. Palynological investigation of amber-bearing layers shows a large prevalence of bisaccates and circumpolles. Particularly, the taeniate bisaccates are frequent (41% and suggest a correlation with the amber-producing species. Amber production and preservation is possibly related to a humid climatic event. 

  15. New records and species of Crepidodera Chevrolat (Coleoptera: Chrysomelidae) in Eocene European amber, with a brief review of described fossil beetles from Bitterfeld amber.

    Science.gov (United States)

    Bukejs, Andris; Biondi, Maurizio; Alekseev, Vitalii I

    2016-11-15

    Based on six relatively well-preserved specimens from Eocene Baltic amber, Crepidodera tertiotertiaria sp. nov. is described. The new species is illustrated and compared with morphologically similar extant and fossil relatives. It is the third described fossil species of Crepidodera Chevrolat. In addition to the new taxon, new fossil records of C. decolorata Nadein & Perkovsky from Baltic and Bitterfeld amber are presented. A key to species of Crepidodera described from fossil resins is provided, and a checklist of Coleoptera described from Bitterfeld amber is compiled.

  16. Blue ghosts: a new method for isolating amber mutants defective in essential genes of Escherichia coli

    DEFF Research Database (Denmark)

    Brown, S; Brickman, E R; Beckwith, J

    1981-01-01

    We describe a technique which permits an easy screening for amber mutants defective in essential genes of Escherichia coli. Using this approach, we have isolated three amber mutants defective in the rho gene. An extension of the technique allows the detection of ochre mutants and transposon inser...

  17. A New Species Of Globicornis (Hadrotoma (Coleoptera, Dermestidae, Megatominae From Baltic Amber

    Directory of Open Access Journals (Sweden)

    Háva J.

    2015-08-01

    Full Text Available The species Globicornis (Hadrotoma ingelehmannae sp. n. from Baltic amber is described, illustrated and compared with all known amber species of Globicornis Latreille, 1829. New species differs by the shape of antennae and black setation on dorsal and ventral surfaces.

  18. New Records Of The Dipteran Genera Triphleba (Phoridae And Prosphyracephala (Diopsidae In Rovno And Baltic Ambers

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2015-06-01

    Full Text Available Dipteran insects constitute 51 % among arthropods of the Rovno Amber. There are 99 species and 23 genera of the Diptera described from the Rovno Amber; however, to date only 32 species are shared with the Baltic Amber fauna, including two species that are treated in this paper. Triphleba schulmanae Brown, 2003 (Phoridae, originally described from the Baltic Amber, is recorded in the Rovno Amber for the first time and its amended description is supplied. Genus Prosphyracephala Hennig, 1965 (Diopsidae, earlier known from the Baltic and Saxonian ambers, the Upper Eocene of Ruby River (Montana, USA and the Lower Oligocene of Céreste (France, is recorded in the Rovno Amber for the first time. Prosphyracephala aff. succini (Loew, 1873 is the first diopsid record from Ukraine. A second specimen of Prosphyracephala kerneggeri Kotrba, 2009 is found in the Baltic amber; the complete wing venation is described for the first time for this species. Vast majority of the Old World Diopsidae are strictly thermophilous. In fact, all of them but the five species of brevicornis group of Sphyracephala Say (three Palearctic and two Nearctic ones frequent tropic and the warmest subtropic areas, however the thermophilous Diopsidae are known in the New World neither in past nor in contemporary fauna.

  19. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa.

    Science.gov (United States)

    Grimaldi, David A; Arillo, Antonio; Cumming, Jeffrey M; Hauser, Martin

    2011-01-01

    Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. etsp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa significantly

  20. New and revised maimetshid wasps from Cretaceous ambers (Hymenoptera, Maimetshidae

    Directory of Open Access Journals (Sweden)

    Vincent Perrichot

    2011-09-01

    Full Text Available New material of the wasp family Maimetshidae (Apocrita is presented from four Cretaceous amber deposits – the Neocomian of Lebanon, the Early Albian of Spain, the latest Albian/earliest Cenomanian of France, and the Campanian of Canada. The new record from Canadian Cretaceous amber extends the temporal and paleogeographical range of the family. New material from France is assignable to Guyotemaimetsha enigmatica Perrichot et al. including the first females for the species, while a series of males and females from Spain are described and figured as Iberomaimetsha Ortega-Blanco, Perrichot, and Engel gen. n., with the two new species Iberomaimetsha rasnitsyni Ortega-Blanco, Perrichot, and Engel sp. n. and I. nihtmara Ortega-Blanco, Delclòs, and Engel sp. n.; a single female from Lebanon is described and figured as Ahiromaimetsha najlae Perrichot, Azar, Nel, and Engel gen. et sp. n., and a single male from Canada is described and figured as Ahstemiam cellula McKellar and Engel gen. et sp. n. The taxa are compared with other maimetshids, a key to genera and species is given, and brief comments made on the family.

  1. Gold nanoparticles combined with highly expressed amber suppressor tRNA: a future antibacterial agent

    Directory of Open Access Journals (Sweden)

    Xiaoda Song

    2010-10-01

    Full Text Available "nAmber suppressor tRNA is a mutant allele coding for a tRNA, whose anticodon is altered in such a way that the suppressor tRNA inserts an amino acid at an amber codon in translation which leads to suppressing (preventing termination. And some Amber suppressor tRNA strains were found. We propose that gold nanoparticles combined with highly expressed amber suppressor tRNA which can be uptake by cells and recognized by AARS (aminoacyl tRNA synthetase will lead to the formation of C-terminally extended proteins. These proteins probably will not work properly, leading bacteria's death. Because of the difference of tRNA between prokaryotic and eukaryotic cells, even between different bacteria species, this amber suppressor tRNA is orthogonal for other species and cannot be recognized by AARS, therefore has no toxicity to other species. May it be an excellent antibacterial agent in the future? In this article we provide a screening method for the highly expressed amber suppressor tRNA using randomly bases mutation, radioactive selection, activity test in vivo, and finally linkage of the amber suppressor tRNA to gold nanoparticles.

  2. Evolutionary and paleobiological implications of Coleoptera (Insecta from Tethyan-influenced Cretaceous ambers

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    David Peris

    2016-07-01

    Full Text Available The intense study of coleopteran inclusions from Spanish (Albian in age and French (Albian–Santonian in age Cretaceous ambers, both of Laurasian origin, has revealed that the majority of samples belong to the Polyphaga suborder and, in contrast to the case of the compression fossils, only one family of Archostemata, one of Adephaga, and no Myxophaga suborders are represented. A total of 30 families from Spain and 16 families from France have been identified (with almost twice bioinclusions identified in Spain than in France; 13 of these families have their most ancient representatives within these ambers. A similar study had previously only been performed on Lebanese ambers (Barremian in age and Gondwanan in origin, recording 36 coleopteran families. Few lists of taxa were available for Myanmar (Burmese amber (early Cenomanian in age and Laurasian in origin. Coleopteran families found in Cretaceous ambers share with their modern relatives mainly saproxylic and detritivorous habits in the larval or adult stages, rather than wood-boring behavior. Fifteen of the coleopteran families occur in both the Lebanese and Spanish ambers; while only five are present in both Spanish and French. Considering the paleogeographic proximity and similarity of age of the Spanish and French ambers, the small number of taxa found in common at both areas is surprising. The ancient origin for the Lebanese and Spanish ambers, the paleogeography (including some barriers for terrestrial biota and the local paleohabitats are factors that may explain the dissimilarity with the French specimens. Wildfires are believed to be a more likely cause of resin production during the Cretaceous than infestation by beetles. Current knowledge of the beetle species found in the Cretaceous ambers is introduced.

  3. Ancient hastisetae of Cretaceous carrion beetles (Coleoptera: Dermestidae) in Myanmar amber.

    Science.gov (United States)

    Poinar, George; Poinar, Roberta

    2016-11-01

    Hastisetae are extremely elaborate and intricate insect setae that occur solely on dermestid larvae (Coleoptera: Dermestidae). The present work characterizes hastisetae found in mid-Cretaceous amber from Myanmar and compares them to hastisetae found on extant dermestid larvae. The presence of hastisetae in Myanmar amber shows that lineages of dermestid beetles had already developed hastisetae by the mid-Cretaceous and their presence allows us to follow the evolutionary development of this particular arthropod structure over the past 100 million years. Hastisetae attached to a parasitic wasp in the same piece of amber indicates that ancient dermestid beetles used their hastisetae for defense, similar to their function today.

  4. 13C Solid State Nuclear Magnetic Resonance and µ-Raman Spectroscopic Characterization of Sicilian Amber.

    Science.gov (United States)

    Barone, Germana; Capitani, Donatella; Mazzoleni, Paolo; Proietti, Noemi; Raneri, Simona; Longobardo, Ugo; Di Tullio, Valeria

    2016-08-01

    (13)C cross-polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) and µ-Raman spectroscopy were applied to characterize Sicilian amber samples. The main goal of this work was to supply a complete study of simetite, highlighting discriminating criteria useful to distinguish Sicilian amber from fossil resins from other regions and laying the foundations for building a spectroscopic database of Sicilian amber. With this aim, a private collection of unrefined simetite samples and fossil resins from the Baltic region and Dominican Republic was analyzed. Overall, the obtained spectra permitted simetite to be distinguished from the other resins. In addition, principal component analysis (PCA) was applied to the spectroscopic data, allowing the clustering of simetite samples with respect to the Baltic and Dominican samples and to group the simetite samples in two sets, depending on their maturity. Finally, the analysis of loadings allowed for a better understanding of the spectral features that mainly influenced the discriminating characteristics of the investigated ambers.

  5. Band structure and optical properties of amber studied by first principles

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Zhi-Fan, E-mail: raozhifan@163.com [Analysis and Testing Center of Yunnan, Kunming University of Science and Technology, Kunming 650093 (China); Zhou, Rong-Feng [Analysis and Testing Center of Yunnan, Kunming University of Science and Technology, Kunming 650093 (China)

    2013-03-01

    The band structure and density of states of amber is studied by the first principles calculation based on density of functional theory. The complex structure of amber has 214 atoms and the band gap is 5.0 eV. The covalent bond is combined C/O atoms with H atoms. The O 2p orbital is the biggest effect near the Fermi level. The optical properties' results show that the reflectivity is low, and the refractive index is 1.65 in visible light range. The highest absorption coefficient peak is at 172 nm and another higher peak is at 136 nm. These convince that the amber would have a pretty sheen and that amber is a good and suitable crystal for jewelry and ornaments.

  6. The range of bioinclusions and pseudoinclusions preserved in a new Turonian (~90 ma) amber occurrence from Southern Australia.

    Science.gov (United States)

    Quinney, Annie; Mays, Chris; Stilwell, Jeffrey D; Zelenitsky, Darla K; Therrien, François

    2015-01-01

    A new Turonian amber occurrence, representing the oldest in situ amber locality in Australia and the southern-most locality in Gondwana, has recently been discovered in the Otway Basin of Victoria. The amber was collected from petroleum cores and many pieces contain a range of inclusions that can provide information on the depositional history of the resin. To date, one species of fern spore (Cyathidites minor) and one species of lycophyte spore (Kraeuselisporites sp?) have been conclusively identified in the amber, along with filamentous microorganisms and degraded plant matter. Several samples are also rife with pseudoinclusions as reported recently in other ambers. The abundance of preserved particulate debris and wind dispersed spores suggest that the Otway amber formed subaerially. Furthermore, based on the range of bioinclusions and forms of pseudoinclusions preserved within a single piece of amber, the locus of hardening for individual samples is variably interpreted as occurring in the tree tops, on the tree trunk or on the ground surface. Notably, specific inclusion assemblages are associated with certain colours of amber. By extension, and in accordance with recent studies, amber colour may be indicative of depositional environment. Variation in the environment of solidification may, therefore, be sufficient to account for the broad range of morphological characteristics preserved in a single amber deposit.

  7. The range of bioinclusions and pseudoinclusions preserved in a new Turonian (~90 ma amber occurrence from Southern Australia.

    Directory of Open Access Journals (Sweden)

    Annie Quinney

    Full Text Available A new Turonian amber occurrence, representing the oldest in situ amber locality in Australia and the southern-most locality in Gondwana, has recently been discovered in the Otway Basin of Victoria. The amber was collected from petroleum cores and many pieces contain a range of inclusions that can provide information on the depositional history of the resin. To date, one species of fern spore (Cyathidites minor and one species of lycophyte spore (Kraeuselisporites sp? have been conclusively identified in the amber, along with filamentous microorganisms and degraded plant matter. Several samples are also rife with pseudoinclusions as reported recently in other ambers. The abundance of preserved particulate debris and wind dispersed spores suggest that the Otway amber formed subaerially. Furthermore, based on the range of bioinclusions and forms of pseudoinclusions preserved within a single piece of amber, the locus of hardening for individual samples is variably interpreted as occurring in the tree tops, on the tree trunk or on the ground surface. Notably, specific inclusion assemblages are associated with certain colours of amber. By extension, and in accordance with recent studies, amber colour may be indicative of depositional environment. Variation in the environment of solidification may, therefore, be sufficient to account for the broad range of morphological characteristics preserved in a single amber deposit.

  8. First Record of Anisoptera (Insecta: Odonata) from mid-Cretaceous Burmese Amber.

    Science.gov (United States)

    Schädel, Mario; Bechly, Günter

    2016-04-18

    The fossil dragonfly Burmalindenia imperfecta gen. et sp. nov. is described from mid-Cretaceous Burmese amber as the first record of the odonate suborder Anisoptera for this locality and one of the few records from amber in general. The inclusion comprises two fragments of the two hind wings of a dragonfly. The fossil can be attributed to a new genus and species of the family Gomphidae, presumably in the subfamily Lindeniinae, and features a strange teratological phenomenon in its wing venation.

  9. Implementation of project Safe in Amber. Verification study for SFR 1 SAR-08

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Gavin; Herben, Martin; Lloyd, Pam; Rose, Danny; Smith, Chris; Barraclough, Ian (Enviros Consulting Ltd (GB))

    2008-03-15

    This report documents an exercise in which AMBER has been used to represent the models used in Project SAFE, a safety assessment undertaken on SFR 1. (AMBER is a flexible, graphical-user-interface based tool that allows users to build their own dynamic compartmental models to represent the migration, degradation and fate of contaminants in an environmental system. AMBER allows the user to assess routine, accidental and long-term contaminant release.) AMBER has been used to undertake assessment calculations on all of the disposal system, including all disposal tunnels and the Silo, the geosphere and several biosphere modules. The near-field conceptual models were implemented with minimal changes to the approach undertaken previously in Project SAFE. Model complexity varied significantly between individual disposal facilities increasing significantly from the BLA to the BTF and BMA tunnels and Silo. Radionuclide transport through the fractured granite geosphere was approximated using a compartment model approach in AMBER. Several biosphere models were implemented in AMBER including reasonable biosphere development, which considered the evolution of the Forsmark area from coastal to lacustrine to agricultural environments in response to land uplift. Parameters were sampled from distributions and simulations were run for 1,000 realisations. In undertaking the comparison of AMBER with the various codes and calculation tools used in Project SAFE it was necessary to undertake a detailed analysis of the modelling approach previously adopted, with particular focus given to the near-field models. As a result some discrepancies in the implementation of the models and documentation were noted. The exercise demonstrates that AMBER is fully capable of representing the features of the SFR 1 disposal system in a safety assessment suitable for SAR-08

  10. Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber

    OpenAIRE

    2016-01-01

    Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic t...

  11. Youngest representative of the extinct genus Microphorites in the Eocene amber of France (Diptera: Dolichopodidae: Microphorinae).

    Science.gov (United States)

    Bramuzzo, Simone; Nel, André

    2017-02-13

    Prior to the present study, seven species of the fossil microphorine (Dolichopodidae s. lat.) genus Microphorites Hennig, 1971 have been described: Microphorites extinctus Hennig, 1971 (type species), M. oculeus Grimaldi & Cumming, 1999, and M. similis Grimaldi & Cumming, 1999 (all from the Early Cretaceous Lebanese amber), M. deploegi Nel et al., 2004 (from the Early Cretaceous of France), M. utrillensis Peñalver, 2008 (from the Early Cretaceous amber of Spain), M. magaliae Perrichot & Engel, 2014 (from the Late Cretaceous amber of France), M. moravicus Tkoč et al., 2016 (possibly from the Paleogene amber of Moravia) (Hennig 1971; Grimaldi & Cumming 1999; Nel et al. 2004; Arillo et al. 2008; Perrichot & Engel 2014; Tkoč et al. 2016). Based on the dating of these amber species, Microphorites could be among the rare insect genera recorded from both the Cretaceous and the Paleogene. Here we describe Microphorites erikai sp. nov., first accurate Eocene Microphorites from the Oise amber (France), on the basis of a complete female specimen.

  12. Game Theory Model of Traffic Participants within Amber Time at Signalized Intersection

    Directory of Open Access Journals (Sweden)

    Weiwei Qi

    2014-01-01

    Full Text Available The traffic light scheme is composed of red, green, and amber lights, and it has been defined clearly for the traffic access of red and green lights; however, the definition of that for the amber light is indistinct, which leads to the appearance of uncertainty factors and serious traffic conflicts during the amber light. At present, the traffic administrations are faced with the decision of whether to forbid passing or not during the amber light in the cities of China. On one hand, it will go against the purpose of setting amber lights if forbidding passing; on the other hand, it may lead to a mess of traffic flow running if not. And meanwhile the drivers are faced with the decision of passing the intersection or stopping during the amber light as well. So the decision-making behavior of traffic administrations and drivers can be converted into a double game model. And through quantification of their earnings in different choice conditions, the optimum decision-making plan under specific conditions could be solved via the Nash equilibrium solution concept. Thus the results will provide a basis for the formulation of the traffic management strategy.

  13. Baltic amber harvestman types (Arachnida: Opiliones: Eupnoi and Dyspnoi

    Directory of Open Access Journals (Sweden)

    J. A. Dunlop

    2006-08-01

    Full Text Available Baltic amber eupnoid and dyspnoid types (Arachnida: Opiliones in the Berendt collection are redescribed from their repository in the Museum für Naturkunde, Berlin. Type specimens of Caddo dentipalpis (Koch & Berendt, 1854, Dicranopalpus ramiger (Koch & Berendt, 1854, Nemastoma (? incertum Koch & Berendt, 1854, Mitostoma (? denticulatum (Koch & Berendt, 1854 and Histricostoma (? tuberculatum (Koch & Berendt, 1854 are all redescribed and the first photographs and camera lucida drawings of this material are presented. N.  (? incertum is removed from synonymy with M.  (? denticulatum. The status of the other Baltic amber harvestman types and their affinities are discussed. The type of Sabacon bachofeni Roewer, 1939 (= S. claviger (Menge, 1854 held in the Bavarian State collection, Munich is also redescribed here, but the repository of three other Roewer harvestman types and all of Menge’s types remains uncertain. The problematic Cheiromachus coriaceus Menge, 1854 is considered a nomen dubium, as is Phalangium succineum Presl, 1822, which may not even be a harvestman. Typenmaterial der Weberknecht-Gruppen Eupnoi und Dyspnoi (Arachnida: Opiliones vom Baltischen Bernstein aus der Berendt-Sammlung des Museums für Naturkunde Berlin wurde bearbeitet. Dabei wurde das Typusmaterial von Caddo dentipalpis (Koch & Berendt, 1854, Dicranopalpus ramiger (Koch & Berendt, 1854, Nemastoma (? incertum Koch & Berendt, 1854, Mitostoma (? denticulatum (Koch & Berendt, 1854 und Histricostoma (? tuberculatum (Koch & Berendt, 1854 revidiert und die ersten Fotografien und camera lucida-Zeichnungen dieses Materials hergestellt. N.  (? incertum wurde aus der Synonymie von M.  (? denticulatum herausgenommen. Der Status der anderen Weberknecht Typen aus dem Baltischen Bernstein und ihre Stellung werden diskutiert. Sabacon bachofeni Roewer, 1939 (= S. claviger (Menge, 1854 wird anhand des Holotypus aus der Bayerischen Staatssammlung M

  14. Eocene and not Cretaceous origin of spider wasps: Fossil evidence from amber

    Directory of Open Access Journals (Sweden)

    Juanita Rodriguez

    2016-02-01

    Full Text Available Spider wasps had long been proposed to originate in the mid-Cretaceous based on the Burmese amber fossil Bryopompilus interfector Engel and Grimaldi, 2006. We performed a morphological examination of this fossil and determined it does not belong to Pompilidae or any other described hymenopteran family. Instead, we place it in the new family Bryopompilidae. The oldest verifiable member of the Pompilidae is from Baltic amber, which suggests the family probably originated in the Eocene, not in the mid-Cretaceous as previously proposed. The origin of spider wasps appears to be correlated with an increase in spider familial diversity in the Cenozoic. We also we add two genera to the extinct pompilid fauna: Tainopompilus gen. nov., and Paleogenia gen. nov., and describe three new species of fossil spider wasps: Anoplius planeta sp. nov., from Dominican amber (Burdigalian to Langhian; Paleogenia wahisi sp. nov., from Baltic amber (Lutetian to Priabonian; and Tainopompilus argentum sp. nov, from Dominican amber (Chattian to Langhian.

  15. Deuterium isotopic exchangeability of resin and amber at low thermal stress under hydrous conditions

    Science.gov (United States)

    Gonzalez, G.; Tappert, R.; Wolfe, A. P.; Muehlenbachs, K.

    2012-04-01

    Hydrous deuterium-exchange experiments have shown that a significant fraction of the original D/H composition of bulk kerogens, bitumens and expelled oils may participate in isotopic exchange reactions during burial diagenesis. However, it is unknown to what extent plant-derived secondary metabolites, namely resins and their fossil counterpart amber, exchange hydrogen isotopes following their biosynthesis. This situation hinders the application of resin D/H measurements in paleoenvironmental reconstruction. Here, we assess explicitly hydrogen exchange in resins and ambers using a series of immersion experiments in deuterated (D-enriched) waters over a period of several months at several temperatures. We are especially interested in assessing whether significant H-isotopic exchange occurs between resins and meteoric waters during early thermal maturation and polymerization. At 90°C, equivalent to ~3km of burial in most diagenetic regimes, modern conifer and angiosperm resins have an average post-metabolic H exchange of 4.6%, compared to only 1.1% for mature, polymerized ambers. At 55°C the degree of exchange is considerably lower: 1.9% for resins and 0.6% for ambers. These results indicate that most D/H isotopic exchange occurs prior to polymerization reactions, thereby confirming that D/H measurements from amber constitute a potentially sensitive proxy for environmental change.

  16. Fossil mesostigmatid mites (Mesostigmata: Gamasina, Microgyniina, Uropodina), associated with longhorn beetles (Coleoptera: Cerambycidae) in Baltic amber

    Science.gov (United States)

    Dunlop, Jason A.; Kontschán, Jenő; Zwanzig, Michael

    2013-04-01

    Fossil mesostigmatid mites are extremely rare. Inclusions assignable to the tortoise mites (Mesostigmata, Uropodina) are described here for the first time from Eocene (ca. 44-49 Ma) Baltic amber. This is the oldest record of Uropodina and documents the first unequivocal amber examples potentially assignable to the extant genus Uroobovella Berlese, 1903 (Uropodoidea: Urodinychidae). Further mites in the same amber pieces are tentatively assigned to Microgynioidea (Microgyniina) and Ascidae (Gamasina), both potentially representing the oldest records of their respective superfamily and family groups. This new material also preserves behavioural ecology in the form of phoretic deutonymphs attached to their carriers via a characteristic anal pedicel. These deutonymphs in amber are intimately associated with longhorn beetles (Coleoptera: Cerambycidae), probably belonging to the extinct species Nothorhina granulicollis Zang, 1905. Modern uropodines have been recorded phoretic on species belonging to several beetle families, including records of living Uroobovella spp. occurring on longhorn beetles. Through these amber inclusions, a uropodine-cerambycid association can now be dated back to at least the Eocene.

  17. Coordinated AMBER and MIDI observations of the Mira variable RR Aql

    CERN Document Server

    Karovicova, Iva; Boboltz, David A; Scholz, Michael

    2008-01-01

    We have used near- and mid-infrared interferometry to investigate the pulsating atmosphere and the circumstellar environment of the Mira variable RR Aql. Observations were taken with the VLTI/AMBER (near infrared) and the VLTI/MIDI (mid infrared) instruments. We have obtained a total of 15 MIDI epochs between Apr 9, 2004 and Jul 28, 2007 covering 4 pulsation cycles and one AMBER epoch on Sep 9, 2006 at phase 2.82. This work is also part of an ongoing project of joint VLTI and VLBA observations to study the connection between stellar pulsation and the mass loss process. Here we present a comparison of the AMBER visibility data to a simple uniform disk model as well as to predictions by recent self-excited dynamic model atmospheres. The best fitting photospheric angular diameter of the model atmosphere at phase 2.82 is 9.9 +/- 2.4 mas.

  18. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator

    Science.gov (United States)

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T.; Singh, Hukam; Hammel, Jörg U.; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-10-01

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

  19. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.

    Science.gov (United States)

    Zheng, Suqing; Tang, Qing; He, Jian; Du, Shiyu; Xu, Shaofang; Wang, Chaojie; Xu, Yong; Lin, Fu

    2016-04-25

    Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.

  20. A New Species of Dactylolabis (Eobothrophorus) from Baltic Amber (Diptera:Limoniidae)

    Institute of Scientific and Technical Information of China (English)

    Wies(l)aw KRZEMINSKI; Iwona KANIA; Ewa KRZEMINSKA

    2010-01-01

    A new species,Dactylolabis (Eobothrophorus) hoffeinsorum sp.nov.from the Baltic amber is described,based on one male.The distinctive characters are the shape of the discal cell in the wing and the shape of the process on tergite Ⅸ.The description of Dactylolabis (Eobothrophorus) lauryni Podenas,2003 is amended,based on an additional specimen.With the new species added herein,the number of species of this subgenus totals four.The wing venation,antennae,and tergai processes of all four species of the subgenus described from the Baltic amber are compared.

  1. The first Aleyrodidae from the Lowermost Eocene Oise amber (Hemiptera: Sternorrhyncha).

    Science.gov (United States)

    Drohojowska, Jowita; Szwedo, Jacek

    2013-01-01

    The first records are provided of the family Aleyrodidae in the Lowermost Eocene amber of Oise, France. The following new taxa in the subfamily Aleurodicinae are described, figured and discussed, together with an identification key: Oisedicus maginus gen. et sp. n., Clodionusfizoli gen. et sp. n., Lukotekia menae gen. et sp. n. and Isaraselis cladiva gen. et sp. n. Unplaced species of Lukotekia are briefly described, and the diversity of the whiteflies from Oise amber is discussed. The importance of fossils for palaeoecological and palaeoclimatological reconstruction is briefly considered.

  2. Electrically driven green, olivine, and amber color nanopyramid light emitting diodes.

    Science.gov (United States)

    Chang, Shih-Pang; Chang, Jet-Rung; Sou, Kuok-Pan; Liu, Mei-Chun; Cheng, Yuh-Jen; Kuo, Hao-Chung; Chang, Chun-Yen

    2013-10-07

    We report the fabrication and studies of electrically driven green, olivine, and amber color nanopyramid GaN light emitting diodes (LEDs). InGaN/GaN multiple quantum wells (MQWs) were grown on the nanopyramid semipolar facets. Compared with the commonly used (0001) c-plane MQWs, the semipolar facet has lower piezoelectric field, resulting in much faster radiative recombination efficiency. This is important for high In content MQWs. The measured internal quantum efficiencies for green, olivine, and amber color LED are 30%, 25%, and 21%, respectively. The radiative and non-radiative lifetime of the semipolar MQWs are also investigated.

  3. Amber lenses to block blue light and improve sleep: a randomized trial.

    Science.gov (United States)

    Burkhart, Kimberly; Phelps, James R

    2009-12-01

    All light is not equal: blue wavelengths are the most potent portion of the visible electromagnetic spectrum for circadian regulation. Therefore, blocking blue light could create a form of physiologic darkness. Because the timing and quantity of light and darkness both affect sleep, evening use of amber lenses to block blue light might affect sleep quality. Mood is also affected by light and sleep; therefore, mood might be affected by blue light blockade. In this study, 20 adult volunteers were randomized to wear either blue-blocking (amber) or yellow-tinted (blocking ultraviolet only) safety glasses for 3 h prior to sleep. Participants completed sleep diaries during a one-week baseline assessment and two weeks' use of glasses. Outcome measures were subjective: change in overall sleep quality and positive/negative affect. Results demonstrated that sleep quality at study outset was poorer in the amber lens than the control group. Two- by three-way ANOVA revealed significant (p sleep over the three weeks and experimental condition. At the end of the study, the amber lens group experienced significant (p improvement in sleep quality relative to the control group and positive affect (p = .005). Mood also improved significantly relative to controls. A replication with more detailed data on the subjects' circadian baseline and objective outcome measures is warranted.

  4. A new genus of highly specialized ants in Cretaceous Burmese amber (Hymenoptera: Formicidae).

    Science.gov (United States)

    Barden, Phillip; Grimaldi, David

    2013-01-01

    A new genus of ants, Zigrasimecia Barden and Grimaldi, is described for a new and uniquely specialized species, Z. tonsora Barden and Grimaldi n.sp., preserved in Cretaceous amber from Myanmar. The amber is radiometrically dated at 99 myo. Zigrasimecia is closely related to another basal genus of ants known only in Burmese and French Cretaceous amber, Sphecomyrmodes Engel and Grimaldi, based in part on the shared possession of a comb of pegs on the clypeal margin, as well as mandible structure. Highly specialized features of Zigrasimecia include extensive development of the clypeal comb, a thick brush of setae on the oral surface of the mandibles and on the labrum, and a head that is broad, flattened, and which bears a crown of blackened, rugose cuticle. Mouthparts are hypothesized to have functioned in a unique manner, showing no clear signs of dentition representative of "chewing" or otherwise processing solid food. Although all ants in Burmese amber are basal, stem-group taxa, there is an unexpected diversity of mouthpart morphologies and probable feeding modes.

  5. The oldest accurate record of Scenopinidae in the Lowermost Eocene amber of France (Diptera: Brachycera).

    Science.gov (United States)

    Garrouste, Romain; Azar, Dany; Nel, Andre

    2016-03-22

    Eocenotrichia magnifica gen. et sp. nov. (Diptera: Scenopinidae: Metatrichini) is described and illustrated from the Lowermost Eocene amber of Oise (France) and represents the oldest definitive window fly fossil. The present discovery in the Earliest Eocene supports the Late Cretaceous-Paleocene age currently proposed for the emergence of Metatrichini.

  6. Cyclic terpenoids of contemporary resinous plant detritus and of fossil woods, ambers and coals

    Energy Technology Data Exchange (ETDEWEB)

    Simoneit, B.R.T.; Grimalt, J.O.; Wang, T.G.; Cox, R.E.; Hatcher, P.G.; Nissenbaum, A.

    1986-01-01

    Cyclic terpenoids present in the solvent extractable material of fossil woods, ambers and brown coals have been analyzed. The sample series chosen consisted of wood remains preserved in Holocene in Jurassic sediments and a set of ambers from the Philippines (copalite), Israel, Canada and Dominican Republic. The brown coals selected were from the Fortuna Garsdorf Mine and Miocene formations on Fiji. The fossil wood extracts contained dominant diterpenoid or sesquiterpenoid skeletons, and aromatized species were present at high concentrations, with a major amount of two-ring aromatic compounds. Tricyclic diterpenoids were the predominant compounds in the ambers. The brown coal extracts were composed of major amounts of one- and two-ring aromatized terpenoids, with a greater proportion of triterpenoid derivatives than in the case of the woods and ambers. This was especially noticeable for the German coal, where the triterpenoids were predominant. Open C-ring aromatized structures were also present in this coal. Steroid compounds were not detectable, but some hopanes were found as minor components in the German brown coal. An overview of the skeletal structure classes identified in each sample, as well as the general mass spectrometric characteristics of the unknown compounds are included in the present paper. It can be concluded from these structural distributions that aromatization is the main process for the transformation of terrestrial cyclic terpenoids during diagenesis, constituting a general pathway for all terpenoids.

  7. A New Thorny Lacewing (Insecta:Neuroptera:Rhachiberothidae) from the Early Cretaceous Amber of Lebanon

    Institute of Scientific and Technical Information of China (English)

    Julian F.PETRULEVI(C)IUS; Dany AZAR; André NEL

    2010-01-01

    A new genus and species of Rhachiberothidae,Raptorapax terribilissima gen.et sp.nov.from the Cretaceous amber of Lebanon is described.The new genus is assigned to the subfamily Paraberothinae.The new material confirms the great diversity of the group in the Cretaceous age and its decrease in diversity in recent times.

  8. A swarm of whiteflies—the first record of gregarious behavior from Eocene Baltic amber

    Science.gov (United States)

    Szwedo, Jacek; Drohojowska, Jowita

    2016-04-01

    A new whitefly Snotra christelae gen. et sp. n. is characterized, illustrated, and described from the Baltic amber. It represents the first record of gregarious behavior of Aleyrodinae (Aleyrodidae) whiteflies in fossil state. Implications of this finding on interpretation of whiteflies and their host-plant relationships and evolutionary traits of the group are discussed.

  9. Photoageing of Baltic amber-influence of daylight radiation behind window glass on surface colour and chemistry

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2011-01-01

    of environmental parameters where amber objects are stored or displayed. To investigate the photodegradation of Baltic amber, the methodology consisted of artificial ageing, in order to initiate degradation of model amber samples, and non-destructive analytical techniques, in order to identify and quantify changes...... in colour and chemical properties. Prism-shaped samples, obtained from a large amber piece, were exposed to different microclimatic conditions, subjected to accelerated photoageing and analysed by spectrocolorimetry, infrared spectroscopy and Raman spectroscopy. The experiments provided results about...... surface discolouration, oxidation of the molecular structure and breakdown of unsaturated carbon-carbon bonds in various environmental conditions, confirming the degrading role of daylight behind window glass. The conclusions of this study can be applied to the development of techniques for preventive...

  10. Solid state {sup 13}C NMR analysis of Brazilian cretaceous ambers

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Ricardo; Azevedo, Debora A., E-mail: ricardopereira@iq.ufrj.b, E-mail: debora@iq.ufrj.b [Universidade Federal do Rio de Janeiro (IQ/UFRJ), Rio de Janeiro, RJ (Brazil). Inst. de Quimica. Lab. de Geoquimica Organica Molecular e Ambiental; San Gil, Rosane A.S. [Universidade Federal do Rio de Janeiro (IQ/UFRJ), RJ (Brazil). Inst. de Quimica. Lab. de RMN de Solidos; Carvalho, Ismar S. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Geociencias. Dept. de Geologia; Fernandes, Antonio Carlos S. [Museu Nacional (MN/UFRJ), RJ (Brazil). Dept. de Geologia e Paleontologia

    2011-07-01

    {sup 13}C cross polarization with magic angle spinning nuclear magnetic resonance ({sup 13}C CPMAS NMR) spectra have been obtained for the first time to three Cretaceous amber samples from South America. The samples were dated to Lower Cretaceous and collected in sediments from the Amazonas, Araripe and Reconcavo basins, Brazil. All samples have very similar spectra, consistent with a common paleobotanical source. Some aspects of the spectra suggest a relationship between Brazilian ambers and Araucariaceae family, such as intense resonances at 38-39 ppm. All samples are constituted by polylabdane structure associated to Class Ib resins, constituted by polymers of labdanoid diterpenes. Finally, information concerning some structural changes during maturation, such as isomerization of {Delta}{sup 8(17)} and {Delta}{sup 12(13)} unsaturations, were obtained by {sup 13}C NMR analyses. The results concerning botanical affinities are in accordance with previous results obtained by gas chromatography-mass spectrometry (GC-MS). (author)

  11. Amino acid racemization in amber-entombed insects: implications for DNA preservation

    Science.gov (United States)

    Bada, J. L.; Wang, X. S.; Poinar, H. N.; Paabo, S.; Poinar, G. O.

    1994-01-01

    DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from 10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

  12. Quesnoin, a novel pentacyclic ent-diterpene from 55 million years Old Oise Amber.

    Science.gov (United States)

    Jossang, Jean; Bel-Kassaoui, Hakima; Jossang, Akino; Seuleiman, Mannan; Nel, André

    2008-01-18

    Amber, fossilized tree resin, found at the Oise River area of the Paris basin (France) was dated as being 55 million years old. Quesnoin, a novel unique pure organic compound, was isolated from Oise amber. 1H and 13C NMR spectroscopic analysis indicated an unknown diterpene skeleton, quesnane. The absolute configurations of the eight chiral centers of quesnoin were determined to be 4S, 5S, 8R, 9S, 10S, 13S, 14R, and 16S by chiral auxiliary (R)- and (S)-phenylglycine methyl ester derivatization. Quesnoin allowed us to disclose the tree producer, corresponding to modern Hymenaea oblongifolia, Fabaceae, a subfamily of Caesalpiniaceae, one of the oldest angiosperm. The presence of the Amazon rainforest tree, H. oblongifolia, indicated that the climate of the Paris basin might have been tropical in the early Eocene period, 55 million years ago.

  13. Spirochete and protist symbionts of a termite (Mastotermes electrodominicus) in Miocene amber.

    Science.gov (United States)

    Wier, Andrew; Dolan, Michael; Grimaldi, David; Guerrero, Ricardo; Wagensberg, Jorge; Margulis, Lynn

    2002-02-05

    Extraordinary preservation in amber of the Miocene termite Mastotermes electrodominicus has led to the discovery of fossil symbiotic microbes. Spirochete bacteria and wood-digesting protists were identified in the intestinal tissue of the insect. Fossil wood (xylem: developing vessel-element cells, fibers, pit connections), protists (most likely xylophagic amitochondriates), an endospore (probably of the filamentous intestinal bacterium Arthromitus = Bacillus), and large spirochetes were seen in thin section by light and transmission electron microscopy. The intestinal microbiota of the living termite Mastotermes darwiniensis, a genus now restricted to northern Australia, markedly resembles that preserved in amber. This is a direct observation of a 20-million-year-old xylophagus termite fossil microbial community.

  14. Amber light-emitting diode comprising a group III-nitride nanowire active region

    Energy Technology Data Exchange (ETDEWEB)

    Wang, George T.; Li, Qiming; Wierer, Jr., Jonathan J.; Koleske, Daniel

    2014-07-22

    A temperature stable (color and efficiency) III-nitride based amber (585 nm) light-emitting diode is based on a novel hybrid nanowire-planar structure. The arrays of GaN nanowires enable radial InGaN/GaN quantum well LED structures with high indium content and high material quality. The high efficiency and temperature stable direct yellow and red phosphor-free emitters enable high efficiency white LEDs based on the RGYB color-mixing approach.

  15. Cyclic terpenoids of contemporary resinous plant detritus and of fossil woods, ambers and coals

    Science.gov (United States)

    Simoneit, B.R.T.; Grimalt, J.O.; Wang, T.-G.; Cox, R.E.; Hatcher, P.G.; Nissenbaum, A.

    1986-01-01

    Cyclic terpenoids present in the solvent extractable material of fossil woods, ambers and brown coals have been analyzed. The sample series chosen consisted of wood remains preserved in Holocene to Jurassic sediments and a set of of ambers from the Philippines (copalite), Israel, Canada and Dominican Republic. The brown coals selected were from the Fortuna Garsdorf Mine and Miocene formations on Fiji. The fossil wood extracts contained dominant diterpenoid or sesquiterpenoid skeletons, and aromatized species were present at high concentrations, with a major amount of two-ring aromatic compounds. Tricyclic diterpenoids were the predominant compounds in the ambers. Aromatized derivatives were the major components, consisting of one or two aromatic ring species with the abietane and occasionally pimarane skeletons. The saturated structures were comprised primarily of the abietane and pimarane skeletons having from three to five carbon (C1, C2, etc.) substituents. Kaurane and phyllocladane isomers were present in only minor amounts. Bicyclic sesquiterpenoids as saturated and partial or fully aromatized forms were also common in these samples, but only traces of sesterterpenoids and triterpenoid derivatives were found. The brown coal extracts were composed of major amounts of one- and two-ring aromatized terpenoids, with a greater proportion of triterpenoid derivatives than in the case of the woods and ambers. This was especially noticeable for the German coal, where the triterpenoids were predominant. Open C-ring aromatized structures were also present in this coal. Steroid compounds were not detectable, but some hopanes were found as minor components in the German brown coal. An overview of the skeletal structure classes identified in each sample, as well as the general mass spectrometric characteristics of the unknown compounds are included in the present paper. It can be concluded from these structural distributions that aromatization is the main process for the

  16. The oldest micropepline beetle from Cretaceous Burmese amber and its phylogenetic implications (Coleoptera: Staphylinidae)

    Science.gov (United States)

    Cai, Chen-Yang; Huang, Di-Ying

    2014-10-01

    The staphylinid subfamily Micropeplinae includes small strongly sclerotized beetles with truncate elytra leaving the most part of abdomen exposed. Fossil micropeplines are rare and confined to Cenozoic representatives of extant genera. Here, we describe the oldest micropepline, Protopeplus cretaceus gen. and sp. n., from the Upper Cretaceous Burmese amber. Fluorescence microscope and confocal laser scanning microscopy (CLSM) were both used to reveal diagnostic features of Micropeplinae and some primitive traits that place Protopeplus very basally within Micropeplinae.

  17. A MODEL OF THE INNOVATIVE AMBER CLUSTER AS A CENTRE OF COOPERATION OF AUTHORITIES - BUSINESS - SCIENCE

    Directory of Open Access Journals (Sweden)

    Gleb B. Trifonov

    2015-01-01

    Full Text Available A mechanism of forming an innovative amber cluster was developed, including structural interconnections of cluster partners,a package of basic innovative technologies, which will createa new value chain, new vacancies, provide contributions to theregional budget.A method of analytical estimation was suggested to assess cluster synergism of partners: authorities, business, science/education, culture, which reflects potential possibilities of thecluster model of region development.

  18. Microplastics in sea coastal zone: Lessons learned from the Baltic amber.

    Science.gov (United States)

    Chubarenko, Irina; Stepanova, Natalia

    2017-05-01

    Baltic amber, adored for its beauty already in Homer's Odyssey (ca. 800 B.C.E), has its material density close to that of wide-spread plastics like polyamide, polystyrene, or acrylic. Migrations of amber stones in the sea and their massive washing ashore have been monitored by Baltic citizens for ages. Based on the collected information, we present the hypothesis on the behaviour of microplastic particles in sea coastal zone. Fresh-to-strong winds generate surface waves, currents and roll-structures, whose joint effect washes ashore from the underwater slope both amber stones and plastics - and carries them back to the sea in a few days. Analysis of underlying hydrophysical processes suggests that sea coastal zone under stormy winds plays a role of a mill for plastics, and negatively buoyant pieces seem to repeatedly migrate between beaches and underwater slopes until they are broken into small enough fragments that can be transported by currents to deeper areas and deposited out of reach of stormy waves. Direct observations on microplastics migrations are urged to prove the hypothesis.

  19. Computed tomography recovers data from historical amber: an example from huntsman spiders

    Science.gov (United States)

    Dunlop, Jason A.; Penney, David; Dalüge, Natalie; Jäger, Peter; McNeil, Andrew; Bradley, Robert S.; Withers, Philip J.; Preziosi, Richard F.

    2011-06-01

    Computed tomography (CT) methods were applied to a problematic fossil spider (Arachnida: Araneae) from the historical Berendt collection of Eocene (ca. 44-49 Ma) Baltic amber. The original specimens of Ocypete crassipes Koch and Berendt 1854 are in dark, oxidised amber and the published descriptions lack detail. Despite this, they were subsequently assigned to the living Pantropical genus Heteropoda Latreille, 1804 and are ostensibly the oldest records of huntsman spiders (Sparassidae) in general. Given their normally large size, and presumptive ability to free themselves more easily from resin, it would be surprising to find a sparassid in amber and traditional (optical) methods of study would likely have left O. crassipes as an equivocal record—probably a nomen dubium. However, phase contrast enhanced X-ray CT revealed exquisite morphological detail and thus `saved' this historical name by revealing characters which confirm that it's a bona fide member both of Sparassidae and the subfamily Eusparassinae. We demonstrate here that CT studies facilitate taxonomic equivalence even between recent spiders and unpromising fossils described in older monographs. In our case, fine structural details such as eye arrangement, cheliceral dentition, and leg characters like a trilobate membrane, spination and claws, allow a precise referral of this fossil to an extant genus as Eusparassus crassipes (Koch and Berendt 1854) comb. nov.

  20. Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

    Science.gov (United States)

    Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

    2004-07-15

    Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

  1. Amberes-Bogotá: interpretaciones de lo doméstico en Ernesto Volkening

    OpenAIRE

    Carlos-Roberto Peña-Barrera

    2010-01-01

    Ernesto Volkening (1908-1983) fue un inmigrante alemán recordado en Colombia desde el ámbito de la crítica y el ensayo. Aunque sus producciones hablan de diversos temas, uno en particular es especial: las impresiones que dejó de su ciudad natal Amberes y algunas añadiduras poéticas de su vivir en Bogotá. En ese sentido, esta investigación tuvo por objeto conocer si en su obra podían encontrarse ideas, pensamientos y fragmentos que pudieran analizarse e interpretarse desde el punto de vista de...

  2. Two flat-backed polydesmidan millipedes from the Miocene Chiapas-amber Lagerstatte, Mexico.

    Directory of Open Access Journals (Sweden)

    Francisco Riquelme

    Full Text Available Two species of fossil polydesmidan millipedes (Diplopoda: Polydesmida embedded in amber are described from Miocene strata near Simojovel, in the Chiapas Highlands, Mexico. Maatidesmus paachtun gen. et sp. nov., placed into Chelodesmidae Cook, 1895, and Anbarrhacus adamantis gen. et sp. nov., assigned in the family Platyrhacidae Pocock, 1895. Morphological data from fossil specimens have been recovered using 3D X-ray micro-computed tomography and regular to infrared-reflected microscopy. Both fossil species are recognizable as new primarily but not exclusively, by collum margin modification and remarkable paranotal and metatergite dorsal sculpture.

  3. Sucinolivolia torpida--a new genus and species of flea-beetles (Coleoptera: Chrysomelidae: Galerucinae) from Baltic amber.

    Science.gov (United States)

    Bukejs, Andris; Biondi, Maurizio; Alekseev, Vitalii I

    2015-12-15

    Sucinolivolia torpida gen. nov. et sp. nov. (Coleoptera: Chrysomelidae: Galerucinae: Alticini) is described and illustrated from Eocene Baltic amber. The new monotypic genus is compared with fossil and extant flea-beetle genera. Sucinolivolia gen. nov. is similar to the extant Livolia Jacoby and Orthaltica Crotch, but difference include the absence of an antebasal pronotal sulcus, not crenulate lateral pronotal margins, possessing very short genae, more robust legs, and the shape of tibiae. Including this new record, six described species of Alticini are known from Baltic amber.

  4. The first Mesozoic microwhip scorpion (Palpigradi): a new genus and species in mid-Cretaceous amber from Myanmar

    Science.gov (United States)

    Engel, Michael S.; Breitkreuz, Laura C. V.; Cai, Chenyang; Alvarado, Mabel; Azar, Dany; Huang, Diying

    2016-04-01

    A fossil palpigrade is described and figured from mid-Cretaceous (Cenomanian) amber from northern Myanmar. Electrokoenenia yaksha Engel and Huang, gen. n. et sp. n., is the first Mesozoic fossil of its order and the only one known as an inclusion in amber, the only other fossil being a series of individuals encased in Pliocene onyx marble and 94-97 million years younger than E. yaksha. The genus is distinguished from other members of the order but is remarkably consistent in observable morphological details when compared to extant relatives, likely reflecting a consistent microhabitat and biological preferences over the last 100 million years.

  5. The first ant-termite syninclusion in amber with CT-scan analysis of taphonomy.

    Directory of Open Access Journals (Sweden)

    David Coty

    Full Text Available We describe here a co-occurrence (i.e. a syninclusion of ants and termites in a piece of Mexican amber (Totolapa deposit, Chiapas, whose importance is two-fold. First, this finding suggests at least a middle Miocene antiquity for the modern, though poorly documented, relationship between Azteca ants and Nasutitermes termites. Second, the presence of a Neivamyrmex army ant documents an in situ raiding behaviour of the same age and within the same community, confirmed by the fact that the army ant is holding one of the termite worker between its mandibles and by the presence of a termite with bitten abdomen. In addition, we present how CT-scan imaging can be an efficient tool to describe the topology of resin flows within amber pieces, and to point out the different states of preservation of the embedded insects. This can help achieving a better understanding of taphonomical processes, and tests ethological and ecological hypotheses in such complex syninclusions.

  6. Computer simulations of interferometric imaging with the VLT interferometer and its AMBER instrument

    CERN Document Server

    Przygodda, F; Hofmann, Karl Heinrich; Weigelt, G

    2001-01-01

    We present computer simulations of interferometric imaging with the Very Large Telescope Interferometer (VLTI) of the European Southern Observatory (ESO) and the Astronomical MultiBEam Recombiner (AMBER) phase-closure instrument. These simulations include both the astrophysical modelling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector read-out noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r_0,object and r_0,ref ranging between 0.9m and 1.2m), different residual tip-tilt error (delta_tt,object and delta_tt,ref ranging between 0.1% and 20% of the Airy disk diameter), and object brightness (K_object=0.7mag to 10.2mag, K_ref=0.7mag). Exem...

  7. A binary engine fuelling HD87643' s complex circumstellar environment, using AMBER/VLTI

    CERN Document Server

    Millour, Florentin; Borges-Fernandes, Marcelo; Meilland, Anthony; Mars, Gilbert; Benoist, C; Thiébaut, E; Stee, Philippe; Hofmann, K -H; Baron, Fabien; Young, John R; Bendjoya, Philippe; Carciofi, A C; De Souza, Armando Domiciano; Driebe, Thomas; Jankov, Slobodan; Kervella, Pierre; Petrov, R G; Robbe-Dubois, Sylvie; Vakili, Farrokh; Waters, L B F M; Weigelt, Gerd

    2009-01-01

    Context. The star HD 87643, exhibiting the ?B[e] phenomenon?, has one of the most extreme infrared excesses for this object class. It harbours a large amount of both hot and cold dust, and is surrounded by an extended re?ection nebula. Aims. One of our major goals was to investigate the presence of a companion in HD87643. In addition, the presence of close dusty material was tested through a combination of multi-wavelength high spatial resolution observations. Methods. We observed HD 87643 with high spatial resolution techniques, using the near-IR AMBER/VLTI interferometer with baselines ranging from 60 m to 130 m and the mid-IR MIDI/VLTI interferometer with baselines ranging from 25 m to 65 m. These observations are complemented by NACO/VLT adaptive-optics-corrected images in the K and L-bands, ESO-2.2m optical Wide-Field Imager large-scale images in the B, V and R-bands, Results. We report the direct detection of a companion to HD 87643 by means of image synthesis using the AMBER/VLTI instrument. The presen...

  8. Mesozoic Evaniidae (Insecta:Hymenoptera) in Spanish Amber:Reanalysis of the Phylogeny of the Evanioidea

    Institute of Scientific and Technical Information of China (English)

    Enrique PE(N)ALVER; Jaime ORTEGA-BLANCO; André NEL; Xavier DELCL(O)S

    2010-01-01

    One new genus and five new species of the family Evaniidae are described from the Early Cretaceous (Albian) Spanish amber of Pe(n)acerrada-Ⅰ (Province of Burgos),San Just and Arroyo de la Pascueta (both in the Province of Teruel):Cretevania alonsoi sp.nov.,C.montoyai sp.nov.,C.alcalai sp.nov.,C.rubusensis sp.nov.,and Iberoevania roblesi gen.and sp.nov.Taxonomic changes include Cretevania pristina (Zhang and Zhang,2000)comb.nov.,C.exquisita (Zhang,Rasnitsyn,Wang and Zhang,2007) comb.nov.,C.vesca (Zhang,Rasnitsyn,Wang and Zhang,2007) comb.nov.,and C.cyrtocerca (Deans,2004) comb.nov.,as a result of the reinterpretation of the genera Procretevania and Eovernevania.The new well preserved specimens of the genus Cretevania,together with the characters shown by the type specimens of the synonymized genera,give new information about their anatomical characters of taxonomical importance,and the genus Cretevania Rasnitsyn,1975 is re-diagnosed.The holotypes of the Russian species in amber have been revised.A cladistic analysis of fossil and extant groups of the superfamily Evanioidea is included.Cretevania had a wide palaeogeographic distribution,with the highest diversity known from Spain.The 13 known Cretevania species show a high interspecific variation mainly in wing characteristics,and a wide range of body and wing size.

  9. Bulk carbon, oxygen, and hydrogen stable isotope composition of recent resins from amber-producing Hymenaea.

    Science.gov (United States)

    Nissenbaum, Arie; Yakir, Dan; Langenheim, Jean H

    2005-01-01

    Resins of Hymenaea, an angiosperm tree genus known to be a copious resin producer and a major source of amber since the Oligo-Miocene, were collected from a wide range of tropical environments from Latin America and Africa, and analyzed for their carbon, hydrogen, and oxygen stable isotope composition. The average value for delta13C in the resins was found to be -27.0+/-1.3 per thousand, which is very similar to the values reported for resins in other studies. Delta18O values for the Hymenaea resins averaged +11.2+/-1.6 per thousand, or about 20 per thousand more depleted than normal plant cellulose. DeltaD values of the resins ranged from -196 to -319 per thousand, with an average of -243+/-30 per thousand. Rough estimates suggest a fractionation of -200 to -210 per thousand between the resins and the environmental water. This value is similar to the -200 per thousand value observed for the fractionation between other plant lipids and environmental water. The present study suggests that the stable isotope composition of fossil resins (amber) has the potential to provide information on ancient environmental waters.

  10. Study of the atmospheric refraction in a single mode instrument - Application to AMBER/VLTI

    CERN Document Server

    Robbe-Dubois, Sylvie; Bresson, Yves; Petrov, Romain G; Carbillet, Marcel; Lecoarer, Etienne; Rantakyrö, Frederik; Tallon-Bosc, Isabelle; Vannier, Martin; Antonelli, Pierre; Martinot-Lagarde, Gregoire; Roussel, Alain; Tasso, Daniel

    2009-01-01

    This paper presents a study of the atmospheric refraction and its effect on the light coupling efficiency in an instrument using single-mode optical fibers. We show the analytical approach which allowed us to assess the need to correct the refraction in J- and H-bands while observing with an 8-m Unit Telescope. We then developed numerical simulations to go further in calculations. The hypotheses on the instrumental characteristics are those of AMBER (Astronomical Multi BEam combineR), the near infrared focal beam combiner of the Very Large Telescope Interferometric mode (VLTI), but most of the conclusions can be generalized to other single-mode instruments. We used the software package caos (Code for Adaptive Optics Systems) to take into account the atmospheric turbulence effect after correction by the ESO system MACAO (Multi-Application Curvature Adaptive Optics). The opto-mechanical study and design of the system correcting the atmospheric refraction on AMBER is then detailed. We showed that the atmospheric...

  11. Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber.

    Science.gov (United States)

    Heinrichs, Jochen; Scheben, Armin; Bechteler, Julia; Lee, Gaik Ee; Schäfer-Verwimp, Alfons; Hedenäs, Lars; Singh, Hukam; Pócs, Tamás; Nascimbene, Paul C; Peralta, Denilson F; Renner, Matt; Schmidt, Alexander R

    2016-01-01

    Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea). We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae.

  12. Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian Indian Amber.

    Directory of Open Access Journals (Sweden)

    Jochen Heinrichs

    Full Text Available Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea. We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae.

  13. An extensible interface for QM/MM molecular dynamics simulations with AMBER.

    Science.gov (United States)

    Götz, Andreas W; Clark, Matthew A; Walker, Ross C

    2014-01-15

    We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.

  14. Near-infrared interferometric observation of the Herbig Ae star HD144432 with VLTI/AMBER

    CERN Document Server

    Chen, Lei; Wang, Yang; Weigelt, Gerd; Hofmann, Karl-Heinz; Kraus, Stefan; Schertl, Dieter; Lagarde, Stephane; Natta, Antonella; Petrov, Roman; Robbe-Dubois, Sylvie; Tatulli, Eric

    2012-01-01

    We study the sub-AU-scale circumstellar environment of the Herbig Ae star HD144432 with near-infrared (NIR) VLTI/AMBER observations to investigate the structure of its inner dust disk. The interferometric observations were carried out with the AMBER instrument in the H and K band. We interpret the measured H- and K-band visibilities, the near- and mid-infrared visibilities from the literature, and the SED of HD144432 by using geometric ring models and ring-shaped temperature-gradient disk models with power-law temperature distributions. We derived a K-band ring-fit radius of 0.17 \\pm 0.01 AU and an H-band radius of 0.18 \\pm 0.01 AU (for a distance of 145 pc). This measured K-band radius of \\sim0.17 AU lies in the range between the dust sublimation radius of \\sim0.13 AU (predicted for a dust sublimation temperature of 1500 K and gray dust) and the prediction of models including backwarming (\\sim0.27 AU). We found that an additional extended halo component is required in both the geometric and temperature-gradi...

  15. Parisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea from the Oise amber with redescription of Palaeognoriste Meunier

    Directory of Open Access Journals (Sweden)

    Vladimir Blagoderov

    2010-06-01

    Full Text Available A new genus and a new species of Lygistorrhinidae, Parisognoriste eocenica is described from the Eocene Oise amber of the Paris Basin. Palaeognoriste sciariforme Meunier, 1904 and Palaeognoriste affine Meunier, 1912 are re-described. Lectotypes are designated for both species of Palaeognoriste. The phylogenetic positions of the new genus and Palaeognoriste Meunier are discussed.

  16. Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

    DEFF Research Database (Denmark)

    Reichert, David E.; Norrby, Per-Ola; Welch, Michael J.

    2001-01-01

    In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER* force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new pa...

  17. Description of Pintomyia (Pifanomyia falcaorum sp. n. (Diptera: Psychodidae: Phlebotominae, a Fossil Sand Fly from Dominican Amber

    Directory of Open Access Journals (Sweden)

    Reginaldo Peçanha Brazil

    2002-06-01

    Full Text Available A new species of sand fly, Pintomyia (Pifanomyia falcaorum is described from an amber originated from the northern mountain range of Dominican Republic. The male sand fly specimen is well preserved and most features used in Phlebotominae taxonomy are seen with remarkable clarity.

  18. Evaluating the use of amber in palaeoatmospheric reconstructions: The carbon-isotope variability of modern and Cretaceous conifer resins

    Science.gov (United States)

    Dal Corso, Jacopo; Schmidt, Alexander R.; Seyfullah, Leyla J.; Preto, Nereo; Ragazzi, Eugenio; Jenkyns, Hugh C.; Delclòs, Xavier; Néraudeau, Didier; Roghi, Guido

    2017-02-01

    Stable carbon-isotope geochemistry of fossilized tree resin (amber) potentially could be a very useful tool to infer the composition of past atmospheres. To test the reliability of amber as a proxy for the atmosphere, we studied the variability of modern resin δ13C at both local and global scales. An amber δ13C curve was then built for the Cretaceous, a period of abundant resin production, and interpreted in light of data from modern resins. Our data show that hardening changes the pristine δ13C value by causing a 13C-depletion in solid resin when compared to fresh liquid-viscous resin, probably due to the loss of 13C-enriched volatiles. Modern resin δ13C values vary as a function of physiological and environmental parameters in ways that are similar to those described for leaves and wood. Resin δ13C varies between plant species and localities, within the same tree and between different plant tissues by up to 6‰, and in general increases with increasing altitudes of the plant-growing site. We show that, as is the case with modern resin, Cretaceous amber δ13C has a high variability, generally higher than that of other fossil material. Despite the high natural variability, amber shows a negative 2.5-3‰ δ13C trend from the middle Early Cretaceous to the Maastrichtian that parallels published terrestrial δ13C records. This trend mirrors changes in the atmospheric δ13C calculated from the δ13C and δ18O of benthic foraminiferal tests, although the magnitude of the shift is larger in plant material than in the atmosphere. Increasing mean annual precipitation and pO2 could have enhanced plant carbon-isotope fractionation during the Late Cretaceous, whereas changing pCO2 levels seem to have had no effect on plant carbon-isotope fractionation. The results of this study suggest that amber is a powerful fossil plant material for palaeoenvironmental and palaeoclimatic reconstructions. Improvement of the resolution of the existing data coupled with more detailed

  19. Characterization of am404, an amber mutation in the simian virus 40 T antigen gene.

    Science.gov (United States)

    Rawlins, D R; Collis, P; Muzyczka, N

    1983-01-01

    We analyzed the biological activity of an amber mutation, am404, at map position 0.27 in the T antigen gene of simian virus 40. Immunoprecipitation of extracts from am404-infected cells demonstrated the presence of an amber protein fragment (am T antigen) of the expected molecular weight (67,000). Differential immunoprecipitation with monoclonal antibody demonstrated that am T antigen was missing the carboxy-terminal antigenic determinants. The amber mutant was shown to be defective for most of the functions associated with wild-type T antigen. The mutant did not replicate autonomously, but this defect could be complemented by a helper virus (D. R. Rawlins and N. Muzyczka, J. Virol. 36:611-616, 1980). The mutant failed to transform nonpermissive rodent cells and did not relieve the host range restriction of adenovirus 2 in monkey cells. However, stimulation of host cell DNA, whose functional region domain has been mapped within that portion of the protein synthesized by the mutant, could be demonstrated in am404-infected cells. A number of unexpected observations were made. First, the am T antigen was produced in unusually large amounts in a simian virus 40-transformed monkey cell line (COS-1), but overproduction was not seen in nontransformed monkey cells regardless of whether or not a helper virus was present. This feature of the mutant was presumably the result of the inability of am T antigen to autoregulate, the level of wild-type T antigen in COS-1 cells, and the unusually short half-life of am T antigen in vivo. Pulse-chase experiments indicated that am T antigen had an intracellular half-life of approximately 10 min. In addition, although the am T antigen retained the major phosphorylation site found in simian virus 40 T antigen, it was not phosphorylated. Thus, phosphorylation of simian virus 40 T antigen is not required for the stimulation of host cell DNA synthesis. Finally, fusion of am404-infected monkey cells with Escherichia coli protoplasts

  20. Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards.

    Science.gov (United States)

    Daza, Juan D; Stanley, Edward L; Wagner, Philipp; Bauer, Aaron M; Grimaldi, David A

    2016-03-01

    Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.

  1. New earwigs in mid-Cretaceous amber from Myanmar (Dermaptera, Neodermaptera

    Directory of Open Access Journals (Sweden)

    Michael Engel

    2011-09-01

    Full Text Available Two new earwigs (Dermaptera recently discovered in mid-Cretaceous (latest Albian amber from Myanmar are described and figured. Astreptolabis ethirosomatia gen. et sp. n. is represented by a peculiar pygidicranoid female, assigned to a new subfamily, Astreptolabidinae subfam. n., and differs from other protodermapterans in the structure of the head, pronotum, tegmina, and cercal forceps. Tytthodiplatys mecynocercus gen. et sp. n. is a distinctive form of first-instar nymph of the Diplatyidae, the earliest record for this basal earwig family. The taxon can be distinguished from other Early Cretaceous nymphs by the structure of the head, antennae, legs, and most notably its filamentous and annulate cerci. The character affinities of these taxa among Neodermaptera are generally discussed as is the identity of an enigmatic ‘earwig-like’ species from the Jurassic of China.

  2. Amber suppression in Escherichia coli by unusual mitochondria-like transfer RNAs.

    Science.gov (United States)

    Bourdeau, V; Steinberg, S V; Ferbeyre, G; Emond, R; Cermakian, N; Cedergren, R

    1998-02-17

    The "cloverleaf" base-pairing pattern was established as the structural paradigm of active tRNA species some 30 years ago. Nevertheless, this pattern does not accommodate the folding of certain mitochondrial tRNAs. For these recalcitrant tRNAs, we have proposed structures having from 5 to 10 base pairs in the anticodon stem rather than the canonical 6. The absence of these types of tRNAs in cytoplasmic translation systems, however, raises the possibility that they may not be bona fide alternate folding patterns for active tRNA molecules. For this reason, we have designed new tRNA genes based on our model of unusual mitochondrial tRNAs, having 7, 8, 9, and 10 base pairs in the anticodon stem with other modifications to the D-stem and connector regions. We show here that these synthetic genes produce tRNAs that actively suppress amber codons in vivo.

  3. Empirical corrections to the Amber RNA force field with Target Metadynamics

    CERN Document Server

    Gil-Ley, Alejandro; Bussi, Giovanni

    2016-01-01

    The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the alpha and beta backbone angles on the modulation of ...

  4. Amberes-Bogotá: interpretaciones de lo doméstico en Ernesto Volkening

    Directory of Open Access Journals (Sweden)

    Carlos-Roberto Peña-Barrera

    2010-12-01

    Full Text Available Ernesto Volkening (1908-1983 fue un inmigrante alemán recordado en Colombia desde el ámbito de la crítica y el ensayo. Aunque sus producciones hablan de diversos temas, uno en particular es especial: las impresiones que dejó de su ciudad natal Amberes y algunas añadiduras poéticas de su vivir en Bogotá. En ese sentido, esta investigación tuvo por objeto conocer si en su obra podían encontrarse ideas, pensamientos y fragmentos que pudieran analizarse e interpretarse desde el punto de vista de lo doméstico. Para ello se abordó su producción, se seleccionaron escritos pertinentes, se resaltaron frases exactas y se comparara todo ello, al final, con algunos argumentos de otros autores. En efecto, su dialéctica y poesía argumentan sobre ello: la ciudad puede ser aprehendida como perteneciente a lo doméstico, porque “desde muy niño había sido para él la cosa más natural del mundo asociar la imagen paterna a la de Amberes; tanto así que el viaje que pensaba emprender le pareció otra manera de encontrarse con su padre”. Tan relevantes son sus pensamientos que siguen siendo vigentes y merecedores de posteriores reflexiones sobre la ciudad, el territorio y lo doméstico de la actualidad.

  5. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

    Science.gov (United States)

    Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

    2011-01-01

    To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

  6. Dark therapy for bipolar disorder using amber lenses for blue light blockade.

    Science.gov (United States)

    Phelps, James

    2008-01-01

    "Dark Therapy", in which complete darkness is used as a mood stabilizer in bipolar disorder, roughly the converse of light therapy for depression, has support in several preliminary studies. Although data are limited, darkness itself appears to organize and stabilize circadian rhythms. Yet insuring complete darkness from 6 p.m. to 8 a.m. the following morning, as used in several studies thus far, is highly impractical and not accepted by patients. However, recent data on the physiology of human circadian rhythm suggests that "virtual darkness" may be achievable by blocking blue wavelengths of light. A recently discovered retinal photoreceptor, whose fibers connect only to the biological clock region of the hypothalamus, has been shown to respond only to a narrow band of wavelengths around 450 nm. Amber-tinted safety glasses, which block transmission of these wavelengths, have already been shown to preserve normal nocturnal melatonin levels in a light environment which otherwise completely suppresses melatonin production. Therefore it may be possible to influence human circadian rhythms by using these lenses at night to blunt the impact of electrical light, particularly the blue light of ubiquitous television screens, by creating a "virtual darkness". One way to investigate this would be to provide the lenses to patients with severe sleep disturbance of probable circadian origin. A preliminary case series herein demonstrates that some patients with bipolar disorder experience reduced sleep-onset latency with this approach, suggesting a circadian effect. If amber lenses can effectively simulate darkness, a broad range of conditions might respond to this inexpensive therapeutic tool: common forms of insomnia; sleep deprivation in nursing mothers; circadian rhythm disruption in shift workers; and perhaps even rapid cycling bipolar disorder, a difficult- to -treat variation of a common illness.

  7. The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

    Science.gov (United States)

    Hu, Yuan; Sherborne, Brad; Lee, Tai-Sung; Case, David A.; York, Darrin M.; Guo, Zhuyan

    2016-07-01

    In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck-Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.

  8. A new genus and species of micro bee fly from the Earliest Eocene French amber (Diptera: Mythicomyiidae: Psiloderoidinae).

    Science.gov (United States)

    Myskowiak, Justine; Garrouste, Romain; Nel, Andre

    2016-05-26

    Mythicomyiidae, or micro bee flies, are tiny flies (0.5-5.0 mm) that are found throughout most parts of the world except the highest altitudes and latitudes (Greathead & Evenhuis 2001). Including all extinct and extant taxa, the Mythicomyiidae currently comprise more than 380 valid taxonomic species distributed among 30 genera. The subfamily Psiloderoidinae is especially well represented among the fossil Mythicomyiidae by seven Cretaceous or Cenozoic genera. We here describe a new genus and a new species of this subfamily based on fossils from the Earliest Eocene of Oise (France). A Psiloderoidinae, Proplatypygus matilei Nel & DePloëg, 2004, is already described in this amber. Another mythicomyiid, Eurodoliopteryx inexpectatus Nel, 2006, is the most frequent bombylioid in this amber (Nel & DePloëg, 2004; Nel, 2006).

  9. Balancing simulation accuracy and efficiency with the Amber united atom force field.

    Science.gov (United States)

    Hsieh, Meng-Juei; Luo, Ray

    2010-03-04

    We have analyzed the quality of a recently proposed Amber united-atom model and its overall efficiency in ab initio folding and thermodynamic sampling of two stable beta-hairpins. It is found that the mean backbone structures are quite consistent between the simulations in the united-atom and its corresponding all-atom models in Amber. More importantly, the simulated beta turns are also consistent between the two models. Finally, the chemical shifts on H alpha are highly consistent between simulations in the two models, although the simulated chemical shifts are lower than experiment, indicating less structured peptides, probably due to the omission of the hydrophobic term in the simulations. More interestingly, the stabilities of both beta-hairpins at room temperature are similar to those derived from the NMR measurement, whether the united-atom or the all-atom model is used. Detailed analysis shows high percentages of backbone torsion angles within the beta region and high percentages of native contacts. Given the reasonable quality of the united-atom model with respect to experimental data, we have further studied the simulation efficiency of the united-atom model over the all-atom model. Our data shows that the united-atom model is a factor of 6-8 faster than the all-atom model as measured with the ab initio first pass folding time for the two tested beta-hairpins. Detailed structural analysis shows that all ab initio folded trajectories enter the native basin, whether the united-atom model or the all-atom model is used. Finally, we have also studied the simulation efficiency of the united-atom model as measured in terms of how fast thermodynamic convergence can be achieved. It is apparent that the united-atom simulations reach convergence faster than the all-atom simulations with respect to both mean potential energies and mean native contacts. These findings show that the efficiency of the united-atom model is clearly beyond the per-step dynamics simulation

  10. Angular diameter estimation of interferometric calibrators. Example of λ Gruis, calibrator for VLTI-AMBER

    Science.gov (United States)

    Cruzalèbes, P.; Jorissen, A.; Sacuto, S.; Bonneau, D.

    2010-06-01

    Context. Accurate long-baseline interferometric measurements require careful calibration with reference stars. Small calibrators with high angular diameter accuracy ensure the true visibility uncertainty to be dominated by the measurement errors. Aims: We review some indirect methods for estimating angular diameter, using various types of input data. Each diameter estimate, obtained for the test-case calibrator star λ Gru, is compared with the value 2.71 mas found in the Bordé calibrator catalogue published in 2002. Methods: Angular size estimations from spectral type, spectral index, in-band magnitude, broadband photometry, and spectrophotometry give close estimates of the angular diameter, with slightly variable uncertainties. Fits on photometry and spectrophotometry need physical atmosphere models with “plausible” stellar parameters. Angular diameter uncertainties were estimated by means of residual bootstrapping confidence intervals. All numerical results and graphical outputs presented in this paper were obtained using the routines developed under PV-WAVE®, which compose the modular software suite SPIDAST, created to calibrate and interprete spectroscopic and interferometric measurements, particularly those obtained with VLTI-AMBER. Results: The final angular diameter estimate 2.70 mas of λ Gru, with 68% confidence interval 2.65-2.81 mas, is obtained by fit of the MARCS model on the ISO-SWS 2.38-27.5 μm spectrum, with the stellar parameters Te = 4250 K, log g = 2.0, z = 0.0 dex, M = 1.0 M⊙, and ξ_t = 2.0 km s-1.

  11. Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM,...

  12. Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

    Science.gov (United States)

    Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

    2016-04-01

    We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

  13. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Walker, Ross C; Lewis, James P; Gómez-Puertas, Paulino; Mendieta, Jesús; Ortega, José

    2014-05-13

    In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.

  14. Immersion mode ice nucleation measurements with the new Portable Immersion Mode Cooling chAmber (PIMCA)

    Science.gov (United States)

    Kohn, Monika; Lohmann, Ulrike; Welti, André; Kanji, Zamin A.

    2016-05-01

    The new Portable Immersion Mode Cooling chAmber (PIMCA) has been developed for online immersion freezing of single-immersed aerosol particles. PIMCA is a vertical extension of the established Portable Ice Nucleation Chamber (PINC). PIMCA immerses aerosol particles into cloud droplets before they enter PINC. Immersion freezing experiments on cloud droplets with a radius of 5-7 μm at a prescribed supercooled temperature (T) and water saturation can be conducted, while other ice nucleation mechanisms (deposition, condensation, and contact mode) are excluded. Validation experiments on reference aerosol (kaolinite, ammonium sulfate, and ammonium nitrate) showed good agreement with theory and literature. The PIMCA-PINC setup was tested in the field during the Zurich AMBient Immersion freezing Study (ZAMBIS) in spring 2014 in Zurich, Switzerland. Significant concentrations of submicron ambient aerosol triggering immersion freezing at T > 236 K were rare. The mean frozen cloud droplet number concentration was estimated to be 7.22·105 L-1 for T ZAMBIS.

  15. Constraining the wind launching region in Herbig Ae stars: AMBER/VLTI spectroscopy of HD104237

    CERN Document Server

    Tatulli, E; Natta, A; Testi, L

    2006-01-01

    We investigate the origin of the $\\mathrm{Br}\\gamma$ emission of the Herbig Ae star HD104237 on Astronomical Unit (AU) scales. Using AMBER/VLTI at a spectral resolution R=1500 spatially resolve the emission in both the BrGamma line and the adjacent continuum. The visibility does not vary between the continuum and the BrGamma line, even though the line is strongly detected in the spectrum, with a peak intensity 35% above the continuum. This demonstrates that the line and continuum emission have similar size scales. We assume that the K-band continuum excess originates in a ``puffed-up'' inner rim of the circumstellar disk, and discuss the likely origin of BrGamma. We conclude that this emission most likely arises from a compact disk wind, launched from a region 0.2-0.5 AU from the star, with a spatial extent similar to that of the near infrared continuum emission region, i.e, very close to the inner rim location.

  16. VLTI/AMBER observations of cold giant stars: atmospheric structures and fundamental parameters

    CERN Document Server

    Arroyo-Torres, B; Marcaide, J M; Wittkowski, M; Guirado, J C; Hauschildt, P H; Quirrenbach, A; Fabregat, J

    2014-01-01

    The main goal of this research is to determine the angular size and the atmospheric structures of cool giant stars and to compare them with hydrostatic stellar model atmospheres, to estimate the fundamental parameters, and to obtain a better understanding of the circumstellar environment. We conducted spectro-interferometric observations of epsilon Oct, beta Peg, NU Pav, and psi Peg in the near-infrared K band (2.13-2.47 microm), and gamma Hya (1.9-2.47 microm) with the VLTI/AMBER instrument at medium spectral resolution. To obtain the fundamental parameters, we compared our data with hydrostatic atmosphere models (PHOENIX). We estimated the Rosseland angular diameters of epsilon Oct, beta Peg, NU Pav, psi Peg, and gamma Hya. Together with distances and bolometric fluxes, we estimated radii, effective temperatures, and luminosities of our targets. In the beta Peg visibility, we observed a molecular layer of CO with a size similar to that modeled with PHOENIX. However, there is an additional slope in absorptio...

  17. VLTI/AMBER spectro-interferometric imaging of VX Sgr's inhomogenous outer atmosphere

    CERN Document Server

    Chiavassa, A; Millour, F; Driebe, T; Wittkowski, M; Plez, B; Thiebeaut, E; Josselin, E; Freytag, B; Scholz, M; Haubois, X

    2009-01-01

    Aims. We aim to explore the photosphere of the very cool late-type star VX Sgr and in particular the existence and characterization of molecular layers above the continuum forming photosphere. Methods. We obtained interferometric observations with the VLTI/AMBER interferometer using the fringe tracker FINITO in the spectral domain 1.45-2.50 micron with a spectral resolution of about 35 and baselines ranging from 15 to 88 meters.We perform independent image reconstruction for different wavelength bins and fit the interferometric data with a geometrical toy model.We also compare the data to 1D dynamical models of Miras atmosphere and to 3D hydrodynamical simulations of red supergiant (RSG) and asymptotic giant branch (AGB) stars. Results. Reconstructed images and visibilities show a strong wavelength dependence. The H-band images display two bright spots whose positions are confirmed by the geometrical toy model. The inhomogeneities are qualitatively predicted by 3D simulations. At about 2,00 micron and in the ...

  18. Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber

    Directory of Open Access Journals (Sweden)

    Leyla J. Seyfullah

    2015-07-01

    Full Text Available Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers, to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.

  19. Yeast Ca(2+)-signal transduction inhibitors isolated from Dominican amber prevent the degranulation of RBL-2H3 cells through the inhibition of Ca(2+)-influx.

    Science.gov (United States)

    Abe, Tomomi; Kobayashi, Miki; Okawa, Yusuke; Inui, Tomoki; Yoshida, Jun; Higashio, Hironori; Shinden, Hisao; Uesugi, Shota; Koshino, Hiroyuki; Kimura, Ken-Ichi

    2016-09-01

    A new norlabdane compound, named kujigamberol has previously been isolated from Kuji amber (but not from Baltic amber) by activity guided fractionation. However, there has been no study of biological compounds in Dominican amber. Biological activities were examined using the hypersensitive mutant yeast (zds1Δ erg3Δ pdr1Δ pdr3Δ) with respect to Ca(2+)-signal transduction, enzymes and rat basophilic leukemia (RBL)-2H3 cells. The structures were elucidated on the basis of spectral analysis including high resolution (HR)-EI-MS, 1D NMR and 2D NMR. Three diterpenoid compounds, 5(10)-halimen-15-oic acid (1), 3-cleroden-15-oic acid (2) and 8-labden-15-oic acid (3), which are different from the bioactive compounds in Kuji and Baltic ambers, were isolated from Dominican amber. They inhibited both calcineurin (CN) (IC50=40.0, 21.2 and 34.2μM) and glycogen synthase kinase-3β (GSK-3β) (IC50=48.9, 43.8 and 41.1μM) which are involved in the growth restored activity against the mutant yeast. The most abundant compound 2 showed inhibitory activity against both degranulation and Ca(2+)-influx in RBL-2H3 cells. The compounds having the growth restoring activity against the mutant yeast have potential as anti-allergic compounds.

  20. Resolving the stellar components of the massive multiple system Herschel 36 with AMBER/VLTI

    Science.gov (United States)

    Sanchez-Bermudez, J.; Alberdi, A.; Schödel, R.; Hummel, C. A.; Arias, J. I.; Barbá, R. H.; Maíz Apellániz, J.; Pott, J.-U.

    2014-12-01

    Context. Massive stars are extremely important for the evolution of the galaxies; there are large gaps in our understanding of their properties and formation, however, mainly because they evolve rapidly, are rare, and distant. Recent findings suggest that most O-stars belong to multiple systems. It may well be that almost all massive stars are born as triples or higher multiples, but their large distances require very high angular resolution to directly detect the companions at milliarcsecond scales. Aims: Herschel 36 is a young massive system located at 1.3 kpc. It has a combined smallest predicted mass of 45 M⊙. Multi-epoch spectroscopic data suggest the existence of at least three gravitationally bound components. Two of them, system Ab, are tightly bound in a spectroscopic binary, and the third one, component Aa, orbits in a wider orbit. Our aim was to image and obtain astrometric and photometric measurements of components Aa and Ab using, for the first time, long-baseline optical interferometry to further constrain its nature. Methods: We observed Herschel 36 with the near-infrared instrument AMBER attached to the ESO VLT Interferometer, which provides an angular resolution of ~2 mas. We used the code BSMEM to perform the interferometric image reconstruction. We fitted the interferometric observables using proprietary IDL routines and the code LitPro. Results: We imaged the Aa + Ab components of Herschel 36 in H and K filters. Component Ab is located at a projected distance of 1.81 mas, at a position angle of ~222° east of north, the flux ratio between components Aa and Ab is close to one. These findings agree with previous predictions about the properties of Herschel 36. The small measured angular separation indicates that system Ab and Ab may be approaching the periastron of their orbits. These results, only achievable with long-baseline near-infrared interferometry, constitute the first step toward a thorough understanding of this massive triple system.

  1. At least 10% shorter C-H bonds in cryogenic protein crystal structures than in current AMBER forcefields.

    Science.gov (United States)

    Pang, Yuan-Ping

    2015-03-06

    High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C-H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C-H bonds in high resolution cryogenic protein structures are 10-14% shorter than those defined in current AMBER forcefields, according to 3709 C-H bonds in the cryogenic protein structures with resolutions of 0.62-0.79 Å. Also, 20 all-atom, isothermal-isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C-H bonds were shortened by 10-14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C-H bonds, respectively. These results show that the 10-14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C-H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations.

  2. Parisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier.

    Science.gov (United States)

    Blagoderov, Vladimir; Hippa, Heikki; Nel, André

    2010-06-30

    A new genus and a new species of Lygistorrhinidae, Parisognoristeeocenica is described from the Eocene Oise amber of the Paris Basin. Parisognoristesciariforme Meunier, 1904 and Parisognoristeaffine Meunier, 1912 are re-described. Lectotypes are designated for both species of Palaeognoriste. The phylogenetic positions of the new genus and Palaeognoriste Meunier are discussed. The paper is an example demonstrating a new approach in cybertaxonomy including automatic generation of manuscript within Virtual Research Environment (Scratchpads), semantic enhancements, and parallel release of the publication on paper and on-line accompanied with registration of new taxa with ZooBank.

  3. Strong carrier localization effect in carrier dynamics of 585 nm InGaN amber light-emitting diodes

    Energy Technology Data Exchange (ETDEWEB)

    Li, Panpan; Li, Hongjian; Li, Zhi; Kang, Junjie; Yi, Xiaoyan; Li, Jinmin; Wang, Guohong [Semiconductor Lighting R and D Center, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China)

    2015-02-21

    Temperature dependence and time-resolved photoluminescence (TRPL) have been carried out to study carrier dynamics for 585 nm InGaN amber light-emitting diodes (LEDs). It is found that in InGaN amber LEDs, peak emission energy only shows a slight blueshift from 588 to 575 nm, as temperature increased from 10 K to 300 K. Moreover, radiative recombination lifetime has demonstrated independent of temperature based TRPL results. These two features indicate that a strong carrier localization effect plays a dominant role in carrier dynamics for InGaN amber LEDs. Also, activation energy of 40.3 meV is obtained through Arrhenius plot of PL intensity versus temperature.

  4. 琥珀酸酐生产新工艺探讨%The Study of New Technology of Producing Amber Anhydride

    Institute of Scientific and Technical Information of China (English)

    吕杨

    2012-01-01

    It introduced the properties of Amber Anhydride and widely used in every field.Introducing the major technology of producing Amber Anhydride.Reviewing new tecnology of producing Amber Anhydride and comparing the major technology with new technology to explaining the superiority of new technology.%介绍了琥珀酸酐的性质及在各个领域的广泛用途,介绍了目前国内琥珀酸酐的主要生产工艺技术方案,综述了琥珀酸酐生产新技术,并对目前国内琥珀酸酐的主要生产工艺和琥珀酸酐生产新工艺进行了比较,突出了新工艺的优势。

  5. VLTI/AMBER spectro-interferometric imaging of VX Sagittarii's inhomogenous outer atmosphere

    Science.gov (United States)

    Chiavassa, A.; Lacour, S.; Millour, F.; Driebe, T.; Wittkowski, M.; Plez, B.; Thiébaut, E.; Josselin, E.; Freytag, B.; Scholz, M.; Haubois, X.

    2010-02-01

    Aims: We aim to explore the photosphere of the very cool late-type star VX Sgr and in particular the characterization of molecular layers above the continuum forming photosphere. Methods: We obtained interferometric observations with the VLTI/AMBER interferometer using the fringe tracker FINITO in the spectral domain 1.45-2.50 μm with a spectral resolution of ≈35 and baselines ranging from 15 to 88 m. We performed independent image reconstruction for different wavelength bins and fit the interferometric data with a geometrical toy model. We also compared the data to 1D dynamical models of Miras atmosphere and to 3D hydrodynamical simulations of red supergiant (RSG) and asymptotic giant branch (AGB) stars. Results: Reconstructed images and visibilities show a strong wavelength dependence. The H-band images display two bright spots whose positions are confirmed by the geometrical toy model. The inhomogeneities are qualitatively predicted by 3D simulations. At ≈2.00 μm and in the region 2.35-2.50 μm, the photosphere appears extended and the radius is larger than in the H band. In this spectral region, the geometrical toy model locates a third bright spot outside the photosphere that can be a feature of the molecular layers. The wavelength dependence of the visibility can be qualitatively explained by 1D dynamical models of Mira atmospheres. The best-fitting photospheric models show a good match with the observed visibilities and give a photospheric diameter of Theta=8.82 ± 0.50 mas. The H2O molecule seems to be the dominant absorber in the molecular layers. Conclusions: We show that the atmosphere of VX Sgr seems to resemble Mira/AGB star model atmospheres more closely than do RSG model atmospheres. In particular, we see molecular (water) layers that are typical of Mira stars. Based on the observations made with VLTI-ESO Paranal, Chile under the programs IDs 081.D-0005(A, B, C, D, E, F, G, H).

  6. Description of a new species, Pintomyia dissimilis nov. sp., a phlebotomine fossil from Dominican Republic amber (Diptera: Psychodidae: Phlebotominae

    Directory of Open Access Journals (Sweden)

    Sanguinette Cristiani

    2009-05-01

    Full Text Available Abstract Background Phlebotomine sandflies are the vectors of etiological agents of leishmaniases in several areas of the world. In the Neotropical Region, the biodiversity of these insects is more than other regions, probably due the long evolutionary period of this group. Miocene amber from Dominican Republic, currently, has a record of 14 extinct species of Phlebotomine sandflies. Results This paper describes a new fossil species of phlebotomine sandfly from amber found in Dominican Republic. This new species is based on morphological characters of a male such as 5° palpomere longer than 3° + 4°, three well-developed spines in the gonostyle, lateral lobe longer than gonocoxite and permit inclusion of the new species in the genus Pintomyia, series serrana. The paramere, with a curvature in the ventral margin, of the middle of the structure, separates the new species from the others fossils or extant species. Conclusion The new species described in the present study named Pintomyia dissimilis nov. sp. is well differenciated from all known species in this genus.

  7. Disk and wind interaction in the young stellar object MWC 297 spatially resolved with VLTI/AMBER

    CERN Document Server

    Malbet, F; De Wit, W J; Kraus, S; Meilland, A; Millour, F; Tatulli, E; Berger, J P; Chesneau, O; Hofmann, Karl Heinrich; Isella, A; Natta, A; Petrov, R; Preibisch, T; Stee, P; Testi, L; Weigelt, G; Antonelli, P; Beckmann, U; Bresson, Y; Chelli, A; Duvert, G; Gluck, L; Kern, P; Lagarde, S; Le Coarer, E; Lisi, F; Perraut, K; Robbe-Dubois, S; Roussel, A; Zins, G; Accardo, M; Acke, B; Agabi, K; Arezki, B; Aristidi, E; Baffa, C; Behrend, J; Blöcker, T; Bonhomme, S; Busoni, S; Cassaing, F; Clausse, J M; Colin, J; Connot, C; Delboulbé, A; Driebe, T; Dugué, M; Feautrier, P; Ferruzzi, D; Forveille, T; Fossat, E; Foy, R; Fraix-Burnet, D; Gallardo, A; Gennari, S; Glentzlin, A; Giani, E; Gil, C; Heiden, M; Heininger, M; Kamm, D; Le Contel, D; Le Contel, J M; López, B; Magnard, Y; Marconi, A; Mars, G; Martinot-Lagarde, G; Mathias, P; Monin, J L; Mouillet, D; Mourard, D; Mege, P; Nussbaum, E; Ohnaka, K; Pacheco, J; Pacini, F; Perrier, C; Puget, P; Rabbia, Y; Rebattu, S; Reynaud, F; Richichi, A; Sacchettini, M; Salinari, P; Schertl, D; Solscheid, W; Stefanini, P; Tallon, M; Tallon-Bosc, I; Tasso, D; Valtier, J C; Vannier, M; Ventura, N; Kiekebusch, M; Rantakyro, F; Schöller, M

    2005-01-01

    The young stellar object MWC 297 has been observed with the VLT interferometer equipped with the AMBER instrument. MWC 297 has been spatially resolved in the continuum with a visibility of 0.50 as well as in the Br gamma emission line where the visibility decrease to a lower value of 0.33. This change in the visibility with the wavelength can be interpreted by the presence of an optically thick disk responsible for the visibility in the continuum and of a stellar wind traced by Br gamma and whose apparent size is 40% larger. We validate this interpretation by building a model of the stellar environment that combines a geometrically thin, optically thick accretion disk model consisting of gas and dust, and a latitude-dependent stellar wind outflowing above the disk surface. The continuum emission and visibilities obtained from this model are fully consistent with the interferometric AMBER data. They agree also with existing optical, near-infrared spectra and other broad-band near-infrared interferometric visib...

  8. On the systematic position of Electrocrania Kusnezov, 1941 with the description of a new species from Baltic amber (Lepidoptera: Micropterigidae).

    Science.gov (United States)

    Kurz, Michael

    2015-11-19

    A new fossil species of Electrocrania Kusnezov is described, i.e. Electrocrania michalskii sp. nov. The male moth in Baltic amber is in a sufficiently good condition to allow its assignment to the family Micropterigidae on the basis of four re-cognized autapomorphies of this family (Kristensen 1998). The unique venation of the specimen places it in the genus Electrocrania stat. rev. and allows a redescription of that genus that has recently been treated as synonym of Micropterix Hübner. It is argued that Electrocrania is a distinct genus within Micropterigidae that is not associated with Micropterix, but probably can be assigned to the "Northern Hemisphere genera"-lineage of Micropterigidae.

  9. On the systematic position of Baltimartyria Skalski, 1995 and description of a new species from Baltic amber (Lepidoptera, Micropterigidae

    Directory of Open Access Journals (Sweden)

    Wolfram Mey

    2011-09-01

    Full Text Available This paper describes a rare case of a male moth in Baltic amber in an excellent position for establishing a species. The moth represents the second species of the genus Baltimartyria Skalski, 1995, described herein as B. rasnitsyni sp. n. The detection of this new species prompts research on the systematic position of the genus within the family Micropterigidae. The genus was found to provide none of the apomorphic characters that would allow placement in one of the monophyletic lineages within the family. The genus is provisionally assigned to the “southern sabatincoid group”, a weakly supported assemblage of Southern Hemisphere genera. The sister genus has still to be determined. Baltimartyria is the first North Hemisphere representative in this group. Some general aspects of historical biogeography relevant for the group are briefly discussed.

  10. Internal quantum efficiency in yellow-amber light emitting AlGaN-InGaN-GaN heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Thi Huong; Gil, Bernard; Valvin, Pierre [Laboratoire Charles Coulomb – UMR 5221, CNRS and University Montpellier, Case courier 074, 34095 Montpellier Cedex 5 (France); Damilano, Benjamin; Lekhal, Kaddour; De Mierry, Philippe [CRHEA-CNRS Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, rue Bernard Gregory, 06560 Valbonne (France)

    2015-09-21

    We determine the internal quantum efficiency of strain-balanced AlGaN-InGaN-GaN hetero-structures designed for yellow-amber light emission, by using a recent model based on the kinetics of the photoluminescence decay initiated by Iwata et al. [J. Appl. Phys. 117, 075701 (2015)]. Our results indicate that low temperature internal quantum efficiencies sit in the 50% range and we measure that adding an AlGaN layer increases the internal quantum efficiency from 50% up to 57% with respect to the GaN-InGaN case. More dramatic, it almost doubles from 2.5% up to 4.3% at room temperature.

  11. A New Species Group in the Genus Tanytarsus van der Wulp(Diptera:Chironomidae)Based on a Fossil Record from Baltic Amber

    Institute of Scientific and Technical Information of China (English)

    Wojciech GI(L)KA

    2010-01-01

    A new fossil chironomid,Tanytarsus serafini,found in Baltic amber is described and illustrated based on adult males.The new species and similar extant species of the genus Tanytarsus van der Wulp are compared.Due to several distinct characters of wing,legs and hypopygium,a new species group for Tanytarsus serafini is proposed,and its diagnostic features are evaluated.

  12. Clumpy dust clouds and extended atmosphere of the AGB star W Hya revealed with VLT/SPHERE-ZIMPOL and VLTI/AMBER

    CERN Document Server

    Ohnaka, Keiichi; Hofmann, Karl-Heinz

    2016-01-01

    We present visible polarimetric imaging observations of the well-studied AGB star W Hya taken with VLT/SPHERE-ZIMPOL as well as high spectral resolution long-baseline interferometric observations with the AMBER instrument of the Very Large Telescope Interferometer (VLTI). We observed W Hya with VLT/SPHERE-ZIMPOL at three wavelengths in the continuum (645, 748, and 820 nm), in the Halpha line at 656.3 nm, and in the TiO band at 717 nm. The VLTI/AMBER observations were carried out in the wavelength region of the CO first overtone lines near 2.3 micron with a spectral resolution of 12000. Taking advantage of the polarimetric imaging capability of SPHERE-ZIMPOL combined with the superb adaptive optics performance, we have succeeded in spatially resolving three clumpy dust clouds located at ~50 mas (~2 Rstar) from the central star, revealing dust formation very close to the star. The AMBER data in the individual CO lines suggest a molecular outer atmosphere extending to ~3 Rstar. Furthermore, the SPHERE-ZIMPOL ima...

  13. Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field.

    Science.gov (United States)

    Agrawal, Paras M; Rice, Betsy M; Zheng, Lianqing; Thompson, Donald L

    2006-12-28

    We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.

  14. Comparison of electrostatic potential around proteins calculated from Amber and AM1 charges: application to mutants of prion protein

    Science.gov (United States)

    Zuegg, Johannes; Bliznyuk, Andrey A.; Gready, Jill E.

    On the basis of arguments of complementary fit of shape and charge polarity or hydrophobicity, molecular electrostatic potentials (MEPs) around proteins are commonly used to deduce likely sites for interaction with ligands or other proteins, including for variations such as mutations. But protein MEPs calculated classically from fixed force field descriptions, including those with implicit solvent models such as in Delphi, do not allow for repolarization of protein residues within the protein system; hence, their representations are likely to be variably inaccurate. Linear-scaling methods now allow calculation of MEPs quantum mechanically for systems as large as proteins, and can account for polarization explicitly. Here we compare MEPs derived from AM1 charge distributions calculated by Mopac2000 with those from the classical Amber force field. Our models are mutants of prion protein (PrP), a protein with an unusually high number of charged residues. The results demonstrate that static point charges, as used in most current force fields, cannot reproduce the MEP of macromolecules. Also, it is not sufficient to account for the influence of nearby atoms connected by chemical bonds; the influence of nearby atoms in space is at least as important. Thus, further progress in the accuracy and wider applicability of force fields requires proper accounting for polarization. Mopac2000 calculations can provide the necessary data for checking new force fields and/or parameter fitting.

  15. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

    Science.gov (United States)

    Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

    2014-01-14

    The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development.

  16. Near-infrared spectro-interferometry of three OH/IR Stars with the VLTI/AMBER instrument

    CERN Document Server

    Ruiz-Velasco, A E; Wachter, A; Schroeder, K -P; Driebe, T

    2011-01-01

    We investigate the molecular and dusty environment of OH/IR stars in order to characterize the mass-loss process during the tip-AGB superwind phase. Employing the AMBER instrument at the VLT Interferometer we obtained near-infrared H- and K-band spectro-interferometric observations of the three OH/IR stars IRAS 13479-5436, IRAS 14086-6907 and IRAS 17020-5254 with a spectral resolution of about 35. We use a two-component geometrical model, consisting of a uniform disk and a Gaussian disk, to obtain characteristic angular sizes of the central stellar sources and their dust envelopes, as well as the flux ratios between these components. Angular uniform disk diameters of the three central components of the objects above have values between 3.2 mas and 5.4 mas. For their dust envelopes, we find FWHM values between 17.1 mas and 25.2 mas. According to distance estimates from the literature, the central stellar components have radii between 900 R_sun and 1400 R_sun, while their dust envelopes reach FWHM values betwee...

  17. The Adaptive Buffered Force QM/MM method in the CP2K and AMBER software packages

    CERN Document Server

    Mones, Letif; Götz, Andreas W; Laino, Teodoro; Walker, Ross C; Leimkuhler, Ben; Csányi, Gábor; Bernstein, Noam

    2014-01-01

    The implementation and validation of the adaptive buffered force QM/MM method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the adaptive buffered-force QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reprod...

  18. Fundamental parameters of 16 late-type stars derived from their angular diameter measured with VLTI/AMBER

    CERN Document Server

    Cruzalèbes, P; Rabbia, Y; Sacuto, S; Chiavassa, A; Pasquato, E; Plez, B; Eriksson, K; Spang, A; Chesneau, O

    2013-01-01

    Thanks to their large angular dimension and brightness, red giants and supergiants are privileged targets for optical long-baseline interferometers. Sixteen red giants and supergiants have been observed with the VLTI/AMBER facility over a two-years period, at medium spectral resolution (R=1500) in the K band. The limb-darkened angular diameters are derived from fits of stellar atmospheric models on the visibility and the triple product data. The angular diameters do not show any significant temporal variation, except for one target: TX Psc, which shows a variation of 4% using visibility data. For the eight targets previously measured by Long-Baseline Interferometry (LBI) in the same spectral range, the difference between our diameters and the literature values is less than 5%, except for TX Psc, which shows a difference of 11%. For the 8 other targets, the present angular diameters are the first measured from LBI. Angular diameters are then used to determine several fundamental stellar parameters, and to loca...

  19. VLTI/AMBER interferometric observations of the recurrent Nova RS Oph 5.5 days after outburst

    CERN Document Server

    Chesneau, O; Millour, F; Hummel, C; De Souza, A D; Bonneau, D; Vannier, M; Rantakyro, F T; Spang, A; Malbet, F; Mourard, D; Bode, M F; O'brien, T J; Skinner, G K; Petrov, R; Stee, P; Tatulli, E; Vakili, F; Chesneau, Olivier; Hummel, Ch.; Stee, Ph.

    2006-01-01

    We report on interferometric AMBER/VLTI observations of the recurrent nova RS Oph five days after its outburst on 2006 Feb 12. Using three baselines from 44 to 86m, and a spectral resolution of 1500, we measured the extension of the emission in the K band continuum and in the BrG and HeI2.06 micron lines. The continuum visibilities were interpreted by fitting simple geometric models consisting of uniform and Gaussian ellipses, ring and binary models. The visibilities and differential phases in the BrG line were interpreted using skewed ring models aiming to perform a limited parametric reconstruction of the extension and kinematics of the line forming region. The limited uv coverage does not allow discrimination between filled models and rings. Binary models are discarded because the measured closure phase in the continuum is close to zero. The visibilities in the lines are at a low level compared to their nearby continuum, consistent with a more extended line forming region for HeI2.06 than BrG. The ellipse ...

  20. The analysis of the kinetics of extraction of resinoids and hypericines from the amber, Hypericum perforatum L.

    Directory of Open Access Journals (Sweden)

    ANDRIJA A. SMELCEROVIC

    2002-06-01

    Full Text Available The kinetics of the extraction of the overall extracted materials (resinoids, total hypericine, hypericine and pseudohypericine from amber (Hypericum perforatum L. was investigated by the procedure of maceration both with and without ultra-sound, using methanol as the extractant. It was found that the period of fast extraction with intensification of the extraction of resinoid by ultra-sound was significantly shorter (about 20 minutes than was needed for the extraction without ultra-sound (about 5 h. Similar results were also obtained for the extraction of the other tested substances. It can be concluded that better drug exploitation can be achieved in a much shorter extraction time by intensification of the extraction using ultra-sound. By preparation of herbal material through pulverization, a significant grade of herbal tissue structure disintegration was achieved, so that turbulent mass transfer plays a dominant role in the extraction. The results show that the coefficient values of fast extraction (b are approximately the same for all the investigated kinetics.

  1. The use of a GIS Red-Amber-Green (RAG) system to define search priorities for burials

    Science.gov (United States)

    Somma, Roberta; Silvestro, Massimiliano; Cascio, Maria; Dawson, Lorna; Donnelly, Laurance; Harrison, Mark; McKinley, Jennifer; Ruffell, Alastair

    2016-04-01

    The aim of this research is to promote among the Italian police, magistrates, and geologists, the applications of a Geographical Information System (GIS)-based RAG system for use in ground searches for burials. To date the RAG system has not been used and documented in Italy and would potentially be useful for searches related to clandestine burial sites. This technique, was originally documented by the British Army in the 1st World War. The RAG method is based on the construction of theme maps. RAG maps can facilitate the deployment of appropriate search assets (such as geophysics, probe or search dogs) and therefore applied to ground searches for the potential location of homicide graves or other buried objects (including weapons, explosives, etc.). RAG maps also may assist in the management of resources such as the deployment of search personnel, search teams and dogs. A GIS RAG (Red-Amber-Green) system related to a search for a homicide grave was applied to a test site in Italy, simulating the concealment of a victim in the area of Alì. This is an area of hill in Sicily, characterized by Palaeozoic phyllites. It was assumed during this test that information was provided by an observer who saw a suspect carrying tools on his land during daylight hours. A desktop study of the rural area was first implemented. Data was collated from previous geological, geomorphological, hydrogeological, geophysical and land use surveys. All these data were stored and independently analysed in a GIS using ArcGIS software. For the development of the GIS-based RAG map a digital elevation model (DEM) including a digital surface model (DTS) and digital terrain model (DTM) types were used. These were integrated with data from soil surveys to provide a preliminary assessment of "diggability" - including the possible thickness of loose superficial deposits and soils. Data were stored in different layers within the GIS. These included the delineation of the search area with consideration

  2. Genetic variations in vitamin D-related pathways and breast cancer risk in African American women in the AMBER consortium.

    Science.gov (United States)

    Yao, Song; Haddad, Stephen A; Hu, Qiang; Liu, Song; Lunetta, Kathryn L; Ruiz-Narvaez, Edward A; Hong, Chi-Chen; Zhu, Qianqian; Sucheston-Campbell, Lara; Cheng, Ting-Yuan David; Bensen, Jeannette T; Johnson, Candace S; Trump, Donald L; Haiman, Christopher A; Olshan, Andrew F; Palmer, Julie R; Ambrosone, Christine B

    2016-05-01

    Studies of genetic variations in vitamin D-related pathways and breast cancer risk have been conducted mostly in populations of European ancestry, and only sparsely in African Americans (AA), who are known for a high prevalence of vitamin D deficiency. We analyzed 24,445 germline variants in 63 genes from vitamin D-related pathways in the African American Breast Cancer Epidemiology and Risk (AMBER) consortium, including 3,663 breast cancer cases and 4,687 controls. Odds ratios (OR) were derived from logistic regression models for overall breast cancer, by estrogen receptor (ER) status (1,983 ER positive and 1,098 ER negative), and for case-only analyses of ER status. None of the three vitamin D-related pathways were associated with breast cancer risk overall or by ER status. Gene-level analyses identified associations with risk for several genes at a nominal p ≤ 0.05, particularly for ER- breast cancer, including rs4647707 in DDB2. In case-only analyses, vitamin D metabolism and signaling pathways were associated with ER- cancer (pathway-level p = 0.02), driven by a single gene CASR (gene-level p = 0.001). The top SNP in CASR was rs112594756 (p = 7 × 10(-5), gene-wide corrected p = 0.01), followed by a second signal from a nearby SNP rs6799828 (p = 1 × 10(-4), corrected p = 0.03). In summary, several variants in vitamin D pathways were associated with breast cancer risk in AA women. In addition, CASR may be related to tumor ER status, supporting a role of vitamin D or calcium in modifying breast cancer phenotypes.

  3. Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Aubert Sylvie

    2009-03-01

    Full Text Available Abstract Background Presenilin proteins are part of a complex of proteins that can cleave many type I transmembrane proteins, including Notch Receptors and the Amyloid Precursor Protein, in the middle of the transmembrane domain. Dominant mutations in the human presenilin genes PS1 and PS2 lead to Familial Alzheimer's disease. Mutations in the Caenorhabditis elegans sel-12 presenilin gene cause a highly penetrant egg-laying defect due to reduction of signalling through the lin-12/Notch receptor. Mutations in six spr genes (for suppressor of presenilin are known to strongly suppress sel-12. Mutations in most strong spr genes suppress sel-12 by de-repressing the transcription of the largely functionally equivalent hop-1 presenilin gene. However, how mutations in the spr-2 gene suppress sel-12 is unknown. Results We show that spr-2 mutations increase the levels of sel-12 transcripts with Premature translation Termination Codons (PTCs in embryos and L1 larvae. mRNA transcripts from sel-12 alleles with PTCs undergo degradation by a process known as Nonsense Mediated Decay (NMD. However, spr-2 mutations do not appear to affect NMD. Mutations in the smg genes, which are required for NMD, can restore sel-12(PTC transcript levels and ameliorate the phenotype of sel-12 mutants with amber PTCs. However, the phenotypic suppression of sel-12 by smg genes is nowhere near as strong as the effect of previously characterized spr mutations including spr-2. Consistent with this, we have identified only two mutations in smg genes among the more than 100 spr mutations recovered in genetic screens. Conclusion spr-2 mutations do not suppress sel-12 by affecting NMD of sel-12(PTC transcripts and appear to have a novel mechanism of suppression. The fact that mutations in smg genes can ameliorate the phenotype of sel-12 alleles with amber PTCs suggests that some read-through of sel-12(amber alleles occurs in smg backgrounds.

  4. The Alberta moving beyond breast cancer (AMBER cohort study: a prospective study of physical activity and health-related fitness in breast cancer survivors

    Directory of Open Access Journals (Sweden)

    Courneya Kerry S

    2012-11-01

    Full Text Available Abstract Background Limited research has examined the association between physical activity, health-related fitness, and disease outcomes in breast cancer survivors. Here, we present the rationale and design of the Alberta Moving Beyond Breast Cancer (AMBER Study, a prospective cohort study designed specifically to examine the role of physical activity and health-related fitness in breast cancer survivorship from the time of diagnosis and for the balance of life. The AMBER Study will examine the role of physical activity and health-related fitness in facilitating treatment completion, alleviating treatment side effects, hastening recovery after treatments, improving long term quality of life, and reducing the risks of disease recurrence, other chronic diseases, and premature death. Methods/Design The AMBER Study will enroll 1500 newly diagnosed, incident, stage I-IIIc breast cancer survivors in Alberta, Canada over a 5 year period. Assessments will be made at baseline (within 90 days of surgery, 1 year, and 3 years consisting of objective and self-reported measurements of physical activity, health-related fitness, blood collection, lymphedema, patient-reported outcomes, and determinants of physical activity. A final assessment at 5 years will measure patient-reported data only. The cohort members will be followed for an additional 5 years for disease outcomes. Discussion The AMBER cohort will answer key questions related to physical activity and health-related fitness in breast cancer survivors including: (1 the independent and interactive associations of physical activity and health-related fitness with disease outcomes (e.g., recurrence, breast cancer-specific mortality, overall survival, treatment completion rates, symptoms and side effects (e.g., pain, lymphedema, fatigue, neuropathy, quality of life, and psychosocial functioning (e.g., anxiety, depression, self-esteem, happiness, (2 the determinants of physical activity and

  5. Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3.

    Science.gov (United States)

    Ciarkowski, Jerzy; Łuczak, Sylwia; Jagieła, Dawid; Sikorska, Emilia; Wójcik, Jacek; Oleszczuk, Marta; Izdebski, Jan

    2012-02-01

    Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-D-Daa-Phe-Daa-NH₂ (Daa=diamino acid): 1 combining D-Dab² (α,γ-diaminobutyryl) with Lys⁴, and 2 -D-Dap² (α,β-diaminopropionyl) with Orn⁴. The ω-amino groups of D-Daa² and Daa⁴ are coupled with C=O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent μ/δ opioid peptides, respectively. To the current task, we took from an earlier work (Filip et al, J. Pept. Sci. 11 (2005) 347-352) the NMR NOE- and J-data in H₂O/D₂O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach (Groth et al, J. Biomol. NMR 15 (1999) 315-330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ(JNHαH) ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ(JNHαH) = 0.8 - 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ(NOE) in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose "overfitted" into the final σ(J) in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an

  6. New genus and species of broad-nosed weevils from Baltic amber and notes on fossils of the subfamily Entiminae (Coleoptera, Curculionidae

    Directory of Open Access Journals (Sweden)

    Nikolai Yunakov

    2011-12-01

    Full Text Available Arostropsis groehni gen. et sp. n. is described from Baltic amber and temporarily placed in the tribe Naupactini. It differs from all recent Naupactini genera with open corbels by very short and flattened scape, distinct lateral carina of the pronotum and elytra, and the rostrum distinctly narrower than the head capsule. The shape of head in the extinct genus is somewhat similar to that of the extant Naupactini genera with enclosed corbels (Platyomus Sahlberg, 1823 and Aptolemus Schoenherr, 1842, but differs in the slender body, open corbels, very short antennal scape and epifrons without a median sulcus (only a longitudinal depression is slightly visible. It is also similar to the Tanymecine genus Pandeleteius Schoenherr, 1834 in general appearance, but distinct by the straight anterior edge of the pronotum, lack of postocular spurs, lobes, and vibrissae, a slightly sloping elytral declivity, lateral ridges on the pronotum, subflattened antennal scape, elongate rostrum, and sparsely setose epistome. A new synonymy of the generic names Protonaupactus Zherikhin, 1971 and Sucinophyllobius Wanat & Borowiec, 1986, syn. n., is established. The Madagascan genus Corecaulus Fairmaire, 1903 is transferred from the tribe Naupactini to the Brachyderini because of its connate claws and the similarity in chaetotaxy of the epistomal area with African and Madagascar Brachyderini genera. A key to the identification of known Baltic amber genera of Entiminae is proposed. A checklist of the prepleistocene fossil Entiminae, based on V.V. Zherikhin’s data, with remarks and corrections, is presented.

  7. AMBER/VLTI high spectral resolution observations of the Br$\\gamma$ emitting region in HD 98922. A compact disc wind launched from the inner disc region

    CERN Document Server

    Garatti, A Caratti o; Lopez, R Garcia; Kraus, S; Schertl, D; Grinin, V P; Weigelt, G; Hofmann, K -H; Massi, F; Lagarde, S; Vannier, M; Malbet, F

    2015-01-01

    We analyse the main physical parameters and the circumstellar environment of the young Herbig Be star HD 98922. We present AMBER/VLTI high spectral resolution (R =12000) interferometric observations across the Br$\\gamma$ line, accompanied by UVES high-resolution spectroscopy and SINFONI-AO assisted near-infrared integral field spectroscopic data. To interpret our observations, we develop a magneto-centrifugally driven disc-wind model. Our analysis of the UVES spectrum shows that HD 98922 is a young (~5x10^5 yr) Herbig Be star (SpT=B9V), located at a distance of 440(+60-50) pc, with a mass accretion rate of ~9+/-3x10^(-7) M_sun yr^(-1). SINFONI K-band AO-assisted imaging shows a spatially resolved circumstellar disc-like region (~140 AU in diameter) with asymmetric brightness distribution. Our AMBER/VLTI UT observations indicate that the Br$\\gamma$ emitting region (radius ~0.31+/-0.04 AU) is smaller than the continuum emitting region (inner dust radius ~0.7+/-0.2 AU), showing significant non-zero V-shaped diff...

  8. Resolving the asymmetric inner wind region of the yellow hypergiant IRC+10420 with VLTI/AMBER in low and high spectral resolution mode

    CERN Document Server

    Driebe, T; Hofmann, K -H; Ohnaka, K; Kraus, S; Millour, F; Murakawa, K; Schertl, D; Weigelt, G; Petrov, R; Wittkowski, M; Hummel, C A; Bouquin, J B Le; Merand, A; Schöller, M; Massi, F; Stee, P; Tatulli, E

    2009-01-01

    We obtained near-infrared long-baseline interferometry of IRC+10420 with the AMBER instrument of ESO's Very Large Telescope Interferometer (VLTI) in low and high spectral resolution (HR) mode to probe the photosphere and the innermost circumstellar environment of this rapidly evolving yellow hypergiant. In the HR observations, the visibilities show a noticeable drop across the Brackett gamma (BrG) line on all three baselines, and we found differential phases up to -25 degrees in the redshifted part of the BrG line and a non-zero closure phase close to the line center. The calibrated visibilities were corrected for AMBER's limited field-of-view to appropriately account for the flux contribution of IRC+10420's extended dust shell. We derived FWHM Gaussian sizes of 1.05 +/- 0.07 and 0.98 +/- 0.10 mas for IRC+10420's continuum-emitting region in the H and K bands, respectively, and the BrG-emitting region can be fitted with a geometric ring model with a diameter of 4.18 +0.19/-0.09 mas, which is approximately 4 t...

  9. Tracing jet emission at the base of a high-mass YSO. First AMBER/VLTI observations of the Br\\gamma emission in IRAS 13481-6124

    CERN Document Server

    Garatti, A Caratti o; Weigelt, G; Schertl, D; Hofmann, K -H; Kraus, S; Oudmaijer, R D; de Wit, W J; Sanna, A; Lopez, R Garcia; Kreplin, A; Ray, T P

    2016-01-01

    To probe the circumstellar environment of IRAS 13481-6124, a 20 M_sun high-mass young stellar object (HMYSO) with a parsec-scale jet and accretion disc, we investigate the origin of its Br\\gamma-emission line through NIR interferometry. We present the first AMBER/VLTI observations of the Br\\gamma-emitting region in an HMYSO at R~1500. Our AMBER/VLTI observations reveal a spatially and spectrally resolved Br\\gamma-line in emission with a strong P Cygni profile, indicating outflowing matter with a terminal velocity of ~500 km/s. Visibilities, differential phases, and closure phases are detected in our observations within the spectral line and in the adjacent continuum. Both total visibilities (continuum plus line emitting region) and pure-line visibilities indicate that the Br\\gamma-emitting region is more compact (2-4 mas in diameter or ~6-13 au at 3.2 kpc) than the continuum-emitting region (~5.4 mas or ~17 au). The absorption feature is also spatially resolved at the longest baselines (81 and 85 m) and has a...

  10. Stable carbon isotopes of C3 plant resins and ambers record changes in atmospheric oxygen since the Triassic

    Science.gov (United States)

    Tappert, Ralf; McKellar, Ryan C.; Wolfe, Alexander P.; Tappert, Michelle C.; Ortega-Blanco, Jaime; Muehlenbachs, Karlis

    2013-11-01

    Estimating the partial pressure of atmospheric oxygen (pO2) in the geological past has been challenging because of the lack of reliable proxies. Here we develop a technique to estimate paleo-pO2 using the stable carbon isotope composition (δ13C) of plant resins-including amber, copal, and resinite-from a wide range of localities and ages (Triassic to modern). Plant resins are particularly suitable as proxies because their highly cross-linked terpenoid structures allow the preservation of pristine δ13C signatures over geological timescales. The distribution of δ13C values of modern resins (n = 126) indicates that (a) resin-producing plant families generally have a similar fractionation behavior during resin biosynthesis, and (b) the fractionation observed in resins is similar to that of bulk plant matter. Resins exhibit a natural variability in δ13C of around 8‰ (δ13C range: -31‰ to -23‰, mean: -27‰), which is caused by local environmental and ecological factors (e.g., water availability, water composition, light exposure, temperature, nutrient availability). To minimize the effects of local conditions and to determine long-term changes in the δ13C of resins, we used mean δ13C values (δ13Cmeanresin) for each geological resin deposit. Fossil resins (n = 412) are generally enriched in 13C compared to their modern counterparts, with shifts in δ13Cmeanresin of up to 6‰. These isotopic shifts follow distinctive trends through time, which are unrelated to post-depositional processes including polymerization and diagenesis. The most enriched fossil resin samples, with a δ13Cmeanresin between -22‰ and -21‰, formed during the Triassic, the mid-Cretaceous, and the early Eocene. Experimental evidence and theoretical considerations suggest that neither change in pCO2 nor in the δ13C of atmospheric CO2 can account for the observed shifts in δ13Cmeanresin. The fractionation of 13C in resin-producing plants (Δ13C), instead, is primarily influenced by

  11. X-shooter, NACO, and AMBER observations of the LBV Pistol Star \\footnote{Based on ESO runs 85.D-0182A, 085.D-0625AC}

    CERN Document Server

    Martayan, Christophe; Bouquin, Jean-Baptiste Le; Merand, Antoine; Montagnier, Guillaume; Selman, Fernando; Girard, Julien; Fox, Andrew; Baade, Dietrich; Fremat, Yves; Lobel, Alex; Martins, Fabrice; Patru, Fabien; Rivinius, Thomas; Sana, Hugues; Stefl, Stan; Zorec, Jean; Semaan, Thierry

    2010-01-01

    We present multi-instruments and multi-wavelengths observations of the famous LBV star Pistol Star. These observations are part of a larger program about early O stars at different metallicities. The Pistol star has been claimed as the most massive star known, with 250 solar masses. We present the preliminary results based on X-Shooter spectra, as well as the observations performed with the VLTI-AMBER and the VLT-NACO adaptive optics. The X-shooter spectrograph allows to obtain simultaneously a spectrum from the UV to the K-band with a resolving power of $\\sim$15000. The preliminary results obtained indicate that Pistol Star has similar properties of Eta Car, including shells of matter, but also the binarity. Other objects of the program, here briefly presented, were selected for their particular nature: early O stars with mass discrepancies between stellar evolution models and observations, discrepancies with the wind momentum luminosity relation.

  12. A new species of Phyllopsora (Lecanorales, lichen-forming Ascomycota) from Dominican amber, with remarks on the fossil history of lichens.

    Science.gov (United States)

    Rikkinen, Jouko; Poinar, George O

    2008-01-01

    Phyllopsora dominicanus sp. nov. (Bacidiaceae, Lecanorales, lichen-forming Ascomycota) is described and illustrated from Dominican amber. The diagnostic features of the lichen include a minute subfolious thallus of lacinulate, ascending squamules, a well-developed upper cortex, and a net-like pseudocortex on the lower surface. The algal symbionts are unicellular green algae, forming a distinct layer immediately below the upper cortex. The fossil demonstrates that distinguishing features of Phyllopsora have remained unchanged for tens of millions of years. The fossil also provides the first detailed views of mycobiont-photobiont contacts in Tertiary green algal lichens. The mycobiont hyphae formed apical and intercalary appressoria by pressing closely against the photobiont cells. This indicates that a conserved maintenance of structure is also seen in the fine details of the fungal-algal interface.

  13. Strain-compensated (Ga,In)N/(Al,Ga)N/GaN multiple quantum wells for improved yellow/amber light emission

    Energy Technology Data Exchange (ETDEWEB)

    Lekhal, K.; Damilano, B., E-mail: bd@crhea.cnrs.fr; De Mierry, P.; Vennéguès, P. [CRHEA-CNRS, Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, Valbonne 06560 (France); Ngo, H. T.; Rosales, D.; Gil, B. [Laboratoire Charles Coulomb, CNRS-INP-UMR 5221, Université Montpellier 2, F-34095 Montpellier (France); Hussain, S. [CRHEA-CNRS, Centre de Recherche sur l' Hétéro-Epitaxie et ses Applications, Centre National de la Recherche Scientifique, Valbonne 06560 (France); Université de Nice Sophia Antipolis, Parc Valrose, 28 av. Valrose, 06108 Nice cedex 2 (France)

    2015-04-06

    Yellow/amber (570–600 nm) emitting In{sub x}Ga{sub 1−x}N/Al{sub y}Ga{sub 1−y}N/GaN multiple quantum wells (QWs) have been grown by metal organic chemical vapor deposition on GaN-on- sapphire templates. When the (Al,Ga)N thickness of the barrier increases, the room temperature photoluminescence is red-shifted while its yield increases. This is attributed to an increase of the QW internal electric field and an improvement of the material quality due to the compensation of the compressive strain of the In{sub x}Ga{sub 1−x}N QWs by the Al{sub y}Ga{sub 1−y}N layers, respectively.

  14. A review and phylogeny of Scarabaeine dung beetle fossils (Coleoptera: Scarabaeidae: Scarabaeinae, with the description of two Canthochilum species from Dominican amber

    Directory of Open Access Journals (Sweden)

    Sergei Tarasov

    2016-05-01

    Full Text Available Despite the increasing rate of systematic research on scarabaeine dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae, their fossil record has remained largely unrevised. In this paper, we review all 33 named scarabaeine fossils and describe two new species from Dominican amber (Canthochilum alleni sp.n., Canthochilum philipsivieorum sp.n.. We provide a catalogue of all fossil Scarabaeinae and evaluate their assignment to this subfamily, based primarily on the original descriptions but also, where possible, by examining the type specimens. We suggest that only 21 fossil taxa can be reliably assigned to the Scarabaeinae, while the remaining 14 should be treated as doubtful Scarabaeinae. The doubtful scarabaeines include the two oldest dung beetle fossils known from the Cretaceous and we suggest excluding them from any assessments of the minimum age of scarabaeine dung beetles. The earliest reliably described scarabaeine fossil appears to be Lobateuchus parisii, known from Oise amber (France, which shifts the minimum age of the Scarabaeinae to the Eocene (53 Ma. We scored the best-preserved fossils, namely Lobateuchus and the two Canthochilum species described herein, into the character matrix used in a recent morphology-based study of dung beetles, and then inferred their phylogenetic relationships with Bayesian and parsimony methods. All analyses yielded consistent phylogenies where the two fossil Canthochilum are placed in a clade with the extant species of Canthochilum, and Lobateuchus is recovered in a clade with the extant genera Ateuchus and Aphengium. Additionally, we evaluated the distribution of dung beetle fossils in the light of current global dung beetle phylogenetic hypotheses, geological time and biogeography. The presence of only extant genera in the late Oligocene and all later records suggests that the main present-day dung beetle lineages had already been established by the late Oligocene–mid Miocene.

  15. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA.

    Science.gov (United States)

    Karakas, Esra; Taveneau, Cyntia; Bressanelli, Stéphane; Marchi, Massimo; Robert, Bruno; Abel, Stéphane

    2017-01-01

    In this paper, we describe the derivation and the validation of original RESP atomic partial charges for the N, N-dimethyl-dodecylamine oxide (LDAO) surfactant. These charges, designed to be fully compatible with all the AMBER force fields, are at first tested against molecular dynamics simulations of pure LDAO micelles and with a fragment of the lipid kinase PIK4A (DI) modeled with the QUARK molecular modeling server. To model the micelle, we used two distinct AMBER force fields (i.e. Amber99SB and Lipid14) and a variety of starting conditions. We find that the micelle structural properties (such as the shape, size, the LDAO headgroup hydration, and alkyl chain conformation) slightly depend on the force field but not on the starting conditions and more importantly are in good agreement with experiments and previous simulations. We also show that the Lipid14 force field should be used instead of the Amber99SB one to better reproduce the C(sp3)C(sp3)C(sp3)C(sp3) conformation in the surfactant alkyl chain. Concerning the simulations with LDAO-DI protein, we carried out different runs at two NaCl concentrations (i.e. 0 and 300 mM) to mimic, in the latter case, the experimental conditions. We notice a small dependence of the simulation results with the LDAO parameters and the salt concentration. However, we find that in the simulations, three out of four tryptophans of the DI protein are not accessible to water in agreement with our fluorescence spectroscopy experiments reported in the paper.

  16. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

    Science.gov (United States)

    Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jurečka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

  17. Effect of some parameters in the response of the Perspex 3042, Lot L amber dosemeters; Efectos de algunos parametros en la respuesta de los dosimetros ambar Perspex 3042, Lote L

    Energy Technology Data Exchange (ETDEWEB)

    Prieto M, E.F.; Barrera G, G. [Centro de Aplicaciones Tecnologicas y Desarrollo Nuclear (CEADEN). Calle 30, No. 502, esq. 5ta. Avenida, Playa, Ciudad de La Habana (Cuba)]. e-mail: efprieto@ceaden.edu.cu

    2004-07-01

    The answer of the dosimetric systems is affected by several factors, for what should know as these factors they influence in each one of the different dosimetric systems and by this way to minimize its effect in the value of the absorbed dose and to obtain exact dose values. One of the dosimetric systems more used in the high dose dosimetry like routine dosemeter for the control of the irradiation process are the Perspex dosemeters, for their speed in the obtaining the information, their easy manipulation and the precision that they present. To this dosemeters group they belong the same as the Red and Clear the Amber, which are adequate for the measurement of the radiation dose in the range of high doses. The objective of the present work is to obtain the calibration curves of the dosemeters Amber Perspex 3042, Lot L under our work conditions, like they are the irradiation temperatures and of storage and to know the influence of the rate dose in the value of the absorbed dose for different measurement wavelengths, as well as, the relationship among the one post-irradiation time and the specific absorbance value induced in function of the absorbed dose. (Author)

  18. When Green and Amber Meet

    Institute of Scientific and Technical Information of China (English)

    Francisco; Little

    2013-01-01

    Through the ages Scotch whisky has been the drink of kings, politicians, entertainers and those who aspire to the finer things in life.It’s traditionally drunk with a splash of water,straight up or with the debonair "on the rocks" by-line.

  19. Las dos versiones de la De Psalterii Anglicani exemplari animaduersio de Benito Arias Montano en la Biblia Políglota de Amberes

    Directory of Open Access Journals (Sweden)

    Dávila Pérez, Antonio

    2014-06-01

    Full Text Available In the eighth and final volume of the Antwerp Polyglot Arias Montano published a short text titled De Psalterii Anglicani Exemplari Animaduersio. In his defense of the Hebrew original of the Old Testament, Montano set out to warn the reader that some of the more esteemed manuscripts by the so-called Hebrew-haters of his time were of little value. For this purpose, Arias Montano examined a Hebrew manuscript of the Psalter considered to be of particular antiquity and significance by the powerful bishop Wilhelm D. Lindanus, and concluded that it was in fact recent and quite worthless in many aspects, thereby fiercely attacking the latter’s scholarly reputation. This attack, based in part on a false accusation, was the beginning of a scholarly controversy lasting over fifteen years. The present essay calls attention to the fact that two versions of the Animaduersio, very different from each other, can be found in surviving copies of the Polyglot Bible. In order to illuminate the circumstances that led to these versions, the author proposes a threefold goal: (1 to gather the Latin text and the Spanish translation of the two versions of the Animaduersio; (2 to examine the reasons why Arias Montano rewrote his text in the light of the private correspondence of both scholars; (3 and to propose an approximate date for each of the versions.En el octavo y último volumen de la Biblia Regia de Amberes Benito Arias Montano publicaba un breve texto titulado De Psalterii Anglicani exemplari animaduersio. En el marco de su defensa del original hebreo del Antiguo Testamento, su autor consideraba necesario advertir al lector de que algunos de los manuscritos más apreciados por los llamados «misohebreos» de su tiempo carecían de todo valor. Para ello, Arias Montano examinó un manuscrito hebreo del salterio elogiado como muy antiguo y relevante por el poderoso obispo Guillermo D. Lindano, y concluía que el códice era reciente y de escaso valor, cargando de

  20. Clumpy dust clouds and extended atmosphere of the AGB star W Hydrae revealed with VLT/SPHERE-ZIMPOL and VLTI/AMBER. II. Time variations between pre-maximum and minimum light

    Science.gov (United States)

    Ohnaka, K.; Weigelt, G.; Hofmann, K.-H.

    2017-01-01

    Aims: Our recent visible polarimetric images of the well-studied AGB star W Hya taken at pre-maximum light (phase 0.92) with VLT/SPHERE-ZIMPOL have revealed clumpy dust clouds close to the star at 2 R⋆. We present second-epoch SPHERE-ZIMPOL observations of W Hya at minimum light (phase 0.54) as well as high-spectral resolution long-baseline interferometric observations with the AMBER instrument at the Very Large Telescope Interferometer (VLTI). Methods: We observed W Hya with VLT/SPHERE-ZIMPOL at three wavelengths in the continuum (645, 748, and 820 nm), in the Hα line at 656.3 nm, and in the TiO band at 717 nm. The VLTI/AMBER observations were carried out in the wavelength region of the CO first overtone lines near 2.3 μm with a spectral resolution of 12 000. Results: The high-spatial resolution polarimetric images obtained with SPHERE-ZIMPOL have allowed us to detect clear time variations in the clumpy dust clouds as close as 34-50 mas (1.4-2.0 R⋆) to the star. We detected the formation of a new dust cloud as well as the disappearance of one of the dust clouds detected at the first epoch. The Hα and TiO emission extends to 150 mas ( 6 R⋆), and the Hα images obtained at two epochs reveal time variations. The degree of linear polarization measured at minimum light, which ranges from 13 to 18%, is higher than that observed at pre-maximum light. The power-law-type limb-darkened disk fit to the AMBER data in the continuum results in a limb-darkened disk diameter of 49.1 ± 1.5 mas and a limb-darkening parameter of 1.16 ± 0.49, indicating that the atmosphere is more extended with weaker limb-darkening compared to pre-maximum light. Our Monte Carlo radiative transfer modeling shows that the second-epoch SPHERE-ZIMPOL data can be explained by a shell of 0.1 μm grains of Al2O3, Mg2SiO4, and MgSiO3 with a 550 nm optical depth of 0.6 ± 0.2 and an inner and outer radii of 1.3 R⋆ and 10 ± 2R⋆, respectively. Our modeling suggests the predominance of small (0

  1. Clumpy dust clouds and extended atmosphere of the AGB star W Hya revealed with VLT/SPHERE-ZIMPOL and VLTI/AMBER II. Time variations between pre-maximum and minimum light

    CERN Document Server

    Ohnaka, Keiichi; Hofmann, Karl-Heinz

    2016-01-01

    Our recent visible polarimetric images of the well-studied AGB star W Hya taken at pre-maximum light (phase 0.92) with VLT/SPHERE-ZIMPOL have revealed clumpy dust clouds close to the star at ~2 Rstar. We present second-epoch SPHERE-ZIMPOL observations of W Hya at minimum light (phase 0.54) in the continuum (645, 748, and 820 nm), in the Halpha line (656.3 nm), and in the TiO band (717 nm) as well as high-spectral resolution long-baseline interferometric observations in 2.3 micron CO lines with the AMBER instrument at the Very Large Telescope Interferometer (VLTI). The high-spatial resolution polarimetric images have allowed us to detect clear time variations in the clumpy dust clouds as close as 34--50~mas (1.4--2.0 Rstar) to the star. We detected the formation of a new dust cloud and the disappearance of one of the dust clouds detected at the first epoch. The Halpha and TiO emission extends to ~150 mas (~6 Rstar), and the Halpha images reveal time variations. The degree of linear polarization is higher at mi...

  2. VLTI-AMBER velocity-resolved aperture-synthesis imaging of Eta Carinae with a spectral resolution of 12000. Studies of the primary star wind and innermost wind-wind collision

    CERN Document Server

    Weigelt, G; Schertl, D; Clementel, N; Corcoran, M F; Damineli, A; de Wit, W -J; Grellmann, R; Groh, J; Guieu, S; Gull, T; Heininger, M; Hillier, D J; Hummel, C A; Kraus, S; Madura, T; Mehner, A; Mérand, A; Millour, F; Moffat, A F J; Ohnaka, K; Patru, F; Petrov, R G; Rengaswamy, S; Richardson, N D; Rivinius, T; Schöller, M; Teodoro, M; Wittkowski, M

    2016-01-01

    Context. The mass loss from massive stars is not understood well. Eta Car is a unique object for studying the massive stellar wind during the LBV phase. It is also an eccentric binary with a period of 5.54 yr. The nature of both stars is uncertain, although we know from X-ray studies that there is a wind-wind collision whose properties change with orbital phase. Methods. Observations of Eta Car were carried out with the ESO VLTI and the AMBER instrument between approximately five and seven months before the August 2014 periastron passage. Velocity-resolved aperture-synthesis images were reconstructed from the spectrally dispersed interferograms. Interferometric studies can provide information on the binary orbit, the primary wind, and the wind collision. Results. We present velocity-resolved aperture-synthesis images reconstructed in more than 100 different spectral channels distributed across the Br Gamma 2.166 micrometer emission line. The intensity distribution of the images strongly depends on wavelength....

  3. Non-invasive determination of ethanol, propylene glycol and water in a multi-component pharmaceutical oral liquid by direct measurement through amber plastic bottles using Fourier transform near-infrared spectroscopy.

    Science.gov (United States)

    Broad, N W; Jee, R D; Moffat, A C; Eaves, M J; Mann, W C; Dziki, W

    2000-11-01

    Fourier transform near-infrared (FT-NIR) spectroscopy was used to quantify rapidly the ethanol (34-49% v/v), propylene glycol (20-35% v/v) and water (11-20% m/m) contents within a multi-component pharmaceutical oral liquid by measurement directly through the amber plastic bottle packaging. Spectra were collected in the range 7302-12,000 cm-1 and calibration models set-up using partial least-squares regression (PLSR) and multiple linear regression. Reference values for the three components were measured using capillary gas chromatography (ethanol and propylene glycol) and Karl Fischer (water) assay procedures. The calibration and test sets consisted of production as well as laboratory batches that were made to extend the concentration ranges beyond the natural production variation. The PLSR models developed gave standard errors of prediction (SEP) of 1.1% v/v for ethanol, 0.9% v/v for propylene glycol and 0.3% m/m for water. For each component the calibration model was validated in terms of: linearity, repeatability, intermediate precision and robustness. All the methods produced statistically favourable outcomes. Ten production batches independent of the calibration and test sets were also challenged against the PLSR models, giving SEP values of 1.3% v/v (ethanol), 1.0% v/v (propylene glycol) and 0.2% m/m (water). NIR transmission spectroscopy allowed all three liquid constituents to be non-invasively measured in under 1 min.

  4. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification.

    Directory of Open Access Journals (Sweden)

    James A J Arpino

    Full Text Available Expanded genetic code approaches are a powerful means to add new and useful chemistry to proteins at defined residues positions. One such use is the introduction of non-biological reactive chemical handles for site-specific biocompatible orthogonal conjugation of proteins. Due to our currently limited information on the impact of non-canonical amino acids (nAAs on the protein structure-function relationship, rational protein engineering is a "hit and miss" approach to selecting suitable sites. Furthermore, dogma suggests surface exposed native residues should be the primary focus for introducing new conjugation chemistry. Here we describe a directed evolution approach to introduce and select for in-frame codon replacement to facilitate engineering proteins with nAAs. To demonstrate the approach, the commonly reprogrammed amber stop codon (TAG was randomly introduced in-frame in two different proteins: the bionanotechnologically important cyt b(562 and therapeutic protein KGF. The target protein is linked at the gene level to sfGFP via a TEV protease site. In absence of a nAA, an in-frame TAG will terminate translation resulting in a non-fluorescent cell phenotype. In the presence of a nAA, TAG will encode for nAA incorporation so instilling a green fluorescence phenotype on E. coli. The presence of endogenously expressed TEV proteases separates in vivo target protein from its fusion to sfGFP if expressed as a soluble fusion product. Using this approach, we incorporated an azide reactive handle and identified residue positions amenable to conjugation with a fluorescence dye via strain-promoted azide-alkyne cycloaddition (SPAAC. Interestingly, best positions for efficient conjugation via SPAAC were residues whose native side chain were buried through analysis of their determined 3D structures and thus may not have been chosen through rational protein engineering. Molecular modeling suggests these buried native residues could become partially

  5. Retractación o pertinacia. Vicisitudes de un tratado parcialmente perdido de Arias Montano al hilo de la polémica en torno a la Biblia Políglota de Amberes

    Directory of Open Access Journals (Sweden)

    Dávila Pérez, Antonio

    2011-12-01

    Full Text Available The aim of this article is to bring to light the origin, chronology and possible contents of a treatise by Arias Montano, partially lost until today. That treatise was the culmination of the long and fierce controversy that Arias Montano and Wilhem van der Lindt were involved in the last quarter of the 16th Century in the context of the polemics between supporters and detractors of the Hebrew original text of the Bible. Yet the main cause of this scientific enmity was a defamatory writing against Lindano published by Arias Montano in the Polyglot Bible of Antwerp. Taking as a starting point Arias Montano’s and Lindano’s Latin correspondence we will try to reconstruct a non-well-known story of complaints and retractions between two theologians whose ultimate goal is to preserve their own fame.

    El objetivo de este artículo es dar a conocer el origen, cronología y posibles contenidos de un tratado de Arias Montano parcialmente perdido hasta el día de hoy. Dicho tratado fue el colofón de la larga controversia que Arias Montano y Guillermo Lindano mantuvieron en el último cuarto del siglo XVI en el marco de la polémica entre defensores y detractores del original hebreo de la Biblia. Pero la causa principal de esta enemistad científica es un escrito difamatorio contra Lindano publicado por Arias Montano en la Biblia Políglota de Amberes. Tomando como punto de partida el epistolario latino de Arias Montano y Lindano se reconstruye aquí una historia no bien conocida de denuncias y retractaciones entre dos teólogos cuyo fin último es velar por su propia fama.

  6. VLTI-AMBER velocity-resolved aperture-synthesis imaging of η Carinae with a spectral resolution of 12 000. Studies of the primary star wind and innermost wind-wind collision zone

    Science.gov (United States)

    Weigelt, G.; Hofmann, K.-H.; Schertl, D.; Clementel, N.; Corcoran, M. F.; Damineli, A.; de Wit, W.-J.; Grellmann, R.; Groh, J.; Guieu, S.; Gull, T.; Heininger, M.; Hillier, D. J.; Hummel, C. A.; Kraus, S.; Madura, T.; Mehner, A.; Mérand, A.; Millour, F.; Moffat, A. F. J.; Ohnaka, K.; Patru, F.; Petrov, R. G.; Rengaswamy, S.; Richardson, N. D.; Rivinius, T.; Schöller, M.; Teodoro, M.; Wittkowski, M.

    2016-10-01

    Context. The mass loss from massive stars is not understood well. η Carinae is a unique object for studying the massive stellar wind during the luminous blue variable phase. It is also an eccentric binary with a period of 5.54 yr. The nature of both stars is uncertain, although we know from X-ray studies that there is a wind-wind collision whose properties change with orbital phase. Aims: We want to investigate the structure and kinematics of η Car's primary star wind and wind-wind collision zone with a high spatial resolution of ~6 mas (~14 au) and high spectral resolution of R = 12 000. Methods: Observations of η Car were carried out with the ESO Very Large Telescope Interferometer (VLTI) and the AMBER instrument between approximately five and seven months before the August 2014 periastron passage. Velocity-resolved aperture-synthesis images were reconstructed from the spectrally dispersed interferograms. Interferometric studies can provide information on the binary orbit, the primary wind, and the wind collision. Results: We present velocity-resolved aperture-synthesis images reconstructed in more than 100 different spectral channels distributed across the Brγ 2.166 μm emission line. The intensity distribution of the images strongly depends on wavelength. At wavelengths corresponding to radial velocities of approximately -140 to - 376 km s-1 measured relative to line center, the intensity distribution has a fan-shaped structure. At the velocity of - 277 km s-1, the position angle of the symmetry axis of the fan is ~126°. The fan-shaped structure extends approximately 8.0 mas (~18.8 au) to the southeast and 5.8 mas (~13.6 au) to the northwest, measured along the symmetry axis at the 16% intensity contour. The shape of the intensity distributions suggests that the obtained images are the first direct images of the innermost wind-wind collision zone. Therefore, the observations provide velocity-dependent image structures that can be used to test three

  7. Multichannel imaging with the AMBER FMCW SAR

    NARCIS (Netherlands)

    Otten, M.P.G.; Rossum, W.L. van; Graaf, M.W. van der; Vlothuizen, W.J.; Tan, R.G.

    2014-01-01

    An X-band Digital Array Synthetic Aperture Radar for a Short Range Tactical UAV is presented. The Frequency Modulated Continuous Wave radar principle in combination with digital beam forming over 24 receive channels is used to achieve low power and advanced imaging SAR capabilities on small platform

  8. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.

    Science.gov (United States)

    Yildirim, Ilyas; Kierzek, Elzbieta; Kierzek, Ryszard; Schatz, George C

    2014-12-11

    When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both

  9. Fútbol e identidades: la actuación de la selección española de fútbol en los Juegos Olímpicos de Amberes y París a través de su impacto en la prensa

    Directory of Open Access Journals (Sweden)

    Juan Antonio Simón Sanjurjo

    2014-03-01

    Full Text Available El presente artículo aborda el análisis histórico de las importantes transformaciones que vivirá el fútbol español en la primera mitad de los años veinte, a partir del estudio de la actuación de la selección española en los Juegos Olímpicos de Amberes (1920 y París (1924. Este estudio también pretende analizar el rol que la prensa y el fútbol tendrá en la construcción de la identidad nacional, así como en la creación de los nuevos ídolos deportivos, en un periodo de progresiva implantación del profesionalismo y en pleno proceso de desarrollo de la sociedad de masas.

  10. 针刺疗法配合琥珀散加减治疗气滞血瘀型卵巢巧克力样囊肿30例%Acupuncture Combined with Amber Powder in the Treatment of 30 Cases of Ovarian Chocolate Cyst with Qi Stagnation and Blood Stasis Type

    Institute of Scientific and Technical Information of China (English)

    韩凤娟; 盛霄燕; 田苗; 周扬; 王秀霞

    2015-01-01

    目的:探究针药结合治疗气滞血瘀型卵巢巧克力样囊肿的临床疗效。方法:60例符合诊断标准的气滞血瘀型卵巢巧克力样囊肿患者随机分为治疗组和对照组。对照组30例给予中药琥珀散加减治疗,治疗组30例在对照组的基础上加针刺治疗,连续用药3个月,经期停止治疗。观察两组治疗前后临床疗效、症状改善情况。结果:两组均可明显缓解患者的临床症状,治疗组和对照组总有效率分别为86.7%和76.7%,治疗组的临床疗效、症状改善情况优于对照组,且复发率和副反应的发生率低于对照组( P<0.05)。结论:针刺疗法配合琥珀散加减治疗气滞血瘀型卵巢巧克力样囊肿,症状明显改善,临床疗效满意。%Objective:To investigate the clinical efficacy of acupuncture combined with Amber powder on ovari-an chocolate cyst with Qi stagnation and blood stasis type.Methods:60 patients met the diagnostic criteria were randomly divided into treatment and control groups.The control group including 30 patients was given medicine Amber powder treatment,and the treatment group including 30 patients was on the basis of treatment in the con-trol group plus acupuncture,with continuous medication for 3 months and menstruation to stop treatment.Ob-serve the clinical efficacy, improvement of symptoms before and after treatment.Results:The two groups could significantly alleviate the clinical symptoms,and in the treatment group and the control group the total effective rates were 86.7%and 76.7%respectively.The clinical efficacy in the treatment group was better than that in the control group, and the relapse rate and incidence of side effects were lower than those in the control group ( P<0 .05 ) .Conclusion:Acupuncture with Amber powder for ovarian chocolate cyst with Qi stagnation and blood stasis type has a satisfactory efficacy,which can improve the symptoms obviously.

  11. Wharfedale(沃夫德尔) Amber

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    沃夫德尔推出Amber琥珀系列新产品,包括AM-20.1、AM-20.2两款书架箱,AM-20.3、AM-20.4、AM-20.5三款落地箱,一款中置音箱AM-20.CENTRE,一款环绕音箱AM-20SR。

  12. AMBER: An X-band FMCW digital beam forming synthetic aperture radar for a tactical UAV

    NARCIS (Netherlands)

    Graaf, M.W. van der; Otten, M.P.G.; Huizing, A.G.; Tan, R.G.; Caro Cuenca, M.; Ruizenaar, M.G.A.

    2013-01-01

    An X-band Digital Array Synthetic Aperture Radar for a Short Range Tactical UAV is presented. This system is demonstrated on a manned helicopter and motor glider. The Frequency Modulated Continuous Wave radar principle in combination with digital beam forming over 24 receive channels is used to meet

  13. Angular diameter estimation of interferometric calibrators - Example of lambda Gruis, calibrator for VLTI-AMBER

    CERN Document Server

    Cruzalebes, P; Sacuto, S; Bonneau, D; 10.1051/0004-6361/200913686

    2010-01-01

    Context. Accurate long-baseline interferometric measurements require careful calibration with reference stars. Small calibrators with high angular diameter accuracy ensure the true visibility uncertainty to be dominated by the measurement errors. Aims. We review some indirect methods for estimating angular diameter, using various types of input data. Each diameter estimate, obtained for the test-case calibrator star lambda Gru, is compared with the value 2.71 mas found in the Bord\\'e calibrator catalogue published in 2002. Methods. Angular size estimations from spectral type, spectral index, in-band magnitude, broadband photometry, and spectrophotometry give close estimates of the angular diameter, with slightly variable uncertainties. Fits on photometry and spectrophotometry need physical atmosphere models with "plausible" stellar parameters. Angular diameter uncertainties were estimated by means of residual bootstrapping confidence intervals. All numerical results and graphical outputs presented in this pap...

  14. Pre-maximum spectro-imaging of the Mira star T Lep with AMBER/VLTI

    CERN Document Server

    Bouquin, Jean-Baptiste Le; Renard, Stephanie; Thiebaut, Eric; Merand, Antoine; Verhoelst, Tijl

    2009-01-01

    Diffuse envelopes around Mira variables are among the most important sources influencing the chemical evolution of galaxies. However they represent an observational challenge because of their complex spectral features and their rapid temporal variability. We constrained the exact brightness distribution of the Mira star TLep with a model-independent analysis. We obtained single-epoch interferometric observations with a dataset continuous in the spectral domain (1.5-2.4mum) and in the spatial domain (baselines ranging from 11 to 96m). We performed a model independent image reconstruction for each spectral bin using the MIRA software. We completed the analysis by modeling the data with a simple star+layer model inspired from the images. Reconstructed images confirm the general picture of a central star partially obscured by the surrounding molecular shell of changing opacity. At 1.7mum, the shell becomes optically thin, with corresponding emission appearing as a ring circling the star. This is the first direct ...

  15. Amber Clifford-Napoleone, Queerness in heavy metal music: metal bent

    OpenAIRE

    Hill, Rosemary Lucy

    2016-01-01

    Metal Bent is an important book that sheds new light on the topic of gender and sexuality in metal music. Its aims are to queer metal and reconfigure discussion of the genre around gender and sexuality, and to move on from thinking about metal as just for “the straight boys” (3). These aims are achieved through a discussion of the style and media coverage of various musicians, and the results of a survey and interviews with queer metal fans. Central are the assertions that metal is queer and ...

  16. 琥珀王国——波兰%Poland: Amber Kingdom

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    提起波兰,人们自然会想到肖邦和居里夫人。肖邦是波兰人引以为骄傲的伟大作曲家和钢琴家。波兰首都华沙举办的五年一度的肖邦国际钢琴大赛,吸引着全世界好手角逐,成为国际音乐界的顶级盛事。出生于华沙的居里夫人是世界上第一个两次获得诺贝尔奖的女科学家,她为人类揭开原子的奥秘作出了巨大贡献。

  17. Latridius Usovae, a new Species of the Minute Brown Scavenger Beetles (Coleoptera, Latridiidae from Rovno Amber

    Directory of Open Access Journals (Sweden)

    Sergi T. A.

    2014-08-01

    Full Text Available Из позднеэоценового ровенского янтаря описан Latridius usovae Sergi et Perkovsky, sp. n. Новый вид отличается от Latridius alexeevi Bukejs, Kirejtshuk et Rucker, 2011 и L. jantaricus Borowiec, 1985 из балтийского янтаря формой переднеспинки, надкрыльев, средних и задних голеней.

  18. X-shooter, NACO, and AMBER observations of the LBV Pistol Star

    NARCIS (Netherlands)

    Martayan, C.; Blomme, R.; Bouquin, J.-B; Merand, A.; Montagnier, G.; Selman, F.; Girard, J.; Fox, A.; Baade, D.; Frémat, Y.; Lobel, A.; Martins, F.; Patru, F.; Rivinius, T.; Sana, H.A.A.; Stefl, S.; Zorec, J.; Semaan, T.

    2011-01-01

    We present multi-instrument and multi-wavelength observations of the famous LBV star Pistol Star. These observations are part of a larger program on early O stars at different metallicities. The Pistol Star has been claimed to be one of the most massive star known, with 250 solar masses. We present

  19. Photoluminescence behavior of amber light emitting GaInN-GaN heterostructures

    Science.gov (United States)

    Thi Ngo, Huong; Rosales, Daniel; Gil, Bernard; Valvin, Pierre; Damilano, Benjamin; Lekhal, Kaddour; de Mierry, Philippe

    2015-03-01

    We present an investigation of optical properties of yellow light emitting (Ga,In) N-based devices grown by metalorganic vapor phase epitaxy (MOVPE) on c-plane sapphire with different designs: well width, indium composition up to 23 percent in the well layer. Using time-resolved photoluminescence measurements collected in range of 8-300K, temperature - dependent photoluminescence decays are determined, they exhibit similar behaviors for all samples. These quantum devices always display a two-mode exponential decay with a long decay time and a short one in a ratio about four to five. The photoluminescence intensities measured from low temperature to room temperature give large values of activation temperature that indicate the increasing of the non-radiative recombination rate when the temperature increases. The average decay times are found by a procedure using fitting sigmoidal functions. These decay times increase exponentially with the indium concentration and the well width due to influence of quantum confined Stark effect on these devices. Finally, in order to estimate the performances of our samples, we plotted the decay times obtained versus product of the indium content and the well width together with others published decay times.

  20. Scalable Synthesis of the Amber Odorant 9-epi-Ambrox through a Biomimetic Cationic Cyclization/Nucleophilic Bromination Reaction.

    Science.gov (United States)

    Fontaneda, Raquel; Alonso, Pedro; Fañanás, Francisco J; Rodríguez, Félix

    2016-09-16

    A novel biomimetic nucleophilic bromocyclization reaction is used in the key step of a new and straightforward synthesis of 9-epi-Ambrox, an organic compound of high interest and value in the context of fragrances. This strategic reaction allows access to 9-epi-Ambrox on a gram scale from a dienyne derivative, easily available from geraniol, following a sequence of seven steps (35% global yield) with just one purification process. Both enantiomers of the molecule were obtained by a challenging enzymatic resolution.

  1. A new genus and species of ibis fly in the Lowermost Eocene amber of Oise (France) (Diptera: Athericidae).

    Science.gov (United States)

    Myskowiak, Justine; Nel, André

    2014-10-02

    A new athericid genus and species, Eoatrichops jeanbernardi, gen. n., sp. n., is described, based on four specimens from the Lowermost Eocene of Oise (France). Its external morphology is analyzed and compared with of all genera of Athericidae. Eoatrichops is very similar to the modern genus Atrichops Verrall, differences concern the wing venation and tibial spur formula. 

  2. Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium.

    Science.gov (United States)

    Zhang, Jianmin; Yao, Song; Hu, Qiang; Zhu, Qianqian; Liu, Song; Lunetta, Kathryn L; Haddad, Stephen A; Yang, Nuo; Shen, He; Hong, Chi-Chen; Sucheston-Campbell, Lara; Ruiz-Narvaez, Edward A; Bensen, Jeannette T; Troester, Melissa A; Bandera, Elisa V; Rosenberg, Lynn; Haiman, Christopher A; Olshan, Andrew F; Palmer, Julie R; Ambrosone, Christine B

    2016-10-01

    The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. Dysfunction of the Hippo pathway components has been linked with breast cancer stem cell regulation, as well as breast tumor progression and metastasis. TAZ, a key component of the Hippo pathway, is highly expressed in triple negative breast cancer; however, the associations of genetic variations in this important pathway with breast cancer risk remain largely unexplored. Here, we analyzed 8309 germline variants in 15 genes from the Hippo pathway with a total of 3663 cases and 4687 controls from the African American Breast Cancer Epidemiology and Risk Consortium. Odds ratios (ORs) were estimated using logistic regression for overall breast cancer, by estrogen receptor (ER) status (1983 ER positive and 1098 ER negative), and for case-only analyses by ER status. The Hippo signaling pathway was significantly associated with ER-negative breast cancer (pathway level P = 0.02). Gene-based analyses revealed that CDH1 was responsible for the pathway association (P CDH1 statistically significant after gene-level adjustment for multiple comparisons (P = 9.2×10(-5), corrected P = 0.02). rs142697907 in PTPN14 was associated with ER-positive breast cancer and rs2456773 in CDK1 with ER-negativity in case-only analysis after gene-level correction for multiple comparisons (corrected P < 0.05). In conclusion, common genetic variations in the Hippo signaling pathway may contribute to both ER-negative and ER+ breast cancer risk in AA women.

  3. VLTI/AMBER differential interferometry of the broad-line region of the quasar 3C273

    CERN Document Server

    Petrov, Romain G; Lagarde, Stéphane; Vannier, Martin; Rakshit, Suvendu; Marconi, Alessandro; Weigelt, Gerd

    2014-01-01

    Unveiling the structure of the Broad Line Region (BLR) of AGNs is critical to understand the quasar phenomenon. Resolving a few BLRs by optical interferometry will bring decisive information to confront, complement and calibrate the reverberation mapping technique, basis of the mass-luminosity relation in quasars. BLRs are much smaller than the angular resolution of the VLT and Keck interferometers and they can be resolved only by differential interferometry very accurate measurements of differential visibility and phase as a function of wavelength. The latter yields the photocenter variation with wavelength, and constrains the size, position and velocity law of various regions of the BLR. AGNs are below the magnitude limit for spectrally resolved interferometry set by currently available fringe trackers. A new "blind" observation method and a data processing based on the accumulation of 2D Fourier power and cross spectra permitted us to obtain the first spectrally resolved interferometric observation of a BL...

  4. 7 CFR 51.2282 - Tolerances for color.

    Science.gov (United States)

    2010-01-01

    ... than light amber). Amber 10 percent. 1 See illustration of this term on color chart. ... Darker than extra light 1 Darker than light 1 Darker than light amber 1 Darker than amber 1 Extra light 15 percent 2 percent (included in 15 percent darker than extra light) Light 15 percent 2...

  5. Application of Argonne's Glass Furnace Model to longhorn glass corporation oxy-fuel furnace for the production of amber glass.

    Energy Technology Data Exchange (ETDEWEB)

    Golchert, B.; Shell, J.; Jones, S.; Energy Systems; Shell Glass Consulting; Anheuser-Busch Packaging Group

    2006-09-06

    The objective of this project is to apply the Argonne National Laboratory's Glass Furnace Model (GFM) to the Longhorn oxy-fuel furnace to improve energy efficiency and to investigate the transport of gases released from the batch/melt into the exhaust. The model will make preliminary estimates of the local concentrations of water, carbon dioxide, elemental oxygen, and other subspecies in the entire combustion space as well as the concentration of these species in the furnace exhaust gas. This information, along with the computed temperature distribution in the combustion space may give indications on possible locations of crown corrosion. An investigation into the optimization of the furnace will be performed by varying several key parameters such as the burner firing pattern, exhaust number/size, and the boost usage (amount and distribution). Results from these parametric studies will be analyzed to determine more efficient methods of operating the furnace that reduce crown corrosion. Finally, computed results from the GFM will be qualitatively correlated to measured values, thus augmenting the validation of the GFM.

  6. VLTI/AMBER spectro-interferometry of the late-type supergiants V766 Cen (=HR 5171 A), σ Oph, BM Sco, and HD 206859

    Science.gov (United States)

    Wittkowski, M.; Arroyo-Torres, B.; Marcaide, J. M.; Abellan, F. J.; Chiavassa, A.; Guirado, J. C.

    2017-01-01

    Aims: We add four warmer late-type supergiants to our previous spectro-interferometric studies of red giants and supergiants. Methods: We measure the near-continuum angular diameter, derive fundamental parameters, discuss the evolutionary stage, and study extended atmospheric atomic and molecular layers. Results: V766 Cen (=HR 5171 A) is found to be a high-luminosity (log L/L⊙ = 5.8 ± 0.4) source of effective temperature 4290 ± 760 K and radius 1490 ± 540 R⊙, located in the Hertzsprung-Russell (HR) diagram close to both the Hayashi limit and Eddington limit; this source is consistent with a 40 M⊙ evolutionary track without rotation and current mass 27-36 M⊙. V766 Cen exhibits Na i in emission arising from a shell of radius 1.5 RPhot and a photocenter displacement of about 0.1 RPhot. It shows strong extended molecular (CO) layers and a dusty circumstellar background component. The other three sources are found to have lower luminosities of about log L/L⊙ = 3.4-3.5, corresponding to 5-9 M⊙ evolutionary tracks. They cover effective temperatures of 3900 K to 5300 K and radii of 60-120 R⊙. They do not show extended molecular layers as observed for higher luminosity RSGs of our sample. BM Sco shows an unusually strong contribution by an over-resolved circumstellar dust component. Conclusions: V766 Cen is a red supergiant located close to the Hayashi limit instead of a yellow hypergiant already evolving back toward warmer effective temperatures as discussed in the literature. Our observations of the Na i line and the extended molecular layers suggest an optically thick pseudo-photosphere at about 1.5 RPhot at the onset of the wind. The stars σ Oph, BM Sco, and HD 206859 are more likely high-mass red giants instead of RSGs as implied by their luminosity class Ib. This leaves us with an unsampled locus in the HR diagram corresponding to luminosities log L/L⊙ 3.8-4.8 or masses 10-13 M⊙, possibly corresponding to the mass region where stars explode as (type II-P) supernovae during the red supergiant stage. With V766 Cen, we now confirm that our previously found relation of increasing strength of extended molecular layers with increasing luminosities extends to double our previous luminosities and up to the Eddington limit. This might further point to steadily increasing radiative winds with increasing luminosity. Based on observations made with the VLT Interferometer (VLTI) at Paranal Observatory under program ID 093.D-0014.

  7. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    Energy Technology Data Exchange (ETDEWEB)

    MacElrevey, Celeste; Wedekind, Joseph E., E-mail: joseph-wedekind@urmc.rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States)

    2005-12-01

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.

  8. Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair.

    Science.gov (United States)

    Ko, Jae-hyeong; Llopis, Paula Montero; Heinritz, Jennifer; Jacobs-Wagner, Christine; Söll, Dieter

    2013-01-01

    While translational read-through of stop codons by suppressor tRNAs is common in many bacteria, archaea and eukaryotes, this phenomenon has not yet been observed in the α-proteobacterium Caulobacter crescentus. Based on a previous report that C. crescentus and Escherichia coli tRNA(His) have distinctive identity elements, we constructed E. coli tRNA(His) CUA, a UAG suppressor tRNA for C. crescentus. By examining the expression of three UAG codon- containing reporter genes (encoding a β-lactamase, the fluorescent mCherry protein, or the C. crescentus xylonate dehydratase), we demonstrated that the E. coli histidyl-tRNA synthetase/tRNA(His) CUA pair enables in vivo UAG suppression in C. crescentus. E. coli histidyl-tRNA synthetase (HisRS) or tRNA(His) CUA alone did not achieve suppression; this indicates that the E. coli HisRS/tRNA(His) CUA pair is orthogonal in C. crescentus. These results illustrate that UAG suppression can be achieved in C. crescentus with an orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pair.

  9. Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair.

    Directory of Open Access Journals (Sweden)

    Jae-hyeong Ko

    Full Text Available While translational read-through of stop codons by suppressor tRNAs is common in many bacteria, archaea and eukaryotes, this phenomenon has not yet been observed in the α-proteobacterium Caulobacter crescentus. Based on a previous report that C. crescentus and Escherichia coli tRNA(His have distinctive identity elements, we constructed E. coli tRNA(His CUA, a UAG suppressor tRNA for C. crescentus. By examining the expression of three UAG codon- containing reporter genes (encoding a β-lactamase, the fluorescent mCherry protein, or the C. crescentus xylonate dehydratase, we demonstrated that the E. coli histidyl-tRNA synthetase/tRNA(His CUA pair enables in vivo UAG suppression in C. crescentus. E. coli histidyl-tRNA synthetase (HisRS or tRNA(His CUA alone did not achieve suppression; this indicates that the E. coli HisRS/tRNA(His CUA pair is orthogonal in C. crescentus. These results illustrate that UAG suppression can be achieved in C. crescentus with an orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pair.

  10. Gene-based analysis of the fibroblast growth factor receptor signaling pathway in relation to breast cancer in African American women: the AMBER consortium.

    Science.gov (United States)

    Ruiz-Narváez, Edward A; Haddad, Stephen A; Lunetta, Kathryn L; Yao, Song; Bensen, Jeannette T; Sucheston-Campbell, Lara E; Hong, Chi-Chen; Haiman, Christopher A; Olshan, Andrew F; Ambrosone, Christine B; Palmer, Julie R

    2016-01-01

    We conducted gene-based analysis in 26 genes in the FGFR signaling pathway to identify genes carrying genetic variation affecting risk of breast cancer and the specific estrogen receptor (ER) subtypes. Tagging single-nucleotide polymorphisms (SNPs) for each gene were selected and genotyped on a customized Illumina Exome Array. Imputation was carried out using 1000 Genomes haplotypes. The analysis included 3237 SNPs in 3663 breast cancer cases (including 1983 ER-positive, and 1098 ER-negative) and 4687 controls from the African American Breast Cancer Epidemiology and Risk consortium, a collaborative project of four large studies of breast cancer in African American women (Carolina Breast Cancer Study, Black Women's Health Study, Women's Circle of Health Study, and Multiethnic Cohort). We used a multi-locus adaptive joint (AdaJoint) test to determine the association of each gene in the FGFR signaling pathway with overall breast cancer and ER subtypes. The FGF1 gene was significantly associated with risk of ER-negative breast cancer (P = 0.001). The FGFR2 gene was associated with risk of overall breast cancer (P = 0.002) and ER-positive breast cancer (P = 0.002). The FGF1 gene affects risk of ER-negative breast cancer in African American women. We confirmed the association of the FGFR2 gene with risk of overall and ER-positive breast cancer. These results highlight the importance of the FGFR signaling pathway in the pathogenesis of breast cancer, and suggest that different genes in the same pathway may be associated with different ER breast cancer subtypes.

  11. Improved Parameterization of Amine-Carboxyate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

    CERN Document Server

    Yoo, Jejoong

    2015-01-01

    Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which have been developed and validated using relatively short simulations of small molecules---become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge--charge interactions. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine--carboxylate and amine--phosphate interactions, which brings MD simulations of basic peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better agreement with experiment. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing additional artifacts.

  12. VLTI/AMBER spectro-interferometry of the late-type supergiants V766 Cen (=HR 5171 A), sigma Oph, BM Sco, and HD 206859

    CERN Document Server

    Wittkowski, M; Marcaide, J M; Abellan, F J; Chiavassa, A; Guirado, J C

    2016-01-01

    We add four warmer late-type supergiants to our previous spectro-interferometric studies of red giants and supergiants. V766 Cen (=HR 5171 A) is found to be a high-luminosity log(L/L_sun)=5.8+-0.4 source of Teff 4290+-760 K and radius 1490+-540 Rsun located close to both the Hayashi and Eddington limits; this source is consistent with a 40 Msun evolutionary track without rotation and current mass 27-36 Msun. It exhibits NaI in emission arising from a shell of radius 1.5 Rphot and a photocenter displacement of about 0.1 Rphot. V766 Cen shows strong extended molecular (CO) layers and a dusty circumstellar background component. This suggest an optically thick pseudo-photosphere at about 1.5 Rphot at the onset of the wind. V766 Cen is a red supergiant located close to the Hayashi limit instead of a yellow hypergiant already evolving back toward warmer Teff as previously discussed. The stars sigma Oph, BM Sco, and HD 206859 are found to have lower luminosities of about log(L/Lsun)=3.4-3.5 and Teff of 3900-5300 K, ...

  13. Kaks miljardit jaotub Balti riikides paljude sektorite vahel / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2004-01-01

    Soome investeerimisfondi Danske Capital Finland loodud investeerimisfond Amber Trust II investeerib Balti riikidesse 2 miljardit krooni. Diagramm: Amber Trust S.C.A. fondi osalused Balti riikide ettevõtetes. Lisa: Turg täis, aga fonde tuleb juurde

  14. Salva pistab rinda hiiglastega / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2006-01-01

    Peamiselt eestlastele kuuluv Salva Kindlustus on turul edukas olnud. Diagrammid: Aktsionärid; Majandusnäitajad. Kommenteerib Peeter Teder. Vt. samas: Amber Trust: Salva Kindlustus on meile korralikult dividende maksnud. Diagramm: Fondi Amber Trust investeeringud

  15. 47 CFR 10.400 - Classification.

    Science.gov (United States)

    2010-10-01

    ... classes of Alert Messages: Presidential Alert; Imminent Threat Alert; and Child Abduction Emergency/AMBER... of greater than 50 percent). (c) Child Abduction Emergency/AMBER Alert. (1) An AMBER Alert is an... the abduction to believe an immediate broadcast alert will help; and (v) The child's name and...

  16. Irving Independent School District, Petitioner v. Henri Tatro, et Ux., Individually and as Next Friend of Amber Tatro, a Minor. On Writ of Certiorari to the United States Court of Appeals for the Fifth Circiut. No. 83-558.

    Science.gov (United States)

    Supreme Court of the U. S., Washington, DC.

    A Supreme Court ruling is presented regarding the provision of clean intermittent catheterization as part of related services mandated under P.L. 94-142, the Education for All Handicapped Children Act. The case argued focused on the needs of a young girl with spina bifida for intermittent catheterization to remove urine from her bladder. The court…

  17. Potentiating effects of honey on antioxidant properties of lemon-flavoured black tea.

    Science.gov (United States)

    Pereira, Carla; Barros, Lillian; Vilas-Boas, Miguel; Ferreira, Isabel C F R

    2013-03-01

    Health benefits including antioxidant potential of black tea (Camellia sinensis), lemon (Citrus limon) and honey bees (Apis mellifera) have been extensively reported. Nevertheless, nothing is reported about the effects of their concomitant use. Herein, those effects were evaluated in infusions of lemon-flavoured black tea with three different kinds of honey (light amber, amber and dark amber) from Lavandula stoechas, Erica sp. pl. and other indigenous floral species from north-east Portugal, a region with high amounts of this food product. Data obtained showed that the use of honey (dark amber>amber>light amber) potentiates the antioxidant activity of lemon-flavoured black tea, increasing the reducing power and lipid peroxidation inhibition properties, as also the antioxidant contents such as phenolics, flavonoids and organic acids including ascorbic acid.

  18. Teledokumentalistika hiilgusest ja viletsusest / Maria Ulfsak

    Index Scriptorium Estoniae

    Ulfsak, Maria, 1981-

    2004-01-01

    Leedu teleprogrammide ja -filmide festivalil "Amber arch" ("Merevaigust arkaad") võitis peapreemia Priit Valkna dokumentaalfilm "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja. Ka teistest festivali filmidest

  19. Understanding the Effects of Infrastructure Changes on Subpopulations: Survey of Current Methods, Models, and Tools

    Science.gov (United States)

    2016-04-01

    50 Figure 14. Links between Infrastructure reconnaissance categories ( USAES ...regional.php) 7 The early August 2014 U.S. airstrikes against the Islamic State in Iraq and Syria were in support of hu- manitarian assistance to...Examples of SWEAT black-red-amber-green rating methodology (re-created from USAES 2005). Area Green Amber Red Black Water Water distribution works

  20. Fringe tracking performance monitoring: FINITO at VLTI

    CERN Document Server

    Merand, A; Berger, J -P; Percheron, I; Poupar, S

    2012-01-01

    Since April 2011, realtime fringe tracking data are recorded simultaneously with data from the VLTI/AMBER interferometric beam combiner. Not only this offers possibilities to post-process AMBER reduced data to obtain more accurate interferometric quantities, it also allows to estimate the performance of the fringe tracking a function of the conditions of seeing, coherence time, flux, etc. First we propose to define fringe tracking performance metrics in the AMBER context, in particular as a function of AMBER's integration time. The main idea is to determine the optimal exposure time for AMBER: short exposures are dominated by readout noise and fringes in long exposures are completely smeared out. Then we present this performance metrics correlated with Paranal local ASM (Ambient Site Monitor) measurements, such as seeing, coherence time or wind speed for example. Finally, we also present some preliminary results of attempts to model and predict fringe tracking performances, using Artificial Neural Networks.

  1. Method for the preparation of photochromic insulating crystals

    Science.gov (United States)

    Abraham, Marvin M.; Boldu, Jose L.; Chen, Yok; Orera, Victor M.

    1986-01-01

    A method for preparing reversible-photochromic magnesium oxide (MgO) crystals. Single crystals of MgO doped with both lithium (Li) and nickel (Ni) are grown by a conventional arc fusion method. The as-grown crystals are characterized by an amber coloration. The crystals lose the amber coloration and become photochromic when they are thermochemically reduced by heating at temperatures greater than 1000.degree. K. in a hydrogen atmosphere. Alternate irradiation with UV and visible light result in rejuvenation and bleaching of the amber coloration, respectively.

  2. Uudised : Ain Anger tuli ooperilauljate konkursil esikohale. Elton Johni fotokogu näitus

    Index Scriptorium Estoniae

    2000-01-01

    A. Anger võitis 11.-14. juuliniu Lätis Jurmalas toimunud rahvusvahelise noorte ooperilauljate konkursi "Amber Sea Voices". E. John korraldab novembris Ameerikas Atlantas oma fotokogu avaliku näituse "Chorus of Light"

  3. The shelf life of dyed polymethylmethacrylate dosimeters

    Science.gov (United States)

    Bett, R.; Watts, M. F.; Plested, M. E.

    2002-03-01

    The long-term stability of the radiation response of Harwell Red 4034 and Amber 3042 Perspex Dosimeters has been monitored for more than 15 years, and the resulting data used in the justification of their shelf-life specifications.

  4. 77 FR 10608 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2012-02-22

    ... requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do not meet the... because distances between them are more compact. These conditions tax visual capacity and driver...

  5. 77 FR 64841 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2012-10-23

    ... recognize the colors of traffic signals and devices showing requirement red, green, and amber (49 CFR 391.41... more compact. These conditions tax visual capacity and driver response just as intensely as...

  6. 76 FR 53710 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2011-08-29

    ... colors of traffic signals and devices showing standard red, green, and amber (49 CFR 391.41(b)(10... generally required because distances between them are more compact. These conditions tax visual capacity...

  7. 75 FR 79081 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-12-17

    ... standard red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do not meet the... because distances between them are more compact. These conditions tax visual capacity and driver...

  8. 78 FR 41188 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2013-07-09

    ... showing requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do... more compact. These conditions tax visual capacity and driver response just as intensely as...

  9. 77 FR 17117 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2012-03-23

    ... recognize the colors of traffic signals and devices showing requirement red, green, and amber (49 CFR 391.41... conditions tax visual capacity and driver response just as intensely as interstate driving conditions....

  10. 78 FR 37274 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2013-06-20

    ... devices showing requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some... distances between them are more compact. These conditions tax visual capacity and driver response just...

  11. 76 FR 2190 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2011-01-12

    ... recognize the colors of traffic signals and devices showing standard red, green, and amber (49 CFR 391.41(b... because distances between them are more compact. These conditions tax visual capacity and driver...

  12. 75 FR 70078 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-11-16

    ... standard red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do not meet the... distances between them are more compact. These conditions tax visual capacity and driver response just...

  13. 78 FR 22602 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2013-04-16

    ... showing requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes that some drivers do... more compact. These conditions tax visual capacity and driver response just as intensely as...

  14. 75 FR 63255 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-10-14

    ... recognize the colors of traffic signals and devices showing standard red, green, and amber (49 CFR 391.41(b... because distances between them are more compact. These conditions tax visual capacity and driver...

  15. 76 FR 67246 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2011-10-31

    ... recognize the colors of traffic signals and devices showing standard red, green, and amber (49 CFR 391.41(b... them are more compact. These conditions tax visual capacity and driver response just as intensely...

  16. 77 FR 3547 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2012-01-24

    ... ability to recognize the colors of traffic signals and devices showing requirement red, green, and amber... more compact. These conditions tax visual capacity and driver response just as intensely as...

  17. 78 FR 76395 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2013-12-17

    ... signals and devices showing requirement red, green, and amber (49 CFR 391.41(b)(10)). FMCSA recognizes... conditions tax visual capacity and driver response just as intensely as interstate driving conditions....

  18. 7 CFR 989.110 - Varietal types.

    Science.gov (United States)

    2010-01-01

    ...) Natural (sun-dried) Seedless includes all sun-dried seedless raisins possessing similar identifiable... Seedless includes all seedless raisins whose color generally varies from golden yellow to dark amber....

  19. Balti riikide firmadesse voolab veel 2 miljardit krooni / Annika Matson

    Index Scriptorium Estoniae

    Matson, Annika, 1976-

    2004-01-01

    Ilmunud ka: Delovõje Vedomosti 15. dets. lk. 33. Fondist Amber Trust II S.C.A., mis hakkab investeerima Balti riikidesse. Lisa: Firebirdi fondid ja Danske Capital praegu Tallinna börsil ligi 400 mln krooniga. Diagrammid

  20. Kuni 30. IV on rahvusraamatukogu haruldaste raamatute saalis...

    Index Scriptorium Estoniae

    2005-01-01

    Näitus "Balti merevaik Palanga merevaigumuuseumist". 21.-24. III oli merevaigufirma Amber näitusmüük raamatukogu fuajees, firma skulptuurikollektsiooni põhjal avati 1996. a. Vilniuses merevaiguskulptuuride muuseum

  1. Vaja on professionaalseid oskusi! / Tiina Lokk ; interv. Maria Ulfsak

    Index Scriptorium Estoniae

    Lokk, Tiina, 1955-

    2004-01-01

    Eesti poolt Leedu teleprogrammide ja -filmide festivalil "Amber arch" žüriis osalenud T. Lokk nähtud filmidest ja peapreemia võitnud Priit Valkna dokumentaalfilmist "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja

  2. Physical, Nutrient, and Biological Measurements of Coastal Waters off Central California in March 2012

    Science.gov (United States)

    2012-10-01

    Oceanography Physical Oceanography Nutrients Nutrients Nutrients Naval Postgraduate School ENS Amber Payne (NOAA)* Cynthia Carrion ...Jolla, CA Cynthia Carrion University of California at Santa Cruz Santa Cruz, CA LT Luke Penrose, USN United States Navy 1 1

  3. The Dependence of Amyloid‐β Dynamics on Protein Force Fields and Water Models

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2015-01-01

    We studied the dynamics of Aβ40, involved in Alzheimer's disease, by using 21 methods combined from Amber03, Amber99sb‐ILDN, Charmm27, Charmm22*, OPLS‐2001, OPLS‐2006, OPLS‐2008, Gromos96‐43a1, Gromos96‐53a6, Gromos96‐54a7, and the water models SPC, TIP3P, TIP4P. Major differences in the structural...

  4. Could submarine groundwater discharge be a significant carbon source to the southern Baltic Sea?** The study reports the results obtained within the framework of the following projects: the statutory activities of the Institute of Oceanology Polish Academy of Sciences theme 2.2, research project No. 2012/05/N/ST10/02761 sponsored by the National Science Centre, and AMBER, the BONUS+EU FP6 Project.

    Directory of Open Access Journals (Sweden)

    Beata Szymczycha

    2014-01-01

    Full Text Available Submarine Groundwater Discharge (SGD is an important yet poorly recognised pathway of material transport to the marine environment. This work reports on the results of dissolved inorganic carbon (DIC and dissolved organic carbon (DOC concentrations and loads in the groundwater seeping into the southern Baltic Sea. Most of the research was carried out in the Bay of Puck (2009–2010, while in 2013 the study was extended to include several other groundwater seepage impacted areas situated along the Polish coastline. The annual average concentrations of DIC and DOC in the groundwater were equal to 64.5±10.0 mg C L−1 and 5.8±0.9 mg C L−1 respectively. The carbon specific flux into the Bay of Puck was estimated at 850 mg m−2 yr−1. The loads of carbon via SGD were scaled up for the Baltic Sea sub-basins and the entire Baltic Sea. The DIC and DOC fluxes via SGD to the Baltic Sea were estimated at 283.6±66.7 kt yr−1 and 25.5±4.2 kt yr−1. The SGD derived carbon load to the Baltic Sea is an important component of the carbon budget, which gives the sea a firmly heterotrophic status.

  5. The nature and fate of natural resins in the geosphere VI. Analysis of fossil resins from Axel Heiberg Island Canadian Arctic

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, K.B. [Argonne National Lab., IL (United States)]|[Amoco Oil Co., Naperville, IL (United States); LePage, B.A. [Univ. of Alberta, Edmonton (Canada). Dept. of Biological Sciences

    1995-06-01

    Ambers are well known and abundant in terrestrial sediments all over the world; however, due largely to the absence of definite morphological characteristics, the precise botanical origin of most amber samples, are at best, often a matter of speculation. This has severely restricted the usefulness of amber in paleobotanical and paleoecological interpretations. The molecular composition and structural characteristics of fossil resins however, may preserve evidence of their botanical origin, which could be of great value in both geochemical, paleobotanical, and paleoenvironmental studies. The remains of a number of exceptionally well-preserved Taxodiaceae-dominated swamp-forest communities have been identified in the sediments of the middle Eocene (45 million years old) Buchanan Lake Formation of Axel Heiberg Island, Canadian Arctic Archipelago. The amber collected from these ancient in situ forests provides a unique opportunity to characterize these resins chemically and taxonomically. Resinite associated with Metasequoia, Pinus and Pseudolarix has been characterized using Pyrolysis-Gas Chromatography-Mass Spectrometry. This method provides a direct analysis of the molecular structure and composition of the resin. In several cases, both bled resin and cone-resin samples have been characterized. The results of these analyses are presented and discussed. The implications of these results for the botanical origins of other ambers represented in the fossil record (including succinite) will also be discussed.

  6. Understanding the Longitudinal Variability of Equatorial Electrodynamics using integrated Ground- and Space-based Observations

    Science.gov (United States)

    Yizengaw, E.; Moldwin, M.; Zesta, E.

    2015-12-01

    The currently funded African Meridian B-Field Education and Research (AMBER) magnetometer array comprises more than thirteen magnetometers stationed globally in the vicinity of geomagnetic equator. One of the main objectives of AMBER network is to understand the longitudinal variability of equatorial electrodynamics as function of local time, magnetic activity, and season. While providing complete meridian observation in the region and filling the largest land-based gap in global magnetometer coverage, the AMBER array addresses two fundamental areas of space physics: first, the processes governing electrodynamics of the equatorial ionosphere as a function of latitude (or L-shell), local time, longitude, magnetic activity, and season, and second, ULF pulsation strength at low/mid-latitude regions and its connection with equatorial electrojet and density fluctuation. The global AMBER network can also be used to augment observations from space-based instruments, such us the triplet SWARM mission and the upcoming ICON missions. Thus, in coordination with space-based and other ground-based observations, the AMBER magnetometer network provides a great opportunity to understand the electrodynamics that governs equatorial ionosphere motions. In this paper we present the longitudinal variability of the equatorial electrodynamics using the combination of instruments onboard SWARM and C/NOFS satellites and ground-based AMBER network. Both ground- and pace-based observations show stronger dayside and evening sector equatorial electrodynamics in the American and Asian sectors compared to the African sector. On the other hand, the African sector is home to stronger and year-round ionospheric bubbles/irregularities compared to the American and Asian sectors. This raises the question if the evening sector equatorial electrodynamics (vertical drift), which is believed to be the main cause for the enhancement of Rayleigh-Taylor (RT) instability growth rate, is stronger in the

  7. Råmaterialer, forarbejder, spild

    DEFF Research Database (Denmark)

    2014-01-01

    Finds from Aggersborg: raw iron, off-cuts and a ?bar, hammer-scale, slag, rough-outs of arrow-heads and leister-prongs, lead waste, copper-alloy raw material and waste, gold and amber waste, raw material, rough-outs and waste of bone, antler and horn, soapstone, pigment?......Finds from Aggersborg: raw iron, off-cuts and a ?bar, hammer-scale, slag, rough-outs of arrow-heads and leister-prongs, lead waste, copper-alloy raw material and waste, gold and amber waste, raw material, rough-outs and waste of bone, antler and horn, soapstone, pigment?...

  8. Sub-Area. 2.5 Demonstration of Promising Energy Storage Technologies Project Type. Flywheel Energy Storage Demonstration Revision: V1.0

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2015-12-30

    In this program, Amber Kinetics designed, built, and tested a sub-­scale 5 kWh engineering prototype flywheel system. Applying lessons learned from the engineering prototype, Amber Kinetics then designed, built and tested full-­size, commercial-­scale 25 kWh flywheel systems. The systems underwent basic functional qualification testing before being installed, sequentially, at the company’s outdoor test site in Alameda, CA for full-­speed field-testing. The primary considerations in testing the prototype units were to demonstrate the functionality of the system, verify the frequencies of resonant modes, and quantify spinning losses and motor/generator efficiency.

  9. Confocal microphotoluminescence of InGaN-based light-emitting diodes

    OpenAIRE

    Okamoto, K.; Kaneta, A; Kawakami, Y.; Fujita, S; Choi, J.; Terazima, M; Mukai, T

    2005-01-01

    Spatially resolved photoluminescence (PL) of InGaN/GaN/AlGaN-based quantum-well-structured light-emitting diodes (LEDs) with a yellow-green light (530 nm) and an amber light (600 nm) was measured by using confocal microscopy. Submicron-scale spatial inhomogeneities of both PL intensities and spectra were found in confocal micro-PL images. We also found clear correlations between PL intensities and peak wavelength for both LEDs. Such correlations for yellow-green and amber LEDs were differen...

  10. Genetically encoded photocrosslinkers locate the high-affinity binding site of antidepressant drugs in the human serotonin transporter

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Andersen, Jacob; Hall, Lena Sørensen;

    2016-01-01

    Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode photocrosslin......Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode...

  11. Pop-Up Store

    OpenAIRE

    Castiñeira Fernández, Agustín

    2016-01-01

    El presente proyecto muestra el proceso de diseño y conceptualización de una tienda “Pop-Up” que será la re-localización temporal para distintos comercios. Los negocios presentes en la calle Meir (Amberes) tendrán que renovar sus edificios para que la ciudad de Amberes sea zona de cero emisiones de CO2 en 2050. Por esta razón el proyecto explora las posibilidades de ofrecer un espacio que sea flexible y móvil, y que pueda adaptarse a distintos tipos de comercios dependiendo de sus necesidades...

  12. [The effect of phospholipid hepatoprotectors on lipid peroxidation in liver and content of cytokines in the blood in experimental pathology caused by isoniazid].

    Science.gov (United States)

    Udut, V V; Vengerovskiĭ, A I; Burkova, V N; Vaizova, O E; Korshunov, D A

    2012-01-01

    The purpose--to investigate the influence of hepatoprotective agents of phospholipids'structure essentiale, eplir and its combinations with amber acid on rats liver functional state, lipoperoxidation and bioenergetics, also tumor necrosis factor-a and interleukin-10 blood content in experimental isoniazid intoxication. These agents demonstrated antioxidant action, decreased the common and indirect bilirubine, tumor necrosis factor-alpha blood content, aminotransferase and alkaline phosphatase activity, increased the interleukin-10 blood content. Isonoazid uncoupled the substrate oxidation with ADP phosphorylation and inhibited the respiratory activity of liver mitochondrions. Essentiale and eplir increased the coupling of oxidation with ATP synthesis, in combination with amber acid improved kinetic characteristics of liver mitochondrions.

  13. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  14. A Simple Molecular Dynamics Lab to Calculate Viscosity as a Function of Temperature

    Science.gov (United States)

    Eckler, Logan H.; Nee, Matthew J.

    2016-01-01

    A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self-diffusion in "n"-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the…

  15. 7 CFR 52.1006 - Color.

    Science.gov (United States)

    2010-01-01

    ... PROCESSED FRUITS AND VEGETABLES, PROCESSED PRODUCTS THEREOF, AND CERTAIN OTHER PROCESSED FOOD PRODUCTS 1 United States Standards for Grades of Dates Factors of Quality § 52.1006 Color. (a) (A) classification... more than 5 percent by count of dates that are light amber in color. (b) (B) classification. If...

  16. Polymeric, Metallic, and Other Glasses in Introductory Chemistry

    Science.gov (United States)

    Hawkes, Stephen J.

    2008-01-01

    Non-ceramic glasses are not adequately discussed in introductory chemistry. Such glasses include polycarbonate, which many corrective lenses are made of, amber, enamel, gelatin, hard candy, coal, refrigerated glycerol, and metallic glasses that have been marketed in recent decades. What is usually discussed in elementary texts is siliceous glass,…

  17. INFRARED INTERFEROMETRY OF MASSIVE YOUNG STELLAR OBJECTS

    Directory of Open Access Journals (Sweden)

    W. J. de Wit

    2010-01-01

    Full Text Available Se discuten la interferometría de AMBER y MIDI, además de observaciones de disco-simple en Subaru de objetos estelares masivos jóvenes. Las observaciones muestran tamaños de escalas lineales entre 10 y 100UA como distancia promedio de nuestras fuentes.

  18. Novel artificial metalloenzymes by in vivo incorporation of metal-binding unnatural amino acids

    NARCIS (Netherlands)

    Drienovska, Ivana; Rioz-Martinez, Ana; Draksharapu, Apparao; Roelfes, Gerard

    2015-01-01

    Artificial metalloenzymes have emerged as an attractive new approach to enantioselective catalysis. Herein, we introduce a novel strategy for preparation of artificial metalloenzymes utilizing amber stop codon suppression methodology for the in vivo incorporation of metal-binding unnatural amino aci

  19. Comparisons of experiment with cellulose models based on electronic structure and empirical force field theories

    Science.gov (United States)

    Studies of cellobiose conformations with HF/6-31G* and B3LYP/6-31+G*quantum theory [1] gave a reference for studies with the much faster empirical methods such as MM3, MM4, CHARMM and AMBER. The quantum studies also enable a substantial reduction in the number of exo-cyclic group orientations that...

  20. Gemstones

    Science.gov (United States)

    Olson, D.W.

    2013-01-01

    The estimated value of natural gemstones produced from U.S. deposits during 2012 was $11.1 million, a slight increase from 2011. U.S. gemstone production included agate, amber, beryl, coral, garnet, jade, jasper, opal, pearl, quartz, sapphire, shell, topaz, tourmaline, turquoise and many other gem materials.

  1. Neutral and ionized gas around the post-Red Supergiant IRC+10420 at au size scales

    CERN Document Server

    Oudmaijer, Rene

    2012-01-01

    IRC +10420 is one of the few known massive stars in rapid transition from the Red Supergiant phase to the Wolf-Rayet or Luminous Blue Variable phase. The star has an ionised wind and using the Br gamma hydrogen recombination emission we assess the mass-loss on spatial scales of order 1 au. We present new VLT Interferometer AMBER data which are combined with all other AMBER data in the literature. The final dataset covers a position angle range of 180 degrees and baselines up to 110 meters. The spectrally dispersed visibilities, differential phases and line flux are conjointly analyzed and modelled. We also present AMBER/FINITO observations which cover a larger wavelength range and allow us to observe the Na I doublet at 2.2 micron. The data are complemented by X-Shooter data, which provide a higher spectral resolution view. The Brackett gamma line and the Na I doublet are both spatially resolved. After correcting the AMBER data for the fact that the lines are not spectrally resolved, we find that Br gamma tra...

  2. Teaching Integration with Layers and Representations: A Case Study

    Science.gov (United States)

    Von Korff, Joshua; Rebello, N. Sanjay

    2012-01-01

    We designed a sequence of seven lessons to facilitate learning of integration in a physics context. We implemented this sequence with a single college sophomore, "Amber," who was concurrently enrolled in a first-semester calculus-based introductory physics course which covered topics in mechanics. We outline the philosophy underpinning these…

  3. 75 FR 61833 - Qualification of Drivers; Exemption Applications; Vision

    Science.gov (United States)

    2010-10-06

    ... recognize the colors of traffic signals and devices showing standard red, green, and amber (49 CFR 391.41(b... conditions tax visual capacity and driver response just as intensely as interstate driving conditions. The... Carriaga, Michael R. Clark, James D. Drabek, Jr., Curtis E. Firari, Percy L. Gaston, Ronald M....

  4. Instrumental Techniques in Archeological Research

    Science.gov (United States)

    1988-09-01

    leather, amber, and mummified material. Evidently this is preliminary work. Schwarcz , H. P., 1986, "ESR Dating of Tooth Enamel," Abstracts of the 1984...Radiocarbon dating Contact: H. P. Schwarcz Technique(s): ESR 79 Illinois State Geological Survey McCrone Associates Inc. State Geological Survey

  5. Unit 1 Cultural relics课程设计(英文)

    Institute of Scientific and Technical Information of China (English)

    郑亮; 杨玲

    2011-01-01

    Teaching content:Unit 1 cultural relicsreading Teaching goals:1)Train the students’reading ability 2 )Learn som ething aboutthe Amber Room 3 )Learn som e useful phrases Teaching Methods & Aids:1)Task-based learning 2 ) CAI (multi-media,com puter,tape recorder,blackboard)

  6. The Growing of Grids

    Science.gov (United States)

    Architectural Record, 1977

    1977-01-01

    The Central Building for the School of Art and Physical Education at Tsukuba University uses eight-inch-square amber-colored glass blocks, steel framing and floor decking, plus pured concrete, to provide simple and flexible spaces for athletes and artists. (Author/MLF)

  7. The nature and fate of natural resins in the geosphere XIII: a probable pinaceous resin from the early Cretaceous (Barremian, Isle of Wight

    Directory of Open Access Journals (Sweden)

    Anderson Ken B

    2008-01-01

    Full Text Available Abstract Terpenoid resin is produced by all families and most genera of the order Coniferales (the conifers, and the distribution of terpenes present in most conifer resins is characteristic of the originating family. Analyses of early Cretaceous (Barremian amber (fossil resin from the English Wealden, Isle of Wight, southern England, by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS, indicate a terpene distribution dominated by abietane- and labdane-type terpenes. Similar distributions are observed in some species of the extant family Pinaceae. The Pinaceae are well represented within the Wealden deposits of southern England, by only one (known species, Pityites solmsii (Seward Seward, whereas the macro-fossil record of these deposits is dominated by the extinct conifer family Cheirolepidiaceae, for which no resin chemistry has been reported. By analogy with modern materials, it is probable that the ambers found in these deposits are derived from an extinct member of the Pinaceae, but given the absence of evidence concerning the chemotaxonomy of the Cheirolepidiaceae, this family cannot be excluded a priori as a possible paleobotanical source. These ambers may therefore be assigned to either the Pinaceae or to the Cheirolepidiaceae. These samples are the oldest ambers to date to yield useful chemotaxonomic data.

  8. India's People, Country, and Great Religions: Two Instructional Learning Packages.

    Science.gov (United States)

    Wales, Largo Ann

    Divided into two parts, this slide narration covers India's history, people, religions, geography, and architecture. The first part, "Introduction: Country, People, and History," covers the general history of India and its people. The history is presented through: (1) the architecture, including the Palace of Winds, the Amber Fort, the Taj Mahal,…

  9. Poliitik: vajame Lähis-Ida gaasi / Jerzy Buzek ; intervjueerinud Jan Jõgis-Laats

    Index Scriptorium Estoniae

    Buzek, Jerzy, 1940-

    2009-01-01

    Poola endise peaministri sõnul on vaja energiaühendust Poola ja Leedu vahel, arutada tuleks projekte, nagu Baltimaade ja Poola kaudu Euroopasse suunduv gaasitorustik Amber, samuti lõunapoolseid gaasiühendusi. Poola peab läbirääkimisi veeldatud gaasi saamiseks ning hakkab seejärel rajama sadamat

  10. M577 Fuze Product Improvement Program: Alternate Materials for Ogive Window.

    Science.gov (United States)

    1984-06-01

    Dow K-Resin Butadine Styrene Phillips Chemical CR-39 Allyl Diglycol Carbonate PPG Trogamid T Polyamide Dynamite Noble Kel-F Teflon 3M Ultem Nylon Dupont...polysulfone and Ultem nylon. Both of these materials have a slight amber tint, the nylon being somewhat darker than the polysulfone. Because of this

  11. Baltikum ja Poola juhiks Vene gaasi mööda maad / Lauri Linnamäe

    Index Scriptorium Estoniae

    Linnamäe, Lauri

    2007-01-01

    Balti riigid ja Poola taotlevad Euroopa Komisjonilt toetust uuringu läbiviimiseks, mis keskenduks 2004. aastal välja pakutud Lätit, Leedut ja Poolat läbiva gaasijuhtme Amber projekti võrdlusele Nord Streami projektiga. Lisa: Nord Stream

  12. 33 CFR 117.1035 - Columbia River.

    Science.gov (United States)

    2010-07-01

    ... on the channel piers start flashing, a downward pointing arrow consisting of amber colored lights is... red lights continue to flash and the downward pointing arrow is displayed, until the lift span returns... begins closing and the centerspan navigation lights turn from green to red. The horn sounds for...

  13. Kak estonski oboroten litovskuju korovu ukral / Jevgenia Garanzha

    Index Scriptorium Estoniae

    Garanža, Jevgenija, 1979-

    2004-01-01

    Leedu teleprogrammide ja -filmide festivalil "Amber arch" ("Merevaigust arkaad") võitis peapreemia Priit Valkna dokumentaalfilm "Hunt", mille tootis Allfilm ETV "Eesti lugude" dokumentaalsarja. Osales ka Vahur Laiapea telesari setudest "Veere pääl". Ulatuslik ülevaade festivalist

  14. Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

    Science.gov (United States)

    2014-10-01

    of these networks, the specific volume and the coefficient of volumetric thermal expansion (CVTE), are shown in Fig. 4. Specific volume is...CVTE values are somewhat lower than expected from experimental measurements of the coefficient of linear thermal expansion ,27 which can be...coefficient of volumetric thermal expansion db equilibrium bond length DCPD dicyclopentadiene GAFF general AMBER force field ID identification K

  15. Choosing a Breast Prosthesis: A Survivor's Perspective

    Science.gov (United States)

    ... Choosing a Breast Prosthesis: A Survivor’s Perspective Choosing a Breast Prosthesis: A Survivor’s Perspective Andrea Zinn June 16, 2015 · Amber ... preferences. Q: Why did you decide to wear a breast form/prosthesis rather than have a reconstruction? ...

  16. Silver Alerts and the Problem of Missing Adults with Dementia

    Science.gov (United States)

    Carr, Dawn; Muschert, Glenn W.; Kinney, Jennifer; Robbins, Emily; Petonito, Gina; Manning, Lydia; Brown, J. Scott

    2010-01-01

    In the months following the introduction of the National AMBER (America's Missing: Broadcast Emergency Response) Alert plan used to locate missing and abducted children, Silver Alert programs began to emerge. These programs use the same infrastructure and approach to find a different missing population, cognitively impaired older adults. By late…

  17. 7 CFR 810.2202 - Definition of other terms.

    Science.gov (United States)

    2010-01-01

    ... Winter wheat, Hard White wheat, Soft White wheat, Unclassed wheat, and Mixed wheat. (1) Durum wheat. All varieties of white (amber) durum wheat. This class is divided into the following three subclasses: (i) Hard... this class. (5) Hard White wheat. All hard endosperm white......

  18. ASPRO and its user's support: the JMMC tools for preparing VLTI Observations

    Science.gov (United States)

    Duchene, Gaspard; Berger, Jean-Philippe; Zins, Gerard; Duvert, Gilles

    2004-12-01

    We will present an overview of the main features of the current and next (to be released at the end of the summer) versions of the ASPRO software that are being developed by the JMMC to prepare VLTI observing programs. To help ASPRO users prepare their AMBER and MIDI proposals, an active helpdesk will also be available.

  19. Escherichia coli and Salmonella typhimurium supX genes specify deoxyribonucleic acid topoisomerase I.

    OpenAIRE

    Trucksis, M; Golub, E I; Zabel, D J; Depew, R E

    1981-01-01

    Mutations of the Escherichia coli or Salmonella typhimurium supX genes eliminated deoxyribonucleic acid topoisomerase I. Suppression of a supX amber mutation partially restored the topoisomerase. Multicopy plasmids carrying supX+ caused overproduction of topoisomerase. Thus, these supX genes were identified as topA genes which specify deoxyribonucleic acid topoisomerase I.

  20. 假眼小绿叶蝉对不同颜色偏嗜性的研究%Study on Preference of Green Leafhopper Empoasca (Empoasca) vitis (G  o¨the) for Different Colors

    Institute of Scientific and Technical Information of China (English)

    赵冬香; 陈宗懋; 程家安

    2001-01-01

    Experiments were made both in laboratory and in tea field aboutthe preference of green leafhopper Empoasca (Empoasca) vitis (G o¨the) to different colors. The result showed that yellow is the most attractive color. Under laboratory conditions,amber yellow was the strongest to attract the leafhoppers. There were no significant difference among amber yellow,lake water blue and gem green,but there showed significant difference between amber yellow and emerald green,snow white ,reddish orange respectively(p<0.05). Among different yellow plates,there had no significant difference in attracting green leafhoppers,but among different yellows and emerald green,indigo-blue and sea-blue,there had significant difference (p<0.05) in attracting. In tea field,amber yellow was the strongest to attract the leafhoppers,there had no significant difference between amber yellow and gem green,and between amber yellow to lake water blue,there were significant difference(p<0.05). The laboratory and field experiments showed that the green leafhopper had a preference for yellow green and pale green.%作者进行了茶树害虫假眼小绿叶蝉对不同颜色偏嗜性的室内和田间试验。结果表明:假眼小绿叶蝉最偏嗜黄色。室内试验中,琥珀黄诱集的虫数最多,且与湖水蓝和宝石绿间的虫数差异不显著,与翠绿、雪白和橘橙间的虫数差异显著(p<0.05)。琥珀黄、油菜花黄和麦杆黄三种不同黄色间诱集的虫数无差异,它们与翠绿、靛青和海青间的虫数达差异显著性水平(p<0.05)。茶园试验中,琥珀黄诱集的虫数最多,与宝石绿间的虫数差异不显著,而与湖水蓝间虫数差异达显著水平(p<0.05)。室内外试验的结果基本一致,即假眼小绿叶蝉偏嗜黄绿色、浅绿色。

  1. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper

    Science.gov (United States)

    Heli, B.; Morales-Narváez, E.; Golmohammadi, H.; Ajji, A.; Merkoçi, A.

    2016-04-01

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and

  2. La presencia de ámbar en los yacimientos prehistóricos (del Paleolítico superior a la Edad del Bronce de la Cornisa Cantábrica y sus fuentes de aprovisionamiento

    Directory of Open Access Journals (Sweden)

    Esteban ÁLVAREZ FERNÁNDEZ

    2009-12-01

    úzcoa (yacimientos de Trikuaizti I y Larrarte, los grupos humanos utilizaron tanto el ámbar autóctono como el alóctono.ABSTRACT: Thirteen prehistoric sites in the Cantabrian Spain with records of amber, of ages ranging from the Upper Paleolithic to the Bronze Age, have been exposed. The geographic origin of these ambers has been studied to improve our the knowledge of the cultural and commercial aspects of the prehistoric societies. We have investigated if the origin of the amber could be local, from the natural Cretaceous amber sources of the Cantabrian Spain, or if it was allochthonous, from the Baltic region in the North of Europe. A comparison of the geographic location of the archaeological sites and the paleontological sources, and a comparison of the IRTF spectra of the ambers from the two kinds of localities, has been accomplished. The Spanish Cretaceous amber has gemological characteristics, as a consequence this amber was a potential material appropriate for the elaboration of ornamental objects using rudimentary instruments. We concluded that the prehistoric archaeological amber of the Cantabrian Spain had in general a local origin, and that it was probably obtained in the surrounding natural sources of the Prehistoric sites. The IRTF spectra of the archaeological ambers analyzed (El Pendo, Cueva Morín, Cueva de La Garma A and Trikuaizti I sites show that they are Cretaceous. Four areas, with close spatial relationship between the archaeological and the palaeontological sites of amber, are proposed as hypothetical source areas where the humans used Cretaceous amber during the Prehistory of the Cantabrian Spain. In contrast, only, the amber from the Larrarte site (Megalithic corresponds to succinite from the Tertiary of the Baltic region. These data indicate that during the Megalithic, at least in a small area of the Guipúzcoa Province (Trikuaizti I and Larrarte sites, the human used local and allochthonous amber.

  3. Botanical origin, colour, granulation, and sensory properties of the Harenna forest honey, Bale, Ethiopia.

    Science.gov (United States)

    Belay, Abera; Solomon, W K; Bultossa, Geremew; Adgaba, Nuru; Melaku, Samuel

    2015-01-15

    In this study, the Harenna forest honey samples were investigated with respect to their botanical origin, granulation, colour and sensory properties. Sixteen honey samples were collected from two representative sites (Chiri, C, and Wabero, W) using random sampling techniques. Botanical origin was investigated using qualitative pollen analysis by counting 500 pollen grains using harmonised methods of melissopalynology. Granulation, colour, and sensory properties of honey were determined by visual observation, using Pfund grader, acceptability and preference tests, respectively. Honey samples were also tested for tetracycline. Honey obtained from Wabero is originated dominantly from Syzygium guineense while Chiri was multifloral. The colour of honey ranged from 34 to 85 with light amber and extra light amber colours. The honey samples were free from tetracycline residue and form coarse granules slowly. Significant variation (p>0.05) in sensory preference and acceptability tests not observed due to hive types and locations.

  4. Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability

    CERN Document Server

    Sakae, Yoshitake

    2013-01-01

    We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $\\psi$ (N-C$^{\\alpha}$-C-N) and $\\zeta$ (C$^{\\beta}$-C$^{\\alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $\\alpha$-helical and $\\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.

  5. Colemanus keeleyorum (Braconidae, Ichneutinae s. l.: a new genus and species of Eocene wasp from the Green River Formation of western North America

    Directory of Open Access Journals (Sweden)

    J. Fisher

    2015-06-01

    Full Text Available A new genus and species of Ichneutinae s. l., Colemanus keeleyorum Fisher, is described from the Eocene Green River Formation in Colorado, USA. Colemanus was placed on a phylogenetic hypothesis using morphological data. Using a parsimony criterion, Colemanus is placed within Proteropini (Ichneutinae s. l.. Reconstructions of well-preserved regions (mesosomal dorsum and wings are included. A previously described species from lower Oligocene Baltic amber is transferred to Colemanus, resulting in the new combination C. contortus (Brues, 1933.

  6. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.

    Science.gov (United States)

    Wang, Jinan; Shao, Qiang; Cossins, Benjamin P; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang

    2016-01-01

    The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design.

  7. Federal and State Responses to the Emergency Response Communications Program. Draft Report, March 1979.

    Science.gov (United States)

    1979-06-01

    comentarios relacionados con el informe titulado "Emergency Response Communications Program". Le agradecer6 estudie este informe y favor de enviarle...sus comentarios respecto al mismo directamente al Contraalmirante Venzke. Anexo I State of Rhode Island and Providence Plantations EXECUTiVE 04AMBER...unconvinced that user requirements have really been developed. No real distinction is made between the way an emergency creates undue demands on the

  8. Izdevuma "Description de l'Égypte" oriģinālgravīras

    OpenAIRE

    Saviča, Mārīte

    2014-01-01

    Raksts par izstādē "Tutanhamona dzintars : Senā Ēģipte = The Amber of Tutankhamun : Ancient Egypt" (Rīgas birža, 2014.g. 14. novembris - 2015.g. 25. janvāris) eksponētajām senajām gravīrām no Latvijas Universitātes Bibliotēkas krājuma.

  9. Traditional Mediterranean Durum Wheat-Based Food Products

    OpenAIRE

    Mandato, Sandra; ABECASSIS, JOEL; Mayer-Laigle, Claire; De Vries, Hugo

    2015-01-01

    Durum wheat plays a major role on nutritional, cultural, economic and social development of the Mediterranean basin, where almost two-thirds of the worldwide annual durum wheat production is consumed. The specific features of durum wheat (glassy texture, amber color, high protein level, etc.) makes it suitable to undergo primary and secondary transformations leading to a lot of diverse food products such as pasta, couscous, bulgur, frekeh, a variety of breads and pastries. For ...

  10. A golden orb-weaver spider (Araneae: Nephilidae: Nephila) from the Middle Jurassic of China

    OpenAIRE

    Paul A Selden; Shih, Chungkun; Ren, Dong

    2011-01-01

    Nephila are large, conspicuous weavers of orb webs composed of golden silk, in tropical and subtropical regions. Nephilids have a sparse fossil record, the oldest described hitherto being Cretaraneus vilaltae from the Cretaceous of Spain. Five species from Neogene Dominican amber and one from the Eocene of Florissant, CO, USA, have been referred to the extant genus Nephila. Here, we report the largest known fossil spider, Nephila jurassica sp. nov., from Middle Jurassic (approx. 165 Ma) strat...

  11. Diagnostic accuracy of PAT-POPS and ManChEWS for admissions of children from the emergency department

    OpenAIRE

    Cotterill, Sarah; Rowland, Andrew G; Kelly, Jacqueline; Lees, Helen; Kamara, Mohammed

    2016-01-01

    Background The Pennine Acute Trust (PAT) Paediatric Observation Priority Score (PAT-POPS) is a specific emergency department (ED) physiological and observational aggregate scoring system, with scores of 0–18. A higher score indicates greater likelihood of admission. The Manchester Children's Early Warning System (ManChEWS) assesses six physiological observations to create a trigger score, classified as Green, Amber or Red. Methods Prospectively collected data were used to calculate PAT-POPS a...

  12. New genera of philopotine spider flies (Diptera, Acroceridae with a key to living and fossil genera

    Directory of Open Access Journals (Sweden)

    Jéssica Gillung

    2011-09-01

    Full Text Available In this paper we describe two new genera of philopotine Acroceridae: Schlingeriella irwini gen. et sp. n. (New Caledonia and Quasi fisheri gen. et sp. n. (Mexico. The Baltic amber species Eulonchiella eocenica Meunier, 1912 is rediagnosed and a neotype designated based on a newly discovered specimen. We also provide a dichotomous key to the world genera of Philopotinae, both living and fossil.

  13. Recent and rapid radiation of the lichen genus Sticta in the Western Indian Ocean islands

    OpenAIRE

    Simon, Antoine; Magain, Nicolas; Goffinet, Bernard; Sérusiaux, Emmanuël

    2016-01-01

    In the framework of a global project on the phylogeny of the lichen genus Sticta (Lobariaceae), extensive sampling was performed on the islands of Reunion and Mauritius as well as in several parts of Madagascar (mainly in two National Parks : Marojejy and Amber Mountain). The aim of this study is to provide the first comprehensive molecular phylogeny of the genus in the Western Indian Ocean islands (and more specifically of a presumably local endemic lineage), and to date its local radiation....

  14. Air Land Sea Bulletin. Issue Number 2012-3, September 2012

    Science.gov (United States)

    2012-09-01

    interagency identity detection equipment at a checkpoint in the Nazyan District, Nangarhar Province, Afghanistan, 10 March 2012. (Photo by SPC Amber Leach ...and neutral networks. Making targeting recommendations requires drawing upon an unders- tanding of the network and network analysis, and the...the DEA working with the Afghans on court authorized wire intercepts). HIGHER HEADQUARTERS LEPS LEPs at higher HQ work with the various enablers

  15. The Effects of Lamp Spectral Distribution on Sky Glow over Observatories

    Science.gov (United States)

    2015-01-01

    MAR 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE The Effects of Lamp Spectral Distribution on Sky Glow...overhead sky glow as a function of distance up to 300 km, from a variety of lamp types, including common gas discharge lamps and several types of LED... lamps . We conclude for both professional, and especially cultural (visual), astronomy, that low-pressure sodium and narrowspectrum amber LED lamps

  16. Documentation of Sensory Information in the Operation of Unmanned Aircraft Systems

    Science.gov (United States)

    2008-10-01

    sual.cue.conssted. of.a.perturbaton.of.the.nose-camera.magery.cons stent . wth.a.turbulence.event ..The.haptc.cue.conssted.of.a. 1-sec. vbraton...23.1322 Warning, caution, and advisory lights 23.1326 Pitot heat indication systems – could use other modes but must include amber light...probable cockpit lighting conditions. 23.1326 Pitot heat indication systems. If a flight instrument pitot heating system is installed to meet the

  17. The Effects of Lamp Spectral Distribution on Sky Glow over Observatories

    Science.gov (United States)

    Luginbuhl, C. B.; Boley, P. A.; Davis, D. R.; Duriscoe, D. M.

    2015-03-01

    Using a wavelength-generalized version of the Garstang (1991) model, we evaluate overhead sky glow as a function of distance up to 300 km, from a variety of lamp types, including common gas discharge lamps and several types of LED lamps. We conclude for both professional, and especially cultural (visual), astronomy, that low-pressure sodium and narrow-spectrum amber LED lamps cause much less sky glow than all broad-spectrum sources.

  18. Mineral resource of the month: gemstones

    Science.gov (United States)

    Olson, Donald W.

    2008-01-01

    Humans have been intrigued by gemstones since prehistoric times. Gemstones have been valued as treasured objects throughout history by all societies in all parts of the world. The first stones known to have been used for making jewelry include amber, amethyst, coral, diamond, emerald, garnet, jade, jasper, lapis lazuli, pearl, rock crystal, ruby, serpentine and turquoise. These stones served as status symbols for the wealthy. Today, arguably, gems are worn more for pleasure and in appreciation of their beauty than to demonstrate wealth.

  19. A large parasitengonid mite (Acari, Erythraeoidea from the Early Cretaceous Crato Formation of Brazil

    Directory of Open Access Journals (Sweden)

    J. A. Dunlop

    2007-08-01

    Full Text Available A new large, fossil mite (Arachnida: Acari, Pararainbowia martilli n. gen. n. sp., is described from the Early Cretaceous (Aptian Crato Formation from Ceará State, Brazil. It is assigned to the Cohort Parasitengona and the superfamily Erythraeoidea, some extant members of which can reach up to seven millimetres in body length. Given that doubts have been raised about the identity of putative Crato feather mite eggs, this new fossil represents the first unequivocal record of Acari from the Crato Formation, the first non-amber record of an erythraeoid mite and the oldest named example of this superfamily. Fossil erythraeoids from Mesozoic and Tertiary ambers are briefly reviewed – including a widely overlooked Late Cretaceous species – with comments on Mesozoic mites in general. Thirteen Baltic amber erythraeoids have been formally described, but much unstudied material from various amber sources remains. Ein neues großes Milbenfossil (Arachnida: Acari, Pararainbowia martilli n. gen. n. sp., wird aus der Crato Formation (Unterkreide, Aptium des Ceará Gebietes in Brasilien beschrieben. Es wird der Kohorte Parasitengona und der Überfamilie Erythraeoidea zugeordnet; die modernen Vertreter erreichen eine Körperlänge bis zu sieben mm. Weil die Identität von Federmilbeneiern aus der Crato Formation in Frage gestellt wurde, ist dieser Neufund der erste klare Hinweis von Acari aus der Crato Formation. Es ist die erste erythraeoide Milbe, die nicht aus dem Bernstein stammt sowie das älteste genannte Beispiel dieser Überfamilie. Fossile erythraeoide Milben aus dem Bernstein des Mesozoikum und des Tertiärs werden kurz zusammengefasst – u. a. eine weitgehend übersehene Art aus der Oberkreide – mit allgemeinen Anmerkungen zu den mesozoischen Milben. Dreizehn erythraeoide Milbenarten sind aus dem baltischen Bernstein genannt und beschrieben worden, aber weiteres unbearbeitetes Material von verschiedenen Bernstein-Fundpunkten liegt noch vor

  20. When using nutritional labels, less is better

    OpenAIRE

    Prevost, Marie; Hot, Pascal; Baciu, Monica; Ruffieux, Bernard; Meary, David; Crosetto, Paolo; Muller, Laurent

    2015-01-01

    New colorful nutrional labels are now used in some countries to help people better evaluate how healthy are food products. But little is known about how we understand and manipulate colored information to evaluate food products. The authors test how people evaluate anonymous food products from nutritional information displayed as numbers (% of daily amount) or as colors (red, amber, green). They anticipate that people will categorize food as bad for their health as soon as the color red is pr...

  1. Human Visual Performance and Flat Panel Display Image Quality

    Science.gov (United States)

    1980-07-01

    In0.42Ga0.58 amber 617 SiC yellow 590 GaN blue 440 GaN green 515 GaAs:Si with green 550 YF3YbEr GaAs:Si with blue 470 YF3:Yb:Tn InSe yellow 590 3.0...nm, from a neon gas. Other gases , and their discharge colors, which have been used in gas dis- charge displays incude argon (blue), cadmium (red

  2. Rock glacier ice as a microbial habitat

    Science.gov (United States)

    Florentine, C. E.; Skidmore, M. L.; Montross, S. N.

    2010-12-01

    Rock glaciers are ubiquitous geomorphic features in alpine environments, recognizable by a talus mantle, steep-toe, lobate shape and that flow due to the inferred presence of internal ice. Rock glaciers consist of both ice and debris, and are abundant in mountain ranges such as the Rocky Mountains, the Andes and the European Alps. Rock glacier ice has not previously been considered as a microbial habitat. However, given recent research showing debris-rich basal layers in glaciers harbor viable microbes, the debris-rich ice in a rock glacier has potential as a microbial habitat. The glacier research has demonstrated increased cell numbers in the debris rich basal ice relative to the clean glacier ice, and the finely-ground debris is considered to be a source of nutrients for the microbes. In August 2009 3 m of surface talus was excavated from the Lone Peak rock glacier, one of ~ 380 in Southwest Montana, to expose the underlying rock glacier ice. The ice contained numerous large rocks making sampling difficult, but 25 cm thick blocks with layers of clean and amber (~ 0.01% debris) ice were sampled. The isotopic, microbiological, and geochemical composition of the clean and amber ice was analyzed. The isotopic data provides some relative age dating for the ice and the geochemical data information on nutrient availability. Differences were observed between the microbial communities in the clean and amber ice by both cell counts and culturing techniques suggesting that as in glacier ice the debris-rich (amber) ice is a more amenable habitat for microbes.

  3. Nuclear Structure of Rhenium-186 Revealed by Neutron-Capture Gamma Rays

    Science.gov (United States)

    2014-03-01

    the non-forbidden transition probabilities, are assumed to follow a Porter -Thomas distribution [21] and its center lies on a mean value given by...rectangles are processing steps and the amber diamond is the conditional or decision point. The remainder of this section will briefly elaborate on...C. E. Porter and R. G. Thomas, "Fluctuations of Nuclear Reaction Widths," Phys. Rev., vol. 104, no. 2, p. 483, 1956. [22] S. Hilaire, "Level

  4. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

  5. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

    Science.gov (United States)

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie; Aspuru-Guzik, Alán; Kleinekathöfer, Ulrich

    2015-08-06

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna-Matthews-Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbital (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.

  6. Teaching integration with layers and representations: A case study

    Directory of Open Access Journals (Sweden)

    Joshua Von Korff

    2012-05-01

    Full Text Available We designed a sequence of seven lessons to facilitate learning of integration in a physics context. We implemented this sequence with a single college sophomore, “Amber,” who was concurrently enrolled in a first-semester calculus-based introductory physics course which covered topics in mechanics. We outline the philosophy underpinning these lessons, which characterizes integration in terms of layers and representations. We describe how Amber learned to give oral presentations in which she told a story about how integration comes from products, sums, and limits in a variety of physics contexts. We conclude that by the end of our lessons, Amber was able to conceptualize and explain integrals using multiple representations. In one case, she was able to solve a novel problem about integration in an unfamiliar context (center of mass. Based on our previous research about integration, we suggest that these achievements would have been unattainable with the use of a single one or two hour lesson.

  7. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    Science.gov (United States)

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  8. Novel recombinant insulin analogue with flexible C-terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water/acetonitrile solution.

    Science.gov (United States)

    Borowicz, Piotr; Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elżbieta; Mikiewicz-Syguła, Diana; Błażej-Sosnowska, Sylwia; Bogiel, Monika; Rusek, Dorota; Kurzynoga, Dariusz; Kozerski, Lech

    2011-11-01

    A tertiary structure of recombinant A22(G)-B31(K)-B32(R)-human insulin monomer (insulin GKR) has been characterized by (1)H, (13)C NMR at natural isotopic abundance using NOESY, TOCSY, (1)H/(13)C-GHSQC, and (1)H/(13)C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculations an ensemble of 20 structures of lowest energy was chosen which represents the tertiary structure of studied insulin. Here we present novel insulin with added A22(G) amino acid which interacts with β-turn environment resulting in high flexibility of B chain C-terminus.

  9. A minute fossil phoretic mite recovered by phase-contrast X-ray computed tomography.

    Science.gov (United States)

    Dunlop, Jason A; Wirth, Stefan; Penney, David; McNeil, Andrew; Bradley, Robert S; Withers, Philip J; Preziosi, Richard F

    2012-06-23

    High-resolution phase-contrast X-ray computed tomography (CT) reveals the phoretic deutonymph of a fossil astigmatid mite (Acariformes: Astigmata) attached to a spider's carapace (Araneae: Dysderidae) in Eocene (44-49 Myr ago) Baltic amber. Details of appendages and a sucker plate were resolved, and the resulting three-dimensional model demonstrates the potential of tomography to recover morphological characters of systematic significance from even the tiniest amber inclusions without the need for a synchrotron. Astigmatids have an extremely sparse palaeontological record. We confirm one of the few convincing fossils, potentially the oldest record of Histiostomatidae. At 176 µm long, we believe this to be the smallest arthropod in amber to be CT-scanned as a complete body fossil, extending the boundaries for what can be recovered using this technique. We also demonstrate a minimum age for the evolution of phoretic behaviour among their deutonymphs, an ecological trait used by extant species to disperse into favourable environments. The occurrence of the fossil on a spider is noteworthy, as modern histiostomatids tend to favour other arthropods as carriers.

  10. The Sky Through Three Giant Eyes

    Science.gov (United States)

    2007-02-01

    AMBER Instrument on VLT Delivers a Wealth of Results The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns

  11. The Great Cometary Show

    Science.gov (United States)

    2007-01-01

    The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns the enigmatic object Eta Carinae. Using AMBER with

  12. How a Huottuja (Piaroa community perceives genuine and false honey from the Venezuelan Amazon, by free-choice profi le sensory method

    Directory of Open Access Journals (Sweden)

    Patricia Vit

    2011-10-01

    Full Text Available Pot honey is the most abundant honey in the forest, produced by many species of stingless bees (Meliponini of the Huottuja (Piaroa community in Paria Grande, Venezuela. However, the commercialization of this honey is low, and false honeys, which are sold in labelled bottles, are easily found in the market. This study has investigated the ability of an untrained panel of Piaroa assessors to differentiate the genuine from the false pot honey using the Free-choice profile. This sensory method allows consumers to use their own words to describe and to quantify sensory attributes of a product. The genuine honeys, light amber Melipona fuscopilosa "isabitto" and dark amber Tetragona clavipes "ajavitte", the false light and dark "angelita" honeys, and the amber Apis mellifera honey, were evaluated. Sensory attributes related to the appearance, color, odor, flavor and mouthfeel were elicited in a qualitative session and were quantified in 10-cm unstructured line scales using individual score sheets. The data were analyzed by Generalized Procrustes Analysis (GPA. The bidimensional plot successfully separated genuine from false pot honeys. The first dimension (39.50% was represented by the low viscosity, fermented odor and sour taste, whereas the second dimension (24.69% was related to fruity and honey odor and flavor. Huottuja assessors differentiated the five honey types in terms of the perceived sensory characteristics.

  13. Erstnachweis von Taiwania, Cryptomeria und Liquidambar aus dem Bitterfelder und Baltischen Bernstein

    Directory of Open Access Journals (Sweden)

    H. Jähnichen

    1998-01-01

    Full Text Available Aus dem untermiozänen Bernstein von Bitterfeld (Sachsen-Anhalt werden erstmalig ein strukturzeigender Zweig von Taiwania schaeferi, ein isoliertes Nadel-Fragment von Cryptomeria sp. sowie ein Fruchtstand von Liquidambar europaea beschrieben. Außerdem muß “Widdringtonites oblongifolius” (Goeppert & Menge Caspary & Klebs 1906/07 pro parte aus dem obereozänen Baltischen Bernstein nach morphologisch-anatomischen Merkmalskomplexen ebenfalls zu Taiwania schaeferi gestellt werden. “Enormicutis eoconferta” — aff. Cryptomeria spec. (Schneider 1986 aus der obereozänen Braunkohle von Nordwestsachsen muß nach morphologisch-anatomischen Details zu Athrotaxis couttsiae (Heer Gardner revidiert werden. First record of Taiwania, Cryptomeria and Liquidambar from Bitterfeld and Baltic amber A structure-bearing twig of Taiwania schaeferi, an isolated needle-fragment of Cryptomeria spec. as also an aggregate fruit of Liquidambar europaea are firstly described from the Lower Miocene amber of Bitterfeld (Saxony-Anhalt. Moreover “Widdringtonites oblongifolius” (Goeppert & Menge Caspary & Klebs 1906/07 p.p. from the Upper Eocene Baltic amber after morphological-anatomical features must be also assigned to Taiwania schaeferi. “Enormicutis eoconferta” — aff. Cryptomeria sp. (Schneider 1986 from the Upper Eocene brown-coal of North Western Saxony after morphological-anatomical details must be revised to Athrotaxis couttsiae (Heer Gardner. doi:10.1002/mmng.19980010112

  14. Performance analysis of orthogonal pairs designed for an expanded eukaryotic genetic code.

    Directory of Open Access Journals (Sweden)

    Sebastian Nehring

    Full Text Available BACKGROUND: The suppression of amber stop codons with non-canonical amino acids (ncAAs is used for the site-specific introduction of many unusual functions into proteins. Specific orthogonal aminoacyl-tRNA synthetase (o-aaRS/amber suppressor tRNA(CUA pairs (o-pairs for the incorporation of ncAAs in S. cerevisiae were previously selected from an E. coli tyrosyl-tRNA synthetase/tRNA(CUA mutant library. Incorporation fidelity relies on the specificity of the o-aaRSs for their ncAAs and the ability to effectively discriminate against their natural substrate Tyr or any other canonical amino acid. METHODOLOGY/PRINCIPAL FINDINGS: We used o-pairs previously developed for ncAAs carrying reactive alkyne-, azido-, or photocrosslinker side chains to suppress an amber mutant of human superoxide dismutase 1 in S. cerevisiae. We found worse incorporation efficiencies of the alkyne- and the photocrosslinker ncAAs than reported earlier. In our hands, amber suppression with the ncAA containing the azido group did not occur at all. In addition to the incorporation experiments in S. cerevisiae, we analyzed the catalytic properties of the o-aaRSs in vitro. Surprisingly, all o-aaRSs showed much higher preference for their natural substrate Tyr than for any of the tested ncAAs. While it is unclear why efficiently recognized Tyr is not inserted at amber codons, we speculate that metabolically inert ncAAs accumulate in the cell, and for this reason they are incorporated despite being weak substrates for the o-aaRSs. CONCLUSIONS/SIGNIFICANCE: O-pairs have been developed for a whole plethora of ncAAs. However, a systematic and detailed analysis of their catalytic properties is still missing. Our study provides a comprehensive scrutiny of o-pairs developed for the site-specific incorporation of reactive ncAAs in S. cerevisiae. It suggests that future development of o-pairs as efficient biotechnological tools will greatly benefit from sound characterization in vivo and in

  15. Optimisation of a system for the co-translational incorporation of a keto amino acid and its application to a tumour-specific Anticalin.

    Science.gov (United States)

    Reichert, Andreas J; Poxleitner, Gabriele; Dauner, Martin; Skerra, Arne

    2015-12-01

    The bioorthogonal keto group has attracted interest for the site-specific chemical conjugation of recombinant proteins under mild conditions, e.g. with aminooxy-functionalised fluorescent probes, radiometal chelates, toxins or polymers. However, the cotranslational incorporation of the corresponding non-canonical amino acid p-acetyl-L-phenylalanine (Apa) into proteins expressed in Escherichia coli by means of amber suppression using a previously described system with a mutated tRNA and an engineered tyrosyl-tRNA synthetase from Methanococcus jannaschii shows limited efficiency and considerable promiscuity towards endogenous amino acids. Employing a one-plasmid system that encodes all three components required for selection, i.e. the modified aminoacyl-tRNA synthetase (aaRS), the cognate amber suppressor tRNA and the enhanced green fluorescent protein equipped with an amber stop codon and serving as reporter, we have generated an Apa-specific aaRS&tRNA pair with considerably improved efficiency (17-fold increased expression) and also fidelity (6-fold). To this end, both the aaRS and the tRNA were subjected to doped random mutagenesis and selection in altogether four evolutionary cycles using fluorescence-activated bacterial cell sorting as well as automated screening of microcultures. The resulting aaRS&tRNA pair was applied to the functionalisation of an Anticalin with specificity towards oncofetal fibronectin by introducing a keto group at a permissible site for subsequent conjugation with a fluorescent dye, thus allowing visualisation of this tumour target under the microscope.

  16. Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl pairs in the Escherichia coli BL21(DE3 cell strain.

    Directory of Open Access Journals (Sweden)

    Keturah A Odoi

    Full Text Available Systematic studies of nonsense and sense suppression of the original and three derivative Methanosarcina mazei PylRS-tRNA(Pyl pairs and cross recognition between nonsense codons and various tRNA(Pyl anticodons in the Escherichia coli BL21(DE3 cell strain are reported. tRNA(CUA(Pyl is orthogonal in E. coli and able to induce strong amber suppression when it is co-expressed with pyrrolysyl-tRNA synthetase (PylRS and charged with a PylRS substrate, N(ε-tert-butoxycarbonyl-L-lysine (BocK. Similar to tRNA(CUA(Pyl, tRNA(UUA(Pyl is also orthogonal in E. coli and can be coupled with PylRS to genetically incorporate BocK at an ochre mutation site. Although tRNA(UUA(Pyl is expected to recognize a UAG codon based on the wobble hypothesis, the PylRS-tRNA(UUA(Pyl pair does not give rise to amber suppression that surpasses the basal amber suppression level in E. coli. E. coli itself displays a relatively high opal suppression level and tryptophan (Trp is incorporated at an opal mutation site. Although the PylRS-tRNA(UCA(Pyl pair can be used to encode BocK at an opal codon, the pair fails to suppress the incorporation of Trp at the same site. tRNA(CCU(Pyl fails to deliver BocK at an AGG codon when co-expressed with PylRS in E. coli.

  17. Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection.

    Science.gov (United States)

    Homs, Maria; Rodriguez-Frias, Francisco; Gregori, Josep; Ruiz, Alicia; Reimundo, Pilar; Casillas, Rosario; Tabernero, David; Godoy, Cristina; Barakat, Salma; Quer, Josep; Riveiro-Barciela, Mar; Roggendorf, Michael; Esteban, Rafael; Buti, Maria

    2016-01-01

    Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV) quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD) treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg). The amber codon encodes the small (unedited) HDAg form and the W codon the large (edited) HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (pquasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.

  18. NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer.

    Science.gov (United States)

    Bocian, Wojciech; Borowicz, Piotr; Mikołajczyk, Jerzy; Sitkowski, Jerzy; Tarnowska, Anna; Bednarek, Elzbieta; Głabski, Tadeusz; Tejchman-Małecka, Bozena; Bogiel, Monika; Kozerski, Lech

    2008-10-01

    A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions.

  19. 与交通有关的词汇

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    交通规则traffic regulation 路标guide post 红绿灯traffic light 红灯red light 绿灯green light 黄灯amber light 岗亭police box 斑马线zebra stripes 车行道cariage-way 此路不通blocked 不准驶入no entry 安全岛safety jsland 停车处parking place 不准停车restricted stop 不准滞留restricted waiting

  20. Work in support of biosphere assessments for solid radioactive waste disposal. 2. biosphere FEP list and biosphere modelling

    Energy Technology Data Exchange (ETDEWEB)

    Egan, M.J.; Maul, P.R.; Watkins, B.M.; Venter, A. [QuantiSci Ltd., Henley-on-Thames (United Kingdom)

    2001-10-01

    In order to assist SSI in its reappraisal of the SFR safety case, QuantiSci has been appointed to develop a systematic framework within which to conduct the review of SKB's post-closure performance assessment (PA). The biosphere FEP list presented here was developed for use as reference material in conducting the review. SSI wishes to develop an independent PA capability for a time-dependent biosphere in preparation for the examination of the revised SFR safety case. This report documents the model development that has been undertaken by QuantiSci using the Amber computer code.

  1. Effects of Bright Light Therapy on Sleep, Cognition, Brain Function, and Neurochemistry in Mild Traumatic Brain Injury

    Science.gov (United States)

    2015-01-01

    of(Greater(Ac0va0on(in(BLUE(vs(AMBER(Condi0on((MSIT(Task)( Hippocampus * functional connectivity between the thalamus and several cortical regions...Ritalin, diet pills.      Cocaine:  snorting, IV, freebase, crack, "speedball".        Narcotics:  heroin,  morphine , Dilaudid, opium, Demerol...Casasanto DJ, Yurgelun-Todd DA, Maldjian JA, Detre JA. Functional activation of the left amygdala and hippocampus during associative encoding

  2. Improving Healthcare Transition Planning and Health-Related Independence for Youth with ASD and their Families

    Science.gov (United States)

    2015-10-01

    included marriage and family in their responses. Discussing current relationships was part of a more complex conversation. Many young adults (n=22...topic].” Other participants were more direct. Sam said he did not want a relationship because he did not want children . Amber, a 25 year old female...who was a lesbian, I had her take me down to Kansas City, and they had a group for gays , transsexuals, lesbians, all the others. I was like, “Holy cr*p

  3. Generic control software connecting astronomical instruments to the reflective memory data recording system of VLTI - bossvlti

    Science.gov (United States)

    Pozna, E.; Ramirez, A.; Mérand, A.; Mueller, A.; Abuter, R.; Frahm, R.; Morel, S.; Schmid, C.; Duc, T. Phan; Delplancke-Ströbele, F.

    2014-07-01

    The quality of data obtained by VLTI instruments may be refined by analyzing the continuous data supplied by the Reflective Memory Network (RMN). Based on 5 years experience providing VLTI instruments (PACMAN, AMBER, MIDI) with RMN data, the procedure has been generalized to make the synchronization with observation trouble-free. The present software interface saves not only months of efforts for each instrument but also provides the benefits of software frameworks. Recent applications (GRAVITY, MATISSE) supply feedback for the software to evolve. The paper highlights the way common features been identified to be able to offer reusable code in due course.

  4. Modulation of allele leakiness and adaptive mutability in Escherichia coli

    Indian Academy of Sciences (India)

    R. Jayaraman

    2000-08-01

    It is shown that partial phenotypic suppression of two ochre mutations (argE3 and lacZU118) and an amber mutation (in argE) by sublethal concentrations of streptomycin in an rpsL+ (streptomycin-sensitive) derivative of the Escherichia coli strain AB1157 greatly enhances their adaptive mutability under selection. Streptomycin also increases adaptive mutability brought about by the ppm mutation described earlier. Inactivation of recA affects neither phenotypic suppression by streptomycin nor replication-associated mutagenesis but abolishes adaptive mutagenesis. These results indicate a causal relationship between allele leakiness and adaptive mutability.

  5. Sleep disorders in Parkinson’s disease

    Directory of Open Access Journals (Sweden)

    Israt Jahan

    2009-10-01

    Full Text Available Israt Jahan1, Robert A Hauser2, Kelly L Sullivan1, Amber Miller1, Theresa A Zesiewicz11Department of Neurology, Parkinson’s Research Foundation, 2Departments of Neurology, Molecular Pharmacology, and Physiology, University of South Florida, Parkinson’s Disease and Movement Disorders Center, Tampa, FL, USAAbstract: Sleep disorders occur commonly in Parkinson’s disease (PD, and reduce quality of life. Sleep-related problems in PD include insomnia, restless legs syndrome, rapid eye movement sleep behavior disorder, sleep apnea, parasomnias, excessive daytime sleepiness, and sleep attacks. This article reviews sleep disorders and their treatment in PD. Keywords: insomnia, restless legs syndrome, sleep apnea

  6. First Aid for Red Cross Inventory Manager

    OpenAIRE

    Alonso Benito, Níobe

    2015-01-01

    El proyecto ha sido realizado en el marco de un programa EPS en Amberes. El producto consiste en un rediseño del Prev-Kit utilizado por la oficina de la Cruz Roja en Merksem en eventos deportivos y socioculturales. El briefing inicial constaba de una serie de requerimientos entre los cuales se encontraban: mejorar el reabastecimiento por parte del encargado del inventario, mejorar la usabilidad, facilitar la limpieza y la adaptación a los posibles cambios de materiales, así com...

  7. Phase Closure Nulling: A "Lyot Mask" on correlated flux of stars

    Science.gov (United States)

    Duvert, G.; Chelli, A.; Malbet F.; Kern, P.

    2010-10-01

    "Phase closure nulling" (PCN in short) is a technique which consists of observing fully resolved stars around the spatial frequency regions where the interferometric visibility amplitude is close to zero. Chelli et al. (2009) have shown that the phase closure in these regions is dominated by the signature of close and faint companions (if present), as if a "Lyot mask" was blocking the correlated flux of the star. This contribution will present the theory of PCN and results obtained on recent AMBER/VLTI and CHARA/MIRC observations, showing the high detection dynamics achieved by this observational technique.

  8. INFLUENCE OF GLASS CULLET IN CEMENT PASTES

    Institute of Scientific and Technical Information of China (English)

    A.Karamberi; E.Chaniotakis; D.Papageorgiou; A.Moutsatsou

    2006-01-01

    The present study investigates glass and cement compatibility with a view to use glass as a cement replacement. Amber, flint and green glasses were chosen due to their prevalence in the Greek market as packaging materials. The factors under investigation were the pozzolanicity of the glass cullet, the hydration rate and the mechanical strength development of the cement pastes, as well as the expansion of the specimens due to alkali-silica reaction.Moreover, the potential enhancement of glass pozzolanic activity was examined. The results of the study were encouraging to show the potentiality of utilising glass cullet in cementitious products.

  9. 四分钟

    Institute of Scientific and Technical Information of China (English)

    姜米粒

    2008-01-01

    片名:四分钟Vief Minuten(2006) 类别:剧情导演:克里斯·克劳斯Chris Kraus编剧:克里斯·克劳斯Chris Kraus主演:里奇·穆勒Richy Muller莫妮卡·布雷多Monika Bleibtreu汉娜·赫斯普朗Hannah Herzsprung安柏·本加德Amber Bongard获奖情况:2006年上海金爵奖2007年德国劳拉奖

  10. The Cretaceous Fossil Burmaculex antiquus Confirmed as the Earliest Known Lineage of Mosquitoes (Diptera: Culicidae).

    Science.gov (United States)

    Borkent, Art; Grimaldi, David A

    2016-01-01

    A second female of mid-Cretaceous Burmaculex antiquus Borkent & Grimaldi, preserved in 99 myo Burmese amber, and the oldest known member of the Culicidae, is described in detail. Although generally opaque and distorted, some character states are added or refined. The discovery of well-developed scales on the legs shows that this feature must now be considered a synapomorphy of both the fossil and all extant members of the family. Previously described synapomorphies and further interpretation here confirm the phylogenetic position of this fossil as the sister group to extant and all known fossil Culicidae. It is placed in the new subfamily Burmaculicinae.

  11. Back in Europe: Quamtana spiders (Araneae: Pholcidae in Germany

    Directory of Open Access Journals (Sweden)

    Huber, Bernhard

    2015-11-01

    Full Text Available Two undescribed species of the African pholcid spider genus Quamtana have been found in German greenhouses and plant markets since 2012. Both species seem to have established stable populations. This genus has not been previously recorded from Europe, except for a fossil specimen in Eocene amber from the Paris Basin that was tentatively assigned to Quamtana and that is estimated to date from 53 million years ago. Since the actual geographic origins of the two species (probably South and/or tropical Africa are unknown, we do not formally describe them.

  12. Enhancement of the Shared Graphics Workspace.

    Science.gov (United States)

    1986-05-01

    RESPONSIBLE INDIVIDUAL 22b. TELEPHONE (Include Area Code) 22c OFFICE SYMBOL Ginger Winn (202) 694-5919 DARPA DO FORM 1473, 84 MAR 83 APR edition may...photograph and the image is less sharp. Text images appear on the SGWS red -green-blue (RGB) monitor in black on amber, with a resolution of 1,024 x 512 pixels...boards no longer send extra characters when an operator presses a button for longer than usual. The system confused the operator by showing all options

  13. Structure and aggregation in model tetramethylurea solutions

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Rini; Patey, G. N., E-mail: patey@chem.ubc.ca [Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1 (Canada)

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X{sub t}, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X{sub t} = 0.005, aggregation is a well established feature of the solution at X{sub t} = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X{sub t} ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X{sub t} = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  14. Stranicy institucional'noj jekonomicheskoj istorii Kjonigsberga/Kaliningrada [Chapters of the institutional economic history of Königsberg/Kaliningrad

    Directory of Open Access Journals (Sweden)

    Nureev Rustem

    2010-01-01

    Full Text Available This article consists of a series of short essays dedicated to a certain period of the 'popular' socioeconomic history (with a particular focus on the institutional development problems of the former East Prussia from Antiquity to present days. The authors tackle the issues of the economic history of amber, the role of the Hansa League in the development of medieval trade, the QWERTY-effects in the rail gauge standards, and the peculiarities of the development of the Kaliningrad region in the post-Soviet period.

  15. Alustava ettevõtja rahaallikad / Eva Palu

    Index Scriptorium Estoniae

    Palu, Eva

    2005-01-01

    Võimalikest finantseerimisallikatest ettevõtte rajamisel. Lisa: Noppeid uuringu "Eesti elanike ettevõtlikkus" järeldustest. Alustavatele ettevõtetele pakutavaid finantseerimisvariante tutvustavad Hansapanga ettevõtete panganduse analüüsi- ja arendusosakonna juhataja Raul Kivari, Eesti Ühispanga ärilaenude arendusjuht Helen Saare, Nordea Panga äriklientide osakonna juhataja Ingo Põder, Parex Panga müügi- ja marketingidirektor Andres Pärloja, BIG-i juhatuse esimees Targo Raus, MTVP tegevjuht Allan Martinson, BaltCapi finantsjuht Martin Kõdar, Amber Trusti nõustaja Indrek Kasela. Diagrammid: Ettevõtlus Eestis

  16. The first mesozoic ants.

    Science.gov (United States)

    Wilson, E O; Carpenter, F M; Brown, W L

    1967-09-01

    Two worker ants preserved in amber of Upper Cretaceous age have been found in New Jersey. They are the first undisputed remains of social insects of Mesozoic age, extending the existence of social life in insects back to approximately 100 million years. They are also the earliest known fossils that can be assigned with certainty to aculeate Hymenoptera. The species, Sphecomyrma freyi, is considered to represent a new subfamily (Sphecomyrminae), more primitive than any previously known ant group. It forms a near-perfect link between certain nonsocial tiphiid wasps and the most primitive myrmecioid ants.

  17. The Employee Diversity Team Wants to Take You around the World in Film | Poster

    Science.gov (United States)

    By Andrea Frydl, Contributing Writer The NCI at Frederick Employee Diversity Team (EDT) has prepared a new display that features a sample of the foreign films from the team’s collection in the Scientific Library. “Foreign films really help stimulate an awareness of different cultures and countries. I think it is a great celebration of diversity to have the Employee Diversity Team promote films from across the globe and make them available to our employees,” said Amber Elia, program analyst, NCI at Frederick Office of Scientific Operations, and member of the EDT.

  18. VLTI status update: a decade of operations and beyond

    CERN Document Server

    Merand, Antoine; Aller-Carpentier, Emmanuel; Andolfato, Luigi; Alonso, Jaime; Berger, Jean-Philippe; Blanchard, Guillaume; Boffin, Henri; Bourget, Pierre; Bristow, Paul; Cid, Claudia; de Wit, Willem-Jan; del Valle, Diego; Delplancke-Stroebele, Franccoise; Derie, Frederic; Faundez, Lorena; Ertel, Steve; Grellmann, Rebekka; Gitton, Philippe; Glindemann, Andreas; Guajardo, Patricia; Guieu, Sylvain; Guisard, Stephane; Guniat, Serge; Haguenauer, Pierre; Herrera, Christian; Hummel, Christian; La Fuente, Carlos; Lopez, Marcelo; Mardones, Pedro; Morel, Sebastien; Mueller, Andre; Percheron, Isabelle; Duc, Than Phan; Pino, Andres; Poupar, Sebastien; Pozna, Eszter; Ramirez, Andres; Rengaswamy, Sridharan; Rivas, Lionel; Rivinius, Thomas; Segovia, Alex; Schmid, Christian; Schoeller, Markus; Schuhler, Nicolas; Woillez, Julien; Wittkowski, Markus

    2014-01-01

    We present the latest update of the European Southern Observatory's Very Large Telescope interferometer (VLTI). The operations of VLTI have greatly improved in the past years: reduction of the execution time; better offering of telescopes configurations; improvements on AMBER limiting magnitudes; study of polarization effects and control for single mode fibres; fringe tracking real time data, etc. We present some of these improvements and also quantify the operational improvements using a performance metric. We take the opportunity of the first decade of operations to reflect on the VLTI community which is analyzed quantitatively and qualitatively. Finally, we present briefly the preparatory work for the arrival of the second generation instruments GRAVITY and MATISSE.

  19. Lesion presenting with a “blue amber” pattern

    Science.gov (United States)

    Pagliarello, Calogero; Peccerillo, Francesca; Zucchi, Alfredo; Tortorella, Rocco Giuseppe; Ricci, Roberto; Stanganelli, Ignazio; Feliciani, Claudio; Di Nuzzo, Sergio

    2016-01-01

    Atypical fibroxanthoma (AFX) is a spindle cell neoplasm with low metastatic potential but high tendency to recur after surgery. Because of the rarity of this lesion and its aspecific clinical features, AFX could be easily misdiagnosed and undertreated by many clinicians who encounter them. Dermoscopy represents a valuable tool for easily assessing skin lesions, even though histological examination is required for final diagnosis. We report a case of a cheek lesion with dermoscopic “blue amber pattern”, easily recognisable and not observed in others skin tumours, which could represent an additional feature useful in differentiating this tumour from other skin neoplasms. PMID:27803916

  20. TRIBUTOS E IMPUESTOS EN DIEGO DE AVENDAÑO. UN CAPÍTULO DE ÉTICA COLONIAL

    Directory of Open Access Journals (Sweden)

    Angel Garcia

    2001-01-01

    Full Text Available En 1668, Diego de Avendaño, jesuita peruano, publicaba en Amberes su Thesaurus Indicus, obra de contenido ético-jurídico, que –en intención del autor– pretendía ser guía para el Consejo de Indias en referencia al recto gobierno de las colonias americanas. El presente trabajo expone la visión que el jesuita presenta en su obra, sobre los diferentes impuestos y tributos en las colonias.

  1. VizieR Online Data Catalog: eta Car velocity-resolved imaging (Weigelt+, 2016)

    Science.gov (United States)

    Weigelt, G.; Hofmann, K.-H.; Schertl, D.; Clementel, N.; Corcoran, M. F.; Damineli, A.; de Wit, W.-J.; Grellmann, R.; Groh, J.; Guieu, S.; Gull, T.; Heininger, M.; Hillier, D. J.; Hummel, C. A.; Kraus, S.; Madura, T.; Mehner, A.; Merand, A.; Millour, F.; Moffat, A. F. J.; Ohnaka, K.; Patru, F.; Petrov, R. G.; Rengaswamy, S.; Richardson, N. D.; Rivinius, T.; Schoeller, M.; Teodoro, M.; Wittkowski, M.

    2016-09-01

    We present the reconstructed images from Fig. 4 of the paper. The interferometric data were taken with the ESO VLTI and the AMBER instrument with high spectral resolution (R=12000) in many spectral channels across the Brackett Gamma line at 2.166 micron. 96 images were reconstructed at velocity channels from -663km/s to 520km/s. The velocity of each channel is coded into the filename. Plate scale is 0.781mas/pixel. North is up, and east to the left. FOV is 50mas. The resolution of the images is ~6 mas. (2 data files).

  2. VLTI status update: a decade of operations and beyond

    Science.gov (United States)

    Mérand, Antoine; Abuter, Roberto; Aller-Carpentier, Emmanuel; Andolfato, Luigi; Alonso, Jaime; Berger, Jean-Philippe; Blanchard, Guillaume; Boffin, Henri; Bourget, Pierre; Bristow, Paul; Cid, Claudia; de Wit, Willem-Jan; del Valle, Diego; Delplancke-Ströbele, Françoise; Derie, Frédéric; Faundez, Lorena; Ertel, Steve; Grellmann, Rebekka; Gitton, Philippe; Glindemann, Andreas; Guajardo, Patricia; Guieu, Sylvain; Guisard, Stéphane; Guniat, Serge; Haguenauer, Pierre; Herrera, Cristian; Hummel, Christian; La Fuente, Carlos; Lopez, Marcelo; Mardones, Pedro; Morel, Sébastien; Müller, André; Percheron, Isabelle; Duc, Than Phan; Pino, Andres; Poupar, Sébastien; Pozna, Eszter; Ramirez, Andres; Rengaswamy, Srihdaran; Rivas, Lionel; Rivinius, Thomas; Segovia, Alex; Schmid, Christian; Schöller, Markus; Schuhler, Nicolas; Woillez, Julien; Wittkowski, Markus

    2014-07-01

    We present the latest update of the European Southern Observatory's Very Large Telescope interferometer (VLTI). The operations of VLTI have greatly improved in the past years: reduction of the execution time; better offering of telescopes configurations; improvements on AMBER limiting magnitudes; study of polarization effects and control for single mode fibres; fringe tracking real time data, etc. We present some of these improvements and also quantify the operational improvements using a performance metric. We take the opportunity of the first decade of operations to reflect on the VLTI community which is analyzed quantitatively and qualitatively. Finally, we present briefly the preparatory work for the arrival of the second generation instruments GRAVITY and MATISSE.

  3. Triangle Area Water Supply Monitoring Project, October 1988 Through September 2001, North Carolina-Description of the Water-Quality Network, Sampling and Analysis Methods, and Quality-Assurance Practices

    Science.gov (United States)

    2004-01-01

    Triazine herbicides in filtered water by GC/MS 1379 1992 – 1993 1–L amber baked glass Chilled. Pesticides in filtered water (Carbopak-B solid-phase...of analysis by the U.S. Geological Survey National Water Quality Laboratory—Determination of organonitrogen herbicides in water by solid-phase...34581 A GC/MS 5 2-Chlorophenol 34586 A GC/MS 5 2- Nitrophenol 34591 A GC/MS 5 Di-N-octylphthalate 34596 A GC/MS 10 2,4-Dichlorophenol 34601 A GC/MS 5

  4. First record of the family Pseudochiridiidae (Arachnida, Pseudoscorpiones) from continental South America--a Pseudochiridium from a Brazilian cave.

    Science.gov (United States)

    Von Schimonsky, Diego Monteiro; Bichuette, Maria Elina; Mahnert, Volker

    2014-12-02

    The small pseudoscorpion family Pseudochiridiidae Chamberlin, 1923 comprises two genera and 12 extant species recorded from Asia (Burma, Christmas Island, Indonesia, India, Nepal, Malaysia, New Guinea, Philippines, Nicobars and Sumba), eastern, central and southern Africa (Chad, D.R. Congo, Kenya, South Africa, Tanzania), Madagascar, Seychelles (Aldabra), North America (Florida) and the Caribbean Islands of Dominican Republic and Cuba (Harvey 2013, Barba & Barroso 2013); one unidentified species is mentioned for the fauna of Mexico (Ceballos 2004). A fossil species has been described from Dominican amber by Judson (2007), who predicted the presence of this family in South America. 

  5. Analysis of a mutation affecting the specificity domain for prohead binding of the bacteriophage lambda terminase.

    OpenAIRE

    1992-01-01

    Genetic studies have identified a specificity domain for prohead binding in the C-terminal 32 amino acids of gpA, the large subunit of bacteriophage lambda terminase (S. Frackman, D. A. Siegele, and M. Feiss, J. Mol. Biol. 180:283-300, 1984). In the present work, an amber mutation, Aam42, in the fifth-to-last codon of the A gene was found to be lethal in nonsuppressing hosts. The mutation, expected to generate gpA lacking the last five amino acids, caused the production of a terminase that cu...

  6. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.

    Science.gov (United States)

    Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2013-01-01

    Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.

  7. Conformational Analysis of Indole Alkaloids Corynantheine and Dihydrocorynantheine by Dynamic 1H NMR Spectroscopy and Computational Methods: Steric Effects of Ethyl vs Vinyl Group

    DEFF Research Database (Denmark)

    Stærk, Dan; Norrby, Per-Ola; Jaroszewski, Jerzy W.

    2001-01-01

    . Line-shape analysis yielded enthalpy of activation DeltaH(double dagger) = 71 +/- 6 kJ/mol, and entropy of activation DeltaS(double dagger) = 33 +/- 6 J/mol(.)K. The major and minor conformation contains the methyl ether group above and below the plane of the ring, respectively, as determined by low...... bulk of the vinyl and the ethyl group. The conformational equilibria involving the side chain rotation as well as inversion of the bridgehead nitrogen in corynantheine and dihydrocorynantheine was studied by force-field (Amber(*) and MMFF) and ab initio (density-functional theory at the B3LYP/6-31G...

  8. Sevilla, puerto y puerta de Europa: la actividad de una compañía comercial flamenca en la segunda mitad del siglo XVI

    Directory of Open Access Journals (Sweden)

    Germán JIMÉNEZ MONTES

    2016-12-01

    Full Text Available En este artículo se analiza la actividad de una compañía comercial flamenca en Sevilla durante los años de 1577 a 1582. A partir del estudio de los negocios (exportaciones, importaciones y letras de cambio de esta firma, con base en Amberes y Brujas, se obtienen conclusiones del papel de los extranjeros en el dinámico ambiente mercantil de la Sevilla del siglo XVI, por un lado, y del incremento de los contactos comerciales y financieros de la ciudad hispalense con otras plazas europeas, como consecuencia precisamente del desarrollo de la Carrera de Indias, por otro.

  9. 广西合浦县九只岭东汉墓%Eastern Han Tombs at Jiuzhiling in Hepu County, Guangxi

    Institute of Scientific and Technical Information of China (English)

    广西壮族自治区文物工作队; 合浦县博物馆

    2003-01-01

    The five tombs at Hepu Jiuzhiling are medium or small in size and “中”- or “凸”-shaped in plan. They are built of bricks except for a brick-and-timber grave. The objects they yielded include pottery, bronzes, irons and talcum articles, as well as jade, gold, silver, crystal, agate, amber and glassornaments. With these grave goods definite in date, the tombs help to make up gaps in the knowledge of the chronology and typology of Han burials in Guangdong and Guangxi. Meanwhile, they undoubtedly much contribute to studying the periodization of Eastern Han graves and the history of the region south of the Five Ridges. Referring to previously obtained research results, the plenty of gold, glass, agate,crystal and amber ornaments unearthed from the tombs must largely be imported goods. This has im-portant value to the study of Han period Hepu Port, the Sea Silk Road, and the overseas trade of South China.

  10. Diterpenoid Biopolymers: New Directions for Renewable Materials Engineering

    Science.gov (United States)

    Hillwig, Matthew L.; Mann, Francis M.; Peters, Reuben J.

    2010-01-01

    Most types of ambers are naturally occurring, relatively hard, durable resinite polymers derived from the exudates of trees. This resource has been coveted for thousands of years due to its numerous useful properties in industrial processes, beauty, and purported medicinal properties. Labdane diterpenoid based ambers represent the most abundant and important resinites on earth. These resinites are a dwindling, non-renewable natural resource, so a new source of such materials needs to be established. Recent advances in sequencing technologies and biochemical engineering are rapidly accelerating the rate of identifying and assigning function to genes involved in terpenoid biosynthesis, as well as producing industrial-scale quantities of desired small-molecules in bacteria and yeast. This has provided new tools for engineering metabolic pathways capable of producing diterpenoid monomers that will enable the production of custom-tailored resinite-like polymers. Furthermore, this biosynthetic toolbox is continuously expanding, providing new possibilities for renewing dwindling stocks of naturally occurring resinite materials and engineering new materials for future applications. PMID:20857504

  11. Debris-carrying camouflage among diverse lineages of Cretaceous insects

    Science.gov (United States)

    Wang, Bo; Xia, Fangyuan; Engel, Michael S.; Perrichot, Vincent; Shi, Gongle; Zhang, Haichun; Chen, Jun; Jarzembowski, Edmund A.; Wappler, Torsten; Rust, Jes

    2016-01-01

    Insects have evolved diverse methods of camouflage that have played an important role in their evolutionary success. Debris-carrying, a behavior of actively harvesting and carrying exogenous materials, is among the most fascinating and complex behaviors because it requires not only an ability to recognize, collect, and carry materials but also evolutionary adaptations in related morphological characteristics. However, the fossil record of such behavior is extremely scarce, and only a single Mesozoic example from Spanish amber has been recorded; therefore, little is known about the early evolution of this complicated behavior and its underlying anatomy. We report a diverse insect assemblage of exceptionally preserved debris carriers from Cretaceous Burmese, French, and Lebanese ambers, including the earliest known chrysopoid larvae (green lacewings), myrmeleontoid larvae (split-footed lacewings and owlflies), and reduviids (assassin bugs). These ancient insects used a variety of debris material, including insect exoskeletons, sand grains, soil dust, leaf trichomes of gleicheniacean ferns, wood fibers, and other vegetal debris. They convergently evolved their debris-carrying behavior through multiple pathways, which expressed a high degree of evolutionary plasticity. We demonstrate that the behavioral repertoire, which is associated with considerable morphological adaptations, was already widespread among insects by at least the Mid-Cretaceous. Together with the previously known Spanish specimen, these fossils are the oldest direct evidence of camouflaging behavior in the fossil record. Our findings provide a novel insight into early evolution of camouflage in insects and ancient ecological associations among plants and insects. PMID:27386568

  12. The development of a standardised diet history tool to support the diagnosis of food allergy.

    Science.gov (United States)

    Skypala, Isabel J; Venter, Carina; Meyer, Rosan; deJong, Nicolette W; Fox, Adam T; Groetch, Marion; Oude Elberink, J N; Sprikkelman, Aline; Diamandi, Louiza; Vlieg-Boerstra, Berber J

    2015-01-01

    The disparity between reported and diagnosed food allergy makes robust diagnosis imperative. The allergy-focussed history is an important starting point, but published literature on its efficacy is sparse. Using a structured approach to connect symptoms, suspected foods and dietary intake, a multi-disciplinary task force of the European Academy of Allergy and Clinical Immunology developed paediatric and adult diet history tools. Both tools are divided into stages using traffic light labelling (red, amber and green). The red stage requires the practitioner to gather relevant information on symptoms, atopic history, food triggers, foods eaten and nutritional issues. The amber stage facilitates interpretation of the responses to the red-stage questions, thus enabling the practitioner to prepare to move forward. The final green stage provides a summary template and test algorithm to support continuation down the diagnostic pathway. These tools will provide a standardised, practical approach to support food allergy diagnosis, ensuring that all relevant information is captured and interpreted in a robust manner. Future work is required to validate their use in diverse age groups, disease entities and in different countries, in order to account for differences in health care systems, food availability and dietary norms.

  13. Nutritional value of cold-pressed rapeseed oil during long term storage as influenced by the type of packaging material, exposure to light & oxygen and storage temperature.

    Science.gov (United States)

    Wroniak, Małgorzata; Rękas, Agnieszka

    2016-02-01

    The effect of various conditions (storage temperature, exposure to light, access of oxygen) and different packaging material (amber glass, amber polyethylene terephthalate) on the nutritional value of cold-pressed rapeseed oil during 12 months of storage was investigated. Quantified quality parameters included: acidity, peroxide value, spectrophotometric indices (K 232 , K 268 ), fatty acid composition, tocopherols and sterols. Storage of oil at 4 °C was found to be most appropriate for maintaining the quality of cold-pressed rapeseed oil. Exposure of oil samples stored at room temperature to light in combination with the access of oxygen caused the most pronounced losses in the total tocopherols (ca. 90-91 % of α-T, and ca. 80-81 % of γ-T), total phytosterols (ca. 15-16 %) and substantial deterioration in oil qualitative properties. Although storage at room temperature is common for use in households, storage of at low temperatures (4 °C) significantly increases the possibility of prolonged shelf life of cold-pressed rapeseed oil.

  14. Revealing the inner circumstellar disk of the T Tauri star S CrA N using the VLTI

    CERN Document Server

    Vural, J; Kraus, S; Weigelt, G; Driebe, T; Benisty, M; Dugué, M; Massi, F; Monin, J -L; Vannier, M

    2012-01-01

    Aims: We investigate the structure of the circumstellar disk of the T Tauri star S CrA N and test whether the observations agree with the standard picture proposed for Herbig Ae stars. Methods: Our observations were carried out with the VLTI/AMBER instrument in the H and K bands with the low spectral resolution mode. For the interpretation of our near-infrared AMBER and archival mid-infrared MIDI visibilities, we employed both geometric and temperature-gradient models. Results: To characterize the disk size, we first fitted geometric models consisting of a stellar point source, a ring-shaped disk, and a halo structure to the visibilities. In the H and K bands, we measured ring-fit radii of 0.73 +- 0.03 mas (corresponding to 0.095 +- 0.018 AU for a distance of 130 pc) and 0.85 +- 0.07 mas (0.111 +- 0.026 AU), respectively. This K-band radius is approximately two times larger than the dust sublimation radius of ~0.05 AU expected for a dust sublimation temperature of 1500 K and gray dust opacities, but approxima...

  15. Influences of Cross Pollination on Pollen Tube Growth and Fruit Set in Zuili Plums (Prunus salicina)

    Institute of Scientific and Technical Information of China (English)

    Hui-Juan Jia; Feng-Jie He; Cai-Zhen Xiong; Fu-Rong Zhu; Goro Okamoto

    2008-01-01

    Zuill plum (Prunus salicina L.) trees usually set fruit poorly, although they produce high quality fruit. To elucidate the causes of the poor fruit set, pollen tube growth Into pistils and fruit set percentage were investigated after cross-, self- and open-pollination. Ovule development in Zuili pistils was also investigated. Pollen tube penetration into the ovules via the obturator and micropyle was best when Zuili pistils were pollinated by cv. Black Amber (P. domestica) pollen grains, although cross-pollinations with Hongxinli and Miili (P. salicina) pollen were more effective than self- and open-pollination. The fruit set percentage was also highest In pistils pollinated with Black Amber pollen grains. Morphological observation of Zuili pistils revealed that the trees produce "double pistils", developing two ovaries from a basal pistil, at a rate as high as 28%. In such abnormal pistils, most ovules were lacking an embryo sac or were entirely degenerated. The percentage of normally developed ovules was 24.3% and 8.9% in normal and double pistils, respectively. From these results, we conclude that the main causes of poor fruit set of Zuili plums are a lack of effective cross-pollination and the production of high percentages of double pistils in which normally developed ovules are scarcely formed.

  16. New long-proboscid lacewings of the mid-Cretaceous provide insights into ancient plant-pollinator interactions

    Science.gov (United States)

    Lu, Xiu-Mei; Zhang, Wei-Wei; Liu, Xing-Yue

    2016-01-01

    Many insects with long-proboscid mouthparts are among the pollinators of seed plants. Several cases of the long-proboscid pollination mode are known between fossil insects (e.g., true flies, scorpionflies, and lacewings) and various extinct gymnosperm lineages, beginning in the Early Permian and increasing during the Middle Jurassic to Early Cretaceous. However, details on the morphology of lacewing proboscides and the relevant pollination habit are largely lacking. Here we report on three lacewing species that belong to two new genera and a described genus from mid-Cretaceous (Albian-Cenomanian) amber of Myanmar. All these species possess relatively long proboscides, which are considered to be modified from maxillary and labial elements, probably functioning as a temporary siphon for feeding on nectar. Remarkably, these proboscides range from 0.4–1.0 mm in length and are attributed to the most diminutive ones among the contemporary long-proboscid insect pollinators. Further, they clearly differ from other long-proboscid lacewings which have a much longer siphon. The phylogenetic analysis indicates that these Burmese long-proboscid lacewings belong to the superfamily Psychopsoidea but cannot be placed into any known family. The present findings represent the first description of the mouthparts of long-proboscid lacewings preserved in amber and highlight the evolutionary diversification of the ancient plant-pollinator interactions. PMID:27149436

  17. The yellow hypergiant HR 5171 A: Resolving a massive interacting binary in the common envelope phase

    CERN Document Server

    Chesneau, O; Chapellier, E; Millour, F; Van Genderen, A M; Nazé, Y; Smith, N; Spang, A; Smoker, J V; Dessart, L; Kanaan, S; Bendjoya, Ph; Feast, M W; Groh, J H; Lobel, A; Nardetto, N; Otero, S; Oudmaijer, R D; Tekola, A G; Whitelock, P A; Arcos, C; Curé, M; Vanzi, L

    2014-01-01

    We initiated long-term optical interferometry monitoring of the diameters of unstable yellow hypergiants (YHG) with the goal of detecting both the long-term evolution of their radius and shorter term formation related to large mass-loss events. We observed HR5171 A with AMBER/VLTI. We also examined archival photometric data in the visual and near-IR spanning more than 60 years, as well as sparse spectroscopic data. HR5171A exhibits a complex appearance. Our AMBER data reveal a surprisingly large star for a YHG R*=1315+/-260Rsun\\ (~6.1AU) at the distance of 3.6+/-0.5kpc. The source is surrounded by an extended nebulosity, and these data also show a large level of asymmetry in the brightness distribution of the system, which we attribute to a newly discovered companion star located in front of the primary star. The companion's signature is also detected in the visual photometry, which indicates an orbital period of Porb=1304+/-6d. Modeling the light curve with the NIGHTFALL program provides clear evidence that ...

  18. Chemical and sensory effects of storing sauvignon Blanc wine in colored bottles under artificial light.

    Science.gov (United States)

    Cáceres-Mella, Alejandro; Flores-Valdivia, Daniela; Laurie, V Felipe; López-Solís, Remigio; Peña-Neira, Álvaro

    2014-07-23

    The chemical and sensory effects of storing Sauvignon Blanc in colored bottles and exposing them to artificial light were examined. The colors of the bottles chosen were Dead Leaf Green, Antique Green, Amber, and Flint. The light was provided by fluorescent tubes with a regime of 16 h of exposure during 8 months of storage. The results indicated that the wine's chemical composition was affected by the type of bottle used. The Flint bottle presented the lowest concentration of total phenols. Yellow coloration was not dependent on the bottle color, as the wine in darker bottles (Amber, Antique Green, and Dead Leaf Green) had considerably more yellow color development than the wine in clear bottles. With regard to the sensory analyses performed, a trend showing an increase in color intensity and a decrease in overall aromas depending on the bottle color was observed. The wine's aromatic description changed significantly during its storage under artificial light conditions, demonstrating a decrease in vegetal aromas and an increase in citrus and tropical flavors that was dependent on the bottle color.

  19. MCPB.py: A Python Based Metal Center Parameter Builder.

    Science.gov (United States)

    Li, Pengfei; Merz, Kenneth M

    2016-04-25

    MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

  20. Occurrences of dendritic gold at the McLaughlin Mine hot-spring gold deposit

    Science.gov (United States)

    Sherlock, R. L.; Lehrman, N. J.

    1995-06-01

    Two styles of gold dendrites are variably developed at the McLaughlin Mine. The most abundant occurrence is hosted by amber-coloured hydrocarbon-rich opal. Silica likely precipitated from a boiling hydrothermal fluid and complexed with immiscible hydrocarbons forming an amorphous hydrocarbon-silica phase. This phase likely scavenged particulate gold by electrostatic attraction to the hydrocarbon-silica phase. The dendritic nature of the gold is secondary and is the result of dewatering of the amorphous hydrocarbon-silica phase and crystallization of gold into syneresis fractures. The second style of dendritic gold is hosted within vein swarms that focused large volumes of fluid flow. The dendrites occur along with hydrocarbon-rich silica at the upper contact of the vein margins which isolated the dendrites allowing sufficient time for them to grow. In a manner similar to the amber-coloured opal, the dendrites may have formed by scavenging particulate gold by electrostatic attraction to the hydrocarbon-silica phase.

  1. Characterization of Plys-proximal morphogenetic genes of transposable bacteriophage Mu.

    Science.gov (United States)

    Siboo, I R; Sieder, F; Kumar, K; Howe, M M; DuBow, M S

    2004-02-01

    Late during the bacteriophage Mu lytic cycle, Mu DNA must be matured and packaged from its dispersed integration sites in the host DNA in order to produce progeny virions. Whereas control of late gene transcription in Mu is becoming well understood, less is known about the phage morphogenetic process. To investigate the latter, we cloned and sequenced a approximately 4.3-kb region of the phage DNA beginning just upstream of the leftmost late promoter Plys. Previous mapping of amber mutations had located the lysis (lys) and proposed DNA maturation genes D and E in this region. When the DNA sequence was analyzed, seven potential open reading frames were found. DNA sequence analysis of amber mutations in genes D and E identified the sixth and seventh open reading frames as D and E, respectively. Cloning and expression of this region enabled production of cell-free protein extracts that specifically recognize the phage-encoded packaging sequence (pac), a characteristic exhibited by phage maturation enzymes. In addition, the E protein was found to share homology with the large subunit of many phage DNA maturation enzymes. These results support the hypothesis that D and E encode subunits of the Mu DNA maturation enzyme.

  2. Diterpenoid biopolymers: new directions for renewable materials engineering.

    Science.gov (United States)

    Hillwig, Matthew L; Mann, Francis M; Peters, Reuben J

    2011-02-01

    Most types of ambers are naturally occurring, relatively hard, durable resinite polymers derived from the exudates of trees. This resource has been coveted for thousands of years due to its numerous useful properties in industrial processes, beauty, and purported medicinal properties. Labdane diterpenoid-based ambers represent the most abundant and important resinites on earth. These resinites are a dwindling nonrenewable natural resource, so a new source of such materials needs to be established. Recent advances in sequencing technologies and biochemical engineering are rapidly accelerating the rate of identifying and assigning function to genes involved in terpenoid biosynthesis, as well as producing industrial-scale quantities of desired small-molecules in bacteria and yeast. This has provided new tools for engineering metabolic pathways capable of producing diterpenoid monomers that will enable the production of custom-tailored resinite-like polymers. Furthermore, this biosynthetic toolbox is continuously expanding, providing new possibilities for renewing dwindling stocks of naturally occurring resinite materials and engineering new materials for future applications.

  3. Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.

    Science.gov (United States)

    Nguyen, Trang Truc; Viet, Man Hoang; Li, Mai Suan

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔG(bind) decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.

  4. After-effects of TFT-LCD display polarity and display colour on the detection of low-contrast objects.

    Science.gov (United States)

    Mayr, Susanne; Buchner, Axel

    2010-07-01

    Participants performed a word-non-word discrimination task within a car control display emulated on a thin film transistor liquid-crystal display (TFT-LCD). The task simulated an information read-out from a TFT-LCD-based instrument panel. Subsequently, participants performed a low-contrast object detection task that simulated the detection of objects during night-time driving. In experiment 1, words/non-words were presented black-on-white (positive polarity) or white-on-black (negative polarity). In experiments 2 and 3, display colour was additionally manipulated. A positive polarity advantage in the discrimination task was consistently observed. In contrast, positive displays interfered more than negative displays with subsequent detection. The detrimental after-effect of positive polarity displays was strong with white and blue, reduced with amber and absent with red displays. Subjective measures showed a preference for blue over red, but a slight advantage for amber over blue. Implications for TFT-LCD design are derived from the results. STATEMENT OF RELEVANCE: When using TFT-LCDs as car instrument panels, positive polarity red TFT-LCDs are very likely to lead to good instrument readability while at the same time minimising - relative to other colours - the negative effects of an illuminated display on low-contrast object detection during night-time driving.

  5. Simulation of carbohydrates, from molecular docking to dynamics in water.

    Science.gov (United States)

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

    Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

  6. The life of massive stars seen through optical/infrared interferometry

    Science.gov (United States)

    Sanchez-Bermudez, J.; Alberdi, A.; Schödel, R.

    2015-05-01

    During the last decade, optical/infrared interferometry has become an essential tool to contribute to the understanding of stellar astrophysics. We present our results in the study of different aspects in the life of massive stars using optical interferometry. Particularly, we focused the discussion in our findings about multiplicity, interactions of the massive stars with the interstellar medium, and the early stages of high-mass stars. Our near-infrared observations comprise both: (i) long-baseline interferometry making use of AMBER/VLTI, and (ii) sparse aperture masking with VLT/NACO/SAM. These data have been obtained by our research group in the previous years, and the results have been published in several peer-reviewed papers. The principles of the optical/near-infrared interferometry are briefly presented. Particularly, we describe how to get the calibrated Interferometric observables. Henceforth, we present our results of two massive systems (HD150136 and Herschel 36) for which we discovered their triple nature using AMBER/VLTI. Finally, we will present the recently found evidence of a disk and a binary system in a very massive young stellar object known as IRS 9A in the NGC 3603 region.

  7. Sequence evolution of putative cytotoxic T cell epitopes in NS3 region of hepatitis C virus

    Institute of Scientific and Technical Information of China (English)

    Hua-Zhang Guo; Ying Yin; Wen-Liang Wang; Chuan-Shan Zhang; Tao Wang; Zhe Wang; Jing Zhang; Hong Cheng; Hai-Tao Wang

    2004-01-01

    AIM: Quasispecies of hepatitis C virus (HCV) are the foundation for rapid sequence evolution of HCV to evade immune surveillance of hosts. The consensus sequence evolution of a segment of HCV NS3 region, which encompasses putative cytotoxic T cell epitopes, was evaluated. METHODS: Three male patients, infected with HCV through multiple transfusions, were identified from clinical symptoms and monitored by aminotransferase for 60 months. Blood samples taken at months 0, 32, and 60 were used for viral RNA extraction. A segment of HCV NS3 region was amplified from the RNA extraction by RT-PCR and subjected to subcloning and sequencing. HLA types of these three patients were determined using complement-dependent microlymphocytotoxic assay. CTL epitopes were predicted using MHC binding motifs.RESULTS: No patient had clinical symptoms or elevation of aspartate/alanine aminotransferase. Two patients showed positive HCV PCR results at all 3 time points. The other one showed a positive HCV PCR result only at month O. A reported HLA-A2-restricted CTL epitope had no alteration in the HLA-A2-negative carrier over 60 months. In the HLA-A2-positive individuals, all the sequences from O month Oshowed an amber mutation on the initial codon of the epitope. Most changes of consensus sequences in the samepatient occurred on predicted cytotoxic T cell epitopes. CONCLUSION: Amber mutation and changes of consensussequence in HCV NS3 region may be related to viral immune escape.

  8. Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools

    Science.gov (United States)

    Boström, Jonas

    2001-12-01

    Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution ( le2.0 Å) X-ray crystallography have been analyzed. The Low-Mode Conformational Search method (with AMBER* and the GB/SA hydration model), as implemented in MacroModel, was found to perform better than the other algorithms. The rule-based method Omega, which is orders of magnitude faster than the other methods, also gave reasonable results but were found to be dependent on the input structure. The methods supporting diverse sampling (Catalyst, Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.

  9. Comparative studies on the structural proteins of T3 and T7 phages

    DEFF Research Database (Denmark)

    Issinger, O G; Falk, H

    1976-01-01

    A comparison of the coat protein patterns of the wild types of the related phages T3 and T7 on SDS polyacrylamide gel electrophoresis was carried out. After infection of the nonpermissive host with T7 amber mutants in genes 7, 11, 12, 13 or 17 and T3 amber mutants in genes 11, 12, 13 and 17...... respectively, noninfectious, DNA containing particles were produced. The protein pattern, as well as electron microscopy of defective particles of T3 and T7 led to the conclusion that the proteins specified by genes 11, 12, 13 and 17 are tail proteins whereas the proteins coded by genes 7, 8, 10, 14, 15 and 16...... enter the head structure. The "serum blocking protein" (gene 17 product) seems to play a different role in the assembly of T3 and T7 tails, since T3 particles defective in gene 17 did not show any tail structure connected with the head whereas T7 particles defective in gene 17 had a tail which looked...

  10. Applying visual attention theory to transportation safety research and design: evaluation of alternative automobile rear lighting systems.

    Science.gov (United States)

    McIntyre, Scott E; Gugerty, Leo

    2014-06-01

    This field experiment takes a novel approach in applying methodologies and theories of visual search to the subject of conspicuity in automobile rear lighting. Traditional rear lighting research has not used the visual search paradigm in experimental design. It is our claim that the visual search design uniquely uncovers visual attention processes operating when drivers search the visual field that current designs fail to capture. This experiment is a validation and extension of previous simulator research on this same topic and demonstrates that detection of red automobile brake lamps will be improved if tail lamps are another color (in this test, amber) rather than the currently mandated red. Results indicate that when drivers miss brake lamp onset in low ambient light, RT and error are reduced in detecting the presence and absence of red brake lamps with multiple lead vehicles when tail lamps are not red compared to current rear lighting which mandates red tail lamps. This performance improvement is attributed to efficient visual processing that automatically segregates tail (amber) and brake (red) lamp colors into distractors and targets respectively.

  11. Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini Mägdefrau.

    Science.gov (United States)

    Kaasalainen, Ulla; Heinrichs, Jochen; Krings, Michael; Myllys, Leena; Grabenhorst, Heinrich; Rikkinen, Jouko; Schmidt, Alexander R

    2015-01-01

    One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon.

  12. Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette

    Directory of Open Access Journals (Sweden)

    Guillaume Borrel

    2014-01-01

    Full Text Available Pyrrolysine (Pyl, the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber   tRNAPyl with an imperfect anticodon stem and a shortened tRNAPyl synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.

  13. The inner circumstellar disk of the UX Ori star V1026 Sco

    CERN Document Server

    Vural, J; Kishimoto, M; Weigelt, G; Hofmann, K -H; Kraus, S; Schertl, D; Dugué, M; Duvert, G; Lagarde, S; Massi, F

    2014-01-01

    The UX Ori type variables (named after the prototype of their class) are intermediate-mass pre-main sequence objects. One of the most likely causes of their variability is the obscuration of the central star by orbiting dust clouds. We investigate the structure of the circumstellar environment of the UX~Ori star V1026 Sco (HD 142666) and test whether the disk inclination is large enough to explain the UX Ori variability. We observed the object in the low-resolution mode of the near-infrared interferometric VLTI/AMBER instrument and derived H- and K-band visibilities and closure phases. We modeled our AMBER observations, published Keck Interferometer observations, archival MIDI/VLTI visibilities, and the spectral energy distribution using geometric and temperature-gradient models. Employing a geometric inclined-ring disk model, we find a ring radius of 0.15 +- 0.06 AU in the H band and 0.18 +- 0.06 AU in the K band. The best-fit temperature-gradient model consists of a star and two concentric, ring-shaped disk...

  14. Detection of an inner gaseous component in a Herbig Be star accretion disk: Near- and mid-infrared spectro-interferometry and radiative transfer modeling of MWC 147

    CERN Document Server

    Kraus, Stefan; Ohnaka, Keiichi

    2007-01-01

    We study the geometry and the physical conditions in the inner (AU-scale) circumstellar region around the young Herbig Be star MWC 147 using long-baseline spectro-interferometry in the near-infrared (NIR K-band, VLTI/AMBER observations and PTI archive data) as well as the mid-infrared (MIR N-band, VLTI/MIDIobservations). The emission from MWC 147 is clearly resolved and has a characteristic physical size of approx. 1.3 AU and 9 AU at 2.2 micron and 11 micron respectively (Gaussian diameter). The spectrally dispersed AMBER and MIDI interferograms both show a strong increase in the characteristic size towards longer wavelengths, much steeper than predicted by analytic disk models assuming power-law radial temperature distributions. We model the interferometric data and the spectral energy distribution of MWC 147 with 2-D, frequency-dependent radiation transfer simulations. This analysis shows that models of spherical envelopes or passive irradiated Keplerian disks (with vertical or curved puffed-up inner rim) c...

  15. Benito Arias Montano y Francisco Arceo: la redacción del De recta curandorum vulnerum ratione

    Directory of Open Access Journals (Sweden)

    Montero Cartelle, Enrique

    2012-12-01

    Full Text Available When comparing language and literary resources in the treatise De recta curandorum vulnerum ratione, written by the 16th practical surgeon Francisco Arceo, to the prologue added by his guest, friend and compatriot, the humanist Arias Montano, it bears so remarkable resemblence that proves the intervention of the latter by arranging the text or even writing it in his own latin style. Furthermore, Arias Montano made the book be annotated and printed in Amberes by Cristobal Plantino’s printing press, one of his dearest friends.La comparación sistemática de la lengua y de los recursos literarios del tratado De recta curandorum vulnerum ratione, obra del cirujano práctico del siglo XVI Francisco Arceo, con la lengua del Prólogo que le puso su huésped, amigo y paisano, el humanista Arias Montano, muestra semejanzas tan significativas que prueban la intervención de este último arreglando el texto o redactándolo con el latín que le caracteriza. Arias Montano, además, hizo anotar la obra y se la publicó en Amberes en la imprenta de su buen amigo Cristóbal Plantino.

  16. 觅情%Soul Searching

    Institute of Scientific and Technical Information of China (English)

    Nora Winslow

    2003-01-01

    @@ Amber swam with the rushing evening tide, coasting on the high-rising waves that continued to clap onto the California beach late into the evening. She had to hurry; tonight was the last night and she needed to make good use of her time. She could feel her hunger and need growing stronger with each passing moment,swelling inside her like the swell of each wave her voluptuous(艳丽的) body rode in on. Amber felt so alive in the water, taking pleasure from it while fearlessly cutting through the waves. She loved the feel of the ocean against her skin and the way it rolled down to the tip of her massive tail, stroking and caressing each scale and fin as if it was a long, lost lover. She dipped and splashed,racing against time and her cardinal(主要的, 最重要的)desire, rising and falling within the surf to reach her destination.

  17. Assessing the levels of food shortage using the traffic light metaphor by analyzing the gathering and consumption of wild food plants, crop parts and crop residues in Konso, Ethiopia

    Directory of Open Access Journals (Sweden)

    Ocho Dechassa

    2012-08-01

    Full Text Available Abstract Background Humanitarian relief agencies use scales to assess levels of critical food shortage to efficiently target and allocate food to the neediest. These scales are often labor-intensive. A lesser used approach is assessing gathering and consumption of wild food plants. This gathering per se is not a reliable signal of emerging food stress. However, the gathering and consumption of some specific plant species could be considered markers of food shortage, as it indicates that people are compelled to eat very poor or even health-threatening food. Methods We used the traffic light metaphor to indicate normal (green, alarmingly low (amber and fully depleted (red food supplies and identified these conditions for Konso (Ethiopia on the basis of wild food plants (WFPs, crop parts (crop parts not used for human consumption under normal conditions; CPs and crop residues (CRs being gathered and consumed. Plant specimens were collected for expert identification and deposition in the National Herbarium. Two hundred twenty individual households free-listed WFPs, CPs, and CRs gathered and consumed during times of food stress. Through focus group discussions, the species list from the free-listing that was further enriched through key informants interviews and own field observations was categorized into species used for green, amber and red conditions. Results The study identified 113 WFPs (120 products/food items whose gathering and consumption reflect the three traffic light metaphors: red, amber and green. We identified 25 food items for the red, 30 food items for the amber and 65 food items for the green metaphor. We also obtained reliable information on 21 different products/food items (from 17 crops normally not consumed as food, reflecting the red or amber metaphor and 10 crop residues (from various crops, plus one recycled stuff which are used as emergency foods in the study area clearly indicating the severity of food stress (red metaphor

  18. STONEWORK OF THE ALTAI POPULATION AT THE 2nd CENTURY B.C. – THE 5 th CENTURY AD

    Directory of Open Access Journals (Sweden)

    V. I. SOENOV

    2015-01-01

    Full Text Available In this work we generalize the results of our study of stonework in Altai at the Hun-Sarmat period, based on the researches of the archaeological sources. It is noted that this craft is represented in the region only by products of stone cutting manufacture, which are basically tools and adornments, among which the most common ones are spindles, grinding bars or whetstones, beads and pendants from various types of stones. Findings of other stone products (incenseburner, stone graters, and plaques are rare. A set of technological operations and tools was quite diverse: to make stone adornments the Altai ancient masters used such operations as cutting, grinding, drilling, and polishing. As a result of the study, we conclude that tools and part of adornments were made of local rocks: rock crystal, calcite, fine-grained white marble, microcrystalgreen slates. Types of stone, from which were made the rest of the found adornments (carnelian, sard, sapphirine, amber, jade etc. were imported. Studies of geological formations in Altai did not show deposits of carnelian, sarder and sapphirine. Deposits of carnelian (serdolik are widespread throughout the world: they are known in the Trans-Baikal region, Yakutia, the Far East, the Crimea, India and Central America. Sard is usually found along with carnelian. In Russia, significant reserves of sard have been found only in the Trans-Baikal region. Sapphirine is a rare variety of chalcedony, its deposits have been found only in India. Natural amber has not been found in Altai; its nearest deposit is located in Burma and the Baltic-Dnepr amber-bearing area. Jade is a widespread decorative stone. The deposits of jade are known in Yakutia, Tuva, China and many other areas, but it was not mined in Altai. Adornments from these types of stones appeared in Altai rather as finished products, than raw materials. The place of their production is to be identified.

  19. Technical Feasibility Assessment of LED Roadway Lighting on the Golden Gate Bridge

    Energy Technology Data Exchange (ETDEWEB)

    Tuenge, Jason R.

    2012-09-01

    Subsequent to preliminary investigations by the Golden Gate Bridge Highway & Transportation District (GGB), in coordination with Pacific Gas & Electric (PG&E), the GATEWAY Demonstration program was asked to evaluate the technical feasibility of replacing existing roadway lighting on the bridge with products utilizing LED technology. GGB and PG&E also indicated interest in induction (i.e., electrodeless fluorescent) technology, since both light source types feature rated lifetimes significantly exceeding those of the existing high-pressure sodium (HPS) and low-pressure sodium (LPS) products. The goal of the study was to identify any solutions which would reduce energy use and maintenance without compromising the quantity or quality of existing illumination. Products used for roadway lighting on the historic bridge must be installed within the existing amber-lensed shoebox-style luminaire housings. It was determined that induction technology does not appear to represent a viable alternative for the roadway luminaires in this application; any energy savings would be attributable to a reduction in light levels. Although no suitable LED retrofit kits were identified for installation within existing luminaire housings, several complete LED luminaires were found to offer energy savings of 6-18%, suggesting custom LED retrofit kits could be developed to match or exceed the performance of the existing shoeboxes. Luminaires utilizing ceramic metal halide (CMH) were also evaluated, and some were found to offer 28% energy savings, but these products might actually increase maintenance due to the shorter rated lamp life. Plasma technology was evaluated, as well, but no suitable products were identified. Analysis provided in this report was completed in May 2012. Although LED technologies are expected to become increasingly viable over time, and product mock-ups may reveal near-term solutions, some options not currently considered by GGB may ultimately merit evaluation. For

  20. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  1. Occurrence, distribution and characteristics of beached plastic production pellets on the island of Malta (central Mediterranean).

    Science.gov (United States)

    Turner, Andrew; Holmes, Luke

    2011-02-01

    The distribution, abundance and chemical characteristics of plastic production pellets on beaches of the island of Malta have been determined. Pellets were observed at all locations visited and were generally most abundant (> 1000m⁻² at the surface) on the backshores of beaches with a westerly aspect. Most pellets were disc-shaped or flattened cylinders and could be categorised as white, yellow, amber or brown. The polymeric matrix of all pellets analysed by infrared spectroscopy was polyethylene and the degree of yellowing or darkening was associated with an increase in the carbonyl index, hence extent of photo-oxidation or aging. Qualitatively, pellets are similar to those reported for other regions of the Mediterranean in surveys spanning three decades, suggesting that they are a general and persistent characteristic of the region.

  2. Extemporaneous Compounding of Oral Acitretin Suspension for Pediatric Patient with Generalized Pustular Psoriasis.

    Science.gov (United States)

    Choo, Winnie

    2016-01-01

    Generalized pustular psoriasis is rare in children, but it can occur and affect an extensive body surface area of a child. Treatment regimens can include medications that are not available in pediatric dosage form. Acitretin is considered one of the treatment options for acute generalized pustular psoriasis in children, but, in Singapore, it is only available as Neotigason capsules. Extemporaneous compounding of the powder content in the capsules was developed for formulating the oral acitretin suspension with a standardized formulation table and compounding process at National Skin Centre. An appropriate beyond-use date of the extemporaneous preparation was assigned after reviewing the photostability data of acitretin, compatibility of the active ingredient and excipients, and United States Pharmacopeia guidelines. It is deemed appropriate to assign a beyond-use date of 14 days when the extemporaneous preparation is stored in amber glass bottles at 2 degrees C to 8 degrees C.

  3. Development of a combined system for identification and classification of adverse drug reactions: Alerts Based on ADR Causality and Severity (ABACUS).

    Science.gov (United States)

    Koh, Yvonne; Yap, Chun Wei; Li, Shu-Chuen

    2010-01-01

    Currently, adverse drug reaction (ADR) causality and severity are assessed using different systems but there is no standard method to combine the results. In this work, a combined ADR causality and severity assessment system, including an online version, was developed. Logical rules were defined to translate the score obtained from the system into three alert zones: green, amber, and red. The alert zones are useful for triaging ADR cases as they help define the seriousness of the ADR and the urgency of the responses required. This new scoring system may be useful for clinicians, investigators, and regulators seeking information on the likelihood of a drug causing an adverse reaction, and whether an adverse reaction is sufficiently dangerous for the drug to be withheld or undergo further investigation.

  4. Extreme adaptations for probable visual courtship behaviour in a Cretaceous dancing damselfly

    Science.gov (United States)

    Zheng, Daran; Nel, André; Jarzembowski, Edmund A.; Chang, Su-Chin; Zhang, Haichun; Xia, Fangyuan; Liu, Haoying; Wang, Bo

    2017-01-01

    Courtship behaviours, frequent among modern insects, have left extremely rare fossil traces. None are known previously for fossil odonatans. Fossil traces of such behaviours are better known among the vertebrates, e.g. the hypertelic antlers of the Pleistocene giant deer Megaloceros giganteus. Here we describe spectacular extremely expanded, pod-like tibiae in males of a platycnemidid damselfly from mid-Cretaceous Burmese amber. Such structures in modern damselflies, help to fend off other suitors as well as attract mating females, increasing the chances of successful mating. Modern Platycnemidinae and Chlorocyphidae convergently acquired similar but less developed structures. The new findings provide suggestive evidence of damselfly courtship behaviour as far back as the mid-Cretaceous. These data show an unexpected morphological disparity in dancing damselfly leg structure, and shed new light on mechanisms of sexual selection involving intra- and intersex reproductive competition during the Cretaceous. PMID:28317876

  5. Combining simulations and solution experiments as a paradigm for RNA force field refinement

    CERN Document Server

    Cesari, Andrea; Bussi, Giovanni

    2016-01-01

    Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data. We here propose a scheme based on the maximum entropy principle to combine simulations with bulk experiments. In the proposed scheme the noise arising from both the measurements and the forward models used to back calculate the experimental observables is explicitly taken into account. The method is tested on RNA nucleosides and is then used to construct chemically consistent corrections to the Amber RNA force field that allow a large set of experimental data on nucleosides and dinucleosides to be correctly reproduced. The transferability of these corrections is assessed against independent data on tetranucleotides and displays a previously unreported agreement with experiments. This procedure can be applied to enforce multiple experimental d...

  6. An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water.

    Science.gov (United States)

    Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O

    2014-07-28

    Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

  7. Thrips pollination of Mesozoic gymnosperms.

    Science.gov (United States)

    Peñalver, Enrique; Labandeira, Conrad C; Barrón, Eduardo; Delclòs, Xavier; Nel, Patricia; Nel, André; Tafforeau, Paul; Soriano, Carmen

    2012-05-29

    Within modern gymnosperms, conifers and Ginkgo are exclusively wind pollinated whereas many gnetaleans and cycads are insect pollinated. For cycads, thrips are specialized pollinators. We report such a specialized pollination mode from Early Cretaceous amber of Spain, wherein four female thrips representing a genus and two species in the family Melanthripidae were covered by abundant Cycadopites pollen grains. These females bear unique ring setae interpreted as specialized structures for pollen grain collection, functionally equivalent to the hook-tipped sensilla and plumose setae on the bodies of bees. The most parsimonious explanation for this structure is parental food provisioning for larvae, indicating subsociality. This association provides direct evidence of specialized collection and transportation of pollen grains and likely gymnosperm pollination by 110-105 million years ago, possibly considerably earlier.

  8. Fuel formula for lighters

    Energy Technology Data Exchange (ETDEWEB)

    Iwayama, I.; Iwayama, A.

    1982-04-10

    A fuel formula that includes a homogenous mixture of benzine, aromatic ether oils, perfume and other perfuming agents, as well as the lowest possible aliphatic alcohol as a component solvent, surfactant, and possibly, a soluble pigment that colors the formula an appropriate color. This formula is used as an aromatic fuel for cigarette lights. The ether oils can be musk, amber, camomille, lavender, mint, anise, rose, camphor, and other aromatic oils; the perfuming agents are: geraniol, linalool, menthol, camphor, benzyl or phenetyl alcohols, phenylacetaldehyde, vanillin, coumarin, and so forth; the pigments are: beta-carotene, sudan dyes, etc.; the low aliphatic alcohols are EtOH, iso-PrOH. Example: 70 parts benzine, 10 parts EtOH, 15 parts oxide mezithylene and 5 parts borneol form a clear liquid that has a camphor aroma when it is lit.

  9. Polyenamines from aromatic diacetylenic diketones and diamines

    Science.gov (United States)

    Hergenrother, Paul M. (Inventor); Bass, Robert G. (Inventor); Sinsky, Mark S. (Inventor); Connell, John W. (Inventor)

    1987-01-01

    The synthesis and characterization of several polyenamine ketones are discussed wherein conjugated diacetylenic diketones and aromatic diamines are used as a route to the formation of high molecular weight polyenamine ketones which exhibit good mechanical properties and can be cast into creasible films. Typical polymerization conditions involved the reaction of stoichiometric amounts of 1,4- or 1,3-PPPO and a diamine at 60 to 130 C in m-cresol at (w/w) solids content of 8 to 26% for a specified period of time under a nitrogen atmosphere. Novel polyenamine ketones were prepared with inherent viscosities as high as 1.99 dl/g and tough, clear amber films with tensile strengths of 12,400 psi and tensile moduli of 397,000 psi were cast from solutions of the polymers in chloroform. In most cases, the elemental analyses for the polyenamine ketones agree within + or - 0.3% of the theoretical values.

  10. Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

    CERN Document Server

    Beauchamp, Kyle A; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-01-01

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using t...

  11. Review and update of the applications of organic petrology: Part 2, geological and multidisciplinary applications

    Science.gov (United States)

    Suarez-Ruiz, Isabel; Flores, Deolinda; Mendonça Filho, João Graciano; Hackley, Paul C.

    2012-01-01

    The present paper is focused on organic petrology applied to unconventional and multidisciplinary investigations and is the second part of a two part review that describes the geological applications and uses of this branch of earth sciences. Therefore, this paper reviews the use of organic petrology in investigations of: (i) ore genesis when organic matter occurs associated with mineralization; (ii) the behavior of organic matter in coal fires (self-heating and self-combustion); (iii) environmental and anthropogenic impacts associated with the management and industrial utilization of coal; (iv) archeology and the nature and geographical provenance of objects of organic nature such as jet, amber, other artifacts and coal from archeological sites; and (v) forensic science connected with criminal behavior or disasters. This second part of the review outlines the most recent research and applications of organic petrology in those fields.

  12. A diverse ant fauna from the mid-cretaceous of Myanmar (Hymenoptera: Formicidae).

    Science.gov (United States)

    Barden, Phillip; Grimaldi, David

    2014-01-01

    A new collection of 24 wingless ant specimens from mid-Cretaceous Burmese amber (Albian-Cenomanian, 99 Ma) comprises nine new species belonging to the genus Sphecomyrmodes Engel and Grimaldi. Described taxa vary considerably with regard to total size, head and body proportion, cuticular sculpturing, and petiole structure while all species are unified by a distinct shared character. The assemblage represents the largest known diversification of closely related Cretaceous ants with respect to species number. These stem-group ants exhibit some characteristics previously known only from their extant counterparts along with presumed plesiomorphic morphology. Consequently, their morphology may inform hypotheses relating to basal relationships and general patterns of ant evolution. These and other uncovered Cretaceous species indicate that stem-group ants are not simply wasp-like, transitional formicids, but rather a group of considerable adaptive diversity, exhibiting innovations analogous to what crown-group ants would echo 100 million years later.

  13. Spheroidal Degeneration of the Cornea

    Directory of Open Access Journals (Sweden)

    Erdem Dinç

    2011-08-01

    Full Text Available A thirty-one-year-old male patient presented with bilateral epiphora and stinging sensation in the cornea. Detailed history revealed that a bilateral corneal scraping had been made regarding the initial diagnosis of fungal keratitis. His bestcorrected visual acuities were 20/20 and 20/30 in right and left eyes, respectively. Biomicroscopy showed bilateral amber colored spherules in the anterior stroma of the central cornea. The diagnosis of spheroidal corneal degeneration was established and symptomatic therapy with artificial tear drops was prescribed. Ultraviolet light is widely accepted to be the main etiological factor in the pathogenesis of spheroidal degeneration. Because of difficulties in the early stages of the diagnostic process of the disease, incorrect diagnoses can be made with inappropriate interventions. (Turk J Ophthalmol 2011; 41: 264-6

  14. Stability of carotenoids recovered from shrimp waste and their use as colorant in fish sausage.

    Science.gov (United States)

    Sachindra, N M; Mahendrakar, N S

    2010-01-01

    The stability of carotenoids recovered from shrimp waste using organic solvents and vegetable oils as affected by antioxidants and pigment carriers was evaluated during storage under different conditions. Solvent extracted carotenoid incorporated into alginate and starch as carriers was stored in metallised polyester and polypropylene pouches. Oil extracted carotenoids were stored in transparent and amber bottles. Also the use of recovered pigments as colorants in fish sausage was evaluated. Antioxidants, packaging material and storage period had a significant effect (p≤0.001) on the reduction of carotenoid content, while type of carrier had marginal effect (p≥0.05) on solvent extracted carotenoids during storage. Carotenoid content in pigmented oil was significantly affected by antioxidants (p≤0.001), packaging material (p≤0.05) and storage period (p≤0.001). Addition of carotenoid to the sausage enhanced the sensory colour, flavour and overall quality score of sausage and the added carotenoid was stable during processing.

  15. Phase closure nulling: results from the 2009 campaign

    Science.gov (United States)

    Duvert, Gilles; Malbet, Fabien; Chelli, Alain; Millan-Gabet, Rafael; Monnier, John D.; Schaefer, Gail H.

    2010-07-01

    We present here a new observational technique, Phase Closure Nulling (PCN), which has the potential to obtain very high contrast detection and spectroscopy of faint companions to bright stars. PCN consists in measuring closure phases of fully resolved objects with a baseline triplet where one of the baselines crosses a null of the object visibility function. For scenes dominated by the presence of a stellar disk, the correlated flux of the star around nulls is essentially canceled out, and in these regions the signature of fainter, unresolved, scene object(s) dominates the imaginary part of the visibility in particular the closure phase. We present here the basics of the PCN method, the initial proof-of-concept observation, the envisioned science cases and report about the first observing campaign made on VLTI/AMBER and CHARA/MIRC using this technique.

  16. Variable Message Signs for road tunnel emergency evacuations.

    Science.gov (United States)

    Ronchi, Enrico; Nilsson, Daniel; Modig, Henric; Walter, Anders Lindgren

    2016-01-01

    This paper investigates the design of Variable Message Signs (VMS) as a way-finding aid for road tunnel emergency evacuations. The use of the Theory of Affordances is suggested to provide recommendations on the design of VMS. A preliminary evaluation of 11 selected VMS systems was performed and 6 of them were further evaluated using an affordance-based within subject stated-preference questionnaire administered to a sample of 62 participants. Results are used to provide recommendations on the characteristics of the VMS systems, such as (1) size of the sign (large or small); (2) use of flashing lights; (3) colour scheme; (4) message coding (i.e., text, pictograms or a combination of them). The best performing VMS features for road tunnel emergency evacuation included the use of larger signs, flashing lights, the combination of emergency exit pictorial symbol in green in one panel and text in amber in the other panel.

  17. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei [Institute of High Performance Computing, A*STAR, 138632 (Singapore)

    2015-12-31

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  18. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

    Science.gov (United States)

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Luo, Ray

    2012-07-19

    As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

  19. Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Zambach, Sine; Christiansen, Henning

    2013-01-01

    suggested, but the structure does not seem to be present in all pyrrolysine incorporating genes. Results We propose a strategy to predict pyrrolysine encoding genes in genomes of archaea and bacteria. We cluster open reading frames interrupted by the amber codon based on sequence similarity. We rank...... these clusters according to several features that may influence pyrrolysine translation. The ranking effects of different features are assessed and we propose a weighted combination of these features which best explains the currently known pyrrolysine incorporating genes. We devote special attention...... to the effect of structural conservation and provide further substantiation to support that structural conservation may be influential – but is not a necessary factor. Finally, from the weighted ranking, we identify a number of potentially pyrrolysine incorporating genes. Conclusions We propose a method...

  20. Comparison of Fourier and model-based estimators in single mode multiaxial interferometry

    CERN Document Server

    Tatulli, E

    2006-01-01

    There are several solutions to code the signal arising from optical long baseline multi-aperture interferometers. In this paper,we focus on the {\\bf non homothetic spatial coding scheme} (multiaxial) with the fringe pattern coded along one dimension on one detector(all-in-one). After describing the physical principles governing single mode interferometers using that sort of recombination scheme, we analyze two different existing methods that measure the source visibility. The first technique, so-called Fourier estimator, consists in integrating the high frequency peak of the power spectral density of the interferogram. The second method, so-called model-based estimator, has been specifically developed for the AMBER instrument of the VLTI and deals with directly modelling the interferogram recorded on the detector. Performances of both estimators are computed in terms of Signal to Noise Ratio (SNR) of the visibility, assuming that the interferograms are perturbed by photon and detector noises. Theoretical expr...

  1. Molecular dynamics simulations of glycerol glass-forming liquid

    Energy Technology Data Exchange (ETDEWEB)

    Blieck, J. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Lerbret, A. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France); Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, CNRS UMR 8024, BAT P5-Cite Scientifique, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2005-10-31

    Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q {approx} 0.6 A{sup -1} are observed. Our results are also found compatible with predictions of the Mode Coupling Theory.

  2. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    Energy Technology Data Exchange (ETDEWEB)

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  3. S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

    DEFF Research Database (Denmark)

    Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

    2002-01-01

    S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

  4. Innovative zoning to support equine influenza eradication from New South Wales, Australia.

    Science.gov (United States)

    Scott-Orr, H

    2011-07-01

    Following detection of equine influenza (EI) in New South Wales, a complete standstill was imposed the next morning on the movement of all horses and donkeys within the state. Premises' biosecurity guidelines became progressively more stringent with time in an effort to stop local spread. The standstill was highly effective as a primary response to stop EI becoming widespread across Australia, but did not prevent spread to properties contiguous to infected premises in areas of high horse density and small property size, nor transmission by fomites nor possible local airborne transmission. Within 2 weeks of the start of the outbreak, a zoning system of Purple (Special Restricted), Red (Restricted), Amber (Control), and Green (Protected) Zones was implemented, and progressively modified as disease distribution changed. The colour coding system proved to be an easy way to communicate zone changes, the approximate level of disease risk and the stringency of movement restrictions to the general public and should be adopted more generally in AUSVETPLAN.

  5. A genetically encoded fluorescent probe in mammalian cells.

    Science.gov (United States)

    Chatterjee, Abhishek; Guo, Jiantao; Lee, Hyun Soo; Schultz, Peter G

    2013-08-28

    Fluorescent reporters are useful in vitro and in vivo probes of protein structure, function, and localization. Here we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), can be site-specifically incorporated into proteins in mammalian cells in response to the TAG codon with high efficiency using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase (aaRS) pair. We further demonstrate that Anap can be used to image the subcellular localization of proteins in live mammalian cells. The small size of Anap, its environment-sensitive fluorescence, and the ability to introduce Anap at specific sites in the proteome by simple mutagenesis make it a unique and valuable tool in eukaryotic cell biology.

  6. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.

    Science.gov (United States)

    Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G

    2016-04-12

    Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.

  7. Assessment of Some Density Functional Theory Methods and Force Field Models in Describing Various Interaction Modes of Benzene Dimer

    Institute of Scientific and Technical Information of China (English)

    Yu-wei Zhou; Igor Ying Zhang; Jian-ming Wu; An-an Wu; Xin Xu

    2011-01-01

    Benzene dimer (bz2) is the simplest prototype of the π-π interactions.Such interactions are ubiquitous in diverse areas of science and molecular engineering.In the present work,we have made assessment on some modern density functional methods including B97-D,BLYP-D3,M06-2X,XYG3,and force field models including CHARMM,AMBER,MM3,AMOEBA on six important interaction modes of bz2.Our results not only highlight the usefulness of these cost-effective methods,which can be used as economic substitutes of the expensive CCSD(T) for complex real-world systems,but also indicate their weakness in the description of the π-π interactions,which points to the future direction for further improvements.

  8. Brood care in a 100-million-year-old scale insect.

    Science.gov (United States)

    Wang, Bo; Xia, Fangyuan; Wappler, Torsten; Simon, Ewa; Zhang, Haichun; Jarzembowski, Edmund A; Szwedo, Jacek

    2015-01-01

    Behavior of extinct organisms can be inferred only indirectly, but occasionally rare fossils document particular behaviors directly. Brood care, a remarkable behavior promoting the survival of the next generation, has evolved independently numerous times among animals including insects. However, fossil evidence of such a complex behavior is exceptionally scarce. Here, we report an ensign scale insect (Hemiptera: Ortheziidae), Wathondara kotejai gen. et sp. nov., from mid-Cretaceous Burmese amber, which preserves eggs within a wax ovisac, and several freshly hatched nymphs. The new fossil is the only Mesozoic record of an adult female scale insect. More importantly, our finding represents the earliest unequivocal direct evidence of brood care in the insect fossil record and demonstrates a remarkably conserved egg-brooding reproductive strategy within scale insects in stasis for nearly 100 million years.

  9. Toward transferable interatomic van der Waals potentials: The role of multipole electrostatics and many-body dispersion without electrons

    CERN Document Server

    Bereau, Tristan

    2014-01-01

    We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi partitioning approach instead. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular potential from dispersion and electrostatics for more than 1,300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. Overall, the method achieves an accuracy well within sophisticated empirical force fields, such as OPLS and Amber FF03, while exhibiting a simple parametrization protocol without the need for experimental inp...

  10. Organic matter of fossil origin in the amberine speleothems from El Soplao Cave (Cantabria, Northern Spain

    Directory of Open Access Journals (Sweden)

    Gázquez Fernando

    2012-01-01

    Full Text Available Unusual amberine-coloured speleothems were recently found in El Soplao Cave (Cantabria, Spain. Chromophore elements such as Fe, Mn, Cd, Co or Ti were not present in significant quantities. Rather, our data show that their colour comes from leachates of fossilized organic material hosted in the carbonaceous Urgonian facies of the host rock. These leachates are related to the Cretaceous amber deposit that has been recently discovered in the vicinity of El Soplao Cave. The presence of humic and fulvic acids of fossil origin were confirmed by IR and Raman spectroscopic analysis of the carbonaceous strata and the speleothems. In addition, the mineralogy of the amberine speleothems was studied. Alternating bands made of calcite and aragonite reveal that periods of humidity and aridity occurred within the cave during the speleothem genesis.

  11. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  12. Phase Closure Nulling: results from the 2009 campaign

    CERN Document Server

    Duvert, Gilles; Chelli, Alain; Millan-Gabet, Rafael; Monnier, John D; Schaefer, Gail H

    2010-01-01

    We present here a new observational technique, Phase Closure Nulling (PCN), which has the potential to obtain very high contrast detection and spectroscopy of faint companions to bright stars. PCN consists in measuring closure phases of fully resolved objects with a baseline triplet where one of the baselines crosses a null of the object visibility function. For scenes dominated by the presence of a stellar disk, the correlated flux of the star around nulls is essentially canceled out, and in these regions the signature of fainter, unresolved, scene object(s) dominates the imaginary part of the visibility in particular the closure phase. We present here the basics of the PCN method, the initial proof-of-concept observation, the envisioned science cases and report about the first observing campaign made on VLTI/AMBER and CHARA/MIRC using this technique.

  13. Infrared source test

    Energy Technology Data Exchange (ETDEWEB)

    Ott, L.

    1994-11-15

    The purpose of the Infrared Source Test (IRST) is to demonstrate the ability to track a ground target with an infrared sensor from an airplane. The system is being developed within the Advance Technology Program`s Theater Missile Defense/Unmanned Aerial Vehicle (UAV) section. The IRST payload consists of an Amber Radiance 1 infrared camera system, a computer, a gimbaled mirror, and a hard disk. The processor is a custom R3000 CPU board made by Risq Modular Systems, Inc. for LLNL. The board has ethernet, SCSI, parallel I/O, and serial ports, a DMA channel, a video (frame buffer) interface, and eight MBytes of main memory. The real-time operating system VxWorks has been ported to the processor. The application code is written in C on a host SUN 4 UNIX workstation. The IRST is the result of a combined effort by physicists, electrical and mechanical engineers, and computer scientists.

  14. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.

    Directory of Open Access Journals (Sweden)

    Luis Felipe Pineda De Castro

    Full Text Available In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.

  15. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes

    Science.gov (United States)

    Pineda De Castro, Luis Felipe; Dopson, Mark

    2016-01-01

    In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow. PMID:27167213

  16. Pristine Early Eocene wood buried deeply in kimberlite from northern Canada.

    Directory of Open Access Journals (Sweden)

    Alexander P Wolfe

    Full Text Available We report exceptional preservation of fossil wood buried deeply in a kimberlite pipe that intruded northwestern Canada's Slave Province 53.3±0.6 million years ago (Ma, revealed during excavation of diamond source rock. The wood originated from forest surrounding the eruption zone and collapsed into the diatreme before resettling in volcaniclastic kimberlite to depths >300 m, where it was mummified in a sterile environment. Anatomy of the unpermineralized wood permits conclusive identification to the genus Metasequoia (Cupressaceae. The wood yields genuine cellulose and occluded amber, both of which have been characterized spectroscopically and isotopically. From cellulose δ(18O and δ(2H measurements, we infer that Early Eocene paleoclimates in the western Canadian subarctic were 12-17°C warmer and four times wetter than present. Canadian kimberlites offer Lagerstätte-quality preservation of wood from a region with limited alternate sources of paleobotanical information.

  17. Pristine Early Eocene wood buried deeply in kimberlite from northern Canada.

    Science.gov (United States)

    Wolfe, Alexander P; Csank, Adam Z; Reyes, Alberto V; McKellar, Ryan C; Tappert, Ralf; Muehlenbachs, Karlis

    2012-01-01

    We report exceptional preservation of fossil wood buried deeply in a kimberlite pipe that intruded northwestern Canada's Slave Province 53.3±0.6 million years ago (Ma), revealed during excavation of diamond source rock. The wood originated from forest surrounding the eruption zone and collapsed into the diatreme before resettling in volcaniclastic kimberlite to depths >300 m, where it was mummified in a sterile environment. Anatomy of the unpermineralized wood permits conclusive identification to the genus Metasequoia (Cupressaceae). The wood yields genuine cellulose and occluded amber, both of which have been characterized spectroscopically and isotopically. From cellulose δ(18)O and δ(2)H measurements, we infer that Early Eocene paleoclimates in the western Canadian subarctic were 12-17°C warmer and four times wetter than present. Canadian kimberlites offer Lagerstätte-quality preservation of wood from a region with limited alternate sources of paleobotanical information.

  18. A deep-learning-based emergency alert system

    Directory of Open Access Journals (Sweden)

    Byungseok Kang

    2016-06-01

    Full Text Available Emergency alert systems serve as a critical link in the chain of crisis communication, and they are essential to minimize loss during emergencies. Acts of terrorism and violence, chemical spills, amber alerts, nuclear facility problems, weather-related emergencies, flu pandemics, and other emergencies all require those responsible such as government officials, building managers, and university administrators to be able to quickly and reliably distribute emergency information to the public. This paper presents our design of a deep-learning-based emergency warning system. The proposed system is considered suitable for application in existing infrastructure such as closed-circuit television and other monitoring devices. The experimental results show that in most cases, our system immediately detects emergencies such as car accidents and natural disasters.

  19. Self-organised criticality in base-pair breathing in DNA with a defect

    CERN Document Server

    Duduiala, Ciprian-Ionut; Laughton, Charles A

    2011-01-01

    We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

  20. Contribution of Solvation Energy in Protein-Peptide Recognition Systems

    Institute of Scientific and Technical Information of China (English)

    LI,Fei; LI,Wei; SHEN,Jia-Cong

    2001-01-01

    The contribution of solvation energy to guding molecualr recognition for six rigid protein-peptide systems had been eval uated by the variation in the number of the identified native like configurations and in the driving force of specific interac tion resulting from the addition of the explicit solvation term in the force field function. The AMBER force field energy and the total energy including the force field energy and the WZS solvation energy were calculated for sampled configurations. The results obtained by the calculations of both force field and total energies were compared with each other. It suggests that specific recognition of the systems in which the ligands possess larger hydrophobic or aromatic residues while the protein re ceptors provide the active surfaces with hydrophobic property.

  1. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation

    Science.gov (United States)

    Paluch, Andrew S.; Parameswaran, Sreeja; Liu, Shuai; Kolavennu, Anasuya; Mobley, David L.

    2015-01-01

    We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.

  2. Neomycin is more efficient than streptomycin in suppressing frameshift mutations.

    Science.gov (United States)

    Phoenix, P; Gravel, M; Herrington, M B; Brakier-Gingras, L

    1985-12-01

    The effects of streptomycin and neomycin on the phenotypic suppression of frameshift mutations in the lacZ gene of Escherichia coli and on the efficiency of suppression of amber mutations in T4 phage by the informational supE tRNA nonsense suppressor were compared. Neomycin stimulated much more efficiently than streptomycin the phenotypic suppression of frameshift mutations. Because neomycin favors mismatches of the central codon base whereas streptomycin favors mismatches of the first codon base, this result suggests that mismatching of the central codon base pair and shifting of the reading frame are two correlated phenomena. In contrast, both streptomycin and neomycin stimulated about equally the efficiency of the tRNA nonsense suppressor, an effect probably related to their interference with the proofreading control in tRNA selection.

  3. HANDICRAFTS, INVASIONS AND MIGRATIONS

    Directory of Open Access Journals (Sweden)

    Perla Shiomara del Carpio Ovando

    2014-01-01

    Full Text Available This research is focused on the migratory movements that have characterized Simojovel de Allende, Chiapas. Both indigenous Tsotsil communities as well as mestizos from different municipalities live in Simojovel, which is a town that has had multiple migratory movements due to different reasons. For example, economical struggle that has led to poverty, the lack of opportunities; the political situation, religious and ethnic persecutions, insecurity and the communitarian division between zapatistas and non-zapatistas. There are also cultural factors that have caused migration in Simojovel such as tradition, generational gaps, young people’s interests for new types of work and ways of living. Simojovel has been characterized by its coffee, tobacco and amber, but also by its migratory activity.

  4. Expanding the genetic code of Mus musculus

    Science.gov (United States)

    Han, Songmi; Yang, Aerin; Lee, Soonjang; Lee, Han-Woong; Park, Chan Bae; Park, Hee-Sung

    2017-01-01

    Here we report the expansion of the genetic code of Mus musculus with various unnatural amino acids including Nɛ-acetyl-lysine. Stable integration of transgenes encoding an engineered Nɛ-acetyl-lysyl-tRNA synthetase (AcKRS)/tRNAPyl pair into the mouse genome enables site-specific incorporation of unnatural amino acids into a target protein in response to the amber codon. We demonstrate temporal and spatial control of protein acetylation in various organs of the transgenic mouse using a recombinant green fluorescent protein (GFPuv) as a model protein. This strategy will provide a powerful tool for systematic in vivo study of cellular proteins in the most commonly used mammalian model organism for human physiology and disease. PMID:28220771

  5. Performance Characteristics of Waste Glass Powder Substituting Portland Cement in Mortar Mixtures

    Science.gov (United States)

    Kara, P.; Csetényi, L. J.; Borosnyói, A.

    2016-04-01

    In the present work, soda-lime glass cullet (flint, amber, green) and special glass cullet (soda-alkaline earth-silicate glass coming from low pressure mercury-discharge lamp cullet and incandescent light bulb borosilicate glass waste cullet) were ground into fine powders in a laboratory planetary ball mill for 30 minutes. CEM I 42.5N Portland cement was applied in mortar mixtures, substituted with waste glass powder at levels of 20% and 30%. Characterisation and testing of waste glass powders included fineness by laser diffraction particle size analysis, specific surface area by nitrogen adsorption technique, particle density by pycnometry and chemical analysis by X-ray fluorescence spectrophotometry. Compressive strength, early age shrinkage cracking and drying shrinkage tests, heat of hydration of mortars, temperature of hydration, X-ray diffraction analysis and volume stability tests were performed to observe the influence of waste glass powder substitution for Portland cement on physical and engineering properties of mortar mixtures.

  6. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  7. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  8. NEESPI focus issues in Environmental Research Letters

    Science.gov (United States)

    Norman, Julian; Groisman, Pavel; Soja, Amber J.

    2010-05-01

    In 2007 and 2009 Environmental Research Letters published focus issues (edited by Pavel Groisman and Amber J Soja) made up of work carried out by NEESPI participants. Here, we present the content of those focus issues as an invaluable resource for researchers working in the NEESPI study area. The first of the two issues, published in 2007 with title 'Northern Hemisphere High Latitude Climate and Environmental Change', presents a diverse collection of articles that are assembled into five groups devoted to studies of climate and hydrology, land cover and land use, the biogeochemical cycle and its feedbacks, the cryosphere, and human dimensions. The second issue, published in 2009, with title 'Climatic and Environmental Change in Northern Eurasia' presents diverse, assorted studies of different aspects of contemporary change, representing the diversity of climates and ecosystems across Northern Eurasia.

  9. “COLATURA DI ALICI “ CETARESE: EVALUATION OF AMINIC PROFILE

    Directory of Open Access Journals (Sweden)

    A Anastasio

    2008-12-01

    Full Text Available “Colatura d’alici”is a speciality made in Cetara, a clear ,amber-coloured liquid that has sharp taste, prepared with the juice coming from the anchovy salting process. The anchovies are caught in the Gulf of Salerno between the mounths of March and July. The colatura is ready at the beginning of December. Histamine poisoning, a food-borne chemical intoxication caused by the consumption of food containing toxic levels of histamine, is a syndrome commonly associated with the consumption of seafood beloging to the Engraulidae and some fish families. Histamine and biogenic amine levels were determined in “colatura di alici di Cetara”. The amine was separated in a HPLC/FL system. Histamine level were lower than the law limits only in one of the examinated products. A reduction of the histamine and amine levels in colatura cetarese can be obtained using a determinate salt concentrations and changing way of seasoning.

  10. Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

    DEFF Research Database (Denmark)

    Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

    2004-01-01

    A quantitative evaluation of 20 second-generation carbohydrate force fields was carried out using ab initio and density functional methods. Geometry-optimized structures (B3LYP/6-31G(d)) and relative energies using augmented correlation consistent basis sets were calculated in gas phase...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error......-generation carbohydrate force fields. No single force field is consistently better than the others for all the test cases. A statistical assessment of the performance of the force fields indicates that CHEAT(95), CFF, certain versions of Amber and of MM3 have the best overall performance, for these gas phase...

  11. Using Colored Cullet for Making Beautiful Glassware

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong-Sang; Matyas, Josef

    2003-03-14

    Eight colored glasses from Fire and Light Originals (FLO) and three container cullet glasses were characterized for the viscosity, density, and thermal expansion, glass transition temperature, dilatometer softening temperature, color chromaticity, Fe(II)/Fe(total) redox ratio, and chemical composition. The results of the characterization were used to evaluate the options for the glass formulation development of colored glasses aimed at increasing the use of recycled container glass cullet. Out of several options considered, the possibility of using clear cullet for FLO’s Citrus colored glass was selected and investigated in this study. It was shown that it is possible to use clear cullet to produce Citrus glass at the cullet oxide ratio of 90 mass% and the final color can be adjusted by controlling the nitrate level and alkali concentrations. From the present study, recommendations for further development efforts are provided to increase the container cullet usage or to replace partially or entirely the clear cullet by the amber cullet.

  12. Molecular dynamics simulations of a single stranded (ss) DNA

    CERN Document Server

    Chatterjee, Subhasish; Thakur, Siddarth; Burin, Alexander

    2012-01-01

    The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.

  13. Hidden flows and waste processing--an analysis of illustrative futures.

    Science.gov (United States)

    Schiller, F; Raffield, T; Angus, A; Herben, M; Young, P J; Longhurst, P J; Pollard, S J T

    2010-12-14

    An existing materials flow model is adapted (using Excel and AMBER model platforms) to account for waste and hidden material flows within a domestic environment. Supported by national waste data, the implications of legislative change, domestic resource depletion and waste technology advances are explored. The revised methodology offers additional functionality for economic parameters that influence waste generation and disposal. We explore this accounting system under hypothetical future waste and resource management scenarios, illustrating the utility of the model. A sensitivity analysis confirms that imports, domestic extraction and their associated hidden flows impact mostly on waste generation. The model offers enhanced utility for policy and decision makers with regard to economic mass balance and strategic waste flows, and may promote further discussion about waste technology choice in the context of reducing carbon budgets.

  14. Predicting Model forComplex Production Process Based on Dynamic Neural Network

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Based on the comparison of several methods of time series predicting, this paper points out that it is nec-essary to use dynamic neural network in modeling of complex production process. Because self-feedback and mutu-al-feedback are adopted among nodes at the same layer in Elman network, it has stronger ability of dynamic ap-proximation, and can describe any non-linear dynamic system. After the structure and mathematical description be-ing given, dynamic back-propagation (BP) algorithm of training weights of Elman neural network is deduced. Atlast, the network is used to predict ash content of black amber in jigging production process. The results show thatthis neural network is powerful in predicting and suitable for modeling, predicting, and controling of complex pro-duction process.

  15. Stop codon reassignments in the wild.

    Science.gov (United States)

    Ivanova, Natalia N; Schwientek, Patrick; Tripp, H James; Rinke, Christian; Pati, Amrita; Huntemann, Marcel; Visel, Axel; Woyke, Tanja; Kyrpides, Nikos C; Rubin, Edward M

    2014-05-23

    The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the >1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments in bacteriophages and of opal in bacteria. Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. The abundance and diversity of genetic codes present in environmental organisms should be considered in the design of engineered organisms with altered genetic codes in order to preclude the exchange of genetic information with naturally occurring species.

  16. AmpC酶的检测技术研究进展

    Institute of Scientific and Technical Information of China (English)

    张秀平

    2006-01-01

    在细菌耐药酶研究机制中,革兰阴性杆菌中的AmpC酶备受临床床关注,使人类对抗AmpC酶的斗争更加艰难。AmpC酶属BushI型酶或AmberC类酶,是不被克拉维酸抑制的“丝氨酸”头孢菌素酶,主要存在于肠杆菌,枸橼酸杆菌,粘质沙雷菌,摩根摩根菌,铜绿假单胞菌等菌属中。AmpC酶可分为诱导型、结构型、质粒型。本文将三型AmpC酶的检测技术综述如下。

  17. Ion concentration dependent tRNA folding energy landscapes

    Science.gov (United States)

    Li, Rongzhong; Cho, Samuel

    2013-03-01

    The RNA folding is highly dependent on the ionic conditions of its environment in the cell because the surrounding ions electrostatically screen the charged phosphates that line the RNA backbone. Recent studies (Cho, Pincus, and Thirumalai, PNAS, 2007; Biyun, Cho, and Thirumalai, JACS, 2011) demonstrated that the coarse-grained model we use accurately captures the RNA folding mechanisms by incorporating a Debye-Huckel potential to screen the electrostatics. We compare the ion-concentration dependent tRNA folding mechanism to the classical thermodynamic melting profiles of Crothers and co-workers, and we observe excellent agreement. We also supported our findings by performing empirical force field MD simulations with CHARMM and AMBER, and we observe remarkably comparable qualitative similarities between the average base-base distances from simulations and the empirically measured base-stacking potentials from the well-known Turner's Rules.

  18. Simulations on the kindling mechanism of the asFP595 fluorescent protein

    Science.gov (United States)

    Grigorenko, Bella L.; Nemukhin, Alexander V.; Savitsky, Alexander P.

    2008-02-01

    We report the results of quantum mechanical - molecular mechanical (QM/MM) simulations aiming to elucidate the mechanism of kindling of the initially non-fluorescent protein asFP595, which is a mutated variant of the chromoprotein asCP from the sea anemone Anemonia sulcata. asFP595 becomes brightly fluorescent (kindles) with emission at 595 nm in response to intense light irradiation at 568 nm. In simulations, we use the flexible effective fragment QM/MM method with the complete active space self-consistent field (CASSCF) wavefunctions in the quantum part and the AMBER force field parameters in the molecular mechanical part. We analyze the computed scans over potential energy surfaces of the ground and excited electronic states and consider details of the working hypothesis that the trans-cis isomerization of the chromophore group inside the protein is responsible for kindling.

  19. Resolved astrometric orbits of ten O-type binaries

    CERN Document Server

    Bouquin, J -B Le; Gosset, E; De Becker, M; Duvert, G; Absil, O; Anthonioz, F; Berger, J -P; Ertel, S; Grellmann, R; Guieu, S; Kervella, P; Rabus, M; Willson, M

    2016-01-01

    Our long term aim is to derive model-independent stellar masses and distances for long period massive binaries by combining apparent astrometric orbit with double-lined radial velocity amplitudes (SB2). We follow-up ten O+O binaries with AMBER, PIONIER and GRAVITY at the VLTI. Here, we report about 130 astrometric observations over the last 7 years. We combine this dataset with distance estimates to compute the total mass of the systems. We also compute preliminary individual component masses for the five systems with available SB2 radial velocities. Nine over the ten binaries have their three dimensional orbit well constrained. Four of them are known colliding wind, non-thermal radio emitters, and thus constitute valuable targets for future high angular resolution radio imaging. Two binaries break the correlation between period and eccentricity tentatively observed in previous studies. It suggests either that massive star formation produce a wide range of systems, or that several binary formation mechanisms ...

  20. Hydrogen Lines in Mira Stars Through Interferometry and Polarimetry

    Science.gov (United States)

    Fabas, N.; Chiavassa, A.; Millour, F.; Wittkowski, M.

    2015-12-01

    Balmer lines in emission are the most prominent features in Mira stars spectra and have a strong potential as a proxy to study the lower atmosphere's dynamics. In Fabas et al. ([1]), we accumulated spectropolarimetric observations of Balmer lines in emission. As the shock is propagating outwards, linear polarization rate increases and the angle of this polarization evolves. Assuming that linear polarization arises from anisotropic scattering, it has the potential of telling us about the geometric structure of the shock as it propagates and the study of such atmospheric structures can typically be performed with interferometry. In 2012, AMBER data on the Mira star omicron Ceti were collected in which the Brackett γ line is studied. The data show signatures in the interferometric observables around this line. Olivier Chesneau was in the jury evaluating the PhD thesis of N. Fabas and he was seduced by the idea to study these shock waves with interferometry and use polarimetry as a complementary study.

  1. Synthesis and Site-Specific Incorporation of Red-Shifted Azobenzene Amino Acids into Proteins.

    Science.gov (United States)

    John, Alford A; Ramil, Carlo P; Tian, Yulin; Cheng, Gang; Lin, Qing

    2015-12-18

    A series of red-shifted azobenzene amino acids were synthesized in moderate-to-excellent yields via a two-step procedure in which tyrosine derivatives were first oxidized to the corresponding quinonoidal spirolactones followed by ceric ammonium nitrate-catalyzed azo formation with the substituted phenylhydrazines. The resulting azobenzene-alanine derivatives exhibited efficient trans/cis photoswitching upon irradiation with a blue (448 nm) or green (530 nm) LED light. Moreover, nine superfolder green fluorescent protein (sfGFP) mutants carrying the azobenzene-alanine analogues were expressed in E. coli in good yields via amber codon suppression with an orthogonal tRNA/PylRS pair, and one of the mutants showed durable photoswitching with the LED light.

  2. Potencial hidrogeniônico de soluções de cloridrato de dobutamina expostas a condições ambientais de unidades de cuidados intensivos neonatais Hydrogen-ion potential of dobutamine hydrochloride solutions exposed to environmental conditions of neonatal intensive care units

    Directory of Open Access Journals (Sweden)

    Lidiane L. Reis

    2009-12-01

    Full Text Available OBJETIVO: Verificar o potencial hidrogeniônico (pH de soluções de cloridrato de dobutamina sob condições ambientais que mimetizam unidades de cuidados intensivos neonatais. MÉTODOS: Analisou-se pH do fármaco em solução glicosada 5% ou NaCl 0,9% segundo temperatura (22 e 37 °C, luz (escuro, lâmpadas fluorescentes ambiente e equipamento de fototerapia e equipos (incolor e âmbar em intervalos de tempo (0, 1, 24, 48, 72 e 96 horas. RESULTADOS: Evidenciaram-se valores próximos de pH do fármaco na apresentação comercial e diluído. Obteve-se média de pH de 3,45±0,19 a 22 °C e de 3,55±0,20 a 37 °C. A média de pH das soluções mantidas no escuro foi de 3,62±0,09, na luz ambiente, de 3,63±0,07, e sob fototerapia, de 3,31±0,16. Soluções em equipos incolores tiveram média menor (3,41±0,24 do que em âmbares (3,52±0,15. Obtiveram-se menores valores de pH nas soluções sob fototerapia em equipos incolores (3,17±0,03 do que em âmbares (3,55±0,03. CONCLUSÃO: Sob a luz da fototerapia houve maior variação do pH das soluções, e o emprego de equipos âmbares minimizou tal efeito.OBJECTIVE: To verify the hydrogen-ion potential (pH of dobutamine hydrochloride solutions under environmental conditions similar to those of neonatal intensive care units. METHODS: We analyzed the pH of the drug diluted in 5% dextrose in water or 0.9% NaCl under different conditions of temperature (22 and 37 °C and light (dark, fluorescent light bulbs, and phototherapy equipment, using colorless and amber intravenous sets at time intervals of 0, 1, 24, 48, 72, and 96 hours. RESULTS: The pH values of the marketed form of the drug and the diluted drug were similar. The pH means were 3.45±0.19 at 22 °C and 3.55±0.20 at 37 °C. The average of the pH according to light conditions were as follows: in the dark = 3.62±0.09, under room light = 3.63±0.07, and exposed to phototherapy = 3.31±0.16. Solutions stored in colorless intravenous sets had a lower

  3. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools.

    Science.gov (United States)

    Boström, J

    2001-12-01

    Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution (Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*\\GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.

  4. The conditions of respect of rules in young and elderly drivers: An exploratory study

    Directory of Open Access Journals (Sweden)

    Didier Le-Gall

    2011-01-01

    Full Text Available This study is concerned with the theoretical field of social representations and conditionality of norms. The aim is to study the perception of driving norms by structuring them around individual and group behaviours. We propose to evaluate driving conditionality with the questionnaire based on conditional scenarios. The tool has been proposed to 40 young drivers and 48 elderly drivers. Results show that the driving representation is conditional for the 2 groups, except with the scenario of wearing seat belt. The more conditional scenarios are the same for the 2 groups (scenarios of speed limit and amber light, with higher scores of conditionality for young drivers. The representation of the driving shows that with the system of legal norms (Highway Code, there is a system of social norms related to the actual practices of the users. This study illustrates an important aspect of road safety: the social perception of rules and its impact on driver behaviour.

  5. Dentinogenesis imperfecta associated with osteogenesis imperfecta: report of two cases.

    Science.gov (United States)

    Tsai, Chia-Ling; Lin, Yng-Tzer; Lin, Yai-Tin

    2003-02-01

    Osteogenesis imperfecta (OI) is a heritable systemic disorder of the connective tissue. Dentinogenesis imperfecta (DI), which is sometimes an accompanying symptom of OI, belongs to a group of genetically conditioned dentin dysplasias and is characterized clinically by an opalescent amber appearance of the dentin. Although the teeth of DI cases wear more easily and excessively compared to normal teeth, they do not appear to be more susceptible to dental caries than normal teeth. Two cases of DI associated with OI are presented in this paper, with 1 case suffering from nursing bottle caries. The purposes of this paper are to present the dental and skeletal characteristics of moderately and mildly involved DI associated with OI, and to discuss the possible methods of dental treatment. Patients with OI and opalescent teeth should be evaluated as soon as the deciduous teeth erupt; immediate dental involvement and oral hygiene instruction can be of help in reducing the necessity of extensive dental care.

  6. Mass-radius relation of low and very low-mass stars revisited with the VLTI

    CERN Document Server

    Demory, B -O; Forveille, T; Queloz, D; Beuzit, J -L; Delfosse, X; Di Folco, E; Kervella, P; Bouquin, J -B Le; Perrier, C

    2009-01-01

    We measured the radii of 7 low and very low-mass stars using long baseline interferometry with the VLTI interferometer and its VINCI and AMBER near-infrared recombiners. We use these new data, together with literature measurements, to examine the luminosity- radius and mass-radius relations for K and M dwarfs. The precision of the new interferometric radii now competes with what can be obtained for double-lined eclipsing binaries. Interferometry provides access to much less active stars, as well as to stars with much better measured distances and luminosities, and therefore complements the information obtained from eclipsing systems. The radii of magnetically quiet late-K to M dwarfs match the predictions of stellar evolution models very well, providing direct confirmation that magnetic activity explains the discrepancy that was recently found for magnetically active eclipsing systems. The radii of the early K dwarfs are well reproduced for a mixing length parameter that approaches the solar value, as qualita...

  7. Археометрия в България през последните десет години

    Directory of Open Access Journals (Sweden)

    Boika Zlateva

    2016-06-01

    Full Text Available Archaeometry in Bulgaria in the last decade. The paper summarizes all papers published by Bulgarian scientists in the field of archaeometry, issued in the last decade. The archaeometric investigations in Bulgaria cover the analyses of chemical composition of bronze, gold, silver, lead, glass, glaze, pottery, mortar, amber, resin and other archaeological objects. For their characterization many instrumental techniques such as AAS, ED-XRF, ICP-AES, INAA, LA-ICP-MS, SEM-EDS, etc. are used. These techniques, together with geophysical methods, archaeomagnetic investigations, dendrochronology and the various dating methods are all covered by the umbrella term ‘archaeometry’. MA programme in archaeometry has been offered in Sofia University ‘St. Kl. Ohridski’ in the last 10 years, whose graduates have been joining archaeological investigations professionally. In this way, archaeology is enriched with new understanding of the role of physics, chemistry, biology and geology.

  8. Andromorphic female of the dragonfly Neurothemis tullia tullia (Drury (Odonata: Libellulidae, central India

    Directory of Open Access Journals (Sweden)

    R.J. Andrew

    2013-01-01

    Full Text Available Neurothemis tullia tullia (Drury is a common dragonfly which occurs in large colonies in swamps and heavily- weeded tanks in different parts of India. It exhibits striking sexual dimorphism in colour and wing spot patterns. The male is dark with a large blue-black spot on the wing base while the female is dull olivaceous and the wing base is amber yellow. The sexes can be easily identified from quite a far distance. Andromorphic females are very rarely found in anisopteran dragonflies. This paper describes and compares not only the coloration and wing spots of the normal male and female with this andromorphic female but also reports about its sexual fitness to produce viable eggs.

  9. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

    Science.gov (United States)

    Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

    2014-12-15

    LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.

  10. Comparative Molecular Mechanics and Quantum Mechanics Study of Microhydration of Nucleic Acid Bases

    CERN Document Server

    Lino, J; Deriabina, A; Velasco, M; Poltev, V

    2013-01-01

    DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives using methods of molecular mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values ...

  11. Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

    DEFF Research Database (Denmark)

    Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas;

    2014-01-01

    Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that t...... possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format....... that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce...

  12. The core and O-polysaccharide structure of the Caulobacter crescentus lipopolysaccharide.

    Science.gov (United States)

    Jones, Michael D; Vinogradov, Evgeny; Nomellini, John F; Smit, John

    2015-01-30

    Here we describe the analysis of the structure of the lipopolysaccharide (LPS) from Caulobacter crescentus strain JS1025, a derivative of C. crescentus CB15 NA1000 with an engineered amber mutation in rsaA, leading to the loss of the protein S-layer and gene CCNA_00471 encoding a putative GDP-L-fucose synthase. LPS was isolated using an aqueous membrane disruption method. Polysaccharide and core oligosaccharide were produced by mild acid hydrolysis and analyzed by nuclear magnetic resonance spectroscopy and chemical methods. Spectra revealed the presence of two polysaccharides, one of them, a rhamnan, could be removed using periodate oxidation. Another polymer, built from 4-amino-4-deoxy-D-rhamnose (perosamine), mannose, and 3-O-methyl-glucose, should be the O-chain of the LPS according to genetic data. The attribution of the rhamnan as a part of LPS or a separate polymer was not possible.

  13. Analysis of the secondary structure of a protein's N-terminal

    Science.gov (United States)

    Floare, C. G.; Bogdan, M.; Horovitz, O.; Mocanu, A.; Tomoaia-Cotisel, M.

    2009-08-01

    The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

  14. Analysis of the secondary structure of a protein's N-terminal

    Energy Technology Data Exchange (ETDEWEB)

    Floare, C G; Bogdan, M [National Institute for R and D of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Horovitz, O; Mocanu, A; Tomoaia-Cotisel, M, E-mail: calin.floare@itim-cj.r [Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Department of Physical Chemistry, 11 Arany Janos, 400028 Cluj-Napoca (Romania)

    2009-08-01

    The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

  15. INFRARED INTERFEROMETRY OF YOUNG STELLAR OBJECTS

    Directory of Open Access Journals (Sweden)

    S. Kraus

    2010-01-01

    Full Text Available Discos circunestelares alrededor de objetos estelares jovenes desempeñan un rol fundamental en el proceso de formación de estrellas y proporcionan una etapa para la formación de planetas. Desde recientemente, la interferometría infrarroja proporciona la resolución espacial requerida para estudiar directamente la distribución del gas y del polvo en la Unidad astroóomica más cercana alrededor de la estrella en formación. Presentamos investigaciones recientes en las cuales empleamos el VLTI e interferométros en infrarrojo cercano y lejano AMBER y MIDI para restringir la geometría y condiciones físicas de discos alrededor de estrellas Herbig Ae/Be y estudiar los procesos del acreción y decreción que ocurren cerca de la estrella central.

  16. Selective-area nanoheteroepitaxy for light emitting diode (LED) applications

    Science.gov (United States)

    Wildeson, Isaac H.

    Over 20% of the electricity in the United States is consumed for lighting, and the majority of this energy is wasted as heat during the lighting process. A solid-state (or light emitting diode (LED)-based) light source has the potential of saving the United States billions of dollars in electricity and reducing megatons of global CO2 emissions annually. While white light LEDs are currently on the market with efficiencies that are superior to incandescent and fluorescent light sources, their high up-front cost is inhibiting mass adoption. One reason for the high cost is the inefficiency of green and amber LEDs that can used to make white light. The inefficiency of green and amber LEDs results in more of these chips being required, and thus a higher cost. Improvements in the performance of green and amber LEDs is also required in order to realize the full potential of solid-state lighting. Nanoheteroepitaxy is an interesting route towards achieving efficient green and amber LEDs as it resolves major challenges that are currently plaguing III-nitride LEDs such as high dislocation densities and limited active region critical thicknesses. A method for fabricating III-nitride nanopyramid LEDs is presented that employs conventional processing used in industry. The present document begins with an overview of the current challenges in III-nitride LEDs and the benefits of nanoheteroepitaxy. A process for controlled selective-area growth of nanopyramid LEDs by organometallic vapor phase epitaxy has been developed throughout the course of this work. Dielectric templates used for the selective-area growth are patterned by two methods, namely porous anodic alumina and electron-beam lithography. The dielectric templates serve as efficient dislocation filters; however, planar defects are initiated during lower temperature growth on the nanopyramids. The quantum wells outline six semipolar planes that form each hexagonal pyramid. Quantum wells grown on these semipolar planes

  17. Pitfalls to avoid when using phage display for snake toxins.

    Science.gov (United States)

    Laustsen, Andreas Hougaard; Lauridsen, Line Præst; Lomonte, Bruno; Andersen, Mikael Rørdam; Lohse, Brian

    2017-02-01

    Antivenoms against bites and stings from snakes, spiders, and scorpions are associated with immunological side effects and high cost of production, since these therapies are still derived from the serum of hyper-immunized production animals. Biotechnological innovations within envenoming therapies are thus warranted, and phage display technology may be a promising avenue for bringing antivenoms into the modern era of biologics. Although phage display technology represents a robust and high-throughput approach for the discovery of antibody-based antitoxins, several pitfalls may present themselves when animal toxins are used as targets for phage display selection. Here, we report selected critical challenges from our own phage display experiments associated with biotinylation of antigens, clone picking, and the presence of amber codons within antibody fragment structures in some phage display libraries. These challenges may be detrimental to the outcome of phage display experiments, and we aim to help other researchers avoiding these pitfalls by presenting their solutions.

  18. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    Science.gov (United States)

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics.

  19. A Simple AIMD Approach to Derive Atomic Charges for Condensed Phase Simulation of Ionic Liquids

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y; Maginn, EJ

    2012-08-23

    The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM] [PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as "AIMD-c charge"). For both ILs, the total charge was found to be +/- 0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-1 charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calculation of isolated ions in a vacuum and resulted in a total charge of unity on each ion. The scaled charge was obtained by uniformly scaling the full charge by 0.8. AIMD-1 and AIMD-b charges were derived from liquid phase ab initio molecular dynamics simulations. The scaled charges have the same total charge on the ions as the AIMD-c charge but different distributions. It was found that simulation results not only depend on the total charge of each ion, but they are also sensitive to the charge distribution within an ion, especially for dynamic and thermodynamic properties. Overall, for the two ILs under study, the AIMD-c charge was found to predict experimental results better than the other four sets of charges, indicating that fitting charges from crystal phase DFT calculations, instead of extensive sampling of the liquid phase configurations, is a simple and reliable way to derive atomic charges for condensed phase ionic liquid simulations.

  20. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  1. Functional and phylogenetic analysis of ureD in Shiga toxin-producing Escherichia coli.

    Science.gov (United States)

    Steyert, Susan R; Rasko, David A; Kaper, James B

    2011-02-01

    Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that can cause severe health complications and utilizes a much lower infectious dose than other E. coli pathotypes. Despite having an intact ure locus, ureDABCEFG, the majority of EHEC strains are phenotypically urease negative under tested conditions. Urease activity potentially assists with survival fitness by enhancing acid tolerance during passage through the stomach or by aiding with colonization in either human or animal reservoirs. Previously, in the EHEC O157:H7 Sakai strain, a point mutation in ureD, encoding a urease chaperone protein, was identified, resulting in a substitution of an amber stop codon for glutamine. This single nucleotide polymorphism (SNP) is observed in the majority of EHEC O157:H7 isolates and correlates with a negative urease phenotype in vitro. We demonstrate that the lack of urease activity in vitro is not solely due to the amber codon in ureD. Our analysis has identified two additional SNPs in ureD affecting amino acid positions 38 and 205, in both cases determining whether the encoded amino acid is leucine or proline. Phylogenetic analysis based on Ure protein sequences from a variety of urease-encoding bacteria demonstrates that the proline at position 38 is highly conserved among Gram-negative bacteria. Experiments reveal that the L38P substitution enhances urease enzyme activity; however, the L205P substitution does not. Multilocus sequence typing analysis for a variety of Shiga toxin-producing E. coli isolates combined with the ureD sequence reveals that except for a subset of the O157:H7 strains, neither the in vitro urease-positive phenotype nor the ureD sequence is phylogenetically restricted.

  2. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  3. Effect of different spectral transmittances through tinted animal cages on circadian metabolism and physiology in Sprague-Dawley rats.

    Science.gov (United States)

    Wren, Melissa A; Dauchy, Robert T; Hanifin, John P; Jablonski, Michael R; Warfield, Benjamin; Brainard, George C; Blask, David E; Hill, Steven M; Ooms, Tara G; Bohm, Rudolf P

    2014-01-01

    The suprachiasmatic nucleus is synchronized by the light:dark cycle and is the master biologic clock that serves as a pacemaker to regulate circadian rhythms. We explored the hypothesis that spectral transmittance (tint) of light through caging alters circadian rhythms of endocrine and metabolic plasma constituents in nonpigmented Sprague-Dawley rats. Rats (Crl:SD; n = 12 per group) were housed in a 12:12-h light:dark environment (300 lx; 123.0 μ W/cm(2); lights on, 0600) in either clear-, amber-, blue-, or red-tinted rodent cages. Blood was collected at 0400, 0800, 1200, 1600, 2000, and 2400 and measured for melatonin, total fatty acids, pH, glucose, lactic acid, corticosterone, insulin, and leptin. As expected, plasma melatonin levels were low during the light phase but higher during the dark phase in all groups; however, when compared with the clear-cage group, rats in amber-, blue-, and red-tinted cages had 29%, 74%, and 48%, respectively, greater total daily melatonin levels due to an increased duration and, in some cases, amplitude of the nocturnal melatonin signal. No differences were found in dietary and water intake, body growth rates, total fatty acids, pH, or glucose among groups. Disruptions in circadian rhythms, manifesting as alterations in phase timing, amplitude, or duration, occurred in the melatonin, lactic acid, corticosterone, insulin, and leptin levels of rats in tinted compared with clear cages. Therefore, the use of variously tinted animal cages significantly alters circadian rhythms in plasma measures of metabolism and physiology in laboratory rats, thus potentially altering the outcomes of scientific investigations.

  4. Labeling proteins on live mammalian cells using click chemistry.

    Science.gov (United States)

    Nikić, Ivana; Kang, Jun Hee; Girona, Gemma Estrada; Aramburu, Iker Valle; Lemke, Edward A

    2015-05-01

    We describe a protocol for the rapid labeling of cell-surface proteins in living mammalian cells using click chemistry. The labeling method is based on strain-promoted alkyne-azide cycloaddition (SPAAC) and strain-promoted inverse-electron-demand Diels-Alder cycloaddition (SPIEDAC) reactions, in which noncanonical amino acids (ncAAs) bearing ring-strained alkynes or alkenes react, respectively, with dyes containing azide or tetrazine groups. To introduce ncAAs site specifically into a protein of interest (POI), we use genetic code expansion technology. The protocol can be described as comprising two steps. In the first step, an Amber stop codon is introduced--by site-directed mutagenesis--at the desired site on the gene encoding the POI. This plasmid is then transfected into mammalian cells, along with another plasmid that encodes an aminoacyl-tRNA synthetase/tRNA (RS/tRNA) pair that is orthogonal to the host's translational machinery. In the presence of the ncAA, the orthogonal RS/tRNA pair specifically suppresses the Amber codon by incorporating the ncAA into the polypeptide chain of the POI. In the second step, the expressed POI is labeled with a suitably reactive dye derivative that is directly supplied to the growth medium. We provide a detailed protocol for using commercially available ncAAs and dyes for labeling the insulin receptor, and we discuss the optimal surface-labeling conditions and the limitations of labeling living mammalian cells. The protocol involves an initial cloning step that can take 4-7 d, followed by the described transfections and labeling reaction steps, which can take 3-4 d.

  5. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  6. Radionuclide release calculations for SAR-08

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Gavin; Miller, Alex; Smith, Graham; Jackson, Duncan (Enviros Consulting Ltd, Wolverhampton (United Kingdom))

    2008-04-15

    Following a review by the Swedish regulatory authorities of the post-closure safety assessment of the SFR 1 disposal facility for low and intermediate waste (L/ILW), SAFE, the SKB has prepared an updated assessment called SAR-08. This report describes the radionuclide release calculations that have been undertaken as part of SAR-08. The information, assumptions and data used in the calculations are reported and the results are presented. The calculations address issues raised in the regulatory review, but also take account of new information including revised inventory data. The scenarios considered include the main case of expected behaviour of the system, with variants; low probability releases, and so-called residual scenarios. Apart from these scenario uncertainties, data uncertainties have been examined using a probabilistic approach. Calculations have been made using the AMBER software. This allows all the component features of the assessment model to be included in one place. AMBER has been previously used to reproduce results the corresponding calculations in the SAFE assessment. It is also used in demonstration of the IAEA's near surface disposal assessment methodology ISAM and has been subject to very substantial verification tests and has been used in verifying other assessment codes. Results are presented as a function of time for the release of radionuclides from the near field, and then from the far field into the biosphere. Radiological impacts of the releases are reported elsewhere. Consideration is given to each radionuclide and to each component part of the repository. The releases from the entire repository are also presented. The peak releases rates are, for most scenarios, due to organic C-14. Other radionuclides which contribute to peak release rates include inorganic C-14, Ni-59 and Ni-63. (author)

  7. The luminous blue variable HR Carinae has a partner. Discovery of a companion with the VLTI

    Science.gov (United States)

    Boffin, Henri M. J.; Rivinius, Thomas; Mérand, Antoine; Mehner, Andrea; LeBouquin, Jean-Baptiste; Pourbaix, Dimitri; de Wit, Willem-Jan; Martayan, Christophe; Guieu, Sylvain

    2016-09-01

    Luminous blue variables (LBVs) are massive stars caught in a post-main sequence phase, during which they lose a significant amount of mass. Since, on one hand, it is thought that the majority of massive stars are close binaries that will interact during their lifetime, and on the other, the most dramatic example of an LBV, η Car, is a binary, it would be useful to find other binary LBVs. We present here interferometric observations of the LBV HR Car done with the AMBER and PIONIER instruments attached to ESO's Very Large Telescope Interferometer (VLTI). Our observations, spanning two years, clearly reveal that HR Car is a binary star. It is not yet possible to fully constrain the orbit, and the orbital period may lie between a few years and several hundred years. We derive a radius for the primary in the system and possibly also resolve the companion. The luminosity ratio in the H-band between the two components is changing with time, going from about 6 to 9. We also tentatively detect the presence of some background flux which remained at the 2% level until January 2016, but then increased to 6% in April 2016. Our AMBER results show that the emission line-forming region of Brγ is more extended than the continuum-emitting region as seen by PIONIER and may indicate some wind-wind interaction. Most importantly, we constrain the total masses of both components, with the most likely range being 33.6 M⊙ and 45 M⊙. Our results show that the LBV HR Car is possibly an η Car analog binary system with smaller masses, with variable components, and further monitoring of this object is definitively called for. Based on data obtained with ESO programmes 092.C-0243, 092.D-0289, 092.D-0296, 094.D-0069, and 596.D-0335.

  8. Revealing the inclined circumstellar disk in the UX Ori system KK Ophiuchi

    Science.gov (United States)

    Kreplin, A.; Weigelt, G.; Kraus, S.; Grinin, V.; Hofmann, K.-H.; Kishimoto, M.; Schertl, D.; Tambovtseva, L.; Clausse, J.-M.; Massi, F.; Perraut, K.; Stee, Ph.

    2013-07-01

    We study the inner sub-AU region of the circumstellar environment of the UX Ori type star KK Oph with near-infrared VLTI/AMBER interferometry. We are particularly interested in the inclination of the star-disk system, and we will use this information to test the current standard picture for UX Ori stars. We recorded spectrally dispersed (R˜35) interferograms in the near-infrared H and K bands with the VLTI/AMBER instrument. The derived visibilities, closure phases and the SED of KK Oph were compared with two-dimensional geometric and radiative transfer models (RADMC). We obtained visibilities at four different position angles. Using two-dimensional geometric models, we derive an axis ratio ˜3.0 corresponding to an inclination of ˜70 degree. A fitted inclined ring model leads to a ring radius of 2.8 ± 0.2 mas, corresponding to 0.44 ± 0.03 AU at a distance of 160 pc, which is larger than the dust sublimation radius of ˜0.1 AU predicted for a dust sublimation temperature of 1500 K. Our derived two-dimensional RADMC model consists of a circumstellar disk with an inclination angle of ˜70 degree and an additional dust envelope. The finding of an ˜70 degree inclined disk around KK Oph is consistent with the prediction that UX Ori objects are seen under large inclination angles, and orbiting clouds in the line of sight cause the observed variability. Furthermore, our results suggest that the orbit of the companion KK Oph B and the disk plane are coplanar.

  9. Revealing the inclined circumstellar disk in the UX Orionis system KK Ophiuchi

    Science.gov (United States)

    Kreplin, A.; Weigelt, G.; Kraus, S.; Grinin, V.; Hofmann, K.-H.; Kishimoto, M.; Schertl, D.; Tambovtseva, L.; Clausse, J.-M.; Massi, F.; Perraut, K.; Stee, Ph.

    2013-03-01

    Aims: We study the inner sub-AU region of the circumstellar environment of the UX Ori-type star KK Oph with near-infrared VLTI/AMBER interferometry. We are particularly interested in the inclination of the star-disk system, and we use this information to test the current standard picture for UX Ori stars. Methods: We recorded spectrally dispersed (R ~ 35) interferograms in the near-infrared H and K bands with the VLTI/AMBER instrument. The derived visibilities, closure phases, and the spectral energy distribution of KK Oph were compared with two-dimensional geometric and radiative transfer models (RADMC). Results: We obtained visibilities at four different position angles. Using two-dimensional geometric models, we derive an axis ratio ~3.0 corresponding to an inclination of ~70°. A fitted inclined ring model leads to a ring radius of 2.8 ± 0.2 mas, corresponding to 0.44 ± 0.03 AU at a distance of 160 pc, which is larger than the dust sublimation radius of ~0.1 AU predicted for a dust sublimation temperature of 1500 K. Our derived two-dimensional RADMC model consists of a circumstellar disk with an inclination angle of ~70° and an additional dust envelope. Conclusions: The finding of an ~70° inclined disk around KK Oph is consistent with the prediction that UX Ori objects are seen under large inclination angles, and orbiting clouds in the line of sight cause the observed variability. Furthermore, our results suggest that the orbit of the companion KK Oph B and the disk plane are coplanar. Based on observations made with ESO telescopes at Paranal Observatory under program ID: 083.D-0224(C) and 088.C-0575(A).

  10. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.

    Science.gov (United States)

    Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A; Almo, Steven C; Gao, Jiali; Suga, Hiroaki; Gerlt, John A

    2014-10-21

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.

  11. Stability of Commercially Available Grape and Compounded Cherry Oral Vancomycin Preparations Stored in Syringes and Cups.

    Science.gov (United States)

    Kirk, Loren; Lewis, Paul; Luu, Yao; Brown, Stacy

    2016-01-01

    The purpose of this study was to evaluate the stability of two preparations of vancomycin oral solution in two different storage containers, capped amber oral-dosing syringes and heat-sealed oral-dosing cups, stored under refrigerated conditions. Commercially available grape-flavored vancomycin oral preparation and compounded vancomycin for intravenous use in cherry syrup oral preparation were divided into 5-mL aliquots into heat-sealed plastic dosing cups and capped oral-dosing syringes. All samples were stored under refrigeration (2°C to 8°C) and evaluated at days 0, 3, 7, 14, 30, 60, and 90. For each evaluation, samples were visually inspected and analyzed for potency using a stability-indicating high-performance liquid chromatographic method with ultraviolet detection. Over the study period, at least 90% of the initial concentrations for the preparation and the product in both storage containers were retained at 60 days. The commercially available oral vancomycin further demonstrated stability within 90% out to 90 days in the syringe and the unit-dose cups. Visual inspection revealed no changes in the grape-flavored vancomycin oral preparation, but a detectable red-dye precipitate could be seen in the crevices of the dosing cups from the vancomycin in cherry syrup oral preparation after 60 days. Commercially available grape-flavored vancomycin oral preparation was stable up to 90 days, and com- pounded vancomycin for intravenous use in cherry syrup oral preparation maintained stability for 60 days when dispensed in capped amber polypropylene oral-dosing syringes and heat-sealed plastic dosing cups when stored at refrigerated conditions.

  12. The clinical effectiveness of reflectance optical spectroscopy for the in vivo diagnosis of oral lesions

    Institute of Scientific and Technical Information of China (English)

    Diana VMessadi; Fariba SYounai; Hong-Hu Liu; Gao Guo; Cun-Yu Wang

    2014-01-01

    Optical spectroscopy devices are being developed and tested for the screening and diagnosis of oral precancer and cancer lesions. This study reports a device that uses white light for detection of suspicious lesions and green-amber light at 545 nm that detect tissue vascularity on patients with several suspicious oral lesions. The clinical grading of vascularity was compared to the histological grading of the biopsied lesions using specific biomarkers. Such a device, in the hands of dentists and other health professionals, could greatly increase the number of oral cancerous lesions detected in early phase. The purpose of this study is to correlate the clinical grading of tissue vascularity in several oral suspicious lesions using the IdentafiH system with the histological grading of the biopsied lesions using specific vascular markers. Twenty-one patients with various oral lesions were enrolled in the study. The lesions were visualized using IdentafiH device with white light illumination, followed by visualization of tissue autofluorescence and tissue reflectance. Tissue biopsied was obtained from the all lesions and both histopathological and immunohistochemical studies using a vascular endothelial biomarker (CD34) were performed on these tissue samples. The clinical vascular grading using the green-amber light at 545 nm and the expression pattern and intensity of staining for CD34 in the different biopsies varied depending on lesions, grading ranged from 1 to 3. The increase in vascularity was observed in abnormal tissues when compared to normal mucosa, but this increase was not limited to carcinoma only as hyperkeratosis and other oral diseases, such as lichen planus, also showed increase in vascularity. Optical spectroscopy is a promising technology for the detection of oral mucosal abnormalities;however, further investigations with a larger population group is required to evaluate the usefulness of these devices in differentiating benign lesions from

  13. Image multispectral sensing: a new and innovative instrument for hyperspectral imaging using dispersive techniques

    Science.gov (United States)

    Hinnrichs, Michele; Massie, Mark A.

    1995-06-01

    IMSS utilizes a very simple optical design that enables a robust and low cost hyperspectral imaging instrument. This technology was developed under a phase II SBIR with the Air Force Philips Lab. (Dr. Paul LeVan), for the midwave IR to perform clutter rejection and target identification based upon IR spectral signatures. The prototype instrument has been field tested on numerous occasions and successfully measured background, aircraft, and misile plume spectra. PAT currently has several contracts to commercialize this technology both for the DoD and the commercial market. Under contract to the BMDO, (Paul McCarley), with matching funds from Amber Engineering, we are developing an F/2.3 system that will be sold by Amber Engineering as an accessory to the Radiance 1 camera. PAT is also under contract with ONR (Mr. Jim Buss), to develop a longwave IR version of IMSS as well as an MWIR version tuned to operate as a 'little sister sensor for target identification' for the Navy's IRST's. The purpose of this paper is to briefly describe the hyperspectral image data that was collected in the field at Long Jump '94, and Santa Ynez Peak using IMSS prototype hyperspectral imager. Examples of spectral images, as well as spectra of different aircraft at various ranges, power settings, and aspect angles, an Atlas liquid hydrocarbon burning missile, and a solid beester. All data presented in this paper are a result of a single spectral scan. The limitation in digital storage of the prototype system do not allow multiple scans in order to improve signal to noise. In spite of this limitation, the performance of the prototype system has proven to be excellent.

  14. Effects of flashing green on driver’s stop/go decision at signalized intersection

    Institute of Scientific and Technical Information of China (English)

    沈家军; 王炜

    2015-01-01

    The primary objective of this work is to explore how drivers react to flashing green at signalized intersections. Through video taping and data procession based on photogrammetry, the operating speeds of vehicles before and after the moment when flashing green started was compared using paired-samples T-test. The critical distances between go and stop decisions was defined through cumulative percentage curve. The boundary of dilemma zone was determined by comparing stop distance and travel distance. Amber-running violation was analyzed on the basis of the travel time to the stop line. And finally, a logistic model for stop and go decisions was constructed. The results shows that the stopping ratios of the first vehicles of west-bound and east-bound approaches are 41.3% and 39.8%, respectively; the amber-light running violation ratios of two approaches are 31.6% and 25.4%, respectively; the operating speed growth ratios of first vehicles selecting to cross intersection after the moment when flashing green started are 26.7% and 17.7%, respectively; and the critical distances are 48 m and 46 m, respectively, which are close to 44 m, the boundary of dilemma zone. The developed decision models demonstrate that the probability of go decision is higher when the distance from the stop line is shorter or operating speed is higher. This indicates that flashing green is an effective way to enhance intersection safety, but it should work together with a strict enforcement. In addition, traffic signs near critical distance and reasonable speed limitation are also beneficial to the safety of intersections.

  15. Initial cos cleavage of bacteriophage lambda concatemers requires proheads and gpFI in vivo.

    Science.gov (United States)

    Sippy, Jean; Feiss, Michael

    2004-04-01

    The development of bacteriophage lambda and double-stranded DNA viruses in general involves the convergence of two separate pathways: DNA replication and head assembly. Clearly, packaging will proceed only if an empty capsid shell, the prohead, is present to receive the DNA, but genetic evidence suggests that proheads play another role in the packaging process. For example, lambda phages with an amber mutation in any head gene or in FI, the gene encoding the accessory packaging protein gpFI, are able to produce normal amounts of DNA concatemers but they are not cut, or matured, into unit length chromosomes for packaging. Similar observations have been made for herpes simplex 1 virus. In the case of lambda, a negative model proposes that in the amber phages, unassembled capsid components are inhibitory to maturation, and a positive model suggests that assembled proheads are required for cutting. We tested the negative model by using a deletion mutant devoid of all prohead genes and FI in an in vivo cos cleavage assay; in this deleted phage, the cohesive ends were not cut. When lambda proheads and gpFI were provided in vivo via a second prophage, cutting was restored, and gpFI was required, results that support the positive model. Phage 21 is a sister phage of lambda, and although its capsid proteins share approximately 60% residue identity with lambda's, phage 21 proheads did not restore cutting, even when provided with the accessory protein gpFI. Models for the role of proheads and gpFI in cos cutting are discussed.

  16. Enhancing effects of organic acids on saltiness of low-sodium salt%有机酸味剂对低钠盐增咸作用的研究

    Institute of Scientific and Technical Information of China (English)

    王仕钰; 张立彦

    2012-01-01

    The combination effects between low-sodium salt and L-malic acid,amber acid,citric acid ,fumaric acid and other organic acids were researched.Using ].0% (w/w)of sodium chloride solution as standard,the sourness and saltiness of the combination solution was evaluated by a special panel.The results showed that= L-malic acid, amber acid,citric acid and fumaric acid all had an obvious effect to enhance the saltiness of low-sodium salt at ].6% ,0.8%, 2.4%, 0.8% (w/w) addition level, respectively.The combination solution which had been added into ].6% L-malic acid had a pure saltiness and good taste,and the saltiness could be increased by 1.33 times.%以1.0%(w/w)的氯化钠溶液为标准参照,重点研究了L一苹果酸、琥珀酸、柠檬酸、富马酸等有机酸味剂与低钠盐的复配效果。通过品尝小组对复配溶液的成度、酸度等进行感官评定,结果表明:当单独添加L-苹果酸、琥珀酸、柠檬酸、富马酸的量依次分别为1.6%、0.8%、2.4%、0.8%(w/w)时,对低钠盐有明显的掩盖苦味及增成效果,其中添加1.6%L-苹果酸的复配溶液成味纯正,综合口感良好,增成效果可达1.33倍。

  17. Total System Performance Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Yong Soo; Kang, Chul Hyung; Lee, Youn Myoung; Han, Ji Woong; Choi, Jong Won; Hahn, Pil Soo; Park, Jeong Hwa; Jeong, Mi Seon

    2007-06-15

    Based on the KAERI FEP list developed through the previous studies, the KAERI FEP Encyclopedia has been developed. Current version is 1.0 which includes all relevant FEPs to compose of two references and all alternative scenarios. Many interaction FEPs between scenario defining FEP(SDF) are created throughout the study. FEPs are classified into many Integrated FEP(IFEP) which eventually become the elements of the RES matrix. The FEAS program one of the component of the KAERI's CYPRUS information system is added to develop the FEP, RES, AC, AMF and finally scenarios. It assists to create transparent way to deal with assessment from the stage of the planning of the R and D to the final stage of the external audit and regulatory body review. Even though MASCOT-K and compartment analysis codes such as AMBER, GoldSim and Ecolego are excellent for TSPA they by in heritage possess a certain limitation especially to identify a proper migration cross sectional area when a relatively big component intersects with a tiny one such as a fracture. It is truly 3D phenomena in nature. MDPSA code is developed which is expected to overcome limitations in compartment models while successfully deals with natural disruptive events. The R and D target for the TSPA is to develop the sufficient scenarios and their variation cases to understand the safety of KRS in every possible aspect. For this, reference scenarios, alternative scenarios covering engineered barrier failure and natural events are developed and assessed respectively for around 100 cases. The stylized template to assess the Korean reference biosphere is developed using the AMBER. Three critical groups, agricultural, freshwater and marine water fishing groups are identified to assess the DCF following the guidelines of ICRP. Based on the QA principles of T2R3, the web based QA system is developed using the procedures in the USNRC 10CFR50 Appendix B. The QA system is combined with the PAID and FEAS to create the

  18. Archaeometric study of glass beads from the 2nd century BC cemetery of Numantia

    Directory of Open Access Journals (Sweden)

    García Heras, Manuel

    2003-06-01

    Full Text Available Recent archaeologícalf ieldwork undertaken in the Celtiberian cremation necropolis of Numantia (Soria, Spain has provided a group of glass beads from the 2nd century BC. Such glass beads were part, together with other metallic and ceramic items, of the offerings deposited with the dead. They are ring-shaped in typology and deep-blue, amber, or semitransparent white in colour. This paper reports results derived from the chemical and microstructural characterization carried out on a representative sample set of this group of beads. The main goal of the research was to find out about their production technology to explore their probable provenance. In addítion, corrosion mechanisms were also assessed to determine the influence of crematíon on the beads' structure. The resulting data suggest that these blue and amber beads were made using soda-lime silicate glass, whereas semi-transparent white ones were manufactured from alumino-silicate glass. It has also determined that some transition metal oxides were used as chromophores, as well as lead oxide for decoration.

    La reciente excavación de la necrópolis celtibérica de Numancia (Garray, Soria ha permitido recuperar un conjunto de cuentas de vidrio del siglo II a.C. Las cuentas, junto con otros objetos de metaly cerámica, formaban parte de las ofrendas depositadas con el difunto, siendo de tipología anular y coloreadas en azul oscuro, ambar y blanco semitransparente. Este trabajo presenta los resultados obtenidos en la caracterización química y microestructural de una muestra representativa de este conjunto. El objetivo principal de la investigación consistió en recabar información sobre su tecnología de manufactura y evaluar su posible procedencia. Asimismo, también se investigaron sus mecanismos de corrosión para determinar si la cremación había inducido cambios en su estructura. Los resultados indican que las cuentas azules y ámbar se realizaron con vidrio de silicato s

  19. Las relaciones financieras entre España y Portugal, 1563-1580

    Directory of Open Access Journals (Sweden)

    Óscar LUCAS VILLANUEVA

    2009-12-01

    Full Text Available RESUMEN: Las economías de Castilla y Portugal durante la segunda mitad del siglo XVI estaban estrechamente ligadas por vínculos financieros. Un espacio económico en desarrollo, el del Atlántico septentrional, comprendía ambos territorios y se organizaba a partir de los grandes centros feriales de Amberes, Lyon y Medina. El gran tráfico mercantil transoceánico se hacía presente en este escenario europeo gracias a la intervención de España y Portugal, pero con papeles bien distintos: España, incontinente, drenando el oro y la plata americanos hacia Europa, Portugal suministrando las apreciadas mercancías orientales. Las ferias de Medina del Campo y los mercaderes castellanos como Simón Ruiz se convierten en colaboradores necesarios de los mercaderes portugueses, pues a través de éstos negociaban los reembolsos o inversiones financieras en las plazas europeas; sin embargo, para ello era preciso un buen conocimiento de los negocios cambiarlos y su oportunidad, atendiendo a la cotización de las distintas monedas y a demanda de dinero en las ferias europeas. De la mano del mercader medinense entran los lisboetas en las grandes finanzas y la concertación de asientos con la Corona, aunque tal vez sin la pujanza que Felipe II hubiese deseado.ABSTRACT: The correspondence studied shows the importance that had, for this period of time (1563-1580, the relationship between Castille and Portugal. The vigorous economic space of the Northern Atlantic, the space in which were inscribed both territories, was organised from the three great market centres of Amberes, Lyon and Medina del Campo. The big transoceanic commercial trade was present in this European scenery thanks to the supervision of Spain an Portugal, but playing a very different role: Spain, draining gold and silver to Europe; and Portugal, supplying the appreciated oriental goods. The fairs of Medina and the Castilian merchants, like Simon Ruiz, were converted in necessary

  20. Nutrient Contents per Serving of Twelve Varieties of Cooked Rice Marketed in Jordan

    Directory of Open Access Journals (Sweden)

    Jafar M. El-Qudah

    2008-01-01

    Full Text Available Jordan imports rice from different countries without any quality preferences. Twelve varieties of cooked rice marketed in Jordan were analyzed. The content per serving of these varieties were computed for energy, protein, carbohydrates, fat, calcium, sodium, potassium, magnesium, manganese, copper, iron and phosphorous. The protein content per serving found to range from 0.49 g for La Cigala rice to 6.2 g for Harvest rice. The fat content for all rice brands was less than 0.37 g per serving. The energy content ranged from 172.12 g/serving for Basmati rice to 212.25 g/serving for Sun White rice. Generally, all rice varieties contain significant amounts of minerals per serving. Ruzzana found to contain the highest level of calcium (38.2 mg/serving and Amber the lowest calcium content (6.7 mg/serving. Magnesium content found to range from 5.7 mg/serving for Royal Umberella rice to 16.3 mg/serving for Ruzzana rice. Consumption of one serving of Harvest cooked rice will cover 13.5% of the daily requirement of protein for females and 11.1% for males. Manganese content of one serving of Harvest, Sun White, Abu bent and La Cigala will cover 22.2% of the daily requirements for females and 14.7% for males, while consumption of one of Basmati, Sos rice or Amber will cover only 11.1% and 8.75 of requirement for females and males respectively. Planning a healthful diet is not a simple task. Dietary Reference Intake planning and assessing the diets of individuals or groups of healthy individuals according to their stage of life and sex. Food choice is a function of many factors, including personal preferences, habits, ethnic heritage and tradition. Dietary guidelines for Americans, consider whole grain products like rice are among the food groups that form the basis of a healthy diet. Including rice as part of a healthy, balanced diet can be linked to overall healthier eating patterns. Rice eaters are more likely to eat a diet consistent with the 2005 Dietary

  1. Critical Dose of Internal Organs Internal Exposure - 13471

    Energy Technology Data Exchange (ETDEWEB)

    Grigoryan, G.; Amirjanyan, A. [Nuclear and Radiation Safety Centre (Armenia); Grigoryan, N. [Yerevan State Medical University 4Tigran Mets,375010 Yerevan (Armenia)

    2013-07-01

    radionuclides that have intake into the organism or absorbed into blood. Transport of different radionuclides between compartments is assumed to follow first order kinetics provided the concentration in red blood cells (RBCs) stays below a nonlinear threshold concentration. When the concentration in RBCs exceeds that threshold, the transfer rate from diffusible plasma to RBCs is assumed to decrease as the concentration in RBCs increases. For the calculations used capabilities AMBER by using the traces of radionuclides in the body. Model for the transfer of radionuclides in the body has been built on the basis of existing models at AMBER for lead. (authors)

  2. Direct detection of the tertiary component in the massive multiple HD 150136 with VLTI

    Science.gov (United States)

    Sanchez-Bermudez, J.; Schödel, R.; Alberdi, A.; Barbá, R. H.; Hummel, C. A.; Maíz Apellániz, J.; Pott, J.-U.

    2013-06-01

    Context. Massive stars are of fundamental importance for almost all aspects of astrophysics, but there still exist large gaps in our understanding of their properties and formation because they are rare and therefore distant. It has been found that most O-stars are multiples. It may well be that almost all massive stars are born as triples or higher multiples, but their large distances require milliarcsecond angular resolution for a direct detection of the companions. Aims: HD 150136 is the nearest system to Earth with >100 M⊙ and provides a unique opportunity to study an extremely massive system. Recently, evidence for the existence of a third component in HD 150136, in addition to the tight spectroscopic binary that forms the main component, was found in spectroscopic observations. Our aim was to image and obtain astrometric and photometric measurements of this component using long-baseline optical interferometry to further constrain the nature of this component. Methods: We observed HD 150136 with the near-infrared instrument AMBER attached to the ESO VLT Interferometer, which provides an angular resolution of 2 mas. The recovered closure phases are robust to systematic errors and provide unique information on the source asymmetry. Therefore, they are of crucial relevance for both image reconstruction and model fitting of the source structure. Results: The third component in HD 150136 is clearly detected in the high-quality data from AMBER. It is located at a projected angular distance of 7.3 mas, or about 13 AU at the line-of-sight distance of HD 150136, at a position angle of 209 degrees east of north, and has a flux ratio of 0.25 with respect to the inner binary. Our findings agree with previous results and have permitted us to improve the orbital solutions of the tertiary around the inner system. Conclusions: We resolved the third component of HD 150136 in J, H and K filters. The luminosity and color of the tertiary agrees with the predictions and shows

  3. El (reconocimiento de la madre en La mitad del alma

    Directory of Open Access Journals (Sweden)

    Sandra J. Schumm

    2011-01-01

    Full Text Available Resumen: La mitad del alma de Carme Riera, en que C rememora a su madre, enfatiza la importancia del reconocimiento de las mujeres en la memoria histórica. Desde el mito griego de Atena, quien ignoraba a su madre Metis, la sociedad patriarcal ha excluido a la madre, lo cual promete que la hija conlleve negación también, según Amber Jacobs en On Matricide. Jacobs observa que en La Oresteia hay crímenes sancionados contra las mujeres, las hijas están deprimidas, existe incesto contra la hija, la reproducción familiar se paraliza, toda la sociedad sufre y la hija se desperdicia también cuando la madre es menospreciada. Jacobs afirma que este desprecio de la madre que transcurría en los mitos griegos continúa en la sociedad y la psicología hoy en día. En esta novela de Riera, la hija protagonista, quien desconoce a su madre, sufre de un estado depresivo, la falta de creatividad y una conexión demasiado fuerte con su padre, semejante a lo que Jacobs observa en los mitos, pero la escritura de C sobre su madre la integrará en la consciencia y mejorará la situación de la hija y, últimamente, la de toda la civilización.Summary: Carme Riera‟s La mitad del alma, in which C recollects her mother, emphasizes the importance of the recognition of women in historic memory. Ever since the Greek myth of Athena, who was ignorant of the existence of her mother, Metis, patriarchal society has excluded the mother, a fact which promises that the daughter will also experience negation, according to Amber Jacobs in On Matricide. Jacobs observes that in La Oresteia there are sanctioned crimes against women, the daughters are depressed, there is incest against the daughter, she is dishonored, family reproduction stops, and all of society suffers when the mother is not appreciated. Jacobs affirms that the distain of the mother that took place in Greek myths continues in society and psychology today. In this novel by Riera, the protagonist/daughter, who

  4. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    ) and amber (587 nm peak) LEDs it achieves 8 m lateral resolution using a CMOS imaging chip (as configured for serial data speeds) or 4 m resolution using USB imaging chips. The imager consists of a modified commercial off-the-shelf CMOS chip camera, amber, blue and white LEDs, as well as a relay lens and dual-band filters to obviate moving parts while supporting both fluorescence wavelengths.

  5. Colour-rendition properties of solid-state lamps

    Science.gov (United States)

    Žukauskas, A.; Vaicekauskas, R.; Shur, M. S.

    2010-09-01

    The applicability of colour-quality metrics to solid-state light sources is validated and the results of the assessment of colour-rendition characteristics of various lamps are presented. The standard colour-rendering index metric or a refined colour-quality scale metric fails to distinguish between two principle colour-rendition properties of illumination: the ability to render object colours with high fidelity and the ability to increase chromatic contrast, especially when the spectra of light sources contain a few narrow-band electroluminescence components. Supplementing these metrics by the known figures of merit that measure the gamut area of a small number of test colour samples does not completely resolve this issue. In contrast, the statistical approach, which is based on sorting a very large number of test colour samples in respect of just-perceivable colour distortions of several kinds, offers a comprehensive assessment of colour-rendition properties of solid-state light sources. In particular, two statistical indices, colour-fidelity index (CFI) and colour-saturation index (CSI), which are the relative numbers of object colours rendered with high fidelity and increased saturation, respectively, are sufficient to reveal and assess three distinct types of solid-state light sources. These are (i) high-fidelity lamps, which cover the entire spectrum with the spectral components present in the wavelength ranges of both 530-610 nm and beyond 610 nm (e.g. trichromatic warm white phosphor-converted (pc) light-emitting diodes (LEDs), red-amber-green-blue LED clusters, complementary clusters of white and coloured LEDs); (ii) colour-saturating lamps, which lack power in the 530-610 nm wavelength range (e.g. red-green-blue or red-cyan-blue LED clusters) and (iii) colour-dulling lamps, which lack power for wavelengths longer than 610 nm (dichromatic daylight pc LEDs and amber-green-blue LED clusters). Owing to a single statistical format, CSI and CFI can be used for

  6. The inner circumstellar disk of the UX Orionis star V1026 Scorpii

    Science.gov (United States)

    Vural, J.; Kreplin, A.; Kishimoto, M.; Weigelt, G.; Hofmann, K.-H.; Kraus, S.; Schertl, D.; Dugué, M.; Duvert, G.; Lagarde, S.; Massi, F.

    2014-04-01

    Context. The UX Ori type variables (named after the prototype of their class) are intermediate-mass pre-main sequence objects. One of the most likely causes of their variability is the obscuration of the central star by orbiting dust clouds. Aims: We investigate the structure of the circumstellar environment of the UX Ori star V1026 Sco (HD 142666) and test whether the disk inclination is large enough to explain the UX Ori variability. Methods: We observed the object in the low-resolution mode of the near-infrared interferometric VLTI/AMBER instrument and derived H- and K-band visibilities and closure phases. We modeled our AMBER observations, published Keck Interferometer observations, archival MIDI/VLTI visibilities, and the spectral energy distribution using geometric and temperature-gradient models. Results: Employing a geometric inclined-ring disk model, we find a ring radius of 0.15 ± 0.06 AU in the H band and 0.18 ± 0.06 AU in the K band. The best-fit temperature-gradient model consists of a star and two concentric, ring-shaped disks. The inner disk has a temperature of 1257+133-53 K at the inner rim and extends from 0.19 ± 0.01 AU to 0.23 ± 0.02 AU. The outer disk begins at 1.35+0.19-0.20 AU and has an inner temperature of 334+35-17 K. The derived inclination of 48.6+2.9-3.6° approximately agrees with the inclination derived with the geometric model (49 ± 5° in the K band and 50 ± 11° in the H band). The position angle of the fitted geometric and temperature-gradient models are 163 ± 9° (K band; 179 ± 17° in the H band) and 169.3+4.2-6.7°, respectively. Conclusions: The narrow width of the inner ring-shaped model disk and the disk gap might be an indication for a puffed-up inner rim shadowing outer parts of the disk. The intermediate inclination of ~50° is consistent with models of UX Ori objects where dust clouds in the inclined disk obscure the central star. Based on observations made with ESO telescopes at the La Silla Paranal Observatory

  7. Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

    Science.gov (United States)

    Pang, Yuan-Ping

    2016-09-01

    Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å(2) for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å(2) for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

  8. HD 85567: A Herbig B[e] star or an interacting B[e] binary

    CERN Document Server

    Wheelwright, H E; Garatti, A Caratti o; Lopez, R Garcia

    2013-01-01

    Context. HD 85567 is an enigmatic object exhibiting the B[e] phenomenon, i.e. an infrared excess and forbidden emission lines in the optical. The object's evolutionary status is uncertain and there are conflicting claims that it is either a young stellar object or an evolved, interacting binary. Aims. To elucidate the reason for the B[e] behaviour of HD 85567, we have observed it with the VLTI and AMBER. Methods. Our observations were conducted in the K-band with moderate spectral resolution (R~1500, i.e. 200 km/s). The spectrum of HD 85567 exhibits Br gamma and CO overtone bandhead emission. The interferometric data obtained consist of spectrally dispersed visibilities, closure phases and differential phases across these spectral features and the K-band continuum. Results. The closure phase observations do not reveal evidence of asymmetry. The apparent size of HD 85567 in the K-band was determined by fitting the visibilities with a ring model. The best fitting radius, 0.8 +/- 0.3 AU, is relatively small maki...

  9. Antioxidant properties of wheat as affected by pearling.

    Science.gov (United States)

    Liyana-Pathirana, Chandrika; Dexter, Jim; Shahidi, Fereidoon

    2006-08-23

    The effects of pearling on the content of phenolics and antioxidant capacity of two Canadian wheat classes, namely, Canada Western Amber Durum; Triticum turgidum L. var. durum; CWAD) and Canada Western Red Spring; Triticum aestivum L.; CWRS) were examined. The antioxidant activity of wheat phenolics was evaluated using oxygen radical absorbance capacity (ORAC), inhibition of photochemiluminescence (PCL), Rancimat method, inhibition of oxidation of low-density lipoprotein, and DNA. The phenolic composition of wheat extracts was determined using high-performance liquid chromatography. The antioxidant capacity of both pearled grains and byproducts significantly decreased as the degree of pearling increased. Among grains, the unprocessed whole grains demonstrated the highest antioxidant capacity. The byproducts always demonstrated higher antioxidant capacity compared to the pearled grains, regardless of the wheat class. The resultant byproducts from 10-20% pearling possessed the highest antioxidant capacity. Processing of cereals may thus exert a significant effect on their antioxidant activity. The concentration of grain antioxidants is drastically reduced during the refining process. As phenolic compounds are concentrated in the outermost layers, the bran fractions resulting from pearling may be used as a natural source of antioxidants and as value-added products in the preparation of functional food ingredients or for enrichment of certain products.

  10. NMR and molecular dynamics studies of the conformational epitope of the type III group B Streptococcus capsular polysaccharide and derivatives.

    Science.gov (United States)

    Brisson, J R; Uhrinova, S; Woods, R J; van der Zwan, M; Jarrell, H C; Paoletti, L C; Kasper, D L; Jennings, H J

    1997-03-18

    The conformational epitope of the type III group B Streptococcus capsular polysaccharide (GBSP III) exhibits unique properties which can be ascribed to the presence of sialic acid in its structure and the requirement for an extended binding site. By means of NMR and molecular dynamics studies on GBSP III and its fragments, the extended epitope of GBSP III was further defined. The influence of sialic acid on the conformational properties of GBSP III was examined by performing conformational analysis on desialylated GBSP III, which is identical to the polysaccharide of Streptococcus pneumoniae type 14, and also on oxidized and reduced GBSP III. Conformational changes were gauged by 1H and 13C chemical shift analysis, NOE, 1D selective TOCSY-NOESY experiments, J(HH) and J(CH) variations, and NOE of OH resonances. Changes in mobility were examined by 13C T1 and T2 measurements. Unrestrained molecular dynamics simulations with explicit water using the AMBER force field and the GLYCAM parameter set were used to assess static and dynamic conformational models, simulate the observable NMR parameters and calculate helical parameters. GBSP III was found to be capable of forming extended helices. Hence, the length dependence of the conformational epitope could be explained by its location on extended helices within the random coil structure of GBSP III. The interaction of sialic acid with the backbone of the PS was also found to be important in defining the conformational epitope of GBSP III.

  11. Variation and correlation of properties in different grades of maple syrup.

    Science.gov (United States)

    Singh, Amritpal S; Jones, A Maxwell P; Saxena, Praveen K

    2014-03-01

    Thirty five commercial maple syrups from twelve producers in Southern Ontario were evaluated for properties including light transmittance, autofluorescence, density, pH, total soluble solids (TSS), glucose and fructose content, total phenol content, antioxidant potential and mineral content (Mg, Mn, P, Zn, Ca, K, Fe and Pb). A high degree of variability was found in many characteristics, often exceeding an order of magnitude. Syrups were categorized based on light transmission at 560 nm into amber (12), dark (13) and very dark (10) using International Maple Syrup Institute (IMSI) guidelines. No statistical differences were found among grades of syrup for density, pH, TSS, glucose, fructose, total reducing sugars, glucose:fructose ratio, magnesium, manganese or potassium. Darker syrups showed significantly higher autofluorescence, total phenol content, antioxidant potential, phosphorous, calcium and total mineral content. Significant negative correlations of percent transmission with total phenol content, antioxidant potential and total mineral content are reported. Significant positive correlations among total phenol content, antioxidant potential and total mineral content are also described. The results from this study suggest that darker syrups tend to contain more beneficial traits and may be applied in developing functional foods and value added products.

  12. Progress in characterizing the multidimensional color quality properties of white LED light sources

    Science.gov (United States)

    Teunissen, Kees; Hoelen, Christoph

    2016-03-01

    With the introduction of solid state light sources, the variety in emission spectra is almost unlimited. However, the set of standardized parameters to characterize a white LED light source, such as correlated color temperature (CCT) and CIE general color rendering index (Ra), is known to be limited and insufficient for describing perceived differences between light sources. Several characterization methods have been proposed over the past decades, but their contribution to perceived color quality has not always been validated. To gain more insight in the relevant characteristics of the emission spectra for specific applications, we have conducted a perception experiment to rate the attractiveness of three sets of objects, including fresh food, packaging materials and skin tones. The objects were illuminated with seven different combinations of Red, Green, Blue, Amber and White LEDs, all with the same CCT and illumination level, but with differences in Ra and color saturation. The results show that, in general, object attractiveness does not correlate well with Ra, but shows a positive correlation with saturation increase for two out of three applications. There is no clear relation between saturation and skin tone attractiveness, partly due to differences in preference between males and females. A relative gamut area index (Ga) represents the average change in saturation and a complementary color vector graphic shows the direction and magnitude of chromatic differences for the eight CIE-1974 test-color samples. Together with the CIE general color rendering index (Ra) they provide useful information for designing and optimizing application specific emission spectra.

  13. Characterization of four-color multi-package white light-emitting diodes combined with various green monochromatic phosphor-converted light-emitting diodes

    Science.gov (United States)

    Oh, Ji Hye; Lee, Keyong Nam; Do, Young Rag

    2012-03-01

    In this study, several combinations of multi-package white light-emitting diodes (LEDs), which combine an InGaN blue LED with green, amber, and red phosphor-converted LEDs (pc-LEDs), were characterized by changing the peak wavelength of green pc-LEDs between 515nm and 560nm (515, 521, 530, 540, 550, 560nm) in color temperature of 6,500K and 3,500K. Various green monochromatic pc-LEDs were fabricated by capping a long-wave pass-filter (LWPF) on top of pc-LEDs to improve luminous efficacy and color purity. LWPF-capped green monochromatic pc-LED can address the drawback of green semiconductor-type III-V LED, such as low luminous efficacy in the region of green gap wavelength. Luminous efficacy and color rendering index (CRI) of multi-package white LEDs are compared with changing the driving current of individual LED in various multi-package white LEDs. This study provides a best combination of four-color multi-package white LEDs which has high luminous efficacy and good CRI.

  14. Unlocking the early fossil record of the arthropod central nervous system

    Science.gov (United States)

    Edgecombe, Gregory D.; Ma, Xiaoya; Strausfeld, Nicholas J.

    2015-01-01

    Extant panarthropods (euarthropods, onychophorans and tardigrades) are hallmarked by stunning morphological and taxonomic diversity, but their central nervous systems (CNS) are relatively conserved. The timing of divergences of the ground pattern CNS organization of the major panarthropod clades has been poorly constrained because of a scarcity of data from their early fossil record. Although the CNS has been documented in three-dimensional detail in insects from Cenozoic ambers, it is widely assumed that these tissues are too prone to decay to withstand other styles of fossilization or geologically older preservation. However, Cambrian Burgess Shale-type compressions have emerged as sources of fossilized brains and nerve cords. CNS in these Cambrian fossils are preserved as carbon films or as iron oxides/hydroxides after pyrite in association with carbon. Experiments with carcasses compacted in fine-grained sediment depict preservation of neural tissue for a more prolonged temporal window than anticipated by decay experiments in other media. CNS and compound eye characters in exceptionally preserved Cambrian fossils predict divergences of the mandibulate and chelicerate ground patterns by Cambrian Stage 3 (ca 518 Ma), a dating that is compatible with molecular estimates for these splits. PMID:26554038

  15. Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand.

    Science.gov (United States)

    Pang, Yuan-Ping

    2015-02-06

    1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

  16. Pre-main-sequence binaries with tidally disrupted discs: the Br gamma in HD 104237

    CERN Document Server

    Garcia, P J V; Dougados, C; Bacciotti, F; Clausse, J -M; Massi, F; Mérand, A; Petrov, R; Weigelt, G

    2013-01-01

    Active pre-main-sequence binaries with separations of around ten stellar radii present a wealth of phenomena unobserved in common systems. The study of these objects is extended from Classical T Tauri stars to the Herbig Ae star HD 104237. Spectro-interferometry with the VLTI/AMBER is presented. It is found that the K-band continuum squared visibilities are compatible with a circumbinary disc with a radius of ~0.5 AU. However, a significant fraction (~50 per cent) of the flux is unresolved and not fully accounted by the stellar photospheres. The stars probably don't hold circumstellar discs, in addition to the circumbinary disk, due to the combined effects of inner magnetospheric truncation and outer tidal truncation. This unresolved flux likely arises in compact structures inside the tidally disrupted circumbinary disc. Most ($\\gtrsim 90$ per cent) of the Br gamma line emission is unresolved. The line-to-continuum spectro-astrometry shifts in time, along the direction of the Ly alpha jet known to be driven b...

  17. QM/MM studies of cisplatin complexes with DNA dimer and octamer

    KAUST Repository

    Gkionis, Konstantinos

    2012-08-01

    Hybrid QM/MM calculations on adducts of cisplatin with DNA dimer and octamer are reported. Starting from the crystal structure of a cisplatin-DNA dimer complex and an NMR structure of a cisplatin-DNA octamer complex, several variants of the ONIOM approach are tested, all employing BHandH for the QM part and AMBER for MM. We demonstrate that a generic set of molecular mechanics parameters for description of Pt-coordination can be used within the subtractive ONIOM scheme without loss of accuracy, such that dedicated parameters for new platinum complexes may not be required. Comparison of optimised structures obtained with different strategies indicates that electrostatic embedding is vital for proper description of the complex, while inclusion of water molecules as explicit solvent further improves performance. The resulting DNA structural parameters are in good general agreement with the experimental structure obtained, particularly when the inherent variability in NMR-derived parameters is taken into account. © 2012 Elsevier B.V.

  18. Distribution and carbon isotope patterns of diterpenoids and triterpenoids in modern temperate C3 trees and their geochemical significance

    Science.gov (United States)

    Diefendorf, Aaron F.; Freeman, Katherine H.; Wing, Scott L.

    2012-05-01

    Tricyclic diterpenoids and pentacyclic triterpenoids are nearly exclusively produced by gymnosperms and angiosperms, respectively. Even though both classes of terpenoids have long been recognized as plant biomarkers, their potential use as phylogenetically specific δ13C proxies remains largely unexplored. Little is known of how terpenoid abundance and carbon isotope composition vary either with plant phylogenetic position, functional group, or during synthesis. Here, we report terpenoid abundances and isotopic data for 44 tree species in 21 families, representing both angiosperms and gymnosperms, and both deciduous and evergreen leaf habits. Di- and triterpenoid abundances are significantly higher in evergreens compared to deciduous species, reflecting differences in growth strategies and increased chemical investment in longer-lived leaves. Carbon isotope abundances of terpenoid lipids are similar to leaf tissues, indicating biosynthetic isotope effects are small for both the MVA (-0.4‰) and MEP (-0.6‰) pathways. Leaf and molecular isotopic patterns for modern plants are consistent with observations of amber, resins and plant biomarkers in ancient sediments. The δ13C values of ancient diterpenoids are higher than triterpenoids by 2-5‰, consistent with observed isotopic differences between gymnosperms and angiosperms leaves, and support the relatively small lipid biosynthetic effects reported here. All other factors being equal, evergreen plants will dominate the abundance of terpenoids contributed to soils, sediments and ancient archives, with similar inputs estimated for angiosperm and gymnosperm trees when scaled by litter flux.

  19. Long-Proboscid Flies as Pollinators of Cretaceous Gymnosperms.

    Science.gov (United States)

    Peñalver, Enrique; Arillo, Antonio; Pérez-de la Fuente, Ricardo; Riccio, Mark L; Delclòs, Xavier; Barrón, Eduardo; Grimaldi, David A

    2015-07-20

    The great evolutionary success of angiosperms has traditionally been explained, in part, by the partnership of these plants with insect pollinators. The main approach to understanding the origins of this pervasive relationship has been study of the pollinators of living cycads, gnetaleans, and basal angiosperms. Among the most morphologically specialized living pollinators are diverse, long-proboscid flies. Early such flies include the brachyceran family Zhangsolvidae, previously known only as compression fossils from the Early Cretaceous of China and Brazil. It belongs to the infraorder Stratiomyomorpha, a group that includes the flower-visiting families Xylomyidae and Stratiomyidae. New zhangsolvid specimens in amber from Spain (ca. 105 mega-annum [Ma]) and Myanmar (100 Ma) reveal a detailed proboscis structure adapted to nectivory. Pollen clumped on a specimen from Spain is Exesipollenites, attributed to a Mesozoic gymnosperm, most likely the Bennettitales. Late Mesozoic scorpionflies with a long proboscis have been proposed as specialized pollinators of various extinct gymnosperms, but pollen has never been observed on or in their bodies. The new discovery is a very rare co-occurrence of pollen with its insect vector and provides substantiating evidence that other long-proboscid Mesozoic insects were gymnosperm pollinators. Evidence is thus now gathering that visitors and probable pollinators of early anthophytes, or seed plants, involved some insects with highly specialized morphological adaptations, which has consequences for interpreting the reproductive modes of Mesozoic gymnosperms and the significance of insect pollination in angiosperm success.

  20. Effects of the interruption of the irradiation process on PMMA Harwell Industry Dosimetry Systems

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Paulo S.; Vasquez, Pablo A.S., E-mail: psantos@ipen.br, E-mail: pavsalva@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    Nowadays, the use of dyed-polymethylmethacrylate dosimetry systems in measurements at industrial irradiations has been broadly, despite the use of alanine dosimeters. Accurate dosimetry measurements are essential for the sterilization applications of medical products as well as the preservation of food by ionizing radiation. Regulations in many countries require in-plant dosimetry to ensure that the specified radiation dose has been delivered to the product. Harwell commercial dosimeters commonly are built to work with measurements between 1 kGy to 50 kGy, this means that a same dosimeter could be used until reach these values. Radiation processing demands partial measurements of the absorbed dose to guarantee the final desired applied absorbed dose depending to the dose rate. In this sense, the total absorbed dose corresponds to the cumulative partial values. In this study, several dosimeters were irradiated at the Multipurpose Gamma Irradiation Facility at IPEN - CNEN/SP to evaluate the response to the interruption of the irradiation process in the total cumulative absorbed dose values considering statistical changes and some processing parameters. When studied the Harwell dyed-polymethylmethacrylate dosimeters Red 4034 and Amber 3042, applying processing interruptions, results shown a coefficient of variation under 7% for industrial irradiation conditions to the total cumulative absorbed dose. (author)

  1. The Use of Chlorophyll Fluorescence Lifetime to Assess Phytoplankton Physiology within a River-Dominated Environment

    Science.gov (United States)

    Hall, Callie M.; Miller, Richard L.; Redalje, Donald G.; Fernandez, Salvador M.

    2002-01-01

    Chlorophyll a fluorescence lifetime was measured for phytoplankton populations inhabiting the three physical zones surrounding the Mississippi River's terminus in the Gulf of Mexico. Observations of river discharge volume, nitrate + nitrite, silicate, phosphate, PAR (Photosynthetically Active Radiation) diffuse attenuation within the water column, salinity, temperature, SPM, and chl a concentration were used to characterize the distribution of chl fluorescence lifetime within a given region within restricted periods of time. 33 stations extending from the Mississippi River plume to the shelf break of the Louisiana coast were surveyed for analysis of chlorophyll fluorescence lifetime during two cruises conducted March 31 - April 6, 2000, and October 24 - November 1, 2000. At each station, two to three depths were chosen for fluorescence lifetime measurement to represent the vertical characteristics of the water column. Where possible, samples were taken from just below the surface and from just above and below the pycnocline. All samples collected were within the 1% light level of the water column (the euphotic zone). Upon collection, samples were transferred to amber Nalgene bottles and left in the dark for at least 15 minutes to reduce the effects of non-photochemical quenching and to insure that photosynthetic reaction centers were open. Before measurements within the phase fluorometer were begun, the instrument was allowed to warm up for no less than one hour.

  2. Partial hessian fitting for determining force constant parameters in molecular mechanics.

    Science.gov (United States)

    Wang, Ruixing; Ozhgibesov, Mikhail; Hirao, Hajime

    2016-10-01

    We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond-stretching, angle-bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least-squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER-type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM-calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal-organic frameworks, the MM-optimized geometry sometimes deviates significantly from the QM-optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond-stretching and angle-bending terms. © 2016 Wiley Periodicals, Inc.

  3. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xianwei [Center for Optics and Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023 (China); State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); Zhang, John Z. H.; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 (China)

    2015-11-14

    Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

  4. [Microbiological and physicochemical evaluation of pasteurized nectar elaborated with tree tomato (Cyphomandra betaceae Sendth)pulp].

    Science.gov (United States)

    Moreno Alvarez, Mario José; Girán, Nathaly; Serrano, Karla; García, David; Belén Camacho, Douglas R

    2003-09-01

    Tree tomato (Cyphomandra betaceae Sendth) is a species from high tropical regions. In Venezuela, it is cultivate at the Andean and Aragua state but its consumption is restricted as fruit-fresh, though it a nutritious and industrial potential due its provitamin A content. In this research four nectars were elaborated in proportion I L pulp/4 L of water (1:4) and addition of ascorbic acid (I: 0%; II: 0.5%; III: 1.0 y IV: 1.5%). The nectars were pasteurized (60 degrees C for 30 min), tuned into amber bottle, and stored under refrigeration conditions (7.0 +/- 1.0 degrees C). Weekly during 21 days the mesophilic bacteria, molds, yeasts, total coliforms (MPN/mL), pH, degree Brix, acidity, total carotenoids, vitamin C and total sugars were evaluated. The mesophilic bacteria content was 0.05) were founded on: pH. degree Brix and total sugars. Significant differences (P < 0.05) were founded in vitamin C and total carotenoids content. Sensorial analysis did not show significant differences between formulations for the smell and flavor attributes, when the color was discriminate during the evaluations. The formulation I (without acid ascorbic) had more preference due its color. In conclusion, the nectars showed useful life of 14-21 days under refrigeration condition storage due to the adequate physicochemical and microbiological quality of the product.

  5. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

    Science.gov (United States)

    Henriksen, Niel M; Davis, Darrell R; Cheatham, Thomas E

    2012-08-01

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to "update" older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  6. The re-design of a theophylline riboswitch for DNT sensing

    Science.gov (United States)

    Chushak, Yaroslav; Kelley-Loughnane, Nancy; Harbaugh, Svetlana; Stone, Morley

    2008-03-01

    Riboswitches are noncoding elements of mRNA that recognize and bind to small molecules and regulate the translation process of downstream genes. As an initial study, we used a theophylline riboswitch that regulates the expression of the Tobacco etch virus (TEV) protease placed downstream of the switch as a controlling element. Upon expression of TEV protease, an optical reporter is cleaved producing change in fluorescence resonance energy transfer (FRET) between BFP and eGFP. We altered the sensing domain of the original construct to create a synthetic riboswitch that responds to the presence of 2,4-dinitrotoluene (DNT) molecules. Computational analysis using Autodock4 and AMBER9 software packages showed that U24A mutant has a significantly higher binding affinity for DNT molecule compared to the original theophylline. Cells expressing the re-designed riboswitch showed a marked optical difference in fluorescence emission in the presence of DNT molecules, leading to the potential of using this construct in biosentinel applications of highly nitrated compounds.

  7. Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.

    Science.gov (United States)

    Aytenfisu, Asaminew H; Liberman, Joseph A; Wedekind, Joseph E; Mathews, David H

    2015-11-01

    Riboswitches are RNA molecules that regulate gene expression using conformational change, affected by binding of small molecule ligands. A crystal structure of a ligand-bound class II preQ1 riboswitch has been determined in a previous structural study. To gain insight into the dynamics of this riboswitch in solution, eight total molecular dynamic simulations, four with and four without ligand, were performed using the Amber force field. In the presence of ligand, all four of the simulations demonstrated rearranged base pairs at the 3' end, consistent with expected base-pairing from comparative sequence analysis in a prior bioinformatic analysis; this suggests the pairing in this region was altered by crystallization. Additionally, in the absence of ligand, three of the simulations demonstrated similar changes in base-pairing at the ligand binding site. Significantly, although most of the riboswitch architecture remained intact in the respective trajectories, the P3 stem was destabilized in the ligand-free simulations in a way that exposed the Shine-Dalgarno sequence. This work illustrates how destabilization of two major groove base triples can influence a nearby H-type pseudoknot and provides a mechanism for control of gene expression by a fold that is frequently found in bacterial riboswitches.

  8. Shell Bed Identification of Kaliwangu Formation and its Sedimentary Cycle Significance, Sumedang, West Java

    Directory of Open Access Journals (Sweden)

    Aswan Aswan

    2014-07-01

    Full Text Available DOI: 10.17014/ijog.v8i1.151Kaliwangu Formation cropping out around Sumedang area contains mollusk fossils dominated by gastropods and bivalves. In terms of sequence stratigraphy, each sedimentary cycle generally consists of four shell bed types: Early Transgressive Systems Tract (Early TST deposited above an erosional surface or sequence boundary, that is characterized by shell disarticulation, trace fossils, gravelly content, no fossil orientation direction, and concretion at the bottom; Late Transgressive Systems Tract (Late TST identified by articulated (conjoined specimen in its life position, that shows a low level abration and fragmentation, adult specimen with complete shells, and variation of taxa; Early Highstand Systems Tract (Early HST characterized by adult taxa that was found locally in their life position with individual articulation, juvenile specimens frequently occured; Late Highstand Systems Tract (Late HST determined as multiple-event concentrations, disarticulated shell domination, and some carbon or amber intercalation indicating terrestrial influence. Shell bed identification done on this rock unit identified nineteen sedimentary cycles.

  9. Prediction of Peptide Binding to Major Histocompatibility II Receptors with Molecular Mechanics and Semi-Empirical Quantum Mechanics Methods

    Directory of Open Access Journals (Sweden)

    James A Platts

    2012-02-01

    Full Text Available Methods for prediction of the binding of peptides to major histocompatibility complex (MHC II receptors are examined, using literature values of IC50 as a benchmark. Two sets of IC50 data for closely structurally related peptides based on hen egg lysozyme (HEL and myelin basic protein (MBP are reported first. This shows that methods based on both molecular mechanics and semi-empirical quantum mechanics can predict binding with good-to-reasonable accuracy, as long as a suitable method for estimation of solvation effects is included. A more diverse set of 22 peptides bound to HLA-DR1 provides a tougher test of such methods, especially since no crystal structure is available for these peptide-MHC complexes. We therefore use sequence based methods such as SYFPEITHI and SVMHC to generate possible binding poses, using a consensus approach to determine the most likely anchor residues, which are then mapped onto the crystal structure of an unrelated peptide bound to the same receptor. This analysis shows that the MM/GBVI method performs particularly well, as does the AMBER94 forcefield with Born solvation model. Indeed, MM/GBVI can be used as an alternative to sequence based methods in generating binding poses, leading to still better accuracy.

  10. Experimental Study on Behavior of Bow-tie Tree Generation by Using Heavy Water

    Science.gov (United States)

    Kumazawa, Takao; Nakagawa, Wataru; Tsurumaru, Hidekazu

    Bow-tie tree (BTT) generated from contaminant, e.g., metal, carbon, amber(over cured resin) or void in insulator is a significant deterioration factor of XLPE power cable. However, essential role of water in generation and progress of BTT is not yet sufficiently cleared. In order to investigate the role of water we paid attention to difference in chemical properties of light water (H2O) and heavy water (D2O), moreover we evaluated influence of isotopic effect due to hydrogen and deuterium on behavior of BTT generation. In accelerated aging test the number of BTT in XLPE sample, in which copper powder of 500ppm was contaminated as BTT cores, dipped in heavy water (D2O:100wt%) decreased to one third compared with light water(D2O:0wt%). Furthermore, the maximum length of BTT decreased with increase in concentration of heavy water. The experimental results show that heavy water exerted a depression effect on generation and progress of BTT. We considered that the depression effect due to hydrogen isotope appeared by inhibiting ionization and elution of BTT cores, because salt-solubility and ionic mobility of heavy water are about 15 to 20% smaller than those of light water. Therefore, the essential role of water seemed to be production and transport of ions in XLPE.

  11. Influence of Water and Ion Diffusion on Generation and Progress of Bow-tie Tree

    Science.gov (United States)

    Kumazawa, Takao; Nakagawa, Wataru; Tsurumaru, Hidekazu

    Bow-tie tree(BTT) generated from contaminant, e.g., metal, carbon, amber(over cured resin) or void is a deterioration factor of XLPE cable. In particular, BTT in contact with inner or outer semi-conductive shield could significantly lower residual AC breakdown voltage of HV power cable. To evaluate influence of water and ion diffusion on generation and progress of BTT, we investigated relationship between water content of XLPE and the generation of BTT by various accelerated aging. The number of BTT in XLPE samples with accelerated aging under open condition, involving evaporation of water in which samples were immersed, was very large compared with closed condition. Furthermore, when samples were intermittently immersed in water, the number of BTT in samples was large compared with samples immersed continuously. In these experiments the generation of BTT seemed to have nothing to do with changes in water content before and after accelerated aging. Therefore, it was suggested that diffusion of ions rather than water in XLPE played an important role in the generation of BTT.

  12. GROMACS: fast, flexible, and free.

    Science.gov (United States)

    Van Der Spoel, David; Lindahl, Erik; Hess, Berk; Groenhof, Gerrit; Mark, Alan E; Berendsen, Herman J C

    2005-12-01

    This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

  13. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    Science.gov (United States)

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  14. A new Cretaceous family of enigmatic two-winged lacewings (Neuroptera

    Directory of Open Access Journals (Sweden)

    V. N. Makarkin

    2013-02-01

    Full Text Available Lacewings (Neuroptera normally bear four well-developed wings. There are a few brachypterous, micropterous or apterous species, found in several extant families; this wing reduction is usually associated with flightlessness. The only documented fossil neuropteran with reduced hind wings (modified to small haltere-like structures is the enigmatic minute genus Mantispidiptera Grimaldi from the Late Cretaceous amber of New Jersey. In this paper, we report a new genus and species from the Early Cretaceous Yixian Formation of China (Dipteromantispa brevisubcosta n. gen. et n. sp. resembling Mantispidiptera. We place these two genera in the new family Dipteromantispidae, n. fam. They bear well-developed forewings with reduced venation, and hind wings that are extremely modified as small structures resembling the halteres of Diptera. Dipteromantispidae n. fam. might be specialized descendants of some early Berothidae or of stem group Mantispidae + Berothidae. We presume that dipteromantispids were active fliers. This is a remarkable example of parallel evolution of wing structures in this neuropteran family and Diptera. doi:10.1002/mmng.201300002

  15. Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts.

    Science.gov (United States)

    Vea, Isabelle M; Grimaldi, David A

    2016-03-22

    The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228-273], and of the neococcoids 60 million years later [210-165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous.

  16. Stability of aflatoxins in solution.

    Science.gov (United States)

    Diaz, Gonzalo J; Cepeda, Sandra M; Martos, Perry A

    2012-01-01

    The stability of aflatoxins B1, B2, G1, and G2 was studied in solutions containing different concentrations of water, acetonitrile, and/or methanol, and in autosampler vials treated with nitric acid or silanized. When stored at room temperature (20 degrees C) for 24 h, aflatoxins G1 and G2 were stable only in solutions containing 100% organic solvent, whereas aflatoxins B1 and B2 were stable in solutions of methanol-water and acetonitrile-water at greater than 60 and 40% organic content, respectively. At 5 degrees C, aflatoxins G1 and G2 showed a significant decrease in concentration only when kept in less than 20% aqueous organic solvent. Significant loss of aflatoxins was realized in standard, commercially available amber type I borosilicate autosampler vials, but chemical etching of the vials with nitric acid or with silanization prevented aflatoxin degradation. These results indicate that aflatoxins are unstable in aqueous solutions and that this instability can be counteracted by the presence of at least 20% organic solvent and keeping the solutions at 5 degrees C or by the use of treated vials.

  17. Practical procedure for discriminating monofloral honey with a broad pollen profile variability using an electronic tongue.

    Science.gov (United States)

    Sousa, Mara E B C; Dias, Luís G; Veloso, Ana C A; Estevinho, Letícia; Peres, António M; Machado, Adélio A S C

    2014-10-01

    Colour and floral origin are key parameters that may influence the honey market. Monofloral light honey are more demanded by consumers, mainly due to their flavour, being more valuable for producers due to their higher price when compared to darker honey. The latter usually have a high anti-oxidant content that increases their healthy potential. This work showed that it is possible to correctly classify monofloral honey with a high variability in floral origin with a potentiometric electronic tongue after making a preliminary selection of honey according their colours: white, amber and dark honey. The results showed that the device had a very satisfactory sensitivity towards floral origin (Castanea sp., Echium sp., Erica sp., Lavandula sp., Prunus sp. and Rubus sp.), allowing a leave-one-out cross validation correct classification of 100%. Therefore, the E-tongue shows potential to be used at analytical laboratory level for honey samples classification according to market and quality parameters, as a practical tool for ensuring monofloral honey authenticity.

  18. Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study

    Science.gov (United States)

    Thai, Nguyen Quoc; Tseng, Ning-Hsuan; Vu, Mui Thi; Nguyen, Tin Trung; Linh, Huynh Quang; Hu, Chin-Kun; Chen, Yun-Ru; Li, Mai Suan

    2016-08-01

    Combining Lipinski's rule with the docking and steered molecular dynamics simulations and using the PubChem data base of about 1.4 million compounds, we have obtained DNA dyes Hoechst 34580 and Hoechst 33342 as top-leads for the Alzheimer's disease. The binding properties of these ligands to amyloid beta (Aβ) fibril were thoroughly studied by in silico and in vitro experiments. Hoechst 34580 and Hoechst 33342 prefer to locate near hydrophobic regions with binding affinity mainly governed by the van der Waals interaction. By the Thioflavin T assay, it was found that the inhibition constant IC50 ≈ 0.86 and 0.68 μM for Hoechst 34580 and Hoechst 33342, respectively. This result qualitatively agrees with the binding free energy estimated using the molecular mechanic-Poisson Boltzmann surface area method and all-atom simulations with the AMBER-f99SB-ILDN force field and water model TIP3P. In addition, DNA dyes have the high capability to cross the blood brain barrier. Thus, both in silico and in vitro experiments have shown that Hoechst 34580 and 33342 are good candidates for treating the Alzheimer's disease by inhibiting Aβ formation.

  19. Effects of Croton rhamnifolioides essential oil on Aedes aegypti oviposition, larval toxicity and trypsin activity.

    Science.gov (United States)

    Santos, Geanne K N; Dutra, Kamilla A; Lira, Camila S; Lima, Bheatriz N; Napoleão, Thiago H; Paiva, Patrícia M G; Maranhão, Claudia A; Brandão, Sofia S F; Navarro, Daniela M A F

    2014-10-14

    Although numerous reports are available concerning the larvicidal potential of essential oils, very few investigations have focused on their mechanisms of action. In the present study, we have investigated the chemical composition of the leaf oil of Croton rhamnifolioides during storage and its effects on oviposition and survival of larvae of the dengue fever mosquito Aedes aegypti. In addition, we have established a possible mechanism of action for the larvicidal activity of the essential oil. GC-MS analyses revealed marked differences in the composition of oil that had been freshly isolated and that of a sample that had been stored in a sealed amber-glass vial under refrigeration for three years. However, both fresh and stored oil exhibited substantial larvicidal activities with LC50 values of 122.35 and 89.03 ppm, respectively, and oviposition deterrent effects against gravid females at concentrations of 50 and 100 µg·mL-1. These results demonstrate that the larvicidal effect of the essential oil was unchanged during three years of storage even though its chemical composition altered. Hence, the essential oil could be used in the preparation of commercial products. In addition, we observed that the trypsin-like activity of mosquito larvae was inhibited in vitro by the essential oil of C. rhamnifolioides, suggesting that the larvicidal effect may be associated with inhibition of this enzyme.

  20. Optical properties of carbon nanostructures produced by laser irradiation on chemically modified multi-walled carbon nanotubes

    Science.gov (United States)

    Santiago, Enrique Vigueras; López, Susana Hernández; Camacho López, Marco A.; Contreras, Delfino Reyes; Farías-Mancilla, Rurik; Flores-Gallardo, Sergio G.; Hernández-Escobar, Claudia A.; Zaragoza-Contreras, E. Armando

    2016-10-01

    This research focused on the nanosecond (Nd: YAG-1064 nm) laser pulse effect on the optical and morphological properties of chemically modified multi-walled carbon nanotubes (MWCNT). Two suspensions of MWCNT in tetrahydrofuran (THF) were prepared, one was submitted to laser pulses for 10 min while the other (blank) was only mechanically homogenized during the same time. Following the laser irradiation, the suspension acquired a yellow-amber color, in contrast to the black translucent appearance of the blank. UV-vis spectroscopy confirmed this observation, showing the blank a higher absorption. Additionally, photoluminescence measurements exhibited a broad blue-green emission band both in the blank and irradiated suspension when excited at 369 nm, showing the blank a lower intensity. However, a modification in the excitation wavelength produced a violet to green tuning in the irradiated suspension, which did not occur in the blank. Lastly, the electron microscopy analysis of the treated nanotubes showed the abundant formation of amorphous carbon, nanocages, and nanotube unzipping, exhibiting the intense surface modification produced by the laser pulse. Nanotube surface modification and the coexistence with the new carbon nanostructures were considered as the conductive conditions for optical properties modification.