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Sample records for abundant functional groups

  1. Differential Abundance of Microbial Functional Groups along the Elevation Gradient from the Coast to the Luquillo Mountains

    EPA Science Inventory

    Microbial communities respond to multiple abiotic and biotic factors that change along elevation gradients. We compare changes in microbial community composition in soil and review previous research on differential abundance of microbial functional groups along an elevation gradi...

  2. Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

    PubMed

    Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

    2016-01-01

    Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally

  3. A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries

    PubMed Central

    Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

    2014-01-01

    The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm−2). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance. PMID:25366060

  4. A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries

    NASA Astrophysics Data System (ADS)

    Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

    2014-11-01

    The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm-2). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance.

  5. THE ABUNDANCES OF HYDROCARBON FUNCTIONAL GROUPS IN THE INTERSTELLAR MEDIUM INFERRED FROM LABORATORY SPECTRA OF HYDROGENATED AND METHYLATED POLYCYCLIC AROMATIC HYDROCARBONS

    SciTech Connect

    Steglich, M.; Jäger, C.; Huisken, F.; Friedrich, M.; Plass, W.; Räder, H.-J.; Müllen, K.; Henning, Th.

    2013-10-01

    Infrared (IR) absorption spectra of individual polycyclic aromatic hydrocarbons (PAHs) containing methyl (-CH{sub 3}), methylene (CH{sub 2}), or diamond-like CH groups and IR spectra of mixtures of methylated and hydrogenated PAHs prepared by gas-phase condensation were measured at room temperature (as grains in pellets) and at low temperature (isolated in Ne matrices). In addition, the PAH blends were subjected to an in-depth molecular structure analysis by means of high-performance liquid chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Supported by calculations at the density functional theory level, the laboratory results were applied to analyze in detail the aliphatic absorption complex of the diffuse interstellar medium at 3.4 μm and to determine the abundances of hydrocarbon functional groups. Assuming that the PAHs are mainly locked in grains, aliphatic CH {sub x} groups (x = 1, 2, 3) would contribute approximately in equal quantities to the 3.4 μm feature (N {sub CHx}/N {sub H} ≈ 10{sup –5}-2 × 10{sup –5}). The abundances, however, may be two to four times lower if a major contribution to the 3.4 μm feature comes from molecules in the gas phase. Aromatic ≅CH groups seem to be almost absent from some lines of sight, but can be nearly as abundant as each of the aliphatic components in other directions (N{sub ≅CH}/N {sub H} ∼< 2 × 10{sup –5}; upper value for grains). Due to comparatively low binding energies, astronomical IR emission sources do not display such heavy excess hydrogenation. At best, especially in protoplanetary nebulae, CH{sub 2} groups bound to aromatic molecules, i.e., excess hydrogens on the molecular periphery only, can survive the presence of a nearby star.

  6. The Abundances of Hydrocarbon Functional Groups in the Interstellar Medium Inferred from Laboratory Spectra of Hydrogenated and Methylated Polycyclic Aromatic Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Steglich, M.; Jäger, C.; Huisken, F.; Friedrich, M.; Plass, W.; Räder, H.-J.; Müllen, K.; Henning, Th.

    2013-10-01

    Infrared (IR) absorption spectra of individual polycyclic aromatic hydrocarbons (PAHs) containing methyl (\\sbondCH3), methylene (\\protect{\\epsfbox{art/apjs484229un01.eps}}CH2), or diamond-like \\protect{\\epsfbox{art/apjs484229un02.eps}}CH groups and IR spectra of mixtures of methylated and hydrogenated PAHs prepared by gas-phase condensation were measured at room temperature (as grains in pellets) and at low temperature (isolated in Ne matrices). In addition, the PAH blends were subjected to an in-depth molecular structure analysis by means of high-performance liquid chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Supported by calculations at the density functional theory level, the laboratory results were applied to analyze in detail the aliphatic absorption complex of the diffuse interstellar medium at 3.4 μm and to determine the abundances of hydrocarbon functional groups. Assuming that the PAHs are mainly locked in grains, aliphatic CH x groups (x = 1, 2, 3) would contribute approximately in equal quantities to the 3.4 μm feature (N CHx /N H ≈ 10-5-2 × 10-5). The abundances, however, may be two to four times lower if a major contribution to the 3.4 μm feature comes from molecules in the gas phase. Aromatic \\epsfbox{art/apjs484229un03.eps} CH groups seem to be almost absent from some lines of sight, but can be nearly as abundant as each of the aliphatic components in other directions (N_{\\epsfbox{art/apjs484229un03.eps} CH}/N H lsim 2 × 10-5 upper value for grains). Due to comparatively low binding energies, astronomical IR emission sources do not display such heavy excess hydrogenation. At best, especially in protoplanetary nebulae, \\protect{\\epsfbox{art/apjs484229un01.eps}}CH2 groups bound to aromatic molecules, i.e., excess hydrogens on the molecular periphery only, can survive the presence of a nearby star.

  7. Model-measurement comparison of functional group abundance in α-pinene and 1,3,5-trimethylbenzene secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Ruggeri, Giulia; Bernhard, Fabian A.; Henderson, Barron H.; Takahama, Satoshi

    2016-07-01

    Secondary organic aerosol (SOA) formed by α-pinene and 1,3,5-trimethylbenzene photooxidation under different NOx regimes is simulated using the Master Chemical Mechanism v3.2 (MCM) coupled with an absorptive gas-particle partitioning module. Vapor pressures for individual compounds are estimated with the SIMPOL.1 group contribution model for determining apportionment of reaction products to each phase. We apply chemoinformatic tools to harvest functional group (FG) composition from the simulations and estimate their contributions to the overall oxygen to carbon ratio. Furthermore, we compare FG abundances in simulated SOA to measurements of FGs reported in previous chamber studies using Fourier transform infrared spectroscopy. These simulations qualitatively capture the dynamics of FG composition of SOA formed from both α-pinene and 1,3,5-trimethylbenzene in low-NOx conditions, especially in the first hours after start of photooxidation. Higher discrepancies are found after several hours of simulation; the nature of these discrepancies indicates sources of uncertainty or types of reactions in the condensed or gas phase missing from current model implementation. Higher discrepancies are found in the case of α-pinene photooxidation under different NOx concentration regimes, which are reasoned through the domination by a few polyfunctional compounds that disproportionately impact the simulated FG abundance in the aerosol phase. This manuscript illustrates the usefulness of FG analysis to complement existing methods for model-measurement evaluation.

  8. Remote sensing data to classify functional groups of vegetation and their distribution and abundance in a semiarid mountain watershed, Idaho, USA

    NASA Astrophysics Data System (ADS)

    Loughridge, R. E.; Benner, S. G.; McNamara, J. P.; Flores, A. N.

    2012-12-01

    In water-limited montane ecosystems, topography is a significant driver of energy balance and soil moisture and therefore governs the distribution and abundance of terrestrial vegetation. Few studies have made a concerted effort to quantify spatial patterns in vegetation along physiographic gradients that control microclimate such as slope, elevation, and aspect. Furthermore, spectral mixing of different vegetation species within individual visible and near-infrared remote sensing pixels makes it difficult to constrain the temporal growth and senescence of individual plant functional types. We report on a study that seeks to understand the interacting roles of topography, soil moisture, and solar radiation on the distribution of different plant functional types within the Dry Creek Experimental Watershed (DCEW). Boise State University maintains the 27 km2 watershed which is located in the Boise Front Mountains of southwest Idaho. It is qualitatively observed in DCEW that low elevations are dominated by sage-steppe ecosystems and high elevations transition to conifer forests. It is also observed that aspect has a major control in which sage-steppe is evident at high elevations on south facing slopes conversely from north facing slopes. To quantify these trends we measured percent ground cover of functional groups (i.e. forbs, grass, shrubs, etc.) at 77 sites within DCEW spanning a large gradient in the controlling biophysiographic variables. In addition, vegetation water content (VWC) and spectral reflectance from the 325 to 1075 nm wavelengths was collected for specific vegetation types at eight permanent soil moisture monitoring sites contained in DCEW throughout the 2012 green-up/senescence transition. To develop a watershed-wide classification we built a supervised multilayer perceptron (MLP) backpropagating artificial neural network (ANN) using temporal Landsat 5 images to classify 4 major groups: sage-steppe, Douglas fir, ponderosa pine, and deciduous trees

  9. Chemical abundances of massive stars in Local Group galaxies

    NASA Astrophysics Data System (ADS)

    Venn, Kim A.; Kaufer, Andreas; Tolstoy, Eline; Kudritzki, Rolf-Peter; Przybilla, Norbert; Smartt, Stephen J.; Lennon, Daniel J.

    The relative abundances of elements in galaxies can provide valuable information on the stellar and chemical evolution of a galaxy. While nebulae can provide abundances for a variety of light elements, stars are the only way to directly determine the abundances of iron-group and s-process and r-process elements in a galaxy. The new 8m and 10m class telescopes and high-efficiency spectrographs now make high-quality spectral observations of bright supergiants possible in dwarf galaxies in the Local Group. We have been concentrating on elemental abundances in the metal-poor dwarf irregular galaxies, NGC 6822, WLM, Sextants A, and GR 8. Comparing abundance ratios to those predicted from their star formation histories, determined from color-magnitude diagrams, and comparing those ratios between these galaxies can give us new insights into the evolution of these dwarf irregular galaxies. Iron-group abundances also allow us to examine the metallicities of the stars in these galaxies directly, which affects their inferred mass loss rates and predicted stellar evolution properties.

  10. Renormalization group functional equations

    SciTech Connect

    Curtright, Thomas L.; Zachos, Cosmas K.

    2011-03-15

    Functional conjugation methods are used to analyze the global structure of various renormalization group trajectories and to gain insight into the interplay between continuous and discrete rescaling. With minimal assumptions, the methods produce continuous flows from step-scaling {sigma} functions and lead to exact functional relations for the local flow {beta} functions, whose solutions may have novel, exotic features, including multiple branches. As a result, fixed points of {sigma} are sometimes not true fixed points under continuous changes in scale and zeroes of {beta} do not necessarily signal fixed points of the flow but instead may only indicate turning points of the trajectories.

  11. Comparing Amino Acid Abundances and Distributions Across Carbonaceous Chondrite Groups

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Callahan, Michael P.; Glavin, Daniel P.; Elsila, Jamie E.; Dworkin, Jason P.

    2012-01-01

    Meteorites are grouped according to bulk properties such as chemical composition and mineralogy. These parameters can vary significantly among the different carbonaceous chondrite groups (CI, CM, CO, CR, CH, CB, CV and CK). We have determined the amino acid abundances of more than 30 primary amino acids in meteorites from each of the eight groups, revealing several interesting trends. There are noticeable differences in the structural diversity and overall abundances of amino acids between meteorites from the different chondrite groups. Because meteorites may have been an important source of amino acids to the prebiotic Earth and these organic compounds are essential for life as we know it, the observed variations of these molecules may have been important for the origins of life.

  12. Lead and uranium group abundances in cosmic rays

    NASA Technical Reports Server (NTRS)

    Yadav, J. S.; Perelygin, V. P.

    1985-01-01

    The importance of Lead and Uranium group abundances in cosmic rays is discussed in understanding their evolution and propagation. The electronic detectors can provide good charge resolution but poor data statistics. The plastic detectors can provide somewhat better statistics but charge resolution deteriorates. The extraterrestrial crystals can provide good statistics but with poor charge resolution. Recent studies of extraterrestrial crystals regarding their calibration to accelerated uranium ion beam and track etch kinetics are discussed. It is hoped that a charge resolution of two charge units can be achieved provided an additional parameter is taken into account. The prospects to study abundances of Lead group, Uranium group and superheavy element in extraterrestrial crystals are discussed, and usefulness of these studies in the light of studies with electronic and plastic detectors is assessed.

  13. Functional Group Analysis.

    ERIC Educational Resources Information Center

    Smith, Walter T., Jr.; Patterson, John M.

    1984-01-01

    Literature on analytical methods related to the functional groups of 17 chemical compounds is reviewed. These compounds include acids, acid azides, alcohols, aldehydes, ketones, amino acids, aromatic hydrocarbons, carbodiimides, carbohydrates, ethers, nitro compounds, nitrosamines, organometallic compounds, peroxides, phenols, silicon compounds,…

  14. SPECTROSCOPIC ABUNDANCES AND MEMBERSHIP IN THE WOLF 630 MOVING GROUP

    SciTech Connect

    Bubar, Eric J.; King, Jeremy R. E-mail: jking2@ces.clemson.ed

    2010-08-15

    The concept of kinematic assemblages evolving from dispersed stellar clusters has remained contentious since Eggen's initial formulation of moving groups in the 1960s. With high-quality parallaxes from the Hipparcos space astrometry mission, distance measurements for thousands of nearby, seemingly isolated stars are currently available. With these distances, a high-resolution spectroscopic abundance analysis can be brought to bear on the alleged members of these moving groups. If a structure is a relic of an open cluster, the members can be expected to be monolithic in age and abundance in as much as homogeneity is observed in young open clusters. In this work, we have examined 34 putative members of the proposed Wolf 630 moving group using high-resolution stellar spectroscopy. The stars of the sample have been chemically tagged to determine abundance homogeneity and confirm the existence of a homogeneous subsample of 19 stars. Fitting the homogeneous subsample with Yale-Yonsei isochrones yields a single evolutionary sequence of {approx}2.7 {+-} 0.5 Gyr. It is concluded that this 19 star subsample of the Wolf 630 moving group sample of 34 stars could represent a dispersed cluster with an ([Fe/H]) = -0.01 {+-} 0.02 and an age of 2.7 {+-} 0.5 Gyr. In addition, chemical abundances of Na and Al in giants are examined for indications of enhancements as observed in field giants of old open clusters; overexcitation/ionization effects are explored in the cooler dwarfs of the sample; and oxygen is derived from the infrared triplet and the forbidden line at {lambda}6300.

  15. Functional group analysis

    SciTech Connect

    Smith, W.T. Jr.; Patterson, J.M.

    1986-04-01

    Analytical methods for functional group analysis are reviewed. Literature reviewed is from the period of December 1983 through November 1985 and presents methods for determining the following compounds: acids, acid halides, active hydrogen, alcohols, aldehydes, ketones, amides, amines, amino acids, anhydrides, aromatic hydrocarbons, azo compounds, carbohydrates, chloramines, esters, ethers, halogen compounds, hydrazines, isothiocyanates, nitro compounds, nitroso compounds, organometallic compounds, oxiranes, peroxides, phenols, phosphorus compounds, quinones, silicon compounds, sulfates, sulfonyl chlorides, thioamides, thiols, and thiosemicarbazones. 150 references.

  16. Cluster functional renormalization group

    NASA Astrophysics Data System (ADS)

    Reuther, Johannes; Thomale, Ronny

    2014-01-01

    Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.

  17. Environmental distribution, abundance and activity of the Miscellaneous Crenarchaeotal Group

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.; Biddle, J.; Teske, A.

    2011-12-01

    Many marine sedimentary microbes have only been identified by 16S rRNA sequences. Consequently, little is known about the types of metabolism, activity levels, or relative abundance of these groups in marine sediments. We found that one of these uncultured groups, called the Miscellaneous Crenarchaeotal Group (MCG), dominated clone libraries made from reverse transcribed 16S rRNA, and 454 pyrosequenced 16S rRNA genes, in the White Oak River estuary. Primers suitable for quantitative PCR were developed for MCG and used to show that 16S rRNA DNA copy numbers from MCG account for nearly all the archaeal 16S rRNA genes present. RT-qPCR shows much less MCG rRNA than total archaeal rRNA, but comparisons of different primers for each group suggest bias in the RNA-based work relative to the DNA-based work. There is no evidence of a population shift with depth below the sulfate-methane transition zone, suggesting that the metabolism of MCG may not be tied to sulfur or methane cycles. We classified 2,771 new sequences within the SSU Silva 106 database that, along with the classified sequences in the Silva database was used to make an MCG database of 4,646 sequences that allowed us to increase the named subgroups of MCG from 7 to 19. Percent terrestrial sequences in each subgroup is positively correlated with percent of the marine sequences that are nearshore, suggesting that membership in the different subgroups is not random, but dictated by environmental selective pressures. Given their high phylogenetic diversity, ubiquitous distribution in anoxic environments, and high DNA copy number relative to total archaea, members of MCG are most likely anaerobic heterotrophs who are integral to the post-depositional marine carbon cycle.

  18. Functional Group Analysis.

    ERIC Educational Resources Information Center

    Smith, Walter T., Jr.; Patterson, John M.

    1980-01-01

    Discusses analytical methods selected from current research articles. Groups information by topics of general interest, including acids, aldehydes and ketones, nitro compounds, phenols, and thiols. Cites 97 references. (CS)

  19. THE ABUNDANCE OF BULLET GROUPS IN ΛCDM

    SciTech Connect

    Fernández-Trincado, J. G.; Forero-Romero, J. E.; Foex, G.; Motta, V.; Verdugo, T. E-mail: je.forero@uniandes.edu.co

    2014-06-01

    We estimate the expected distribution of displacements between the two dominant dark matter (DM) peaks (DM-DM displacements) and between the DM and gaseous baryon peak (DM-gas displacements) in DM halos with masses larger than 10{sup 13} h {sup –1} M {sub ☉}. As a benchmark, we use the observation of SL2S J08544–0121, which is the lowest mass system (1.0 × 10{sup 14} h {sup –1} M {sub ☉}) observed so far, featuring a bi-modal DM distribution with a dislocated gas component. We find that (50 ± 10)% of the DM halos with circular velocities in the range 300-700 km s{sup –1} (groups) show DM-DM displacements equal to or larger than 186 ± 30 h {sup –1} kpc as observed in SL2S J08544–0121. For DM halos with circular velocities larger than 700 km s{sup –1} (clusters) this fraction rises to (70 ± 10)%. Using the same simulation, we estimate the DM-gas displacements and find that 0.1%-1.0% of the groups should present separations equal to or larger than 87 ± 14 h {sup –1} kpc, corresponding to our observational benchmark; for clusters, this fraction rises to (7 ± 3)%, consistent with previous studies of DM to baryon separations. Considering both constraints on the DM-DM and DM-gas displacements, we find that the number density of groups similar to SL2S J08544–0121 is ∼6.0 × 10{sup –7} Mpc{sup –3}, three times larger than the estimated value for clusters. These results open up the possibility for a new statistical test of ΛCDM by looking for DM-gas displacements in low mass clusters and groups.

  20. Iron-group Abundances in the Metal-poor Main-Sequence Turnoff Star HD~84937

    NASA Astrophysics Data System (ADS)

    Sneden, Christopher; Cowan, John J.; Kobayashi, Chiaki; Pignatari, Marco; Lawler, James E.; Den Hartog, Elizabeth A.; Wood, Michael P.

    2016-01-01

    We have derived new, very accurate abundances of the Fe-group elements Sc through Zn (Z = 21-30) in the bright main-sequence turnoff star HD 84937 based on high-resolution spectra covering the visible and ultraviolet spectral regions. New or recent laboratory transition data for 14 species of seven elements have been used. Abundances from more than 600 lines of non-Fe species have been combined with about 550 Fe lines in HD 84937 to yield abundance ratios of high precision. The abundances have been determined from both neutral and ionized transitions, which generally are in agreement with each other. We find no substantial departures from the standard LTE Saha ionization balance in this [Fe/H] = -2.32 star. Noteworthy among the abundances are [Co/Fe] = +0.14 and [Cu/Fe] = -0.83, in agreement with past studies of abundance trends in this and other low-metallicity stars, and < [{{Sc,Ti,V/Fe}}]> = +0.31, which has not been noted previously. A detailed examination of scandium, titanium, and vanadium abundances in large-sample spectroscopic surveys reveals that they are positively correlated in stars with [Fe/H] < -2 HD 84937 lies at the high end of this correlation. These trends constrain the synthesis mechanisms of Fe-group elements. We also examine the Galactic chemical evolution abundance trends of the Fe-group elements, including a new nucleosynthesis model with jet-like explosion effects.

  1. Potential environmental functions of widespread, abundant, uncultured marine archaea

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.; Schreiber, L.; Petersen, D. G.; Schramm, A.; Jorgensen, B.

    2012-12-01

    The vast majority of marine subsurface microorganisms are uncultivated, and therefore have unknown metabolisms. Much of the prokaryotes present in the marine subsurface are archaea, and, in turn, much of the archaea fall into the Miscellaneous Crenarchaeotal Group. These organisms are widely distributed globally and are phylogenetically diverse, comprising 17 distinct subgroups, defined by 16S rRNA genes (Kubo et al. 2012). The subgroups do not seem to have any well-defined environmental distribution (i.e., they are all present in different types of marine and terrestrial environments). However, the abundance of sequences from a certain environment type differs among subgroups, and may provide clues to their role in these environments. We sequenced the genome of a single cell of MCG extracted directly from marine sediments. Although coverage was low (~30%), the data quality was high. Conserved genes show that MCG is deeply branching within the newly named "Thaumarchaeota", and contains a complete pathway for the degradation or extracellular proteins. A further search through metagenomic data shows that this process may be widespread in marine sediments. We hypothesize that MCG archaea may be important in anaerobic protein decomposition in marine sediments. Reference Kubo et al., 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments. ISME Journal, in press, doi:10.1038/ismej.2012.37.

  2. Learning the Functional Groups: Keys to Success.

    ERIC Educational Resources Information Center

    Byrd, Shannon; Hildreth, David P.

    2001-01-01

    Points out the difficulties students have when they are expected to learn functional groups, which are frameworks for chemical and physical properties of molecules. Presents a classification key for functional groups categorized by 10 common functional groups. (YDS)

  3. Measurements of the Fe-group abundance in energetic solar particles

    NASA Technical Reports Server (NTRS)

    Bertsch, D. L.; Fichtel, C. E.; Pellerin, C. J.; Reames, D. V.

    1972-01-01

    The abundance of Fe-group nuclei in the energetic solar particles was measured twice in the 24 January 1971 event and once in the 2 September 1971 event. Including earlier results from the 2 September 1966 event, the Fe-group abundance was found to be in the range from 3% to 6% of the oxygen nuclei in the energy interval from 21 to 50 MeV/nucleon, in those events where the Fe-group abundance could be measured. Fe-nuclei have a different charge-to-mass ratio from that of the C, N, O nuclei, so small variations in the Fe abundance in solar particles are expected. In the three exposures where the statistics were adequate to construct an energy spectrum, the Fe-group nuclei were seen to have an energy/nucleon spectrum similar to that of the C, N, O nuclei; however, the energy/nucleon range was limited. The abundance for the Fe-group nuclei is consistent with the present solar spectroscopic abundance estimates.

  4. Radial pulsation as a function of hydrogen abundance

    NASA Astrophysics Data System (ADS)

    Jeffery, C. S.; Saio, H.

    2016-05-01

    Using linear non-adiabatic pulsation analysis, we explore the radial-mode (p-mode) stability of stars across a wide range of mass (0.2 ≤ M ≤ 50{ M_{{⊙}}}), composition (0 ≤ X ≤ 0.7, Z = 0.001, 0.02), effective temperature (3000 ≤ Teff ≤ 40 000 K), and luminosity (0.01 ≤ L/M ≤ 100 000 solar units). We identify the instability boundaries associated with low- to high-order radial oscillations (0 ≤ n ≤ 16). The instability boundaries are a strong function of both composition and radial order (n). With decreasing hydrogen abundance we find that (i) the classical blue edge of the Cepheid instability strip shifts to higher effective temperature and luminosity, and (ii) high-order modes are more easily excited and small islands of high radial-order instability develop, some of which correspond with real stars. Driving in all cases is by the classical κ-mechanism and/or strange modes. We identify regions of parameter space where new classes of pulsating variable may, in future, be discovered. The majority of these are associated with reduced hydrogen abundance in the envelope; one has not been identified previously.

  5. CHEMICAL ABUNDANCES OF SEVEN IRREGULAR AND THREE TIDAL DWARF GALAXIES IN THE M81 GROUP

    SciTech Connect

    Croxall, Kevin V.; Van Zee, Liese; Lee, Henry; Miller, Bryan W.; Skillman, Evan D.; Lee, Janice C.; Cote, Stephanie; Kennicutt, Robert C. E-mail: vanzee@astro.indiana.ed E-mail: skillman@astro.umn.ed E-mail: stephanie.cote@nrc-cnrc.gc.c E-mail: bmiller@gemini.ed

    2009-11-01

    We have derived nebular abundances for 10 dwarf galaxies belonging to the M81 Group, including several galaxies which do not have abundances previously reported in the literature. For each galaxy, multiple H II regions were observed with GMOS-N at the Gemini Observatory in order to determine abundances of several elements (oxygen, nitrogen, sulfur, neon, and argon). For seven galaxies, at least one H II region had a detection of the temperature sensitive [O III] lambda4363 line, allowing a 'direct' determination of the oxygen abundance. No abundance gradients were detected in the targeted galaxies, and the observed oxygen abundances are typically in agreement with the well-known metallicity-luminosity relation. However, three candidate 'tidal dwarf' galaxies lie well off this relation: UGC 5336, Garland, and KDG 61. The nature of these systems suggests that UGC 5336 and Garland are indeed recently formed systems, whereas KDG 61 is most likely a dwarf spheroidal galaxy which lies along the same line of sight as the M81 tidal debris field. We propose that these H II regions formed from previously enriched gas which was stripped from nearby massive galaxies (e.g., NGC 3077 and M81) during a recent tidal interaction.

  6. Fe-Group Elements in the Metal-Poor Star HD 84937: Abundances and their Implications

    NASA Astrophysics Data System (ADS)

    Sneden, Chris; Cowan, John J.; Kobayashi, Chiaki; Pignatari, Marco; Lawler, James E.; Den Hartog, Elizabeth; Wood, Michael P.

    2016-01-01

    We have derived accurate relative abundances of the Fe-group elements Sc through Zn in the very metal-poor main-sequence turnoff star HD 84937. For this study we analyzed high resolution, high signal-to-noise HST/STIS and VLT/UVES spectra over a total wavelength range 2300-7000 Å. We employed only recent or newly-applied reliable laboratory transition data for all species. Abundances from more than 600 lines of non-Fe species were combined with about 550 Fe lines in HD 84937 to yield abundance ratios of high precision. From parallel analyses of solar photospheric spectra we also derived new solar abundances of these elements. This in turn yielded internally-consistent relative HD 84937 abundances with respect to the Sun. For seven of the ten Fe-group elements the HD 84937 abundances were from both neutral and ionized transitions. In all of these cases the neutral and ionized species yield the same abundances within the measurement uncertainties. Therefore standard Saha ionization balance appears to hold in the HD 84937 atmosphere. We derived metallicity [Fe/H] = -2.32 with sample standard deviation of 0.06. Solid evidence is seen for departures from the solar abundance mix in HD 84937, for example [Co/Fe] = +0.14, [Cu/Fe] = -0.83, and <[Sc,Ti,V/Fe]> = +0.31. Combining our Sc, Ti, and V abundances for this star with those from large-sample spectroscopic surveys suggests that these elements are positively correlated in stars with [Fe/H] < -2. HD 84937 is unusually enriched in Sc, Ti, and V. Our analysis strongly suggests that different types of supernovae with a large scatter of explosion energies and asymmetries contributed to the creation of the Fe-group elements early in the Galaxy's history.This work has been supported in part by NASA grant NNX10AN93G (J.E.L.), by NSF grants AST-1211055 (J.E.L.), AST-1211585 (C.S.), PHY-1430152 (through JINA, J.J.C. and M.P.), EU MIRGCT-2006-046520 (M.P.), and by the ``Lendlet-2014'' Programme of the Hungarian Academy of

  7. Functional group diversity in dendrimers.

    PubMed

    Sivanandan, Kulandaivelu; Vutukuri, Dharmarao; Thayumanavan, S

    2002-10-17

    [structure: see text] A methodology for synthesizing dendrons with different peripheral functionalities is described. The benzyl ether-based dendrons reported here were synthesized using allyl and methoxymethyl ether-based protection-deprotection strategies.

  8. DISTINCTIVE LOCALIZATION OF GROUP 3 LATE EMBRYOGENESIS ABUNDANT SYNTHESIZING CELLS DURING BRINE SHRIMP DEVELOPMENT.

    PubMed

    Kim, Bo Yong; Song, Hwa Young; Kim, Mi Young; Lee, Bong Hee; Kim, Kyung Joo; Jo, Kyung Jin; Kim, Suhng Wook; Lee, Seung Gwan; Lee, Boo Hyung

    2015-07-01

    Despite numerous studies on late embryogenesis abundant (LEA) proteins, their functions, roles, and localizations during developmental stages in arthropods remain unknown. LEA proteins protect crucial proteins against osmotic stress during the development and growth of various organisms. Thus, in this study, fluorescence in situ hybridization was used to determine the crucial regions protected against osmotic stress as well as the distinctive localization of group 3 (G3) LEA(+) cells during brine shrimp development. Several cell types were found to synthesize G3 LEA RNA, including neurons, muscular cells, APH-1(+) cells, and renal cells. The G3 LEA(+) neuronal cell bodies outside of the mushroom body projected their axonal bundles to the central body, but those inside the mushroom body projected their axonal bundles toward the deutocerebrum without innervating the central body. The cell bodies inside the mushroom body received axons of the G3 LEA(+) sensory cells at the medial ventral cup of the nauplius eye. Several glands were found to synthesize G3 LEA RNA during the nauplius stages of brine shrimp, including the sinus, antennal I and II, salt, and three ectodermal glands. This study provides the first demonstration of the formation of G3 LEA(+) sinus glands at the emergence stages of brine shrimp. These results suggest that G3 LEA protein is synthesized in several cell types. In particular, specific glands play crucial roles during the emergence and nauplius stages of brine shrimp. PMID:25781424

  9. A Functional Analytic Approach to Group Psychotherapy

    ERIC Educational Resources Information Center

    Vandenberghe, Luc

    2009-01-01

    This article provides a particular view on the use of Functional Analytical Psychotherapy (FAP) in a group therapy format. This view is based on the author's experiences as a supervisor of Functional Analytical Psychotherapy Groups, including groups for women with depression and groups for chronic pain patients. The contexts in which this approach…

  10. Population Signatures in Planetary Nebulae from Abundances of Fe-group and Neutron-Capture Elements

    NASA Astrophysics Data System (ADS)

    Dinerstein, Harriet L.; Geballe, Thomas R.; Sterling, N. C.

    2015-08-01

    There are two categories of elements for which abundances are measured in planetary nebulae (PNe). The first are species whose abundances may be modified by nuclear reactions in the star prior to PN formation, such as He, C, N, and nuclei made by slow neutron captures (Karakas & Lattanzio 2014, PASA, 31, 30). In contrast, elements unaffected by evolution should indicate the star’s initial composition. These include S, Ar, Cl, and (with certain exceptions) O and Ne, most of which are alpha species. A long-missing piece of the puzzle has been the abundances of the Fe-group elements. We cannot determine a meaningful elemental abundance from the gas-phase Fe lines seen in PNe, since Fe is heavily depleted into dust. Another approach is to use a different element as a proxy for Fe. Dinerstein & Geballe (2001, ApJ, 562, 515) identified a line at 3.625 μm as due to Zn, the least refractory Fe-group element. Observations of this line in Milky Way PNe yield -1 ≤ [Zn/H] ≤ 0 (Smith, Zijlstra, & Dinerstein 2014, MNRAS, 441, 3161; Dinerstein et al. 2015, in preparation). Substituting Zn for Fe, PNe can be placed in the [alpha/Fe] vs. [Fe/H] diagram used to characterize stellar populations. Dividing our sample into probable thin and thick disk members using the kinematic criterion of Peimbert’s Type II and III classes (1978, IAU Symp. 76, 215), we find that they occupy similar regions in [alpha/Fe] vs. [Fe/H] phase space as the stars of those populations. Elevated [alpha/Fe] values at subsolar [Fe/H], which tend to be higher for thick than thin disk PNe, cause degeneracies that make alpha species ambiguous metallicity indicators. This is important for self-enrichment studies, since if the initial abundance of an element is lower than projected from an alpha species, internal synthesis may be required to produce even a solar final abundance. Low observed abundances of the n-capture element Se suggest that many Type III PNe may have subsolar initial abundances of n

  11. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

    PubMed Central

    Kubo, Kyoko; Lloyd, Karen G; F Biddle, Jennifer; Amann, Rudolf; Teske, Andreas; Knittel, Katrin

    2012-01-01

    Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes. PMID:22551871

  12. The Measurement of Iron-Group Isotopic Abundances in the Cosmic Rays Using the Magpie Detector

    NASA Astrophysics Data System (ADS)

    Yanasak, Nathan Eugene

    This thesis details the analysis of data from the MAGPIE detector, a balloon-borne detector designed to measure cosmic ray isotope abundances between 300 and 900 MeV/a μ in the Fe group. MAGPIE consists of a magnetic spectrometer for measuring particle rigidity, and nine stacks of CR-39 plastic nuclear track detectors for measuring charge and velocity. After an Antarctic flight in December of 1991 during which ~2000 Fe nuclei were collected, damage occurred to the spectrometer during the landing of the balloon payload, limiting the analysis to cosmic ray particles that stop in the plastic stack. This limited the energy range of data to between 100 MeV/a μ and 400 MeV/a μ for Fe group elements. The measurement of Fe group isotopes is an important one. Because nuclei from this group have the highest binding energy of all the elements, they represent the primary products during late stellar nucleosynthesis. This characteristic makes Fe group isotopes unique in their ability to probe the interior environment during the final stages of stellar evolution. In addition, the primary decay channel by e- capture for some of the Ni and Co isotopes makes these isotopes ideal for probing the time delay between production of cosmic rays and their acceleration. Finally, the radioactive isotope 54Mn has a mean lifetime that is comparable to residence time of lighter elements in the galaxy, which has been measured using the 10Be isotopic abundance. Both of these abundances are produced primarily through spallation during propagation, and Mn can measure the average density of the propagation medium and residence time for Fe group elements with isotopic abundance measurements of stable spallation products. After etching, the MAGPIE CR-39 plastic was scanned for tracks using an automated microscope and image processing system. This system offers a data acquisition method that is as efficient and much quicker than techniques using a microscope and reticle. Cosmic ray data were

  13. Relating Functional Groups to the Periodic Table

    ERIC Educational Resources Information Center

    Struyf, Jef

    2009-01-01

    An introduction to organic chemistry functional groups and their ionic variants is presented. Functional groups are ordered by the position of their specific (hetero) atom in the periodic table. Lewis structures are compared with their corresponding condensed formulas. (Contains 5 tables.)

  14. Organic Functional Group Playing Card Deck

    NASA Astrophysics Data System (ADS)

    Welsh, Michael J.

    2003-04-01

    The recognition and identification of organic functional groups, while essential for chemistry and biology majors, is also very useful for non-science majors in the study of molecules in art and life. In order to make this task more palatable for the non-science major (art and communications students), the images of a traditional playing deck of cards (heart, spade, diamond, and club) have been replaced with four representations of common organic functional groups. The hierarchy rules for naming two groups in a molecule is loosely incorporated to represent the sequence (King, Queen, Jack, ?, Ace) of the deck. Students practice recognizing and identifying organic groups by playing simple card games of "Old Maid" and "Go Fish". To play games like "Poker" or "Gin", a student must not only recognize the functional groups, but also master a naming hierarchy for the organic groups.

  15. Life strategies of a ubiquitous and abundant subsurface archaeal group Bathyarchaeota

    NASA Astrophysics Data System (ADS)

    He, Y.; Li, M.; Perumal, V.; Feng, X.; Sievert, S. M.; Wang, F.

    2015-12-01

    Archaea belonging to the Miscellaneous Crenarchaeota Group (MCG, "Candidatus Bathyarchaeota") are widespread and abundant in the deep biosphere, yet their life strategies and ecological roles remain elusive. Metagenomic sequencing of a sample enriched in Bathyarchaeota (up to 74%) that originated from Guaymas Basin deep-sea vent sediments revealed 6 partial to nearly completed Bathyarchaeota genomic bins. ranging ~900kb-3.3Mb. The Bathyarchaeota bin size ranged from approximately 0.9 to 3.3 Mb, with coverage ranging from approximately 10× to 28×. The phylogeny based on 110 concatenated conserved archaeal single copy genes confirmed the placement of Bathyarchaeota into a novel archaeal phylum. Genes encoding for enzymes involved in the degradation of organic polymers such as protein, cellulose, chitin, and aromatic compounds, were identified. In addition, genes encoding glycolysis/gluconeogenesis, beta-oxidation pathways and the tricarboxylic acid cycle (except citrate synthase) were present in all genomic bins highlighting the heterotrophic life style of Bathyarchaeota. The presence of a wide variety of transporters of organic compounds further supports the versatile heterotrophic metabolism of Bathyarchaeota. This study highlights the life strategies of a ubiquitous and abundant subsurface archaeal group that thrives under energy-limited conditions, and expands the metabolic potentials of Archaea that play important roles in carbon cycling in marine sediments.

  16. Density and abundance of badger social groups in England and Wales in 2011-2013

    NASA Astrophysics Data System (ADS)

    Judge, Johanna; Wilson, Gavin J.; MacArthur, Roy; Delahay, Richard J.; McDonald, Robbie A.

    2014-01-01

    In the United Kingdom, European badgers Meles meles are a protected species and an important wildlife reservoir of bovine tuberculosis. We conducted a survey of badger dens (main setts) in 1614 1 km squares across England and Wales, between November 2011 and March 2013. Using main setts as a proxy for badger social groups, the estimated mean density of badger social groups in England and Wales was 0.485 km-2 (95% confidence interval 0.449-0.521) and the estimated abundance of social groups was 71,600 (66,400-76,900). In the 25 years since the first survey in 1985-88, the annual rate of increase in the estimated number of badger social groups was 2.6% (2.2-2.9%), equating to an 88% (70-105%) increase across England and Wales. In England, we estimate there has been an increase of 103% (83-123%) in badger social groups, while in Wales there has been little change (-25 to +49%).

  17. Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

    PubMed

    Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

    2016-02-01

    Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

  18. Identifying copepod functional groups from species functional traits

    PubMed Central

    Benedetti, Fabio; Gasparini, Stéphane; Ayata, Sakina-Dorothée

    2016-01-01

    We gathered information on the functional traits of the most representative copepod species in the Mediterranean Sea. Our database includes 191 species described by 7 traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Cluster analysis in the functional trait space revealed that Mediterranean copepods can be separated into groups with distinct ecological roles. PMID:26811565

  19. The Group Abundance Fraction: A statistically robust measure of particle composition and of spatial structure in images

    NASA Astrophysics Data System (ADS)

    Roelof, Edmond C.

    2015-01-01

    When two processes (A and B) are measured by counting instruments, we wish to present the results as an "abundance" along with an associated uncertainty. When the number of individual counts of either component is low, the usual ratio (A/B) is statistically ill-defined because there is a finite probability of zero counts in the denominator. However, the "Group Abundance Fraction" (F), e.g., A/(A+B), is a statistically robust parameter (under the condition that there must be at least one total count between A and B in order to constitute a measurement). We rigorously derive expectation values (over a conditional Poisson statistical ensemble) for and its standard deviation σF that are valid for all values of total counts greater than one. We then derive useful estimators for these ensemble expectation values in terms of simple algebraic functions of the actual observed accumulated counts. We also incorporate the practical effects of instrument response functions and background rates. The results are not restricted to particle species composition (or spectra), but are also applicable when A and B represent counts in adjacent "pixels" of spatial images formed by the particles.

  20. Using plant functional traits as a link between land use and bee foraging abundance

    NASA Astrophysics Data System (ADS)

    Pakeman, R. J.; Stockan, J.

    2013-07-01

    Many recent studies have shown that plant functional traits can be used to predict the response of plant assemblages to management or other environmental change. A further challenge is to use them to predict changes in the assemblages of other groups. Using data from a study of the impact of land use on biodiversity, the linkages between management drivers, a range of plant functional traits and the overall foraging numbers and assemblage of bees was assessed. Bee foraging numbers were only weakly predicted by plant traits, though bee foraging assemblage was closely related to a number of different groups of plant traits (flower colour and Forage Index, as well as taxonomic group). In turn, the selected traits were significantly correlated to some of the response traits that linked the plant assemblage to management, indicating that there was a predictive pathway from management to bee abundance and assemblage structure. However, models developed with just the environmental drivers proved superior at predicting both bee numbers and assemblage. Plant traits proved to be a moderately effective predictor of bee assemblage structure. However, the use of plant traits as a link between the bees and management did not offer any improvement on models directly developed from management variables. This suggests that the bee assemblage is responding to traits that have not been quantified and that developing these trophic linkage models may have to take a different approach.

  1. Identification, localization, and functional implications of an abundant nematode annexin

    PubMed Central

    1996-01-01

    Cultures of the nematode C. elegans were examined for the presence of calcium-dependent, phospholipid-binding proteins of the annexin class. A single protein of apparent mass on SDS-polyacrylamide gels of 32 kD was isolated from soluble extracts of nematode cultures on the basis of its ability to bind to phospholipids in a calcium-dependent manner. After verification of the protein as an annexin by peptide sequencing, an antiserum to the protein was prepared and used to isolate a corresponding cDNA from an expression library in phage lambda gt11. The encoded protein, herein referred to as the nex-1 annexin, has a mass of 35 kD and is 36-42% identical in sequence to 10 known mammalian annexins. Several unique modifications were found in the portions of the sequence corresponding to calcium-binding sites. Possible phosphorylation sites in the NH2-terminal domain of the nematode annexin correspond to those of mammalian annexins. The gene for this annexin (nex-1) was physically mapped to chromosome III in the vicinity of the dpy-17 genetic marker. Two other annexin genes (nex-2 and nex-3) were also identified in chromosome III sequences reported by the nematode genomic sequencing project (Sulston, J., Z. Du, K. Thomas, R. Wilson, L. Hillier, R. Staden, N. Halloran, P. Green, J. Thierry-Mieg, L. Qiu, et al. 1992. Nature (Lond.). 356:37-41). The nex-1 annexin was localized in the nematode by immunofluorescence and by electron microscopy using immunogold labeling. The protein is associated with membrane systems of the secretory gland cells of the pharynx, with sites of cuticle formation in the grinder in the pharynx, with yolk granules in oocytes, with the uterine wall and vulva, and with membrane systems in the spermathecal valve. The presence of the annexin in association with the membranes of the spermathecal valve suggests a novel function of the protein in the folding and unfolding of these membranes as eggs pass through the valve. The localizations also indicate

  2. The abundance and organization of polypeptides associated with antigens of the Rh blood group system.

    PubMed

    Gardner, B; Anstee, D J; Mawby, W J; Tanner, M J; von dem Borne, A E

    1991-06-01

    Twelve murine monoclonal antibodies, which react with human red cells of common Rh phenotype but give weak or negative reactions with Rh null erythrocytes, were used in quantitative binding assays and competitive binding assays to investigate the abundance and organization of polypeptides involved in the expression of antigens of the Rh blood group system. Antibodies of the R6A-type (R6A, BRIC-69, BRIC-207) and the 2D10-type (MB-2D10, LA18.18, LA23.40) recognize related structures and 100,000-200,000 molecules of each antibody bind maximally to erythrocytes of common Rh phenotype. Antibodies of the BRIC-125 type (BRICs 32, 122, 125, 126, 168, 211) recognize structures that are unrelated to those recognized by R6A-type and 2D10-type antibodies and between 10,000 and 50,000 antibody molecules bind maximally to erythrocytes of the common Rh phenotype. The binding of antibodies of the R6A-type and the 2D10-type, but not of antibodies of the BRIC-125-type could be partially inhibited by human anti-D antibodies (polyclonal and monoclonal) and a murine anti-e-like antibody. These results are consistent with evidence (Moore & Green 1987; Avent et al., 1988b) that the Rh blood group antigens are associated with a complex that comprises two groups of related polypeptides of M(r) 30,000 and M(r) 35,000-100,000, respectively, and suggest that there are 1-2 x 10(5) copies of this complex per erythrocyte. The polypeptide recognized by antibodies of the BRIC-125 type is likely to be associated with this complex. PMID:9259831

  3. The abundance and organization of polypeptides associated with antigens of the Rh blood group system.

    PubMed

    Gardner, B; Anstee, D J; Mawby, W J; Tanner, M J; von dem Borne, A E

    1991-06-01

    Twelve murine monoclonal antibodies, which react with human red cells of common Rh phenotype but give weak or negative reactions with Rh null erythrocytes, were used in quantitative binding assays and competitive binding assays to investigate the abundance and organization of polypeptides involved in the expression of antigens of the Rh blood group system. Antibodies of the R6A-type (R6A, BRIC-69, BRIC-207) and the 2D10-type (MB-2D10, LA18.18, LA23.40) recognize related structures and 100,000-200,000 molecules of each antibody bind maximally to erythrocytes of common Rh phenotype. Antibodies of the BRIC-125 type (BRICs 32, 122, 125, 126, 168, 211) recognize structures that are unrelated to those recognized by R6A-type and 2D10-type antibodies and between 10,000 and 50,000 antibody molecules bind maximally to erythrocytes of the common Rh phenotype. The binding of antibodies of the R6A-type and the 2D10-type, but not of antibodies of the BRIC-125-type could be partially inhibited by human anti-D antibodies (polyclonal and monoclonal) and a murine anti-e-like antibody. These results are consistent with evidence (Moore & Green 1987; Avent et al., 1988b) that the Rh blood group antigens are associated with a complex that comprises two groups of related polypeptides of M(r) 30,000 and M(r) 35,000-100,000, respectively, and suggest that there are 1-2 x 10(5) copies of this complex per erythrocyte. The polypeptide recognized by antibodies of the BRIC-125 type is likely to be associated with this complex.

  4. Functional group diversity of bee pollinators increases crop yield

    PubMed Central

    Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

    2008-01-01

    Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees. PMID:18595841

  5. Functional group diversity of bee pollinators increases crop yield.

    PubMed

    Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

    2008-10-01

    Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees.

  6. Interaction network among functional drug groups

    PubMed Central

    2013-01-01

    Background More attention has been being paid to combinatorial effects of drugs to treat complex diseases or to avoid adverse combinations of drug cocktail. Although drug interaction information has been increasingly accumulated, a novel approach like network-based method is needed to analyse that information systematically and intuitively Results Beyond focussing on drug-drug interactions, we examined interactions between functional drug groups. In this work, functional drug groups were defined based on the Anatomical Therapeutic Chemical (ATC) Classification System. We defined criteria whether two functional drug groups are related. Then we constructed the interaction network of drug groups. The resulting network provides intuitive interpretations. We further constructed another network based on interaction sharing ratio of the first network. Subsequent analysis of the networks showed that some features of drugs can be well described by this kind of interaction even for the case of structurally dissimilar drugs. Conclusion Our networks in this work provide intuitive insights into interactions among drug groups rather than those among single drugs. In addition, information on these interactions can be used as a useful source to describe mechanisms and features of drugs. PMID:24555875

  7. Cold-Regulated Cereal Chloroplast Late Embryogenesis Abundant-Like Proteins. Molecular Characterization and Functional Analyses

    PubMed Central

    NDong, Christian; Danyluk, Jean; Wilson, Kenneth E.; Pocock, Tessa; Huner, Norman P.A.; Sarhan, Fathey

    2002-01-01

    Cold acclimation and freezing tolerance are the result of complex interaction between low temperature, light, and photosystem II (PSII) excitation pressure. Previous results have shown that expression of the Wcs19 gene is correlated with PSII excitation pressure measured in vivo as the relative reduction state of PSII. Using cDNA library screening and data mining, we have identified three different groups of proteins, late embryogenesis abundant (LEA) 3-L1, LEA3-L2, and LEA3-L3, sharing identities with WCS19. These groups represent a new class of proteins in cereals related to group 3 LEA proteins. They share important characteristics such as a sorting signal that is predicted to target them to either the chloroplast or mitochondria and a C-terminal sequence that may be involved in oligomerization. The results of subcellular fractionation, immunolocalization by electron microscopy and the analyses of target sequences within the Wcs19 gene are consistent with the localization of WCS19 within the chloroplast stroma of wheat (Triticum aestivum) and rye (Secale cereale). Western analysis showed that the accumulation of chloroplastic LEA3-L2 proteins is correlated with the capacity of different wheat and rye cultivars to develop freezing tolerance. Arabidopsis was transformed with the Wcs19 gene and the transgenic plants showed a significant increase in their freezing tolerance. This increase was only evident in cold-acclimated plants. The putative function of this protein in the enhancement of freezing tolerance is discussed. PMID:12114590

  8. Galaxy and Group Baryonic Mass Functions for the RESOLVE Survey

    NASA Astrophysics Data System (ADS)

    Eckert, Kathleen D.; Kannappan, Sheila; Moffett, Amanda J.; Baker, Ashley; Stark, David; Berlind, Andreas A.; Storey-Fisher, Kate; Erickcek, Adrienne L.; Norris, Mark A.; Resolve Team

    2015-01-01

    We present a comparison of the galaxy and group baryonic mass functions for a subvolume of the RESOLVE (Resolved Spectroscopy Of a Local VolumE) survey. RESOLVE occupies A and B semester volumes totaling ~52,000 cubic Mpc, complete in baryonic mass to ~10^9.3 Msun and 10^9.0 Msun respectively, with galaxies and groups ranging in halo mass from 10^11-10^14 Msun. The A semester volume is surrounded by the larger ECO catalog, which lacks complete HI data but occupies ~561,000 cubic Mpc. We define the observed baryonic mass of a galaxy or group to be the sum of its stellar and cold atomic hydrogen components, with the latter inferred indirectly for much of ECO. For groups, we infer the total baryonic mass by summing the observed components of each constituent galaxy and add the likely hot halo gas based on prescriptions from observations and semi-analytic models. We perform subhalo/halo abundance matching between observed galaxies/groups and dark matter simulations, and we compare derived halo properties based on matching on luminosity vs. on observed baryonic mass (or on inferred total baryonic mass for groups). We also present a status update on the galaxy and group velocity functions for these surveys, which will allow for more direct comparison with dark matter simulations. This project was supported by NSF funding for the RESOLVE survey (AST-0955368).

  9. Monitoring change in the abundance and distribution of insects using butterflies and other indicator groups

    PubMed Central

    Thomas, J.A

    2005-01-01

    Conservative estimates suggest that 50–90% of the existing insect species on Earth have still to be discovered, yet the named insects alone comprise more than half of all known species of organism. With such poor baseline knowledge, monitoring change in insect diversity poses a formidable challenge to scientists and most attempts to generalize involve large extrapolations from a few well-studied taxa. Butterflies are often the only group for which accurate measures of change can be obtained. Four schemes, used successfully to assess change in British butterflies, that are increasingly being applied across the world are described: Red Data Books (RDB) list the best judgements of experts of the conservation status of species in their field of expertise; mapping schemes plot the changing distributions of species at scales of 1–100 km2; transect monitoring schemes generate time series of changes in abundance in sample populations of species on fixed sites across the UK; and occasional surveys measure the number, boundaries and size of all populations of a (usually RDB) species at intervals of 10–30 years. All schemes describe consistent patterns of change, but if they are to be more generally useful, it is important to understand how well butterflies are representative of other taxa. Comparisons with similarly measured changes in native bird and plant species suggest that butterflies have declined more rapidly that these other groups in Britain; it should soon be possible to test whether this pattern exists elsewhere. It is also demonstrated that extinction rates in British butterflies are similar to those in a range of other insect groups over 100 years once recording bias is accounted for, although probably lower than in aquatic or parasitic taxa. It is concluded that butterflies represent adequate indicators of change for many terrestrial insect groups, but recommended that similar schemes be extended to other popular groups, especially dragonflies

  10. Dominant Functional Group Effects on the Invasion Resistance at Different Resource Levels

    PubMed Central

    Wang, Jiang; Ge, Yuan; Zhang, Chong B.; Bai, Yi; Du, Zhao K.

    2013-01-01

    Background Functional group composition may affect invasion in two ways the effect of abundance, i.e. dominance of functional group; and the effect of traits, i.e. identity of functional groups. However, few studies have focused on the role of abundance of functional group on invasion resistance. Moreover, how resource availability influences the role of the dominant functional group in invasion resistance is even less understood. Methodology/Principal Findings In this experiment, we established experimental pots using four different functional groups (annual grass, perennial grass, deciduous shrub or arbor and evergreen shrub or arbor), and the dominant functional group was manipulated. These experimental pots were respectively constructed at different soil nitrogen levels (control and fertilized). After one year of growth, we added seeds of 20 different species (five species per functional group) to the experimental pots. Fertilization significantly increased the overall invasion success, while dominant functional group had little effect on overall invasion success. When invaders were grouped into functional groups, invaders generally had lower success in pots dominated by the same functional group in the control pots. However, individual invaders of the same functional group exhibited different invasion patterns. Fertilization generally increased success of invaders in pots dominated by the same than by another functional group. However, fertilization led to great differences for individual invaders. Conclusions/Significance The results showed that the dominant functional group, independent of functional group identity, had a significant effect on the composition of invaders. We suggest that the limiting similarity hypothesis may be applicable at the functional group level, and limiting similarity may have a limited role for individual invaders as shown by the inconsistent effects of dominant functional group and fertilization. PMID:24167565

  11. The circular velocity function of group galaxies

    SciTech Connect

    Abramson, Louis E.; Williams, Rik J.; Benson, Andrew J.; Kollmeier, Juna A.; Mulchaey, John S.

    2014-09-20

    A robust prediction of ΛCDM cosmology is the halo circular velocity function (CVF), a dynamical cousin of the halo mass function. The correspondence between theoretical and observed CVFs is uncertain, however: cluster galaxies are reported to exhibit a power-law CVF consistent with N-body simulations, but that of the field is distinctly Schechter-like, flattened compared to ΛCDM expectations at circular velocities v {sub c} ≲ 200 km s{sup –1}. Groups offer a powerful probe of the role environment plays in this discrepancy as they bridge the field and clusters. Here, we construct the CVF for a large, mass- and multiplicity-complete sample of group galaxies from the Sloan Digital Sky Survey. Using independent photometric v {sub c} estimators, we find no transition from field to ΛCDM-shaped CVF above v {sub c} = 50 km s{sup –1} as a function of group halo mass. All groups with 12.4 ≲ log M {sub halo}/M {sub ☉} ≲ 15.1 (Local Group analogs to rich clusters) display similar Schechter-like CVFs marginally suppressed at low v {sub c} compared to that of the field. Conversely, some agreement with N-body results emerges for samples saturated with late-type galaxies, with isolated late-types displaying a CVF similar in shape to ΛCDM predictions. We conclude that the flattening of the low-v {sub c} slope in groups is due to their depressed late-type fractions—environment affecting the CVF only to the extent that it correlates with this quantity—and that previous cluster analyses may suffer from interloper contamination. These results serve as useful benchmarks for cosmological simulations of galaxy formation.

  12. The Abundances of the Fe Group Elements in Early B Stars in the Magellanic Clouds and Bridge

    NASA Astrophysics Data System (ADS)

    Peters, Geraldine J.; Adelman, Saul J.

    2016-01-01

    The abundances of three Fe Group elements (V, Cr, and Fe) in 9 early main-sequence band B stars in the LMC, 7 in the SMC , and two in the Magellanic Bridge have been determined from archival FUSE observations and the Hubeny/Lanz NLTE programs TLUSTY/SYNSPEC. Lines from the Fe group elements, except for a few weak multiplets of Fe III, are not observable in the optical spectral region. The best set of lines in the FUSE spectral region are Fe III (UV1), V III 1150 Å, and Cr III 1137 Å. The abundances of these elements in early B stars are a marker for recent SNe Ia activity, as a single exploding white dwarf can deliver 0.5 solar masses of Ni-56 that decays into Fe to the ISM. The Fe group abundances in an older population of stars primarily reflect SNe II activity, in which a single explosion delivers only 0.07 solar masses of Ni-56 to the ISM (the rest remains trapped in the neutron star). The abundances of the Fe group elements in early B stars not only track SNe Ia activity but are also important for computing evolutionary tracks for massive stars. In general, the Fe abundance relative to the sun's value is comparable to the mean abundances for the lighter elements in the Clouds/Bridge but the values of [V,Cr/Fe]sun are smaller. This presentation will discuss the spatial distribution of the Fe Group elements in the Magellanic Clouds, and compare it with our galaxy in which the abundance of Fe declines with radial distance from the center. Support from NASA grants NAG5-13212, NNX10AD66G, STScI HST-GO-13346.22, and USC's Women in Science and Engineering (WiSE) program is greatly appreciated.

  13. The Abundances of the Fe Group Elements in Early B Stars in the Magellanic Clouds and Our Galaxy

    NASA Astrophysics Data System (ADS)

    Peters, Geraldine Joan; Adelman, Saul Joseph

    2015-08-01

    The abundances of the Fe-peak elements (Ti, V, Cr, Mn, Fe, Co, and Ni) are of interest as they are important for assessing opacities for stellar evolution calculations, confirming theoretical calculations of explosive nucleosynthesis, and inferring the past history of supernova activity in a galaxy. FUSE FUV spectra of early B stars in the LMC and SMC and HST/STIS FUV/NUV spectra of nearby B stars in our galaxy are analyzed with the Hubeny/Lanz programs TLUSTY/SYNSPEC to determine abundance for the Fe group elements and produce a map of these abundances in the Magellanic Clouds (MC) and Magellanic Bridge (MB). Except for four weak multiplets of Fe III there are no measurable lines from the Fe group in the optical region. The Fe group species found in the FUV spectra of early B stars are primarily in the second stage of ionization. The best set of lines in the FUSE spectral region are Fe III (UV1), V III 1150 Å, and Cr III 1137 Å. Analysis of the galactic B stars provides a good assessment of the reliability of the atomic parameters that are used for the MC calculations. Twenty-two early B stars in the MC and MB and five in our galaxy were analyzed. In general the Fe group abundances range from solar to slightly below solar in our region of the galaxy. But in the MCs the abundances of V, Cr, and Fe tend to be significantly lower than the mean metal abundances for the galaxy. Maps of the Fe group abundances and their variations in the LMC and SMC, tracers of recent enrichment of the ISM from supernova activity, are shown. Support from NASA grants NAG5-13212, NNX10AD66G, STScI HST-GO-13346.22, and USC’s Women in Science and Engineering (WiSE) program is greatly appreciated.

  14. [Functional feeding groups of macroinvertebrates in Gaira river, Colombia].

    PubMed

    Rodríguez-Barrios, Javier; Ospina-Tórres, Rodulfo; Turizo-Correa, Rodrigo

    2011-12-01

    Tropical rivers are frequently described on their biodiversity but few studies have considered the ecological value of this richness in their food webs. We determined the trophic structure of aquatic macroinvertebrate communities (expressed in the richness and abundance of taxa and biomass proportions of different functional feeding groups) at the level of the river, stretch and microhabitats (functional units - UFs). We evaluated the spatial and temporal variation of these descriptors during wet and dry events, and selected three sites associated with different altitudinal belts. We reported 109 taxa, with 11167 individuals who contributed 107.11g of biomass. Density of macroinvertebrates was favored with increasing height, and biomass showed the opposite pattern (K-W = 10.1, d.f. = 1, p < 0.05), due to the addition of large crustaceans (Macrobrachium), and the taxa diversity was higher in the middle stretch of the river (H'=3.16). The Gaira stream runs through a mid-sized river basin, for this reason we found mainly bedrock (epilithon = 50.5%), gravel and sand (43.7%). The functional unit with more habitat and food resources that contains a higher abundance of leaf litter macroinvertebrates was foliage followed by epilithon, fine sediment and gravel-sand (K-W = 25.3, d.f. = 3, p < 0.05). The biomass values of these organisms were higher in leaves followed by gravel-sands, epilithon and sediment (K-W = 15.3, d.f. = 3, p < 0.05). Autochthonous biomass input by different functional feeding groups can be considered very low, but they define the functionality of the stream, being represented almost exclusively by shredders (Macrobrachium, 73%), present only in the lower reaches, followed by shredder Leptonema with 15%, located mostly in the upper reaches and predatory stoneflies of the genus Anacroneuria to 6.56%, which dominated in the middle stretch of stream. Excluding Macrobrachium from the analysis, there was dominance of Anacroneuria in the lower reaches

  15. Topology of Protein Interaction Network Shapes Protein Abundances and Strengths of Their Functional and Nonspecific Interactions

    SciTech Connect

    Maslov, S.; Heo, M.; Shakhnovich, E.

    2011-03-08

    How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein-protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a 'frustration' effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture-mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.

  16. Abundances of Local Group Globular Clusters Using High Resolution Integrated Light Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sakari, Charli; McWilliam, A.; Venn, K.; Shetrone, M. D.; Dotter, A. L.; Mackey, D.

    2014-01-01

    Abundances and kinematics of extragalactic globular clusters provide valuable clues about galaxy and globular cluster formation in a wide variety of environments. In order to obtain such information about distant, unresolved systems, specific observational techniques are required. An Integrated Light Spectrum (ILS) provides a single spectrum from an entire stellar population, and can therefore be used to determine integrated cluster abundances. This dissertation investigates the accuracy of high resolution ILS analysis methods, using ILS (taken with the Hobby-Eberly Telescope) of globular clusters associated with the Milky Way (47 Tuc, M3, M13, NGC 7006, and M15) and then applies the method to globular clusters in the outer halo of M31 (from the Pan-Andromeda Archaeological Survey, or PAndAS). Results show that: a) as expected, the high resolution method reproduces individual stellar abundances for elements that do not vary within a cluster; b) the presence of multiple populations does affect the abundances of elements that vary within the cluster; c) certain abundance ratios are very sensitive to systematic effects, while others are not; and d) certain abundance ratios (e.g. [Ca/Fe]) can be accurately obtained from unresolved systems. Applications of ILABUNDS to the PAndAS clusters reveal that accretion may have played an important role in the formation of M31's outer halo.

  17. Functional trait responses to grazing are mediated by soil moisture and plant functional group identity.

    PubMed

    Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

    2015-12-11

    Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization.

  18. Functional trait responses to grazing are mediated by soil moisture and plant functional group identity.

    PubMed

    Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

    2015-01-01

    Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization. PMID:26655858

  19. Functional trait responses to grazing are mediated by soil moisture and plant functional group identity

    PubMed Central

    Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

    2015-01-01

    Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance–resistance strategies to grazing and mixed acquisitive–conservative strategies in resource utilization. PMID:26655858

  20. The (32)S/(33)S abundance as a function of galactocentric radius in the Milky Way

    NASA Technical Reports Server (NTRS)

    Greenhouse, M. A.; Thronson, H. A., Jr.

    1986-01-01

    Astration of heavy elements by the stars of the Milky Way forms a fossil record which may preserve spacial distribution of the mass function for the stars in the galaxy. Sulfur is among the last common element for which the relative abundance of its various isotopes have yet to be completely measured within our galaxy. Explosive oxygen burning in massive stars is thought to be the process which dominates sulfur production within stars. There models predict that the various isotopes (S-32, S-33, S-34) are formed in relative abundance which depend strongly upon the mass of the parent star. This relative abundance is thought to be unaffected by subsequent stellar procesing since all important sinks of sulfur destroy it without regard for isotopic form. Hence the spacial variation of the mass function (MF) can be studied by measuring the abundance variation of sulfur isotopes in the galaxy provided that the product yields for these isotopes are known accurately as a function of stellar mass.

  1. Plant functional group diversity promotes soil protist diversity.

    PubMed

    Ledeganck, Pieter; Nijs, Ivan; Beyens, Louis

    2003-07-01

    We tested whether effects of plant diversity can propagate through food webs, down to heterotrophic protists not linked directly to plants. To this end we synthesised grassland ecosystems with varying numbers of plant functional groups (FGN) and assessed corresponding changes in testate amoebae communities. The number of plant species was kept constant. When FGN was increased from 1 to 3, species number and total community density of live testate amoebae were enhanced according to a linear and a saturating function, respectively. From FGN 1 to 2, the appearance of new testate amoebae species did not affect the presence of the resident species, whereas, from FGN 2 to 3 about one quarter of the resident testate amoebae species was replaced, without altering the total species number. Overall, density by species increased, while evenness of the testate amoebae community was not affected by FGN; although Trinema lineare, one of the most common species, became more abundant. The observed relationship between plant functional group diversity and testate amoebae diversity could shed new light on the biogeographical distribution patterns of protists.

  2. Plant functional group diversity promotes soil protist diversity.

    PubMed

    Ledeganck, Pieter; Nijs, Ivan; Beyens, Louis

    2003-07-01

    We tested whether effects of plant diversity can propagate through food webs, down to heterotrophic protists not linked directly to plants. To this end we synthesised grassland ecosystems with varying numbers of plant functional groups (FGN) and assessed corresponding changes in testate amoebae communities. The number of plant species was kept constant. When FGN was increased from 1 to 3, species number and total community density of live testate amoebae were enhanced according to a linear and a saturating function, respectively. From FGN 1 to 2, the appearance of new testate amoebae species did not affect the presence of the resident species, whereas, from FGN 2 to 3 about one quarter of the resident testate amoebae species was replaced, without altering the total species number. Overall, density by species increased, while evenness of the testate amoebae community was not affected by FGN; although Trinema lineare, one of the most common species, became more abundant. The observed relationship between plant functional group diversity and testate amoebae diversity could shed new light on the biogeographical distribution patterns of protists. PMID:13677451

  3. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    PubMed

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  4. Functional traits predict relationship between plant abundance dynamic and long-term climate warming

    PubMed Central

    Soudzilovskaia, Nadejda A.; Elumeeva, Tatiana G.; Onipchenko, Vladimir G.; Shidakov, Islam I.; Salpagarova, Fatima S.; Khubiev, Anzor B.; Tekeev, Dzhamal K.; Cornelissen, Johannes H. C.

    2013-01-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year’s shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  5. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    PubMed

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change.

  6. Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales.

    PubMed

    Newbold, Tim; Butchart, Stuart H M; Sekercioğlu, Cağan H; Purves, Drew W; Scharlemann, Jörn P W

    2012-01-01

    Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R(2): 5.6 × 10(-7) to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2): 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.

  7. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli

    PubMed Central

    Gao, Jie; Lan, Ting

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty–three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers. PMID:26781930

  8. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli.

    PubMed

    Gao, Jie; Lan, Ting

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty-three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers. PMID:26781930

  9. Biogeographical boundaries, functional group structure and diversity of Rocky Shore communities along the Argentinean coast.

    PubMed

    Wieters, Evie A; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; Navarrete, Sergio A

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10's km) and local (10's m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3-4 main 'groups' of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or "insurance", against spatial variability

  10. The Abundances of the Fe Group Elements in Three Early B Stars in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Peters, G. J.; Adelman, S. J.

    2005-12-01

    The photospheric abundances of V, Cr, and Fe have been determined for three sharp-lined early B stars in the Large Magellanic Cloud using FUV spectra obtained from the Far Ultraviolet Spectroscopic Explorer (FUSE) and the Kurucz LTE model atmosphere/spectrum synthesis codes ATLAS9/SYNTHE. The program stars include NGC1818/D1, NGC2004/B15, and NGC2004/B30 (star designations are from Robertson 1974, A&AS, 15, 261). The calculations were carried through with model parameters close to those adopted by Korn et al. (2000, A&A, 353, 655). Values of Teff, log g, ξ T, and v sin I are 25000/4.0/0/30, 20000/3.1/6/25, and 23500/3.3/14/30 for NGC1818/D1, NGC2004/B15, and NGC2004/B30, respectively. The abundances quoted below are in sequence for the latter stars. The vanadium abundances, [V/H], determined from V III λ λ 1150,1152 (UV 2), are -0.6, -0.9, and -0.9 dex. Cr was determined from Cr III λ λ 1118,1136. Values of -0.5, -0.8, and -0.7 dex were found. Uncertainties in the V and Cr abundances are ˜0.3 dex. The Fe abundance is primarily from 7 lines of Fe III (UV 1) in the region λ λ 1122-32. Values are -0.8±0.3, ˜-1.1, and -0.4±0.3. Since there is no evidence for N enhancement in the program stars ([N/H] ˜ -0.9, -1.0, and -0.6 from the N III doublet at 1183,1184 Å) the photospheric abundances have probably not been altered by mixing of processed material from the star's interior and the derived abundances represent pristine values for the two young clusters in the LMC. It should be noted that the N and Fe abundances derived for NGC1818/D1 are about 0.5 dex lower than those determined by Korn et al. from much weaker optical lines. We will discuss possible reasons for the discrepancy. The generally low abundances for the Fe group elements in these young cluster B stars imply that supernova activity has been minimal in the regions of the LMC in which the stars were formed. GJP appreciates support from NASA grant NAG5-13212.

  11. Plant functional group composition modifies the effects of precipitation change on grassland ecosystem function.

    PubMed

    Fry, Ellen L; Manning, Pete; Allen, David G P; Hurst, Alex; Everwand, Georg; Rimmler, Martin; Power, Sally A

    2013-01-01

    Temperate grassland ecosystems face a future of precipitation change, which can alter community composition and ecosystem functions through reduced soil moisture and waterlogging. There is evidence that functionally diverse plant communities contain a wider range of water use and resource capture strategies, resulting in greater resistance of ecosystem function to precipitation change. To investigate this interaction between composition and precipitation change we performed a field experiment for three years in successional grassland in southern England. This consisted of two treatments. The first, precipitation change, simulated end of century predictions, and consisted of a summer drought phase alongside winter rainfall addition. The second, functional group identity, divided the plant community into three groups based on their functional traits- broadly described as perennials, caespitose grasses and annuals- and removed these groups in a factorial design. Ecosystem functions related to C, N and water cycling were measured regularly. Effects of functional groupidentity were apparent, with the dominant trend being that process rates were higher under control conditions where a range of perennial species were present. E.g. litter decomposition rates were significantly higher in plots containing several perennial species, the group with the highest average leaf N content. Process rates were also very strongly affected by the precipitation change treatmentwhen perennial plant species were dominant, but not where the community contained a high abundance of annual species and caespitose grasses. This contrasting response could be attributable to differing rooting patterns (shallower structures under annual plants, and deeper roots under perennials) and faster nutrient uptake in annuals compared to perennials. Our results indicate that precipitation change will have a smaller effect on key process rates in grasslandscontaining a range of perennial and annual species

  12. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater.

    PubMed

    Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz; Cannistraci, Carlo V; Ravasi, Timothy; Hentschel, Ute

    2014-12-01

    The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

  13. Organic amendments enhance microbial diversity and abundance of functional genes in Australian Soils

    NASA Astrophysics Data System (ADS)

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2016-04-01

    Food and cash crops play important roles in Australia's economy with black, grey and red clay soil, widely use for growing cotton, wheat, corn and other crops in rotation. While the majority of cotton growers use nitrogen and phosphate fertilizers only in the form of agrochemicals, a few experiment with the addition of manure or composted plant material before planting. We hypothesized that the use of such organic amendments would enhance the soil microbial function through increased microbial diversity and abundance, thus contribute to improved soil sustainability. To test the hypothesis we collected soil samples from two cotton-growing farms in close geographical proximity and with mostly similar production practices other than one grower has been using composted plants as organic amendment and the second farmer uses only agrochemicals. We applied the Biolog Ecoplate system to study the metabolic signature of microbial communities and used qPCR to estimate the abundance of functional genes in the soil. The soil treated with organic amendments clearly showed higher metabolic activity of a more diverse range of carbon sources as well as higher abundance of genes involved in the nitrogen and phosphorous cycles. Since microbes undertake a large number of soil functions, the use of organic amendments can contribute to the sustainability of agricultural soils.

  14. Preconversion catalytic deoxygenation of phenolic functional groups

    SciTech Connect

    Kubiak, C.P.

    1991-01-01

    The deoxygenation of phenols is a conceptually simple, but unusually difficult chemical transformation to achieve. Aryl carbon-oxygen bond cleavage is a chemical transformation of importance in coal liquefaction and the upgrading of coal liquids as well as in the synthesis of natural products. This proposed research offers the possibility of effecting the selective catalytic deoxygenation of phenolic functional groups using CO. A program of research for the catalytic deoxygenation of phenols, via a low energy mechanistic pathway that is based on the use of the CO/CO{sub 2} couple to remove phenolic oxygen atoms, is underway. We are focusing on systems which have significant promise as catalysts: Ir(triphos)OPh, (Pt(triphos)OPh){sup +} and Rh(triphos)OPh. Our studies of phenol deoxygenation focus on monitoring the reactions for the elementary processes upon which catalytic activity will depend: CO insertion into M-OPh bonds, CO{sub 2} elimination from aryloxy carbonyls {l brace}M-C(O)-O-Ph{r brace}, followed by formation of a coordinated benzyne intermediate.

  15. Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees.

    PubMed

    Samant, Suvidha; Huo, Tian; Dawson, Jeffrey O; Hahn, Dittmar

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations. PMID:26143359

  16. Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees.

    PubMed

    Samant, Suvidha; Huo, Tian; Dawson, Jeffrey O; Hahn, Dittmar

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations.

  17. Biogeographical Boundaries, Functional Group Structure and Diversity of Rocky Shore Communities along the Argentinean Coast

    PubMed Central

    Wieters, Evie A.; McQuaid, Christopher; Palomo, Gabriela; Pappalardo, Paula; Navarrete, Sergio A.

    2012-01-01

    We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10′s km) and local (10′s m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3–4 main ‘groups’ of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or “insurance”, against spatial

  18. Linking Carbonic Anhydrase Abundance and Diversity in Soils to Ecological Function

    NASA Astrophysics Data System (ADS)

    Pang, E.; Meredith, L. K.; Welander, P. V.

    2015-12-01

    Carbonic anhydrase (CA) is an ancient enzyme widespread among bacteria, archaea, and eukarya that catalyzes the following reaction: CO2 + H2O ⇌ HCO3- + H+. Its functions are critical for key cellular processes such as concentrating CO2 for autotrophic growth, pH regulation, and pathogen survival in hosts. Currently, there are six known CA classes (α, β, γ, δ, η, ζ) arising from several distinct evolutionary lineages. CA are widespread in sequenced genomes, with many organisms containing multiple classes of CA or multiple CA of the same class. Soils host rich microbial communities with diverse and important ecological functions, but the diversity and abundance of CA in soils has not been explored. CA appears to play an important, but poorly understood, role in some biogeochemical cycles such as those of CO2 and its oxygen isotope composition and also carbonyl sulfide (COS), which are potential tracers in predictive carbon cycle models. Recognizing the prevalence and functional significance of CA in soils, we used a combined bioinformatics and molecular biology approach to address fundamental questions regarding the abundance, diversity, and function of CA in soils. To characterize the abundance and diversity of the different CA classes in soils, we analyzed existing soil metagenomic and metatranscriptomic data from the DOE Joint Genome Institute databases. Out of the six classes of CA, we only found the α, β, and γ classes to be present in soils, with the β class being the most abundant. We also looked at genomes of sequenced soil microorganisms to learn what combination of CA classes they contain, from which we can begin to predict the physiological role of CA. To characterize the functional roles of the different CA classes in soils, we collected soil samples from a variety of biomes with diverse chemical and physical properties and quantified the rate of two CA-mediated processes: soil uptake of COS and acceleration of the oxygen isotope exchange

  19. Temperature-dependent nuclear partition functions and abundances in the stellar interior

    NASA Astrophysics Data System (ADS)

    Nabi, Jameel-Un; Nasser Tawfik, Abdel; Ezzelarab, Nada; Abas Khan, Ali

    2016-05-01

    We calculate the temperature-dependent nuclear partition functions (TDNPFs) and nuclear abundances for 728 nuclei, assuming nuclear statistical equilibrium (NSE). The theories of stellar evolution support NSE. Discrete nuclear energy levels have been calculated microscopically, using the pn-QRPA theory, up to an excitation energy of 10 MeV in the calculation of the TDNPFs. This feature of our paper distinguishes it from previous calculations. Experimental data is also incorporated wherever available to ensure the reliability of our results. Beyond 10 MeV, we employ a simple Fermi gas model and perform integration over the nuclear level densities to approximate the TDNPFs. We calculate nuclidic abundances, using the Saha equation, as a function of three parameters: stellar density, stellar temperature and the lepton-to-baryon content of stellar matter. All these physical parameters are considered to be extremely important in the stellar interior. The results obtained in this paper show that the equilibrium configuration of nuclei remains unaltered by increasing the stellar density (only the calculated nuclear abundances increase by roughly the same order of magnitude). Increasing the stellar temperature smoothes the equilibrium configuration showing peaks at the neutron-number magic nuclei.

  20. [Response of Phytoplankton Functional Groups to Eutrophication in Summer at Xiaoguan Reservoir].

    PubMed

    Li, Lei; Li, Qiu-hua; Jiao, Shu-lin; Li, Yue; Xiao, Jing; Deng, Long; Sun, Rong-guo; Gao, Yong-chun; Luo, Lan

    2015-12-01

    Hydrology and Water Resources Bureau of Guizhou Province, Guiyang 550002, China) Abstract: In order to explore the distribution characteristics of phytoplankton functional groups, eutrophication characteristics and response of phytoplankton functional groups to eutrophication in Xiaoguan Reservoir, phytoplankton and water samples were taken once a week from 25th July 2014 to 27th September 2014. The results showed that there were 22 phytoplankton functional groups, groups S1, D, J, B, G, MP, L₀, SN, X1, Y, Xph, F, T and W1 were comparatively common functional groups, Wherein, S1, D and J were the dominant functional groups. Weekly dynamics of phytoplankton functional groups were: S1-->S1-->S1-->S1-->S1--S1-->S1-->J/D/S1-->Sl1- >/1D. group Sl1dominated over other groups, the cell abundance of S1 appeared two peaks at week 5 and week 7 respectively, but there was a slump at week 8, and rose again at last, compared to two peaks before, the cell abundance had dropped from 10⁸cells · L⁻¹ to 10⁷cells · L⁻¹ Water flush caused by discharge gate opening artificially was the main reason. Based on the three methods of eutrophication evaluation, the water was in moderately eutrophic and eutrophic states in Xiaoguan Reservoir in the summer of 2014. Multivariate analysis (RDA) indicated transparency was the main factor affecting the distribution of phytoplankton functional groups, and nutrients were no longer the limiting factor. The study suggested that phytoplankton functional groups could make a good response to eutrophication: groups S1 and J adapted to the turbid eutrophic water bodies, D adapted to shallow turbid waters and was sensitive to nutrient depletion. Also, common functional groups like G, X1, WW1 F etc. mostly adapted to eutrophic water bodies.

  1. Modeling wetland blackbird populations as a function of waterfowl abundance in the prairie pothole region of the United States and Canada

    USGS Publications Warehouse

    Forcey, G.M.; Linz, G.M.; Thogmartin, W.E.; Bleier, W.J.

    2008-01-01

    Blackbirds share wetland habitat with many waterfowl species in Bird Conservation Region 11 (BCR 11), the prairie potholes. Because of similar habitat preferences, there may be associations between blackbird populations and populations of one or more species of waterfowl in BCR11. This study models populations of red-winged blackbirds and yellow-headed blackbirds as a function of multiple waterfowl species using data from the North American Breeding Bird Survey within BCR11. For each blackbird species, we created a global model with blackbird abundance modeled as a function of 11 waterfowl species; nuisance effects (year, route, and observer) also were included in the model. Hierarchical Poisson regression models were fit using Markov chain Monte Carlo methods in WinBUGS 1.4.1. Waterfowl abundances were weakly associated with blackbird numbers, and no single waterfowl species showed a strong correlation with any blackbird species. These findings suggest waterfowl abundance from a single species is not likely a good bioindicator of blackbird abundance; however, a global model provided good fit for predicting red-winged blackbird abundance. Increased model complexity may be required for accurate predictions of blackbird abundance; the amount of data required to construct appropriate models may limit this approach for predicting blackbird abundance in the prairie potholes. Copyright ?? Taylor & Francis Group, LLC.

  2. Relative abundance of water-group ions in Saturn's inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Perry, Mark E.; Cravens, Thomas; Tokar, Robert; Smith, Howard T.; Perryman, Rebecca; Waite, J. Hunter; McNutt, Ralph L.

    2016-10-01

    At nineteen different times over seven years, the Cassini Ion Neutral Mass Spectrometer (INMS) measured the relative fractions of water-group ions in the inner magnetosphere of Saturn near the equatorial plane between 3.8 and 6.5 Saturn radii (RS). INMS samples only a small portion of velocity space in any one measurement, but the measurements span a broad range of velocity space. The data show that H2O+ comprises the bulk of the ions near 4.0 RS, and that its fraction decreases with increasing distance from 4.0 RS, the source of neutral water at Enceladus. At 4.0 RS, the fraction of H2O+ ranges from 60% to 100%, with an average of 80%. At 6.5 RS, the three main water-group constituents, H2O+, OH+, and O+, are nearly equal. H3O+, which dominates the water-group ion fractions in the Enceladus plume, is 10% or less in Saturn's magnetosphere outside the plume. The relative ion fractions show other variations that are not clearly linked to any of the studied parameters including velocity, density, and the orbit-phase-dependent activity of Enceladus.

  3. Functional group diversity increases with modularity in complex food webs.

    PubMed

    Montoya, D; Yallop, M L; Memmott, J

    2015-01-01

    Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web.

  4. Functional group diversity increases with modularity in complex food webs

    PubMed Central

    Montoya, D.; Yallop, M.L.; Memmott, J.

    2015-01-01

    Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web. PMID:26059871

  5. On the Abundance of Water in Extrasolar Planetary Systems as a Function of Stellar Metallicity

    NASA Astrophysics Data System (ADS)

    Dominguez, Gerardo

    2016-06-01

    The discovery, to date, of several hundred confirmed extra solar planets and a statistical analysis of their properties has revealed intriguing patterns in the abundance and types of extrasolar planets. The metallicity of the host star appears to be a driver in determining extrasolar planetary system characteristics, although a mechanistic understanding of these relationships is not currently available. Understanding the broad relationship(s) between the characteristics of extrasolar planets and stellar metallicity thus appears timely.Recent work examining the timescales for water production in protoplanetary disks suggest that ionizing radiation required to drive surface chemistry in protoplanetary disks is insufficient and production timescales too slow to account for a significant amount of water in protoplanetary disks. Here we focus on the timescales for water production in cold molecular clouds and examine the relationship of this timescale as a function of molecular cloud metallicity. To do this, we consider the distribution of surface area concentration (dA/dV) in molecular clouds as a function of their metallicity and various MRN-like dust grain size distributions. We find that molecular cloud metallicity is a significant factor in determining upper-limits to the availability of water in molecular clouds and by extension, protoplanetary disks. The spectral index of the MRN distribution affects the upper-limits to H2O abundance, but the effect is not as significant as metallicity. We find that the ratio of H2O/SiO2 produced in a molecular cloud of solar metallicity can easily account for Earth’s present day ratio , supporting the “wet” hypothesis for the origins of Earth’s water. Future studies will focus on the retention of water on interstellar dust grain surfaces in protoplanetary disk environments inside the water line, the abundance of other volatile species, more detailed estimates of H2O destruction timescales in molecular clouds, and

  6. Preconversion catalytic deoxygenation of phenolic functional groups

    SciTech Connect

    Kubiak, C.P.

    1990-01-01

    The deoxygenation of phenols is a conceptually simple, but unusually difficult chemical transformation of importance in organic synthesis and commercial coal liquefaction. The phenolic C-O bond energy of 103 kcal/mol is as strong as a benzene C-H bond and over 10 kcal/mol stronger than the C-O bonds of methanol and ethanol. The deoxygenation of phenols by CO is a viable process. metallolactones, created via late transition metal orthometallation of aryloxycarbonyl ligands, may provide the essential low energy pathway for elimination of CO{sub 2}, formation of a benzyne hydride intermediate, and thereby formation of the phenyl group. In the present Pt(OAr){sub 2}(dpps) system the phenyl group produced by phenol deoxygenation is eliminated with an aryloxycarbonyl ligand to yield phenylbenzoates. For this reason we are focusing our ongoing efforts on systems which contain one aryloxide, thus removing the possibility of reductive elimination of the phenyl group prior to elimination of free arenes.

  7. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    NASA Astrophysics Data System (ADS)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  8. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  9. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  10. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    PubMed Central

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  11. Differences in ecological structure, function, and native species abundance between native and invaded Hawaiian streams.

    PubMed

    Holitzki, Tara M; MacKenzie, Richard A; Wiegner, Tracy N; McDermid, Karla J

    2013-09-01

    Poeciliids, one of the most invasive species worldwide, are found on almost every continent and have been identified as an "invasive species of concern" in the United States, New Zealand, and Australia. Despite their global prevalence, few studies have quantified their impacts on tropical stream ecosystem structure, function, and biodiversity. Utilizing Hawaiian streams as model ecosystems, we documented how ecological structure, function, and native species abundance differed between poeciliid-free and poeciliid-invaded tropical streams. Stream nutrient yields, benthic biofilm biomass, densities of macroinvertebrates and fish, and community structures of benthic algae, macroinvertebrates, and fish were compared between streams with and without established poeciliid populations on the island of Hawai'i, Hawaii, USA. Sum nitrate (sigmaNO3(-) = NO3(-) + NO2(-)), total nitrogen, and total organic carbon yields were eight times, six times, and five times higher, respectively, in poeciliid streams than in poeciliid-free streams. Benthic biofilm ash-free dry mass was 1.5x higher in poeciliid streams than in poeciliid-free streams. Percentage contributions of chironomids and hydroptilid caddisflies to macroinvertebrate densities were lower in poeciliid streams compared to poeciliid-free streams, while percentage contributions of Cheumatopsyche analis caddisflies, Dugesia sp. flatworms, and oligochaetes were higher. Additionally, mean densities of native gobies were two times lower in poeciliid streams than in poeciliid-free ones, with poeciliid densities being approximately eight times higher than native fish densities. Our results, coupled with the wide distribution of invasive poeciliids across Hawaii and elsewhere in the tropics, suggest that poeciliids may negatively impact the ecosystem structure, function, and native species abundance of tropical streams they invade. This underscores the need for increased public awareness to prevent future introductions and for

  12. Atom-efficient regioselective 1,2-dearomatization of functionalized pyridines by an earth-abundant organolanthanide catalyst

    NASA Astrophysics Data System (ADS)

    Dudnik, Alexander S.; Weidner, Victoria L.; Motta, Alessandro; Delferro, Massimiliano; Marks, Tobin J.

    2014-12-01

    Developing earth-abundant, non-platinum metal catalysts for high-value chemical transformations is a critical challenge to contemporary chemical synthesis. Dearomatization of pyridine derivatives is an important transformation to access a wide range of valuable nitrogenous natural products, pharmaceuticals and materials. Here, we report an efficient 1,2-regioselective organolanthanide-catalysed pyridine dearomatization process using pinacolborane, which is compatible with a broad range of pyridines and functional groups and employs equimolar reagent stoichiometry. Regarding the mechanism, derivation of the rate law from NMR spectroscopic and kinetic measurements suggests first order in catalyst concentration, fractional order in pyridine concentration and inverse first order in pinacolborane concentration, with C=N insertion into the La-H bond as turnover-determining. An energetic span analysis affords a more detailed understanding of experimental activity trends and the unusual kinetic behaviour, and proposes the catalyst ‘resting’ state and potential deactivation pathways.

  13. [2]Rotaxane with multiple functional groups.

    PubMed

    Saha, Subrata; Santra, Saikat; Akhuli, Bidyut; Ghosh, Pradyut

    2014-11-21

    High-yield syntheses of Cu(II)- and Ni(II)-templated [2]pseudorotaxane precursors (CuPRT and NiPRT, respectively) were achieved by threading bis(azide)bis(amide)-2,2'-bipyridine axle into a bis(amide)tris(amine) macrocycle. Single-crystal X-ray structural analysis of CuPRT revealed complete threading of the axle fragment into the wheel cavity, where strong aromatic π-π stacking interactions between two parallel arene moieties of the wheel and the pyridyl unit of axle are operative in addition to metal ion templation. Attachment of a newly developed bulky stopper molecule with a terminal alkyne to CuPRT via a Cu(I)-catalyzed azide-alkyne cycloaddition reaction failed as a result of dethreading of the azide-terminated axle under the reaction conditions. However, the synthesis of a metal-free [2]rotaxane containing triazole with other functionalities in the axle was achieved in ∼45% yield upon coupling between azide-terminated NiPRT and the alkyne-terminated stopper. The [2]rotaxane was characterized by mass spectrometry, 1D and 2D NMR (COSY, DOSY, and ROESY) experiments. Comparative solution-state NMR studies of the [2]rotaxane in its unprotonated and protonated states were carried out to locate the position of the wheel on the axle of the metal-free [2]rotaxane. Furthermore, a variable-temperature (1)H NMR study in DMSO-d6 of [2]rotaxane supported the kinetic inertness of the interlocked structure, where the newly developed stopper prevents dethreading of the 30-membered wheel from the axle.

  14. Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3.

    PubMed

    Gómez, Fernando; Moreira, David; Benzerara, Karim; López-García, Purificación

    2011-01-01

    Culture-independent molecular methods based on the amplification, cloning and sequencing of small-subunit (SSU) rRNA genes are a powerful tool to study the diversity of prokaryotic and eukaryotic microorganisms for which morphological features are not conspicuous. In recent years, molecular data from environmental surveys have revealed several clades of protists lacking cultured and/or described members. Among them are various clades of marine stramenopiles (heterokonts), which are thought to play an essential ecological role as grazers, being abundant and distributed in oceans worldwide. In this work, we show that Solenicola setigera, a distinctive widespread colonial marine protist, is a member of the environmental clade MArine STramenopile 3 (MAST-3). Solenicola is generally considered as a parasite or an epiphyte of the diatom Leptocylindrus mediterraneus. So far, the ultrastructural, morphological and ecological data available were insufficient to elucidate its phylogenetic position, even at the division or class level. We determined SSU rRNA gene sequences of S. setigera specimens sampled from different locations and seasons in the type locality, the Gulf of Lions, France. They were closely related, though not identical, which, together with morphological differences under electron microscopy, suggest the occurrence of several species. Solenicola sequences were well nested within the MAST-3 clade in phylogenetic trees. Since Solenicola is the first identified member of this abundant marine clade, we propose the name Solenicolida for the MAST-3 phylogenetic group.

  15. The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit.

    PubMed

    Cuevas-Velazquez, Cesar L; Saab-Rincón, Gloria; Reyes, José Luis; Covarrubias, Alejandra A

    2016-05-13

    Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics. PMID:27006402

  16. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling.

    PubMed

    Bode, Antonio; Estévez, M Graciela; Varela, Manuel; Vilar, José A

    2015-09-01

    Phytoplankton is a sentinel of marine ecosystem change. Composed by many species with different life-history strategies, it rapidly responds to environment changes. An analysis of the abundance of 54 phytoplankton species in Galicia (NW Spain) between 1989 and 2008 to determine the main components of temporal variability in relation to climate and upwelling showed that most of this variability was stochastic, as seasonality and long term trends contributed to relatively small fractions of the series. In general, trends appeared as non linear, and species clustered in 4 groups according to the trend pattern but there was no defined pattern for diatoms, dinoflagellates or other groups. While, in general, total abundance increased, no clear trend was found for 23 species, 14 species decreased, 4 species increased during the early 1990s, and only 13 species showed a general increase through the series. In contrast, series of local environmental conditions (temperature, stratification, nutrients) and climate-related variables (atmospheric pressure indices, upwelling winds) showed a high fraction of their variability in deterministic seasonality and trends. As a result, each species responded independently to environmental and climate variability, measured by generalized additive models. Most species showed a positive relationship with nutrient concentrations but only a few showed a direct relationship with stratification and upwelling. Climate variables had only measurable effects on some species but no common response emerged. Because its adaptation to frequent disturbances, phytoplankton communities in upwelling ecosystems appear less sensitive to changes in regional climate than other communities characterized by short and well defined productive periods.

  17. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling.

    PubMed

    Bode, Antonio; Estévez, M Graciela; Varela, Manuel; Vilar, José A

    2015-09-01

    Phytoplankton is a sentinel of marine ecosystem change. Composed by many species with different life-history strategies, it rapidly responds to environment changes. An analysis of the abundance of 54 phytoplankton species in Galicia (NW Spain) between 1989 and 2008 to determine the main components of temporal variability in relation to climate and upwelling showed that most of this variability was stochastic, as seasonality and long term trends contributed to relatively small fractions of the series. In general, trends appeared as non linear, and species clustered in 4 groups according to the trend pattern but there was no defined pattern for diatoms, dinoflagellates or other groups. While, in general, total abundance increased, no clear trend was found for 23 species, 14 species decreased, 4 species increased during the early 1990s, and only 13 species showed a general increase through the series. In contrast, series of local environmental conditions (temperature, stratification, nutrients) and climate-related variables (atmospheric pressure indices, upwelling winds) showed a high fraction of their variability in deterministic seasonality and trends. As a result, each species responded independently to environmental and climate variability, measured by generalized additive models. Most species showed a positive relationship with nutrient concentrations but only a few showed a direct relationship with stratification and upwelling. Climate variables had only measurable effects on some species but no common response emerged. Because its adaptation to frequent disturbances, phytoplankton communities in upwelling ecosystems appear less sensitive to changes in regional climate than other communities characterized by short and well defined productive periods. PMID:26283032

  18. Wigner functions from the two-dimensional wavelet group.

    PubMed

    Ali, S T; Krasowska, A E; Murenzi, R

    2000-12-01

    Following a general procedure developed previously [Ann. Henri Poincaré 1, 685 (2000)], here we construct Wigner functions on a phase space related to the similitude group in two dimensions. Since the group space in this case is topologically homeomorphic to the phase space in question, the Wigner functions so constructed may also be considered as being functions on the group space itself. Previously the similitude group was used to construct wavelets for two-dimensional image analysis; we discuss here the connection between the wavelet transform and the Wigner function.

  19. Integrating abundance and functional traits reveals new global hotspots of fish diversity.

    PubMed

    Stuart-Smith, Rick D; Bates, Amanda E; Lefcheck, Jonathan S; Duffy, J Emmett; Baker, Susan C; Thomson, Russell J; Stuart-Smith, Jemina F; Hill, Nicole A; Kininmonth, Stuart J; Airoldi, Laura; Becerro, Mikel A; Campbell, Stuart J; Dawson, Terence P; Navarrete, Sergio A; Soler, German A; Strain, Elisabeth M A; Willis, Trevor J; Edgar, Graham J

    2013-09-26

    Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of

  20. Efficient solar water oxidation using photovoltaic devices functionalized with earth-abundant oxygen evolving catalysts.

    PubMed

    Cristino, Vito; Berardi, Serena; Caramori, Stefano; Argazzi, Roberto; Carli, Stefano; Meda, Laura; Tacca, Alessandra; Bignozzi, Carlo Alberto

    2013-08-21

    Indium tin oxide (ITO) surfaces of triple junction photovoltaic cells were functionalized with oxygen evolving catalysts (OECs) based on amorphous hydrous earth-abundant metal oxides (metal = Fe, Ni, Co), obtained by straightforward Successive Ionic Layer Adsorption and Reaction (SILAR) in an aqueous environment. Functionalization with Fe(iii) oxides gave the best results, leading to photoanodes capable of efficiently splitting water, with photocurrent densities up to 6 ± 1 mA cm(-2) at 0 V vs. the reversible hydrogen electrode (RHE) under AM 1.5 G simulated sunlight illumination. The resulting Solar To Hydrogen (STH) conversion efficiencies, measured in two electrodes configuration, were in the range 3.7-5%, depending on the counter electrode that was employed. Investigations on the stability showed that these photoanodes were able to sustain 120 minutes of continuous illumination with a < 10% photocurrent loss at 0 V vs. RHE. Pristine photoanodic response of the cells could be fully restored by an additional SILAR cycle, evidencing that the observed loss is due to the detachment of the more weakly surface bound catalyst.

  1. Sniffing for Clues to the Dinosaurs Demise: Measurement of Osmium Isotope Compositions and Platinum Group Element Abundances in Volcanic Emissions

    NASA Astrophysics Data System (ADS)

    Sims, K. W.; Peucker-Ehrenbrink, B.; Mather, T.; Pyle, D.; Martin, R.; Gauthier, P.; Aiuppa, A.

    2005-12-01

    Platinum Group Elements (PGE: Os, Ir, Rh, Ru, Pt, Pd) and osmium isotopes measured in marine and terrestrial sediment, snow and ice records are important paleo-tracers of riverine, hydrothermal, extraterrestrial, volcanic and anthropogenic inputs into the global surficial environment. For instance, the marine Os isotope record across the Cretaceous-Tertiary Boundary (KTB) indicates that the onset of the main phase of Deccan volcanism and the transient late Maastrichtian warming preceded the large extraterrestrial impact and the related KTB mass extinction by several hundred thousand years [Ravizza and Peucker-Ehrenbrink, 2003]. Distinguishing extraterrestrial from volcanic PGE sources has been difficult due to the similarity in Os isotopic compositions, complex PGE fractionations, and our lack of knowledge of the Os isotopic composition and PGE abundances in volcanic aerosols. These difficulties have fueled vigorous debate about extraterrestrial vs. volcanic triggers of mass extinctions in the geologic record. To assess the volcanic contribution to the global Re-Os-PGE cycle we have initiated a study of Os isotopic compositions and PGE abundances in volcanic emissions from volcanoes around the globe. Here we report preliminary data on PGE abundances and Os isotopes measured in gas and aerosol filter samples from Vulcan Masaya, Nicaragua and Mt Etna, Italy. Samples were analyzed by ID-ICPMS (ThermoFinnigan ELEMENT 2 and NEPTUNE) at the Woods Hole Oceanographic Institution. Osmium isotope compositions of the filters are unradiogenic (0.1272 to 0.187). Osmium concentrations range from 28 to 97 pg/cubic meter and are 3-4 orders of magnitude lower than those measured by Krahenbuhl et al. [1992] during the spring 1984 eruption of Mauna Loa just after the lava fountaining phase. Normalized PGE abundance patterns are fractionated relative to carbonaceous chondrites and two important features distinguish the pattern from other important PGE sources: 1) Os/Ir is much higher

  2. Replicating Small Group Research Using the Functional Theory.

    ERIC Educational Resources Information Center

    Cragan, John F.; Wright, David W.

    A replication study tested functional theory utilizing untrained full-fledged groups. One hundred forty undergraduate students who were enrolled in a small group communication course at a large midwestern university participated in small group discussions analyzing a plagiarism case used in an original study by R. Y. Hirokawa. Results indicated…

  3. Functional Analytic Psychotherapy for Interpersonal Process Groups: A Behavioral Application

    ERIC Educational Resources Information Center

    Hoekstra, Renee

    2008-01-01

    This paper is an adaptation of Kohlenberg and Tsai's work, Functional Analytical Psychotherapy (1991), or FAP, to group psychotherapy. This author applied a behavioral rationale for interpersonal process groups by illustrating key points with a hypothetical client. Suggestions are also provided for starting groups, identifying goals, educating…

  4. A Group 6 Late Embryogenesis Abundant Protein from Common Bean Is a Disordered Protein with Extended Helical Structure and Oligomer-forming Properties*

    PubMed Central

    Rivera-Najera, Lucero Y.; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O.; García-Hernández, Enrique; Solórzano, Rosa M.; Reyes, José L.; Covarrubias, Alejandra A.

    2014-01-01

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  5. A group 6 late embryogenesis abundant protein from common bean is a disordered protein with extended helical structure and oligomer-forming properties.

    PubMed

    Rivera-Najera, Lucero Y; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O; García-Hernández, Enrique; Solórzano, Rosa M; Reyes, José L; Covarrubias, Alejandra A

    2014-11-14

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  6. Differential Item Functioning Detection across Two Methods of Defining Group Comparisons: Pairwise and Composite Group Comparisons

    ERIC Educational Resources Information Center

    Sari, Halil Ibrahim; Huggins, Anne Corinne

    2015-01-01

    This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF…

  7. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  8. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data. PMID:26881747

  9. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  10. Effect of Habitat Size, Quality, and Isolation on Functional Groups of Beetles in Hollow Oaks

    PubMed Central

    Pilskog, Hanne Eik; Birkemoe, Tone; Framstad, Erik; Sverdrup-Thygeson, Anne

    2016-01-01

    One of the largest threats to biodiversity is land use change and habitat loss. Hollow oaks (Quercus spp. L.) are well-defined patches that are hotspots for biodiversity and red-listed species, but they are often rare and fragmented in the landscape. We investigated the effect of patch size, habitat quality, and isolation on functional groups and red-listed saproxylic beetles in hollow oaks (n = 40) in Norway. The groups were defined by host tree association, trophic grouping, and red-listed status. Habitat quality, represented by tree form was most important in explaining species richness for most groups. Patch size, represented by circumference and amount of dead branches, was most important in explaining abundance. Isolation, that is single oaks compared with oaks in groups, had a negative effect on the abundance of beetles feeding both on wood and fungi (xylomycethopagous), as well as on species associated with broadleaved trees (oak semi-specialists), but did not affect species richness. This indicates that at this scale and in this landscape, isolated oaks are as species rich and valuable for conservation as other oaks, although some functional groups may be more vulnerable to isolation than others. The red-listed species only responded to patch size, indicating that oaks with large circumference and many dead branches are especially important for red-listed species and for conservation. PMID:26945089

  11. Effect of Habitat Size, Quality, and Isolation on Functional Groups of Beetles in Hollow Oaks.

    PubMed

    Pilskog, Hanne Eik; Birkemoe, Tone; Framstad, Erik; Sverdrup-Thygeson, Anne

    2016-01-01

    One of the largest threats to biodiversity is land use change and habitat loss. Hollow oaks (Quercus spp. L.) are well-defined patches that are hotspots for biodiversity and red-listed species, but they are often rare and fragmented in the landscape. We investigated the effect of patch size, habitat quality, and isolation on functional groups and red-listed saproxylic beetles in hollow oaks (n = 40) in Norway. The groups were defined by host tree association, trophic grouping, and red-listed status. Habitat quality, represented by tree form was most important in explaining species richness for most groups. Patch size, represented by circumference and amount of dead branches, was most important in explaining abundance. Isolation, that is single oaks compared with oaks in groups, had a negative effect on the abundance of beetles feeding both on wood and fungi (xylomycethopagous), as well as on species associated with broadleaved trees (oak semi-specialists), but did not affect species richness. This indicates that at this scale and in this landscape, isolated oaks are as species rich and valuable for conservation as other oaks, although some functional groups may be more vulnerable to isolation than others. The red-listed species only responded to patch size, indicating that oaks with large circumference and many dead branches are especially important for red-listed species and for conservation. PMID:26945089

  12. Single or functionalized fullerenes interacting with heme group

    NASA Astrophysics Data System (ADS)

    Costa, Wallison Chaves; Diniz, Eduardo Moraes

    2014-09-01

    The heme group is responsible for iron transportation through the bloodstream, where iron participates in redox reactions, electron transfer, gases detection etc. The efficiency of such processes can be reduced if the whole heme molecule or even the iron is somehow altered from its original oxidation state, which can be caused by interactions with nanoparticles as fullerenes. To verify how such particles alter the geometry and electronic structure of heme molecule, here we report first principles calculations based on density functional theory of heme group interacting with single C60 fullerene or with C60 functionalized with small functional groups (-CH3, -COOH, -NH2, -OH). The calculations shown that the system heme + nanoparticle has a different spin state in comparison with heme group if the fullerene is functionalized. Also a functional group can provide a stronger binding between nanoparticle and heme molecule or inhibit the chemical bonding in comparison with single fullerene results. In addition heme molecule loses electrons to the nanoparticles and some systems exhibited a geometry distortion in heme group, depending on the binding energy. Furthermore, one find that such nanoparticles induce a formation of spin up states in heme group. Moreover, there exist modifications in density of states near the Fermi energy. Although of such changes in heme electronic structure and geometry, the iron atom remains in the heme group with the same oxidation state, so that processes that involve the iron might not be affected, only those that depend on the whole heme molecule.

  13. FGO: A novel ontology for identification of ligand functional group

    PubMed Central

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2007-01-01

    Small molecules play crucial role in the modulation of biological functions by interacting with specific macromolecules. Hence small molecule interactions are captured by a variety of experimental methods to estimate and propose correlations between molecular structures to their biological activities. The tremendous expanse in publicly available small molecules is also driving new efforts to better understand interactions involving small molecules particularly in area of drug docking and pharmacogenomics. We have studied and designed a functional group identification system with the associated ontology for it. The functional group identification system can detect the functional group components from given ligand structure with specific coordinate information. Functional group ontology (FGO) proposed by us is a structured classification of chemical functional group which acts as an important source of prior knowledge that may be automatically integrated to support identification, categorization and predictive data analysis tasks. We have used a new annotation method which can be used to construct the original structure from given ontological expression using exact coordinate information. Here, we also discuss about ontology-driven similarity measure of functional groups and uses of such novel ontology for pharmacophore searching and de-novo ligand designing. PMID:18288335

  14. Abundance- and functional-based mechanisms of plant diversity loss with fertilization in the presence and absence of herbivores.

    PubMed

    Yang, Zhongling; Hautier, Yann; Borer, Elizabeth T; Zhang, Chunhui; Du, Guozhen

    2015-09-01

    Nutrient supply and herbivores can regulate plant species composition, biodiversity and functioning of terrestrial ecosystems. Nutrient enrichment frequently increases plant productivity and decreases diversity while herbivores tend to maintain plant diversity in productive systems. However, the mechanisms by which nutrient enrichment and herbivores regulate plant diversity remain unclear. Abundance-based mechanisms propose that fertilization leads to the extinction of rare species due to random loss of individuals of all species. In contrast, functional-based mechanisms propose that species exclusion is based on functional traits which are disadvantageous under fertilized conditions. We tested mechanistic links between fertilization and diversity loss in the presence or absence of consumers using data from a 4-year fertilization and fencing experiment in an alpine meadow. We found that both abundance- and functional-based mechanisms simultaneously affected species loss in the absence of herbivores while only abundance-based mechanisms affected species loss in the presence of herbivores. Our results indicate that an abundance-based mechanism may consistently play a role in the loss of plant diversity with fertilization, and that diversity decline is driven primarily by the loss of rare species regardless of a plant's functional traits and whether or not herbivores are present. Increasing efforts to conserve rare species in the context of ecosystem eutrophication is a central challenge for grazed grassland ecosystems.

  15. Diversity and abundance of dung beetles (Coleoptera: Scaraebidae) at several different ecosystem functions in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Din, Abdullah Muhaimin Mohammad; Yaakop, Salmah; Hazmi, Izfa Riza

    2015-09-01

    Dung beetles has known for its bioindicator characteristic. Sensitive towards forest disturbance, dung beetles population and diversity will be less in disturbed and modified area. The objective of this study is to evaluate the diversity and distribution of dung beetles in different type of ecosystems in Peninsular Malaysia. Fifteen baited pitfall traps aligned in three transects were used in this study. Samples were collected after 24 h and repeated three time collections and identified afterwards. Two ecosystem types were selected, which are forested and agricultural ecosystem (livestock and plantation). A total of 4249 individuals, 47 species, in 11 genera was successfully collected from all localities. The H' index for Fraser Hill, Langkawi, Bangi Reserve Forest, Selangor (HSB), Sungkai Reserve Forest, Perak (SRF), Chini Lake, Bera Lake, chicken farm, goat farm, Longan plantation, and palm oil plantation were 1.58, 1.74, 2.17, 2.63, 1.80, 1.52, 1.63, 0.46, 0.00 and 1.98 respectively.Forest ecosystem, SRF shows the highest abundance (1486 individuals) and diversity, while for agricultural ecosystem,palm oil plantation shows the highest with 273 individuals and 16 species. Based onDetrended Correspondence Analysis (DCA) shows two groups that separate forest ecosystem with the agricultural ecosystem, with palm oil is the nearest to the forest. Palm oil ecosystem can sustain a dung beetles population due to the area can provide the requirements for the dung beetles to survive, such as food which comes from local domestic cows, shade from sunlight provide by the palm oil trees, and ground cover from small plants and shrubs.Even though modified ecosystem should have lower diversity of dung beetles, but some factors must be measured as well in order to have a better point of view.

  16. Conformation of a Group 2 Late Embryogenesis Abundant Protein from Soybean. Evidence of Poly (l-Proline)-type II Structure1

    PubMed Central

    Soulages, Jose L.; Kim, Kangmin; Arrese, Estela L.; Walters, Christina; Cushman, John C.

    2003-01-01

    Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (l-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (l-proline)-type II-like helical conformation at 12°C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80°C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt α-helical structure and to interact with phospholipid bilayers through amphipathic α-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic

  17. Functional Group and Substructure Searching as a Tool in Metabolomics

    PubMed Central

    Kotera, Masaaki; McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

    2008-01-01

    Background A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. Methodology We have developed a database named “Biochemical Substructure Search Catalogue” (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. Conclusions This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed. PMID:18253485

  18. Matrix intensification alters avian functional group composition in adjacent rainforest fragments.

    PubMed

    Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

    2013-01-01

    Conversion of farmland land-use matrices to surface mining is an increasing threat to the habitat quality of forest remnants and their constituent biota, with consequences for ecosystem functionality. We evaluated the effects of matrix type on bird community composition and the abundance and evenness within avian functional groups in south-west Ghana. We hypothesized that surface mining near remnants may result in a shift in functional composition of avifaunal communities, potentially disrupting ecological processes within tropical forest ecosystems. Matrix intensification and proximity to the remnant edge strongly influenced the abundance of members of several functional guilds. Obligate frugivores, strict terrestrial insectivores, lower and upper strata birds, and insect gleaners were most negatively affected by adjacent mining matrices, suggesting certain ecosystem processes such as seed dispersal may be disrupted by landscape change in this region. Evenness of these functional guilds was also lower in remnants adjacent to surface mining, regardless of the distance from remnant edge, with the exception of strict terrestrial insectivores. These shifts suggest matrix intensification can influence avian functional group composition and related ecosystem-level processes in adjacent forest remnants. The management of matrix habitat quality near and within mine concessions is important for improving efforts to preserveavian biodiversity in landscapes undergoing intensification such as through increased surface mining. PMID:24058634

  19. Use of stoichiometry to predict the abundance and functioning of root symbioses

    NASA Astrophysics Data System (ADS)

    Johnson, N. C.

    2012-04-01

    Plants form nutritional symbioses with fungi and bacteria and the importance of these partnerships varies with the mineral fertility of soil. There is strong evidence that plants acclimate and adapt to their local soil conditions through root symbioses; nitrogen limitation is ameliorated by symbiosis with diazotrophic prokaryotes and mycorrhizas ameliorate phosphorus limitation. Corollaries of ecological stoichiometry may be useful for predicting the abundance and functioning of mycorrhizas and N-fixation symbioses. A series of field experiments show that arbuscular mycorrhizal (AM) symbioses in grasslands in North America and in the African Serengeti are most beneficial to plant nutrition when plants are phosphorus limited and have sufficient nitrogen and carbon. A reciprocal inoculation experiment shows that locally adapted communities of AM fungi, associated soil organisms and plants arise such that mutualistic benefits are maximized; both AM fungi and plants grew best in their "home" soil-symbiont combination compared to "away" soil-symbiont combinations. Plants in their home combination acquired more limiting resource (either phosphorus or nitrogen) and consequently grew larger; similarly, AM fungi in their home combination formed more arbuscules and extraradical hyphae. Genetic analysis of the AM fungi inside plant roots indicate that these results correspond to variation in the community composition of AM fungi and also to variation in the symbiotic performance of local isolates of one particular species of AM fungus. The next step is to conduct landscape scale studies of root symbioses to test the hypothesis that plants cultivate microbial communities in and around their roots such that the species and ecotypes of microorganisms within these communities is customized for optimal nutrient acquisition under site-specific environmental conditions. If locally adapted communities of root and rhizosphere organisms are common, then plants may be optimizing their

  20. Functional Grouping in Residential Homes for People with Intellectual Disabilities.

    ERIC Educational Resources Information Center

    Mansell, Jim; Beadle-Brown, Julie; Macdonald, Susan; Ashman, Bev

    2003-01-01

    The effects of functional grouping of 303 people with intellectual disabilities on care practices in English group homes were investigated. Residents who were non-ambulant were rated as receiving care with less interpersonal warmth and residents with severe challenging behavior were rated as receiving care with less interpersonal warmth and…

  1. Using the Group Presentation to Foster Functional Skills.

    ERIC Educational Resources Information Center

    King, Kim M.

    1990-01-01

    Suggests using group presentations as a method for instructors with large introductory courses to help students gain functional skills and also make the courses more interesting. Provides examples of group presentation projects. States goals of projects as showing how sociology can be used in everyday life and providing a review of the examination…

  2. Quantitative distribution and functional groups of intertidal macrofaunal assemblages in Fildes Peninsula, King George Island, South Shetland Islands, Southern Ocean.

    PubMed

    Liu, Xiaoshou; Wang, Lu; Li, Shuai; Huo, Yuanzi; He, Peimin; Zhang, Zhinan

    2015-10-15

    To evaluate spatial distribution pattern of intertidal macrofauna, quantitative investigation was performed in January to February, 2013 around Fildes Peninsula, King George Island, South Shetland Islands. A total of 34 species were identified, which were dominated by Mollusca, Annelida and Arthropoda. CLUSTER analysis showed that macrofaunal assemblages at sand-bottom sites belonged to one group, which was dominated by Lumbricillus sp. and Kidderia subquadrata. Macrofaunal assemblages at gravel-bottom sites were divided into three groups while Nacella concinna was the dominant species at most sites. The highest values of biomass and Shannon-Wiener diversity index were found in gravel sediment and the highest value of abundance was in sand sediment of eastern coast. In terms of functional group, detritivorous and planktophagous groups had the highest values of abundance and biomass, respectively. Correlation analysis showed that macrofaunal abundance and biomass had significant positive correlations with contents of sediment chlorophyll a, phaeophorbide and organic matter.

  3. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation.

    PubMed

    Boswell, Leaf C; Menze, Michael A; Hand, Steven C

    2014-01-01

    Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA. PMID:25244376

  4. Background field functional renormalization group for absorbing state phase transitions.

    PubMed

    Buchhold, Michael; Diehl, Sebastian

    2016-07-01

    We present a functional renormalization group approach for the active to inactive phase transition in directed percolation-type systems, in which the transition is approached from the active, finite density phase. By expanding the effective potential for the density field around its minimum, we obtain a background field action functional, which serves as a starting point for the functional renormalization group approach. Due to the presence of the background field, the corresponding nonperturbative flow equations yield remarkably good estimates for the critical exponents of the directed percolation universality class, even in low dimensions. PMID:27575107

  5. Background field functional renormalization group for absorbing state phase transitions

    NASA Astrophysics Data System (ADS)

    Buchhold, Michael; Diehl, Sebastian

    2016-07-01

    We present a functional renormalization group approach for the active to inactive phase transition in directed percolation-type systems, in which the transition is approached from the active, finite density phase. By expanding the effective potential for the density field around its minimum, we obtain a background field action functional, which serves as a starting point for the functional renormalization group approach. Due to the presence of the background field, the corresponding nonperturbative flow equations yield remarkably good estimates for the critical exponents of the directed percolation universality class, even in low dimensions.

  6. Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

    PubMed

    Merlin, Chloé; Devers, Marion; Béguet, Jérémie; Boggio, Baptiste; Rouard, Nadine; Martin-Laurent, Fabrice

    2016-03-01

    The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil

  7. Detection of rare functional variants using group ISIS.

    PubMed

    Niu, Yue S; Hao, Ning; An, Lingling

    2011-11-29

    Genome-wide association studies have been firmly established in investigations of the associations between common genetic variants and complex traits or diseases. However, a large portion of complex traits and diseases cannot be explained well by common variants. Detecting rare functional variants becomes a trend and a necessity. Because rare variants have such a small minor allele frequency (e.g., <0.05), detecting functional rare variants is challenging. Group iterative sure independence screening (ISIS), a fast group selection tool, was developed to select important genes and the single-nucleotide polymorphisms within. The performance of the group ISIS and group penalization methods is compared for detecting important genes in the Genetic Analysis Workshop 17 data. The results suggest that the group ISIS is an efficient tool to discover genes and single-nucleotide polymorphisms associated to phenotypes.

  8. Runoff source or sink? Biocrust hydrological function strongly depends on the relative abundance of mosses

    NASA Astrophysics Data System (ADS)

    Bowker, M. A.; Eldridge, D. J.; Maestre, F. T.

    2012-04-01

    The redistribution of water in semi-arid environments is critical for overall ecosystem productivity. To a large degree, ecosystem engineers may determine the redistribution of water. Biological soil crusts (biocrusts) are one such group of ecosystem engineers. Their effects on infiltration have been somewhat controversial, varying from place to place and ranging from strongly positive to strongly negative. In addition, they coexist with and are modified by additional ecosystem engineers. We used a systems approach to examine the interactive effects of multiple engineers on infiltration processes across two analogous sets of interactors. First in Spain, we examined interactions among Stipa tenacissima, biocrusts, and the European rabbit; and in Australia, the interaction between biocrusts and the bilby (a rabbit-like marsupial). We focused on the effects of particular community properties of biocrusts such as species richness, total cover, species composition, and spatial patterning to characterize their variable effects on infiltration. We measured the early (sorptivity) and later (steady-state infiltration) stages of infiltration at two supply potentials using disk permeameters, which allowed us to determine the relative effects of different engineers and soil micropores on water flow through large macropores. In the Spanish case, structural equation modeling showed that both Stipa and biocrust cover exerted substantial and equal positive effects on infiltration under ponding, whereas indirectly, rabbit disturbance negatively affected infiltration by reducing crust cover; rabbits had negligible direct effects. The biocrust influence could be partitioned roughly equally between total cover and composition. All lichen species were negatively related to infiltration and almost all mosses were positively related to infiltration. In the Australian study, bilby forage pits had a direct and strong positive influence on steady state infiltration under ponding and most

  9. Single or functionalized fullerenes interacting with heme group

    SciTech Connect

    Costa, Wallison Chaves; Diniz, Eduardo Moraes

    2014-09-15

    The heme group is responsible for iron transportation through the bloodstream, where iron participates in redox reactions, electron transfer, gases detection etc. The efficiency of such processes can be reduced if the whole heme molecule or even the iron is somehow altered from its original oxidation state, which can be caused by interactions with nanoparticles as fullerenes. To verify how such particles alter the geometry and electronic structure of heme molecule, here we report first principles calculations based on density functional theory of heme group interacting with single C{sub 60} fullerene or with C{sub 60} functionalized with small functional groups (−CH{sub 3}, −COOH, −NH{sub 2}, −OH). The calculations shown that the system heme + nanoparticle has a different spin state in comparison with heme group if the fullerene is functionalized. Also a functional group can provide a stronger binding between nanoparticle and heme molecule or inhibit the chemical bonding in comparison with single fullerene results. In addition heme molecule loses electrons to the nanoparticles and some systems exhibited a geometry distortion in heme group, depending on the binding energy. Furthermore, one find that such nanoparticles induce a formation of spin up states in heme group. Moreover, there exist modifications in density of states near the Fermi energy. Although of such changes in heme electronic structure and geometry, the iron atom remains in the heme group with the same oxidation state, so that processes that involve the iron might not be affected, only those that depend on the whole heme molecule.

  10. Platinum-group element abundance and distribution in chromite deposits of the Acoje Block, Zambales Ophiolite Complex, Philippines

    USGS Publications Warehouse

    Bacuta, G.C.; Kay, R.W.; Gibbs, A.K.; Lipin, B.R.

    1990-01-01

    Platinum-group elements (PGE) occur in ore-grade concentration in some of the chromite deposits related to the ultramafic section of the Acoje Block of the Zambales Ophiolite Complex. The deposits are of three types: Type 1 - associated with cumulate peridotites at the base of the crust; Type 2 - in dunite pods from the top 1 km of mantle harzburgite; and Type 3 - like Type 2, but in deeper levels of the harzburgite. Most of the deposites have chromite compositions that are high in Cr with Cr/(Cr + Al) (expressed as chromium index, Cr#) > 0.6; high-Al (Cr# Pd, thought to be characteristic of PGE-barren deposits) and positive slope (Ir < Pd, characteristic of PGE-rich deposits). Iridium, Ru and Os commonly occur as micron-size laurite (sulfide) inclusions in unfractured chromite. Laurite and native Os are also found as inclusions in interstitial sulfides. Platinum and Pd occur as alloy inclusions (and possibly as solid solution) in interstitial Ni-Cu sulfides and as tellurobismuthides in serpentine and altered sulfides. Variability of PGE distribution may be explained by alteration, crystal fractionation or partial melting processes. Alteration and metamorphism were ruled out, because PGE contents do not correlate with degree of serpentinization or the abundance and type (hydroxyl versus non-hydroxyl) of silicate inclusions in chromite. Preliminary Os isotopic data do not support crustal contamination as a source of the PGEs in the Acoje deposits. The anomalous PGE concentrations in Type 1 high-Cr chromite deposits are attributed to two stages of enrichment: an early enrichment of their mantle source from previous melting events and a later stage of sulfide segregation accompanying chromite crystallization. High-Al chromite deposits which crystallized from basalts derived from relatively low degrees of melting owe their low PGE content to partitioning of PGEs in sulfides and alloys that remain in the mantle. High-Cr deposits crystallized from melts that were

  11. Functional Gene Group Summarization by Clustering MEDLINE Abstract Sentences

    PubMed Central

    Yang, Jianji; Cohen, Aaron M.; Hersh, William R.

    2006-01-01

    Tools to automatically summarize functional gene group information from the biomedical literature will help genomics researchers both better interpret gene expression data and understand biological pathways. In this study, we built a system that takes in a set of genes and MEDLINE records and outputs clusters of genes along with summaries of each cluster by sentence extraction from MEDLINE abstracts. Our preliminary use-case evaluation shows that this approach can identify gene clusters similar to manually generated groupings. PMID:17238770

  12. The carbon functional group budget of a peatland

    NASA Astrophysics Data System (ADS)

    Moody, Catherine; Worrall, Fred; Clay, Gareth; Apperley, David

    2016-04-01

    Organic matter samples were taken from each organic matter reservoir and fluvial flux found in a peatland and analysed by elemental analysis for carbon, hydrogen, nitrogen and oxygen content, and by 13C solid state nuclear magnetic resonance (NMR) for functional group composition. The samples analysed were: aboveground, belowground, heather, mosses and sedges, litter layer, four different depths from a peat core, and monthly samples of fluvial particulate and dissolved organic matter. All organic matter samples were taken from a 100% peat catchment within Moor House National Nature Reserve in the North Pennines, UK. The proportion of carbon atoms from each of the eight carbon functional groups (C-alkyl, N-alkyl/methoxyl C, O-alkyl, O2-alkyl/acetal C, aromatic/unsaturated C, phenolic C, aldehyde/ketone C and amide/carboxyl C) from each type of organic matter were combined with an existing carbon budget from the same site, to give a functional group carbon budget. The budget results show that the ecosystem is accumulating N-alkyl/methoxyl C, O-alkyl, O2-alkyl/acetal C and phenolic C groups, but losing C-alkyl, aromatic/unsaturated C, amide/carboxyl C and aldehyde/ketone C. Comparing the functional group compositions between the sampled organic matter pools shows that DOM arises from two distinct sources; from the peat itself and from a vegetation source.

  13. From infinite to two dimensions through the functional renormalization group.

    PubMed

    Taranto, C; Andergassen, S; Bauer, J; Held, K; Katanin, A; Metzner, W; Rohringer, G; Toschi, A

    2014-05-16

    We present a novel scheme for an unbiased, nonperturbative treatment of strongly correlated fermions. The proposed approach combines two of the most successful many-body methods, the dynamical mean field theory and the functional renormalization group. Physically, this allows for a systematic inclusion of nonlocal correlations via the functional renormalization group flow equations, after the local correlations are taken into account nonperturbatively by the dynamical mean field theory. To demonstrate the feasibility of the approach, we present numerical results for the two-dimensional Hubbard model at half filling. PMID:24877952

  14. Species, functional groups, and thresholds in ecological resilience

    USGS Publications Warehouse

    Sundstrom, Shana M.; Allen, Craig R.; Barichievy, Chris

    2012-01-01

    The cross-scale resilience model states that ecological resilience is generated in part from the distribution of functions within and across scales in a system. Resilience is a measure of a system's ability to remain organized around a particular set of mutually reinforcing processes and structures, known as a regime. We define scale as the geographic extent over which a process operates and the frequency with which a process occurs. Species can be categorized into functional groups that are a link between ecosystem processes and structures and ecological resilience. We applied the cross-scale resilience model to avian species in a grassland ecosystem. A species’ morphology is shaped in part by its interaction with ecological structure and pattern, so animal body mass reflects the spatial and temporal distribution of resources. We used the log-transformed rank-ordered body masses of breeding birds associated with grasslands to identify aggregations and discontinuities in the distribution of those body masses. We assessed cross-scale resilience on the basis of 3 metrics: overall number of functional groups, number of functional groups within an aggregation, and the redundancy of functional groups across aggregations. We assessed how the loss of threatened species would affect cross-scale resilience by removing threatened species from the data set and recalculating values of the 3 metrics. We also determined whether more function was retained than expected after the loss of threatened species by comparing observed loss with simulated random loss in a Monte Carlo process. The observed distribution of function compared with the random simulated loss of function indicated that more functionality in the observed data set was retained than expected. On the basis of our results, we believe an ecosystem with a full complement of species can sustain considerable species losses without affecting the distribution of functions within and across aggregations, although

  15. Species, functional groups, and thresholds in ecological resilience.

    PubMed

    Sundstrom, Shana M; Allen, Craig R; Barichievy, Chris

    2012-04-01

    The cross-scale resilience model states that ecological resilience is generated in part from the distribution of functions within and across scales in a system. Resilience is a measure of a system's ability to remain organized around a particular set of mutually reinforcing processes and structures, known as a regime. We define scale as the geographic extent over which a process operates and the frequency with which a process occurs. Species can be categorized into functional groups that are a link between ecosystem processes and structures and ecological resilience. We applied the cross-scale resilience model to avian species in a grassland ecosystem. A species' morphology is shaped in part by its interaction with ecological structure and pattern, so animal body mass reflects the spatial and temporal distribution of resources. We used the log-transformed rank-ordered body masses of breeding birds associated with grasslands to identify aggregations and discontinuities in the distribution of those body masses. We assessed cross-scale resilience on the basis of 3 metrics: overall number of functional groups, number of functional groups within an aggregation, and the redundancy of functional groups across aggregations. We assessed how the loss of threatened species would affect cross-scale resilience by removing threatened species from the data set and recalculating values of the 3 metrics. We also determined whether more function was retained than expected after the loss of threatened species by comparing observed loss with simulated random loss in a Monte Carlo process. The observed distribution of function compared with the random simulated loss of function indicated that more functionality in the observed data set was retained than expected. On the basis of our results, we believe an ecosystem with a full complement of species can sustain considerable species losses without affecting the distribution of functions within and across aggregations, although ecological

  16. The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete

    PubMed Central

    Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis

    2014-01-01

    A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

  17. Chapter 8. Resident Group Influences on Team Functioning

    ERIC Educational Resources Information Center

    Burford, Gale E.; Fulcher, Leon C.

    2006-01-01

    Research has documented important interplays between the diagnostic characteristics of residents in group care centers and the functioning of staff teams responsible for the delivery of services. Factors that impact on the quality of working life satisfactions and frustrations are variable over time and may originate from within the team, the…

  18. Assemblage patterns of fish functional groups relative to habitat connectivity and conditions in floodplain lakes

    USGS Publications Warehouse

    Miyazono, S.; Aycock, J.N.; Miranda, L.E.; Tietjen, T.E.

    2010-01-01

    We evaluated the influences of habitat connectivity and local environmental factors on the distribution and abundance patterns of fish functional groups in 17 floodplain lakes in the Yazoo River Basin, USA. The results of univariate and multivariate analyses showed that species-environmental relationships varied with the functional groups. Species richness and assemblage structure of periodic strategists showed strong and positive correlations with habitat connectivity. Densities of most equilibrium and opportunistic strategists decreased with habitat connectivity. Densities of certain equilibrium and opportunistic strategists increased with turbidity. Forested wetlands around the lakes were positively related to the densities of periodic and equilibrium strategists. These results suggest that decreases in habitat connectivity, forested wetland buffers and water quality resulting from environmental manipulations may cause local extinction of certain fish taxa and accelerate the dominance of tolerant fishes in floodplain lakes. ?? 2010 John Wiley & Sons A/S.

  19. The functional importance of blood group-active molecules in human red blood cells.

    PubMed

    Anstee, D J

    2011-01-01

    Antigens of 23 of the 30 human blood group systems are defined by the amino acid sequence of red cell membrane proteins. The antigens of DI, RH, RHAG, MNS, GE and CO systems are carried on blood group-active proteins (Band 3, D and CE polypeptides, RhAG, Glycophorins A and B, Glycophorins C and D and Aquaporin 1, respectively) which are expressed at high levels (>200,000 copies/red cell). These major proteins contribute to essential red cell functions either directly as membrane transporters and by providing linkage to the underlying red cell skeleton or by facilitating the membrane assembly of the protein complexes involved in these processes. The proteins expressing antigens of the remaining 17 blood group systems are much less abundant (<20,000 copies/red cell) and their functional importance for the circulating red cell is largely unknown. Human gene knock-outs (null phenotypes) have been described for many of these minor blood group-active proteins, but only absence of Kx glycoprotein has been clearly linked with pathology directly related to the function of circulating red cells. Recent evidence suggesting the normal quality control system for glycoprotein synthesis is altered during the latter stages of red cell production raises the possibility that many of these low abundance blood group-active proteins are vestigial. In sickle cell disease and polycythaemia vera, elevated Lutheran glycoprotein expression may contribute to pathology. Dyserythropoiesis with reduced antigen expression can result from mutations in the erythroid transcription factors GATA-1 and EKLF.

  20. Functional group accessibility in hydrogen bonded polymer blends

    NASA Astrophysics Data System (ADS)

    Pehlert, George James

    Intramolecular screening and functional group accessibility are important concepts in hydrogen bonded polymer blends. Intramolecular screening results from the fact that the units in a polymer are linked together via covalent bonds (chain connectivity). This linking together of the units results in an increase in the number of same chain contacts (self-association) due to the chains bending back upon themselves, both locally and through long range effects. Because of this effect, the number of interchain contacts (interassociation) in a polymer blend is significantly lower than that observed in an analogous low molecular weight mixture. In addition to intramolecular screening, evidence has been found showing that the accessibility of functional groups is affected by factors such as the functional groups being too close to one another along the (co)polymer chain and steric shielding due to the presence of bulky or long chain side groups. The effect of these factors on the scaling and transferability of self-association and interassociation equilibrium constants is discussed, together with ramifications in terms of the predictions of miscibility windows and maps (using the association model) for hydrogen bonded polymer blends.

  1. Nonylphenol biodegradation, functional gene abundance and bacterial community in bioaugmented sediment: effect of external carbon source.

    PubMed

    Wang, Zhao; Dai, Yu; Zhao, Qun; Li, Ningning; Zhou, Qiheng; Xie, Shuguang

    2015-08-01

    Nonylphenol (NP) biodegradation in river sediment using Stenotrophomonas strain Y1 and Sphingobium strain Y2 were proved to be an effective strategy to remediate NP pollution in our earlier study. The purpose of this study is to investigate the influence of glucose addition on their ability to degrade NP in both liquid cultures and sediment microcosms. The shift in bacterial community structure and relative abundance of NP degraders in sediment microcosms were characterized using terminal restriction fragment length polymorphism analysis. The proportion of NP-degrading alkB and sMO genes was assessed using quantitative polymerase chain reaction (PCR) assay. The growth of Stenotrophomonas strain Y1 and its NP biodegradation efficiency were inhibited by glucose supplementation, while the relative abundance of alkB gene increased. However, NP degradation, as well as the growth of added degraders and proportion of sMO gene, was enhanced in the glucose-amended sediment microcosms inoculated with Sphingobium strain Y2. Moreover, external glucose addition altered bacterial community structures in bioaugmented sediment microcosms, depending on the level of glucose dosage.

  2. [Study on Characteristics of Terahertz Spectra of Organic Functional Groups].

    PubMed

    Ma, Chun-qian; Xu, Xiang-dong; Zou, Rui-jiao; Liu, Yi-ke; He, Qiong; Jiang, Ya-dong; Huang, Rui; Wen, Yue-jiang; Sun, Zi-qiang

    2015-04-01

    Fourier transform infrared (FTIR) was exploited to measure terahertz (THz) spectra in the wave number range of 30-300 cm(-1) for saturated straight chain organic molecules at room temperature. The results reveal that different organic functional groups exhibit different THz spectral characteristics. The absorption peaks of vibration modes of organic crystal lattice locate in high frequency range of THz, while those of vibration modes of intermolecular hydrogen (H) bonds appear in low frequency range of THz. Moreover, a typical absorption peak of intermolecular H bonds caused by saturated straight-chain monohydric alcohol hydroxyl functional groups locates at 57 cm(-1), while a characteristic absorption peak of intermolecular hydrogen bonds caused by triacontanoic acid carboxyl functional groups appears at 74 cm(-1). The intermolecular H bonds not only result in that the THz absorbing abilities of triacontanol and triacontanoic acid are significantly stronger than that of triacontane, but also cause regular red-shift and blue-shift of the THz absorption peaks of triacontanoic acid, as compared with those of triacontanol. In addition, density functional theory (DFT) B3LYP/6-311G(d,p) basis set was employed to simulate the THz spectra of saturated straight-chain alkane, alkanol and acid, respectively. The simulation results indicate that for the organic molecules with stronger intermolecular H bonds, lower consistent degree of the THz spectrum simulated from monomer molecule with the THz spectrum experimentally measured will occur. Moreover, the simulation results of dimer structures agree well with the measured spectra as compared to those simulated from monomer molecule structures. The results presented in this work are of great significance not only to the study of the THz spectral characteristics of other organic functional groups, but also to the clarification of the vibration modes of organic molecules. Particularly, our results are also helpful for clarifying

  3. Anthropogenic disturbances influencing ciliate functional feeding groups in impacted tropical streams.

    PubMed

    Segovia, Bianca Trevizan; Lansac-Toha, Fernando Miranda; de Meira, Bianca Ramos; Cabral, Adalgisa Fernanda; Lansac-Tôha, Fabio Amodêo; Velho, Luiz Felipe Machado

    2016-10-01

    Anthropogenic disturbances change the trophic structure of streams, ultimately affecting ecosystem functioning. We investigated the effects of human disturbances, mainly organic pollution, on ciliate functional feeding groups (FFG) in 10 tropical streams near agricultural and urban habitats, in the dry and rainy seasons. We hypothesised that the organic pollution would affect the ciliate composition and that the richness and abundance of ciliate FFG would be associated with different disturbances, such that an increase in the load of organic matter would result in an increase in the percentage of bacterivores ciliates, while streams with low organic matter concentration and wide canopy openness will determine a higher contribution of algivorous ciliates. Our results corroborate our hypothesis of an increased development of bacterivorous ciliates with increasing organic pollution, but only in the abundance of this FFG. Also, algivorous ciliates were found to be related to riparian vegetation clearing. Thus, ciliate FFG accurately reflected different anthropogenic disturbances, revealing a change in the trophic structure of the streams. In addition, we found that organic pollution can lead to both taxonomic and functional homogenization of the ciliate community, which implies serious consequences for ecosystem functioning.

  4. Groups as units of functional analysis, individuals as proximate mechanisms.

    PubMed

    Wilson, David Sloan

    2014-06-01

    Whenever selection operates at a given level of a multitier hierarchy, units at that level should become the object of functional analysis, and units at lower levels should be studied as proximate mechanisms. This intuition already exists for the study of genes in individuals, when individuals are the unit of selection. It is only beginning to be applied for the study of individuals in groups, when groups are the unit of selection. Smaldino's target article is an important step in this direction with an emphasis on human cultural evolution, but the same algorithm applies to all multilevel evolutionary processes.

  5. Oxygen functional groups in graphitic carbon nitride for enhanced photocatalysis.

    PubMed

    Liu, Shizhen; Li, Degang; Sun, Hongqi; Ang, Ha Ming; Tadé, Moses O; Wang, Shaobin

    2016-04-15

    Metal-free semiconductors offer a new opportunity for environmental photocatalysis toward a potential breakthrough in high photo efficiency with complete prevention of metal leaching. In this study, graphitic carbon nitride (GCN) modified by oxygen functional groups was synthesized by a hydrothermal treatment of pristine GCN at different temperatures with H2O2. Insights into the emerging characteristics of the modified GCN in photocatalysis were obtained by determining the optical properties, band structure, electrochemical activity and pollutant degradation efficiency. It was found that the introduction of GCN with oxygen functional groups can enhance light absorption and accelerate electron transfer so as to improve the photocatalytic reaction efficiency. The photoinduced reactive radicals and the associated photodegradation were investigated by in situ electron paramagnetic resonance (EPR). The reactive radicals, O2(-) and OH, were responsible for organic degradation.

  6. Properties of graphene inks stabilized by different functional groups

    NASA Astrophysics Data System (ADS)

    Wei, Di; Li, Hongwei; Han, Dongxue; Zhang, Qixian; Niu, Li; Yang, Huafeng; Bower, Chris; Andrew, Piers; Ryhänen, Tapani

    2011-06-01

    Different graphene inks have been synthesized by chemical methods. These uniform dispersions were stabilized by various functional groups such as room temperature ionic liquid, polyaniline, polyelectrolyte (poly[2,5-bis(3-sulfonatopropoxy)-1,4-ethynylphenylene-alt-1,4-ethynylphenylene] sodium salt) and poly(styrenesulfonate) (PSS). The dispersions can be easily cast into high-quality, free-standing films but with very different physiochemical properties such as surface tension and adhesion. SEM and AFM methods have been applied to have a detailed study of the properties of the inks. It is found that graphenes modified by p-type polyaniline show the highest surface tension. Diverse surface adhesive properties to the substrate are also found with various functional groups. The different viscoelasticities of graphene inks were related to the microscopic structure of their coating layer and subsequently related to the configuration, chemistry and molecular dimensions of the modifying molecules to establish the property-structure relationship. Modifications of graphene inks made from chemical reduction cannot only enable cost-effective processing for printable electronics but also extend the applications into, for example, self-assembly of graphene via bottom-up nano-architecture and surface energy engineering of the graphenes. To fabricate useful devices, understanding the surface properties of graphene inks is very important. It is the first paper of this kind to study the surface tension and adhesion of graphene influenced by different functional groups.

  7. Functional renormalization group analysis of tensorial group field theories on Rd

    NASA Astrophysics Data System (ADS)

    Geloun, Joseph Ben; Martini, Riccardo; Oriti, Daniele

    2016-07-01

    Rank-d tensorial group field theories are quantum field theories (QFTs) defined on a group manifold G×d , which represent a nonlocal generalization of standard QFT and a candidate formalism for quantum gravity, since, when endowed with appropriate data, they can be interpreted as defining a field theoretic description of the fundamental building blocks of quantum spacetime. Their renormalization analysis is crucial both for establishing their consistency as quantum field theories and for studying the emergence of continuum spacetime and geometry from them. In this paper, we study the renormalization group flow of two simple classes of tensorial group field theories (TGFTs), defined for the group G =R for arbitrary rank, both without and with gauge invariance conditions, by means of functional renormalization group techniques. The issue of IR divergences is tackled by the definition of a proper thermodynamic limit for TGFTs. We map the phase diagram of such models, in a simple truncation, and identify both UV and IR fixed points of the RG flow. Encouragingly, for all the models we study, we find evidence for the existence of a phase transition of condensation type.

  8. Slug responses to grassland cutting and fertilizer application under plant functional group removal

    NASA Astrophysics Data System (ADS)

    Everwand, Georg; Scherber, Christoph; Tscharntke, Teja

    2013-04-01

    Current studies on trophic interactions in biodiversity experiments have largely relied on artificially sown gradients in plant diversity, but removal experiments with their more natural plant community composition are more realistic. Slugs are a major part of the invertebrate herbivore community, with some species being common pests in agriculture. We therefore investigated how strongly slugs are influenced by grassland management, plant biodiversity and composition. Here we analysed the effects of cutting frequency, fertilizer application and plant functional group composition on slug densities and their contribution to herbivory on Rumex acetosa in a removal experiment within a >100-year old grassland in Northern Germany. The experiment was laid out as a Latin rectangle with full factorial combinations of (i) plant functional group removal (3 levels) using herbicides, (ii) fertilizer application (2 levels) and (iii) cutting frequency (2 levels). The resulting 12 treatment combinations were replicated 6 times, resulting in 72 plots. We collected a total of 1020 individuals belonging to three species Arion distinctus (60.4% of individuals), Deroceras reticulatum (34.7%) and Arion lusitanicus (4.9%) using a cover board technique and additionally measured herbivore damage to R. acetosa. We found the highest slug abundance on plots with a low cutting frequency and high food resource availability (increased cover of forbs and taller vegetation). Fertilizer application had no significant effect on slug abundance, but caused higher herbivore damage to on R. acetosa, possibly as a result of increased tissue quality. The negative effect of higher cutting frequency on slug abundance was lowest in control plots with their naturally developed graminoid-forb communities (cutting reduced slug density by 6% in the control vs. 29% in herbicide plots). Our experiments therefore support the idea that more natural plant species compositions reduce the impact of disturbances (e

  9. The effects of knee injury on skeletal muscle function, Na+, K+-ATPase content, and isoform abundance

    PubMed Central

    Perry, Ben D; Levinger, Pazit; Morris, Hayden G; Petersen, Aaron C; Garnham, Andrew P; Levinger, Itamar; McKenna, Michael J

    2015-01-01

    While training upregulates skeletal muscle Na+, K+-ATPase (NKA), the effects of knee injury and associated disuse on muscle NKA remain unknown. This was therefore investigated in six healthy young adults with a torn anterior cruciate ligament, (KI; four females, two males; age 25.0 ± 4.9 years; injury duration 15 ± 17 weeks; mean ± SD) and seven age- and BMI-matched asymptomatic controls (CON; five females, two males). Each participant underwent a vastus lateralis muscle biopsy, on both legs in KI and one leg in CON. Muscle was analyzed for muscle fiber type and cross-sectional area (CSA), NKA content ([3H]ouabain binding), and α1–3 and β1–2 isoform abundance. Participants also completed physical activity and knee function questionnaires (KI only); and underwent quadriceps peak isometric strength, thigh CSA and postural sway assessments in both injured and noninjured legs. NKA content was 20.1% lower in the knee-injured leg than the noninjured leg and 22.5% lower than CON. NKA α2 abundance was 63.0% lower in the knee-injured leg than the noninjured leg, with no differences in other NKA isoforms. Isometric strength and thigh CSA were 21.7% and 7.1% lower in the injured leg than the noninjured leg, respectively. In KI, postural sway did not differ between legs, but for two-legged standing was 43% higher than CON. Hence, muscle NKA content and α2 abundance were reduced in severe knee injury, which may contribute to impaired muscle function. Restoration of muscle NKA may be important in rehabilitation of muscle function after knee and other lower limb injury. PMID:25677549

  10. Characterization of Sea Lettuce Surface Functional Groups by Potentiometric Titrations

    NASA Astrophysics Data System (ADS)

    Ebling, A. M.; Schijf, J.

    2008-12-01

    In pursuit of our ultimate goal to better understand the prodigious capacity of the marine macroalga Ulva lactuca (sea lettuce) for adsorbing a broad range of dissolved trace metals from seawater, we performed an initial characterization of its surface functional groups. Specifically, the number of distinct functional groups as well as their individual bulk concentrations and acid dissociation constants (pKas) were determined by potentiometric titrations in NaCl solutions of various ionic strengths (I = 0.01-5.0 M), under inert nitrogen atmosphere at 25°C. Depending on the ionic strength, Ulva samples were manually titrated down to pH 2 or 3 with 1 N HCl and then up to pH 10 with 1 N NaOH in steps of 0.1-0.2 units, continuously monitoring pH with a glass combination electrode. Titrations of a dehydrated Ulva standard reference material (BCR-279) were compared with fresh Ulva tissue cultured in our laboratory. A titration in filtered natural seawater was also compared with one in an NaCl solution of equal ionic strength. Equilibrium constants for the ionization of water in NaCl solutions as a function of ionic strength were obtained from the literature. Fits to the titration data ([H]T vs. pH) were performed with the FITEQL4.0 computer code using non-electrostatic 3-, 4-, and 5-site models, either by fixing ionic strength at its experimental value or by allowing it to be extrapolated to zero, while considering all functional group pKas and bulk concentrations as adjustable parameters. Since pKas and bulk concentrations were found to be strongly correlated, the latter were also fixed in some cases to further constrain the pKas. Whereas these calculations are currently ongoing, preliminary results point to three, possibly four, functional groups with pKas of about 4.1, 6.3, and 9.5 at I = 0. Bulk concentrations of the three groups are very similar, about 5-6×10-4 mol/g based on dry weight, which suggests that all are homogeneously distributed over the surface and

  11. Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands

    PubMed Central

    Reverchon, Frédérique; Bai, Shahla H.; Liu, Xian; Blumfield, Timothy J.

    2015-01-01

    Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ15N), and inorganic N pools. Soil pH and δ15N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4+ concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and denitrification

  12. Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands.

    PubMed

    Reverchon, Frédérique; Bai, Shahla H; Liu, Xian; Blumfield, Timothy J

    2015-01-01

    Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ(15)N), and inorganic N pools. Soil pH and δ(15)N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4 (+) concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and

  13. Geographic differences between functional groups in patterns of bird species richness in North America

    NASA Astrophysics Data System (ADS)

    Carnicer, Jofre; Díaz-Delgado, Ricardo

    2008-03-01

    Geographic divergences in patterns of species richness were studied for the terrestrial birds of North America using Breeding Bird Survey (BBS) census data subdivided for guild and migratory groups. Our aim was to study if species richness patterns for North American birds were best viewed as the convergent response of different groups to a common mechanism or as the result of several different processes. We observed opposite geographical patterns of species richness and differences in the variables associated with species richness depending on the guild or migratory status considered. Several ecological variables seem to regulate large-scale patterns of terrestrial bird species richness in North America, mainly temperature-, productivity- and landscape habitat structure-related variables. These variables are diverse and group-specific. For instance, the results supported the productivity hypothesis in migratory and frugivore groups and the winter tolerance hypothesis in residents. Habitat structure was also identified as an important factor driving species richness, total abundance and community body mass variation. Overall, our results indicate that the large-scale patterns of bird species richness are the result of several divergent, group-specific processes, and that understanding diversity gradients requires the identification of the functional ecological groups included.

  14. Intracellular localization of a group II chaperonin indicates a membrane-related function

    NASA Technical Reports Server (NTRS)

    Trent, Jonathan D.; Kagawa, Hiromi K.; Paavola, Chad D.; McMillan, R. Andrew; Howard, Jeanie; Jahnke, Linda; Lavin, Colleen; Embaye, Tsegereda; Henze, Christopher E.

    2003-01-01

    Chaperonins are protein complexes that are believed to function as part of a protein folding system in the cytoplasm of the cell. We observed, however, that the group II chaperonins known as rosettasomes in the hyperthermophilic archaeon Sulfolobus shibatae, are not cytoplasmic but membrane associated. This association was observed in cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C by using immunofluorescence microscopy and in thick sections of rapidly frozen cells grown at 76 degrees C by using immunogold electron microscopy. We observed that increased abundance of rosettasomes after heat shock correlated with decreased membrane permeability at lethal temperature (92 degrees C). This change in permeability was not seen in cells heat-shocked in the presence of the amino acid analogue azetidine 2-carboxylic acid, indicating functional protein synthesis influences permeability. Azetidine experiments also indicated that observed heat-induced changes in lipid composition in S. shibatae could not account for changes in membrane permeability. Rosettasomes purified from cultures grown at 60 degrees C and 76 degrees C or heat-shocked at 85 degrees C bind to liposomes made from either the bipolar tetraether lipids of Sulfolobus or a variety of artificial lipid mixtures. The presence of rosettasomes did not significantly change the transition temperature of liposomes, as indicated by differential scanning calorimetry, or the proton permeability of liposomes, as indicated by pyranine fluorescence. We propose that these group II chaperonins function as a structural element in the natural membrane based on their intracellular location, the correlation between their functional abundance and membrane permeability, and their potential distribution on the membrane surface.

  15. Organized thiol functional groups in mesoporous core shell colloids

    SciTech Connect

    Marchena, Martin H.; Granada, Mara; Bordoni, Andrea V.; Joselevich, Maria; Troiani, Horacio; Williams, Federico J.; Wolosiuk, Alejandro

    2012-03-15

    The co-condensation in situ of tetraethoxysilane (TEOS) and mercaptopropyltrimethoxysilane (MPTMS) using cetyltrimethylammonium bromide (CTAB) as a template results in the synthesis of multilayered mesoporous structured SiO{sub 2} colloids with 'onion-like' chemical environments. Thiol groups were anchored to an inner selected SiO{sub 2} porous layer in a bilayered core shell particle producing different chemical regions inside the colloidal layered structure. X-Ray Photoelectron Spectroscopy (XPS) shows a preferential anchoring of the -SH groups in the double layer shell system, while porosimetry and simple chemical modifications confirm that pores are accessible. We can envision the synthesis of interesting colloidal objects with defined chemical environments with highly controlled properties. - Graphical abstract: Mesoporous core shell SiO{sub 2} colloids with organized thiol groups. Highlights: Black-Right-Pointing-Pointer Double shell mesoporous silica colloids templated with CTAB. Black-Right-Pointing-Pointer Sequential deposition of mesoporous SiO{sub 2} layers with different chemistries. Black-Right-Pointing-Pointer XPS shows the selective functionalization of mesoporous layers with thiol groups.

  16. Symmetry groups, density-matrix equations and covariant Wigner functions

    NASA Astrophysics Data System (ADS)

    Santana, A. E.; Neto, A. Matos; Vianna, J. D. M.; Khanna, F. C.

    2000-06-01

    A representation theory for Lie groups is developed taking the Hilbert space, say Hw, of the w∗-algebra standard representation as the representation space. In this context the states describing physical systems are amplitude wave functions but closely connected with the notion of the density matrix. Then, based on symmetry properties, a general physical interpretation for the dual variables of thermal theories, in particular the thermofield dynamics (TFD) formalism, is introduced. The kinematic symmetries, Galilei and Poincaré, are studied and (density) amplitude matrix equations are derived for both of these cases. In the same context of group theory, the notion of phase space in quantum theory is analysed. Thus, in the non-relativistic situation, the concept of density amplitude is introduced, and as an example, a spin-half system is algebraically studied; Wigner function representations for the amplitude density matrices are derived and the connection of TFD and the usual Wigner-function methods are analysed. For the Poincaré symmetries the relativistic density matrix equations are studied for the scalar and spinorial fields. The relativistic phase space is built following the lines of the non-relativistic case. So, for the scalar field, the kinetic theory is introduced via the Klein-Gordon density-matrix equation, and a derivation of the Jüttiner distribution is presented as an example, thus making it possible to compare with the standard approaches. The analysis of the phase space for the Dirac field is carried out in connection with the dual spinor structure induced by the Dirac-field density-matrix equation, with the physical content relying on the symmetry groups. Gauge invariance is considered and, as a basic result, it is shown that the Heinz density operator (which has been used to develope a gauge covariant kinetic theory) is a particular solution for the (Klein-Gordon and Dirac) density-matrix equation.

  17. Molecular dynamics simulations of functionalized carbon nanotubes in water: Effects of type and position of functional groups

    NASA Astrophysics Data System (ADS)

    Foroutan, Masumeh; Moshari, Mahshad

    2010-11-01

    In this work the behavior of the (8,2) single walled carbon nanotubes (CNTs) and functionalized carbon nanotubes (FCNTs) with four functional groups in water were studied using molecular dynamic (MD) simulation method. Glutamine as a long chain functional group and carboxyl as a short chain functional group have been used as functional groups in FCNTs. Four functional groups in each FCNT were localized at two positions: (i) all four functional groups were in the sidewalls of nanotube, (ii) two functional groups were at the ends and two functional groups were in the sidewalls of nanotube. The intermolecular interaction energies between CNTs or FCNTs and water molecules, the plots of radial distribution function and the diffusion coefficients of CNTs and FCNTs in water were computed for investigating the effects of type and position of functional groups on the behavior of FCNTs in water. The obtained results from three methods are consistent with each others. Results showed that the position of the functional groups in FCNTs has an important role in the interaction of hydrophilic groups of FCNTs with water molecules. Furthermore we also investigated the behavior of FCNTs with sixteen carboxyl functional groups in water. The presence of these large numbers of carboxyl functional groups on the carbon nanotubes prevents water molecules from moving towards hydrophilic carboxyl functional groups. This demonstrates the advantage of using lower number of functional groups each containing many hydrophilic groups like glutamine functional group.

  18. Identifying functional sites based on prediction of charged group behavior.

    PubMed

    Ondrechen, Mary Jo

    2004-09-01

    This protocol describes the implementation and interpretation of THEMATICS, a simple computational predictor of functional information for proteins from the three-dimensional structure. This method is based on the computation of the electrical potential function for the protein and the calculation of the predicted titration curves for each of the titratable groups in the protein. While most of the titratable residues in a protein have predicted titration behavior that fits the Henderson-Hasselbalch equation, the ionizable residues in the active site generally deviate dramatically from the typical behavior. From the calculated titration curves, one identifies those residues that deviate significantly from Henderson-Hasselbalch behavior. A cluster of two or more of such deviant titratable residues in physical proximity is a reliable predictor of active-site location.

  19. Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

    PubMed Central

    Alexander, Harriet; Rouco, Mónica; Haley, Sheean T.; Wilson, Samuel T.; Karl, David M.; Dyhrman, Sonya T.

    2015-01-01

    A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate. PMID:26460011

  20. Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean.

    PubMed

    Alexander, Harriet; Rouco, Mónica; Haley, Sheean T; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

    2015-11-01

    A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate. PMID:26460011

  1. Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean.

    PubMed

    Alexander, Harriet; Rouco, Mónica; Haley, Sheean T; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

    2015-11-01

    A diverse microbial assemblage in the ocean is responsible for nearly half of global primary production. It has been hypothesized and experimentally demonstrated that nutrient loading can stimulate blooms of large eukaryotic phytoplankton in oligotrophic systems. Although central to balancing biogeochemical models, knowledge of the metabolic traits that govern the dynamics of these bloom-forming phytoplankton is limited. We used eukaryotic metatranscriptomic techniques to identify the metabolic basis of functional group-specific traits that may drive the shift between net heterotrophy and autotrophy in the oligotrophic ocean. Replicated blooms were simulated by deep seawater (DSW) addition to mimic nutrient loading in the North Pacific Subtropical Gyre, and the transcriptional responses of phytoplankton functional groups were assayed. Responses of the diatom, haptophyte, and dinoflagellate functional groups in simulated blooms were unique, with diatoms and haptophytes significantly (95% confidence) shifting their quantitative metabolic fingerprint from the in situ condition, whereas dinoflagellates showed little response. Significantly differentially abundant genes identified the importance of colimitation by nutrients, metals, and vitamins in eukaryotic phytoplankton metabolism and bloom formation in this system. The variable transcript allocation ratio, used to quantify transcript reallocation following DSW amendment, differed for diatoms and haptophytes, reflecting the long-standing paradigm of phytoplankton r- and K-type growth strategies. Although the underlying metabolic potential of the large eukaryotic phytoplankton was consistently present, the lack of a bloom during the study period suggests a crucial dependence on physical and biogeochemical forcing, which are susceptible to alteration with changing climate.

  2. Coumestan inhibits radical-induced oxidation of DNA: is hydroxyl a necessary functional group?

    PubMed

    Xi, Gao-Lei; Liu, Zai-Qun

    2014-06-18

    Coumestan is a natural tetracycle with a C═C bond shared by a coumarin moiety and a benzofuran moiety. In addition to the function of the hydroxyl group on the antioxidant activity of coumestan, it is worth exploring the influence of the oxygen-abundant scaffold on the antioxidant activity as well. In this work, seven coumestans containing electron-withdrawing and electron-donating groups were synthesized to evaluate the abilities to trap 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) cationic radical (ABTS(•+)), 2,2'-diphenyl-1-picrylhydrazyl radical (DPPH), and galvinoxyl radical, respectively, and to inhibit the oxidations of DNA mediated by (•)OH, Cu(2+)/glutathione (GSH), and 2,2'-azobis(2-amidinopropane hydrochloride) (AAPH), respectively. It was found that all of the coumestans used herein can quench the aforementioned radicals and can inhibit (•)OH-, Cu(2+)/GSH-, and AAPH-induced oxidations of DNA. In particular, substituent-free coumestan exhibits higher ability to quench DPPH and to inhibit AAPH-induced oxidation of DNA than Trolox. In addition, nonsubstituted coumestan shows a similar ability to inhibit (•)OH- and Cu(2+)/GSH-induced oxidations of DNA relative to that of Trolox. The antioxidant effectiveness of the coumestan can be attributed to the lactone in the coumarin moiety and, therefore, a hydroxyl group may not be a necessary functional group for coumestan to be an antioxidant.

  3. FTIR Analysis of Functional Groups in Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Shokri, S. M.; McKenzie, G.; Dransfield, T. J.

    2012-12-01

    Secondary organic aerosols (SOA) are suspensions of particulate matter composed of compounds formed from chemical reactions of organic species in the atmosphere. Atmospheric particulate matter can have impacts on climate, the environment and human health. Standardized techniques to analyze the characteristics and composition of complex secondary organic aerosols are necessary to further investigate the formation of SOA and provide a better understanding of the reaction pathways of organic species in the atmosphere. While Aerosol Mass Spectrometry (AMS) can provide detailed information about the elemental composition of a sample, it reveals little about the chemical moieties which make up the particles. This work probes aerosol particles deposited on Teflon filters using FTIR, based on the protocols of Russell, et al. (Journal of Geophysical Research - Atmospheres, 114, 2009) and the spectral fitting algorithm of Takahama, et al (submitted, 2012). To validate the necessary calibration curves for the analysis of complex samples, primary aerosols of key compounds (e.g., citric acid, ammonium sulfate, sodium benzoate) were generated, and the accumulated masses of the aerosol samples were related to their IR absorption intensity. These validated calibration curves were then used to classify and quantify functional groups in SOA samples generated in chamber studies by MIT's Kroll group. The fitting algorithm currently quantifies the following functionalities: alcohols, alkanes, alkenes, amines, aromatics, carbonyls and carboxylic acids.

  4. Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!

    PubMed Central

    Lacroix, Thomas; Loux, Valentin; Gendrault, Annie; Hoebeke, Mark; Gibrat, Jean-François

    2014-01-01

    High-throughput techniques have considerably increased the potential of comparative genomics whilst simultaneously posing many new challenges. One of those challenges involves efficiently mining the large amount of data produced and exploring the landscape of both conserved and idiosyncratic genomic regions across multiple genomes. Domains of application of these analyses are diverse: identification of evolutionary events, inference of gene functions, detection of niche-specific genes or phylogenetic profiling. Insyght is a comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and (iii) a genomic organization view designed to improve the legibility of rearrangements and distinctive loci. The latter display combines symbolic and proportional graphical paradigms. Synchronized navigation across multiple species and interoperability between the views are core features of Insyght. A gene filter mechanism is provided that helps the user to build a biologically relevant gene set according to multiple criteria such as presence/absence of homologues and/or various annotations. We illustrate the use of Insyght with scenarios. Currently, only Bacteria and Archaea are supported. A public instance is available at http://genome.jouy.inra.fr/Insyght. The tool is freely downloadable for private data set analysis. PMID:25249626

  5. Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor

    NASA Astrophysics Data System (ADS)

    Li, Zhi-Ling; Nan, Jun; Huang, Cong; Liang, Bin; Liu, Wen-Zong; Cheng, Hao-Yi; Zhang, Chunfang; Zhang, Dongdong; Kong, Deyong; Kanamaru, Kyoko; Kobayashi, Tetsuo; Wang, Ai-Jie; Katayama, Arata

    2016-01-01

    Functional interplays of microbial activity, genetic diversity and contaminant transformation are poorly understood in reactors for mineralizing halogenated aromatics anaerobically. Here, we investigated abundance and distribution of potential microbes and functional genes associated with pentachlorophenol (PCP) anaerobic mineralization in a continuous-flow cylindrical reactor (15 cm in length). PCP dechlorination and the metabolite (phenol) were observed at segments 0–8 cm from inlet, where key microbes, including potential reductive dechlorinators (Dehalobacter, Sulfurospirillum, Desulfitobacterium and Desulfovibrio spp.) and phenol degraders (Cryptanaerobacter and Syntrophus spp.), as well as putative functional genes, including putative chlorophenol reductive dehalogenase (cprA) and benzoyl-CoA reductase (bamB), were highly enriched simultaneously. Five types of putative cprAs, three types of putative bamBs and seven types of putative nitrogenase reductase (nifHs) were determined, with their copy numbers decreased gradually from inlet to outlet. Distribution of chemicals, bacteria and putative genes confirmed PCP dechlorination and phenol degradation accomplished in segments 0–5 cm and 0–8 cm, respectively, contributing to a high PCP mineralization rate of 3.86 μM d‑1. Through long-term incubation, dechlorination, phenol degradation and nitrogen fixation bacteria coexisted and functioned simultaneously near inlet (0–8 cm), verified the feasibility of anaerobic mineralization of halogenated aromatics in the compact reactor containing multiple functional microbes.

  6. Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor.

    PubMed

    Li, Zhi-Ling; Nan, Jun; Huang, Cong; Liang, Bin; Liu, Wen-Zong; Cheng, Hao-Yi; Zhang, Chunfang; Zhang, Dongdong; Kong, Deyong; Kanamaru, Kyoko; Kobayashi, Tetsuo; Wang, Ai-Jie; Katayama, Arata

    2016-01-01

    Functional interplays of microbial activity, genetic diversity and contaminant transformation are poorly understood in reactors for mineralizing halogenated aromatics anaerobically. Here, we investigated abundance and distribution of potential microbes and functional genes associated with pentachlorophenol (PCP) anaerobic mineralization in a continuous-flow cylindrical reactor (15 cm in length). PCP dechlorination and the metabolite (phenol) were observed at segments 0-8 cm from inlet, where key microbes, including potential reductive dechlorinators (Dehalobacter, Sulfurospirillum, Desulfitobacterium and Desulfovibrio spp.) and phenol degraders (Cryptanaerobacter and Syntrophus spp.), as well as putative functional genes, including putative chlorophenol reductive dehalogenase (cprA) and benzoyl-CoA reductase (bamB), were highly enriched simultaneously. Five types of putative cprAs, three types of putative bamBs and seven types of putative nitrogenase reductase (nifHs) were determined, with their copy numbers decreased gradually from inlet to outlet. Distribution of chemicals, bacteria and putative genes confirmed PCP dechlorination and phenol degradation accomplished in segments 0-5 cm and 0-8 cm, respectively, contributing to a high PCP mineralization rate of 3.86 μM d(-1). Through long-term incubation, dechlorination, phenol degradation and nitrogen fixation bacteria coexisted and functioned simultaneously near inlet (0-8 cm), verified the feasibility of anaerobic mineralization of halogenated aromatics in the compact reactor containing multiple functional microbes. PMID:26750760

  7. Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor

    NASA Astrophysics Data System (ADS)

    Li, Zhi-Ling; Nan, Jun; Huang, Cong; Liang, Bin; Liu, Wen-Zong; Cheng, Hao-Yi; Zhang, Chunfang; Zhang, Dongdong; Kong, Deyong; Kanamaru, Kyoko; Kobayashi, Tetsuo; Wang, Ai-Jie; Katayama, Arata

    2016-01-01

    Functional interplays of microbial activity, genetic diversity and contaminant transformation are poorly understood in reactors for mineralizing halogenated aromatics anaerobically. Here, we investigated abundance and distribution of potential microbes and functional genes associated with pentachlorophenol (PCP) anaerobic mineralization in a continuous-flow cylindrical reactor (15 cm in length). PCP dechlorination and the metabolite (phenol) were observed at segments 0-8 cm from inlet, where key microbes, including potential reductive dechlorinators (Dehalobacter, Sulfurospirillum, Desulfitobacterium and Desulfovibrio spp.) and phenol degraders (Cryptanaerobacter and Syntrophus spp.), as well as putative functional genes, including putative chlorophenol reductive dehalogenase (cprA) and benzoyl-CoA reductase (bamB), were highly enriched simultaneously. Five types of putative cprAs, three types of putative bamBs and seven types of putative nitrogenase reductase (nifHs) were determined, with their copy numbers decreased gradually from inlet to outlet. Distribution of chemicals, bacteria and putative genes confirmed PCP dechlorination and phenol degradation accomplished in segments 0-5 cm and 0-8 cm, respectively, contributing to a high PCP mineralization rate of 3.86 μM d-1. Through long-term incubation, dechlorination, phenol degradation and nitrogen fixation bacteria coexisted and functioned simultaneously near inlet (0-8 cm), verified the feasibility of anaerobic mineralization of halogenated aromatics in the compact reactor containing multiple functional microbes.

  8. Functional group based Ligand binding affinity scoring function at atomic environmental level

    PubMed Central

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2009-01-01

    Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure. PMID:19255647

  9. Sterol 14 alpha-demethylase, an abundant and essential mixed-function oxidase.

    PubMed

    Waterman, Michael R; Lepesheva, Galina I

    2005-12-01

    Sterol 14alpha-demethylase (CYP51) is the most widely distributed of all members of the cytochrome P450 gene superfamily and the only CYP family found in both prokaryotes and eukaryotes. It is well known as a drug target for microbial pathogenic infections. Studies of CYP51 gene regulation have been carried out primarily in animals because its regulation is similar to those of other genes involved in the cholesterol biosynthetic pathway. The function of CYP51 has been studied widely throughout biology including in animals, plants, yeast/fungi, protozoa, and bacteria. The structure has been determined by X-ray crystallography for the soluble prokaryotic form of CYP51 from Mycobacterium tuberculosis. Together these studies provide the most detailed understanding of any single cytochrome P450 and this minireview summarizes this information.

  10. Variation in Plant Traits Explains Global Biogeographic Variation in the Abundance of Major Forest Functional Types

    NASA Astrophysics Data System (ADS)

    Wang, Y.

    2015-12-01

    Contrasting leaf types (needle vs. broadleaf) with different lifespans (annual vs. perennial) represent different adaptive strategies of plants under different environmental conditions. Previous studies explained adaptive advantages of different strategies using empirical models but cannot adequately explain the co-dominance of multiple plant functional types (PFTs) as observed in many parts of the world. Here we used a process-based model to explore whether observed inter- and intra-PFT variation in key plant traits can explain global biogeographic variation in co-dominance of major forest functional types. Using a parameter screening method, we identified the four most important plant traits for simulating annual net primary production (NPP) using the Australian Community Atmosphere-Biosphere-Land Exchange model (CABLE). Using ensemble CABLE simulations, we estimated the fraction of global land cover attributed to each PFT by comparing the simulated NPP for all three PFTs at each land point, globally. Our results were consistent with land area cover fractions of major forest types estimated from remote sensing data products; i.e., evergreen needle-leaf forests dominate in boreal regions, evergreen broadleaf forests dominate in tropical regions, and deciduous broadleaf forests are distributed widely across a broad range of environmental conditions. More importantly our approach successfully explained a paradox that has puzzled ecologists for over a century: why evergreen leaf types dominate in both boreal and tropical regions. We conclude that variation in and co-variation between key plant traits can explain significant fractions of global biogeographic variation of three major forest types, and should be taken into account when simulating global vegetation dynamics.

  11. The Araucaria Project: The Distance to the Sculptor Group Galaxy NGC 55 from a Newly Discovered Abundant Cepheid Population

    NASA Astrophysics Data System (ADS)

    Pietrzyński, Grzegorz; Gieren, Wolfgang; Soszyński, Igor; Udalski, Andrzej; Bresolin, Fabio; Kudritzki, Rolf-Peter; Mennickent, Ronald; Walker, Alistair; Garcia, Alejandro; Szewczyk, Olaf; Szymański, MichaŁ; Kubiak, Marcin; Wyrzykowski, Łukasz

    2006-12-01

    We have detected, for the first time, Cepheid variables in the Sculptor Group SB(s)m galaxy NGC 55. From wide-field images obtained in the optical V and I bands during 77 nights in 2002-2003, we have found 143 Cepheids with periods ranging from 5.6 to 175.9 days; 133 of these objects have periods longer than 10 days, making NGC 55 to date the galaxy with the largest known number of long-period Cepheids in the Sculptor Group. We construct period-luminosity relations from our data and obtain distance moduli corrected for the small foreground reddening to NGC 55 of 26.79+/-0.04 mag (internal error) in V, 26.66+/-0.03 mag in I, and 26.40+/-0.05 mag in the reddening-independent V-I Wesenheit index. The trend of increasing distance moduli with shorter wavelength hints at the existence of significant reddening intrinsic to NGC 55, which affects the measured Cepheid magnitudes. From our data we determine the intrinsic mean reddening of the Cepheids in NGC 55 as E(B-V)=0.102 mag, which brings the distance determinations from the different bands into excellent agreement. Our best distance estimate for NGC 55 from the present optical Cepheid photometry is 26.40+/-0.05 (internal error) +/-0.09 mag (systematic error). This value is tied to an assumed LMC distance of 18.50 mag. Our quoted systematic error of the present NGC 55 Cepheid distance does not take into account the current uncertainty in the distance of the fiducial LMC galaxy itself. Within the small respective uncertainties, the Sculptor Group galaxies NGC 55 and NGC 300 are at the same distance of 1.9 Mpc, strengthening the case for a physical association of these galaxies. Based on observations obtained with the 1.3 m Warsaw telescope at Las Campanas Observatory, Chile.

  12. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames.

    PubMed

    Cross, Frederick R

    2015-12-23

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence ('uORFs'): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard 'scanning' model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5' untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral.

  13. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames

    PubMed Central

    Cross, Frederick R.

    2015-01-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence (‘uORFs’): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard ‘scanning’ model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5′ untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral. PMID:26701783

  14. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames.

    PubMed

    Cross, Frederick R

    2016-02-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence ('uORFs'): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard 'scanning' model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5' untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral. PMID:26701783

  15. Highlighting functional groups in self-assembled overlayers with specific functionalized scanning tunnelling microscopy tips

    NASA Astrophysics Data System (ADS)

    Volcke, Cedric; Simonis, Priscilla; Thiry, Paul A.; Lambin, Philippe; Culot, Christine; Humbert, Christophe

    2005-11-01

    Overlayers of a fatty acid (palmitic and lauric acid) formed at the interface between a solution of this molecule in phenyloctane and the basal plane of graphite are studied by in situ scanning tunnelling microscopy. The layers organize into lamellae, which are formed by a close packing arrangement of molecules parallel to the graphite surface. Chemical modification of the STM tips used allowed identification of the functional group. Indeed, the gold tips used are functionalized with 4-mercaptobenzoic acid (4-MBA) and 4-mercaptotoluene (4-MT). The same functional group on a sample is then 'seen' as a dark and a bright spot when imaged with 4-MBA and 4-MT modified tips, respectively. This contrast distinction is related to interactions (or a lack of them) between the carboxyl group on the sample and molecules on the tip, which can facilitate (or hinder) the electron tunnelling.

  16. Sleeping functional group drives coral-reef recovery.

    PubMed

    Bellwood, David R; Hughes, Terry P; Hoey, Andrew S

    2006-12-19

    The world's coral reefs are in decline, with many exhibiting a phase shift from coral to macroalgal dominance . This change is often associated with habitat loss and overharvesting of herbivorous fishes, particularly parrotfishes and surgeonfishes . The challenge is to reverse this decline and enhance the resilience of coral-reef ecosystems . We demonstrate, by using a large-scale experimentally induced phase shift, that the rapid reversal from a macroalgal-dominated to a coral- and epilithic algal-dominated state was not a result of herbivory by parrotfishes or surgeonfishes. Surprisingly, phase-shift reversal was primarily driven by a single batfish species (Platax pinnatus), a fish previously regarded as an invertebrate feeder. The 43 herbivorous fishes in the local fauna played only a minor role, suggesting that biodiversity may not offer the protection we hoped for in complex ecosystems. Our findings highlight the dangers faced by coral reefs and other threatened complex ecosystems: Species or functional groups that prevent phase shifts may not be able to reverse phase shifts once they occur. Nevertheless, reversal is possible. The critical issue is to identify and protect those groups that underpin the resilience and regeneration of complex ecosystems.

  17. The Cockayne syndrome group B protein is a functional dimer.

    PubMed

    Christiansen, Mette; Thorslund, Tina; Jochimsen, Bjarne; Bohr, Vilhelm A; Stevnsner, Tinna

    2005-09-01

    Cockayne syndrome (CS) is a rare inherited human genetic disorder characterized by developmental abnormalities, UV sensitivity, and premature aging. The CS group B (CSB) protein belongs to the SNF2-family of DNA-dependent ATPases and is implicated in transcription elongation, transcription coupled repair, and base excision repair. It is a DNA stimulated ATPase and remodels chromatin in vitro. We demonstrate for the first time that full-length CSB positively cooperates in ATP hydrolysis as a function of protein concentration. We have investigated the quaternary structure of CSB using a combination of protein-protein complex trapping experiments and gel filtration, and found that CSB forms a dimer in solution. Chromatography studies revealed that enzymatically active CSB has an apparent molecular mass of approximately 360 kDa, consistent with dimerization of CSB. Importantly, in vivo protein cross-linking showed the presence of the CSB dimer in the nucleus of HeLa cells. We further show that dimerization occurs through the central ATPase domain of the protein. These results have implications for the mechanism of action of CSB, and suggest that other SNF2-family members might also function as dimers. PMID:16128801

  18. Observations of Adolescent Peer Group Interactions as a Function of Within- and Between-Group Centrality Status

    ERIC Educational Resources Information Center

    Ellis, Wendy E.; Dumas, Tara M.; Mahdy, Jasmine C.; Wolfe, David A.

    2012-01-01

    Observations of adolescent (n = 258; M age = 15.45) peer group triads (n = 86) were analyzed to identify conversation and interaction styles as a function of within-group and between-group centrality status. Group members' discussions about hypothetical dilemmas were coded for agreements, disagreements, commands, and opinions. Interactions during…

  19. Nucleotide substitutions revealing specific functions of Polycomb group genes.

    PubMed

    Bajusz, Izabella; Sipos, László; Pirity, Melinda K

    2015-04-01

    POLYCOMB group (PCG) proteins belong to the family of epigenetic regulators of genes playing important roles in differentiation and development. Mutants of PcG genes were isolated first in the fruit fly, Drosophila melanogaster, resulting in spectacular segmental transformations due to the ectopic expression of homeotic genes. Homologs of Drosophila PcG genes were also identified in plants and in vertebrates and subsequent experiments revealed the general role of PCG proteins in the maintenance of the repressed state of chromatin through cell divisions. The past decades of gene targeting experiments have allowed us to make significant strides towards understanding how the network of PCG proteins influences multiple aspects of cellular fate determination during development. Being involved in the transmission of specific expression profiles of different cell lineages, PCG proteins were found to control wide spectra of unrelated epigenetic processes in vertebrates, such as stem cell plasticity and renewal, genomic imprinting and inactivation of X-chromosome. PCG proteins also affect regulation of metabolic genes being important for switching programs between pluripotency and differentiation. Insight into the precise roles of PCG proteins in normal physiological processes has emerged from studies employing cell culture-based systems and genetically modified animals. Here we summarize the findings obtained from PcG mutant fruit flies and mice generated to date with a focus on PRC1 and PRC2 members altered by nucleotide substitutions resulting in specific alleles. We also include a compilation of lessons learned from these models about the in vivo functions of this complex protein family. With multiple knockout lines, sophisticated approaches to study the consequences of peculiar missense point mutations, and insights from complementary gain-of-function systems in hand, we are now in a unique position to significantly advance our understanding of the molecular basis of

  20. Woody plant encroachment into grasslands: spatial patterns of functional group distribution and community development.

    PubMed

    Liu, Feng; Archer, Steven R; Gelwick, Frances; Bai, Edith; Boutton, Thomas W; Wu, Xinyuan Ben

    2013-01-01

    Woody plant encroachment into grasslands has been globally widespread. The woody species invading grasslands represent a variety of contrasting plant functional groups and growth forms. Are some woody plant functional types (PFTs) better suited to invade grasslands than others? To what extent do local patterns of distribution and abundance of woody PFTs invading grasslands reflect intrinsic topoedaphic properties versus plant-induced changes in soil properties? We addressed these questions in the Southern Great Plains, United States at a subtropical grassland known to have been encroached upon by woody species over the past 50-100 years. A total of 20 woody species (9 tree-statured; 11 shrub-statured) were encountered along a transect extending from an upland into a playa basin. About half of the encroaching woody plants were potential N2-fixers (55% of species), but they contributed only 7% to 16 % of the total basal area. Most species and the PFTs they represent were ubiquitously distributed along the topoedaphic gradient, but with varying abundances. Overstory-understory comparisons suggest that while future species composition of these woody communities is likely to change, PFT composition is not. Canonical correspondence analysis (CCA) ordination and variance partitioning (Partial CCA) indicated that woody species and PFT composition in developing woody communities was primarily influenced by intrinsic landscape location variables (e.g., soil texture) and secondarily by plant-induced changes in soil organic carbon and total nitrogen content. The ubiquitous distribution of species and PFTs suggests that woody plants are generally well-suited to a broad range of grassland topoedaphic settings. However, here we only examined categorical and non-quantitative functional traits. Although intrinsic soil properties exerted more control over the floristics of grassland-to-woodland succession did plant modifications of soil carbon and nitrogen concentrations, the latter

  1. Woody plant encroachment into grasslands: spatial patterns of functional group distribution and community development.

    PubMed

    Liu, Feng; Archer, Steven R; Gelwick, Frances; Bai, Edith; Boutton, Thomas W; Wu, Xinyuan Ben

    2013-01-01

    Woody plant encroachment into grasslands has been globally widespread. The woody species invading grasslands represent a variety of contrasting plant functional groups and growth forms. Are some woody plant functional types (PFTs) better suited to invade grasslands than others? To what extent do local patterns of distribution and abundance of woody PFTs invading grasslands reflect intrinsic topoedaphic properties versus plant-induced changes in soil properties? We addressed these questions in the Southern Great Plains, United States at a subtropical grassland known to have been encroached upon by woody species over the past 50-100 years. A total of 20 woody species (9 tree-statured; 11 shrub-statured) were encountered along a transect extending from an upland into a playa basin. About half of the encroaching woody plants were potential N2-fixers (55% of species), but they contributed only 7% to 16 % of the total basal area. Most species and the PFTs they represent were ubiquitously distributed along the topoedaphic gradient, but with varying abundances. Overstory-understory comparisons suggest that while future species composition of these woody communities is likely to change, PFT composition is not. Canonical correspondence analysis (CCA) ordination and variance partitioning (Partial CCA) indicated that woody species and PFT composition in developing woody communities was primarily influenced by intrinsic landscape location variables (e.g., soil texture) and secondarily by plant-induced changes in soil organic carbon and total nitrogen content. The ubiquitous distribution of species and PFTs suggests that woody plants are generally well-suited to a broad range of grassland topoedaphic settings. However, here we only examined categorical and non-quantitative functional traits. Although intrinsic soil properties exerted more control over the floristics of grassland-to-woodland succession did plant modifications of soil carbon and nitrogen concentrations, the latter

  2. Woody Plant Encroachment into Grasslands: Spatial Patterns of Functional Group Distribution and Community Development

    PubMed Central

    Liu, Feng; Archer, Steven R.; Gelwick, Frances; Bai, Edith; Boutton, Thomas W.; Wu, Xinyuan Ben

    2013-01-01

    Woody plant encroachment into grasslands has been globally widespread. The woody species invading grasslands represent a variety of contrasting plant functional groups and growth forms. Are some woody plant functional types (PFTs) better suited to invade grasslands than others? To what extent do local patterns of distribution and abundance of woody PFTs invading grasslands reflect intrinsic topoedaphic properties versus plant-induced changes in soil properties? We addressed these questions in the Southern Great Plains, United States at a subtropical grassland known to have been encroached upon by woody species over the past 50-100 years. A total of 20 woody species (9 tree-statured; 11 shrub-statured) were encountered along a transect extending from an upland into a playa basin. About half of the encroaching woody plants were potential N2-fixers (55% of species), but they contributed only 7% to 16 % of the total basal area. Most species and the PFTs they represent were ubiquitously distributed along the topoedaphic gradient, but with varying abundances. Overstory-understory comparisons suggest that while future species composition of these woody communities is likely to change, PFT composition is not. Canonical correspondence analysis (CCA) ordination and variance partitioning (Partial CCA) indicated that woody species and PFT composition in developing woody communities was primarily influenced by intrinsic landscape location variables (e.g., soil texture) and secondarily by plant-induced changes in soil organic carbon and total nitrogen content. The ubiquitous distribution of species and PFTs suggests that woody plants are generally well-suited to a broad range of grassland topoedaphic settings. However, here we only examined categorical and non-quantitative functional traits. Although intrinsic soil properties exerted more control over the floristics of grassland-to-woodland succession did plant modifications of soil carbon and nitrogen concentrations, the latter

  3. Functional movement screen scores in a group of running athletes.

    PubMed

    Loudon, Janice K; Parkerson-Mitchell, Amy J; Hildebrand, Laurie D; Teague, Connie

    2014-04-01

    The purpose of this study was to determine the mean values of the functional movement screen (FMS) in a group of long-distance runners. The secondary aims were to investigate whether the FMS performance differed between sexes and between young and older runners. Forty-three runners, 16 women (mean age = 33.5 years, height = 165.2 cm, weight = 56.3 kg, and body mass index [BMI] = 20.6) and 27 men (mean age = 39.3 years, height = 177.6 cm, weight = 75.8 kg, and BMI = 24.2) performed the FMS. All the runners were injury-free and ran >30 km·wk. Independent t-tests were performed on the composite scores to examine the differences between men and women and also between young (<40 years) and older runners (>40 years). Contingency tables (2 × 2) were developed for each of the 7 screening tests to further look at the differences in groups for each single test. The χ values were calculated to determine significant differences. Statistical significance was set at p ≤ 0.05. There was no significant difference in the composite score between women and men. There were significant differences between the sexes in the push-up and straight leg test scores, with the women scoring better on each test. A significant difference was found in the composite scores between younger and older runners (p < 0.000). Additional score differences were found for the squat, hurdle step, and in-line lunge tests with the younger runners scoring better. This study provided mean values for the FMS in a cohort of long-distance runners. These values can be used as a reference for comparing FMST scores in other runners who are screened with this tool.

  4. Highly adaptive tests for group differences in brain functional connectivity.

    PubMed

    Kim, Junghi; Pan, Wei

    2015-01-01

    Resting-state functional magnetic resonance imaging (rs-fMRI) and other technologies have been offering evidence and insights showing that altered brain functional networks are associated with neurological illnesses such as Alzheimer's disease. Exploring brain networks of clinical populations compared to those of controls would be a key inquiry to reveal underlying neurological processes related to such illnesses. For such a purpose, group-level inference is a necessary first step in order to establish whether there are any genuinely disrupted brain subnetworks. Such an analysis is also challenging due to the high dimensionality of the parameters in a network model and high noise levels in neuroimaging data. We are still in the early stage of method development as highlighted by Varoquaux and Craddock (2013) that "there is currently no unique solution, but a spectrum of related methods and analytical strategies" to learn and compare brain connectivity. In practice the important issue of how to choose several critical parameters in estimating a network, such as what association measure to use and what is the sparsity of the estimated network, has not been carefully addressed, largely because the answers are unknown yet. For example, even though the choice of tuning parameters in model estimation has been extensively discussed in the literature, as to be shown here, an optimal choice of a parameter for network estimation may not be optimal in the current context of hypothesis testing. Arbitrarily choosing or mis-specifying such parameters may lead to extremely low-powered tests. Here we develop highly adaptive tests to detect group differences in brain connectivity while accounting for unknown optimal choices of some tuning parameters. The proposed tests combine statistical evidence against a null hypothesis from multiple sources across a range of plausible tuning parameter values reflecting uncertainty with the unknown truth. These highly adaptive tests are not only

  5. Highly adaptive tests for group differences in brain functional connectivity.

    PubMed

    Kim, Junghi; Pan, Wei

    2015-01-01

    Resting-state functional magnetic resonance imaging (rs-fMRI) and other technologies have been offering evidence and insights showing that altered brain functional networks are associated with neurological illnesses such as Alzheimer's disease. Exploring brain networks of clinical populations compared to those of controls would be a key inquiry to reveal underlying neurological processes related to such illnesses. For such a purpose, group-level inference is a necessary first step in order to establish whether there are any genuinely disrupted brain subnetworks. Such an analysis is also challenging due to the high dimensionality of the parameters in a network model and high noise levels in neuroimaging data. We are still in the early stage of method development as highlighted by Varoquaux and Craddock (2013) that "there is currently no unique solution, but a spectrum of related methods and analytical strategies" to learn and compare brain connectivity. In practice the important issue of how to choose several critical parameters in estimating a network, such as what association measure to use and what is the sparsity of the estimated network, has not been carefully addressed, largely because the answers are unknown yet. For example, even though the choice of tuning parameters in model estimation has been extensively discussed in the literature, as to be shown here, an optimal choice of a parameter for network estimation may not be optimal in the current context of hypothesis testing. Arbitrarily choosing or mis-specifying such parameters may lead to extremely low-powered tests. Here we develop highly adaptive tests to detect group differences in brain connectivity while accounting for unknown optimal choices of some tuning parameters. The proposed tests combine statistical evidence against a null hypothesis from multiple sources across a range of plausible tuning parameter values reflecting uncertainty with the unknown truth. These highly adaptive tests are not only

  6. A conceptual basis to encode and detect organic functional groups in XML.

    PubMed

    Sankar, Punnaivanam; Krief, Alain; Vijayasarathi, Durairaj

    2013-06-01

    A conceptual basis to define and detect organic functional groups is developed. The basic model of a functional group is termed as a primary functional group and is characterized by a group center composed of one or more group center atoms bonded to terminal atoms and skeletal carbon atoms. The generic group center patterns are identified from the structures of known functional groups. Accordingly, a chemical ontology 'Font' is developed to organize the existing functional groups as well as the new ones to be defined by the chemists. The basic model is extended to accommodate various combinations of primary functional groups as functional group assemblies. A concept of skeletal group is proposed to define the characteristic groups composed of only carbon atoms to be regarded as equivalent to functional groups. The combination of primary functional groups with skeletal groups is categorized as skeletal group assembly. In order to make the model suitable for reaction modeling purpose, a Graphical User Interface (GUI) is developed to define the functional groups and to encode in XML format appropriate to detect them in chemical structures. The system is capable of detecting multiple instances of primary functional groups as well as the overlapping poly-functional groups as the respective assemblies. PMID:23666030

  7. The Mechanism and Function of Group II Chaperonins.

    PubMed

    Lopez, Tom; Dalton, Kevin; Frydman, Judith

    2015-09-11

    Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis. PMID:25936650

  8. Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality.

    PubMed

    Kushwaha, Rekha; Downie, A Bruce; Payne, Christina M

    2013-01-01

    A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

  9. Protein covalent immobilization via its scarce thiol versus abundant amine groups: Effect on orientation, cell binding domain exposure and conformational lability.

    PubMed

    Ba, O M; Hindie, M; Marmey, P; Gallet, O; Anselme, K; Ponche, A; Duncan, A C

    2015-10-01

    Quantity, orientation, conformation and covalent linkage of naturally cell adhesive proteins adsorbed or covalently linked to a surface, are known to influence the preservation of their subsequent long term cell adhesion properties and bioactivity. In the present work, we explore two different strategies for the covalent linking of plasma fibronectin (pFN) - used as a cell adhesive model protein, onto a polystyrene (PS) surface. One is aimed at tethering the protein to the surface in a semi-oriented fashion (via one of the 4 free thiol reactive groups on the protein) with a heterofunctional coupling agent (SSMPB method). The other aims to immobilize the protein in a more random fashion by reaction between the abundant pendant primary amine bearing amino acids of the pFN and activated carboxylic surface functions obtained after glutaric anhydride surface treatment (GA method). The overall goal will be to verify the hypothesis of a correlation between covalent immobilization of a model cell adhesive protein to a PS surface in a semi-oriented configuration (versus randomly oriented) with promotion of enhanced exposure of the protein's cell binding domain. This in turn would lead to enhanced cell adhesion. Ideally the goal is to elaborate substrates exhibiting a long term stable protein monolayer with preserved cell adhesive properties and bioactivity for biomaterial and/or cell adhesion commercial plate applications. However, the initial restrictive objective of this paper is to first quantitatively and qualitatively investigate the reversibly (merely adsorbed) versus covalently irreversibly bound protein to the surface after the immobilization procedure. Although immobilized surface amounts were similar (close to the monolayer range) for all immobilization approaches, covalent grafting showed improved retention and stronger "tethering" of the pFN protein to the surface (roughly 40%) after SDS rinsing compared to that for mere adsorption (0%) suggesting an added value

  10. Plant Species and Functional Group Combinations Affect Green Roof Ecosystem Functions

    PubMed Central

    Lundholm, Jeremy; MacIvor, J. Scott; MacDougall, Zachary; Ranalli, Melissa

    2010-01-01

    Background Green roofs perform ecosystem services such as summer roof temperature reduction and stormwater capture that directly contribute to lower building energy use and potential economic savings. These services are in turn related to ecosystem functions performed by the vegetation layer such as radiation reflection and transpiration, but little work has examined the role of plant species composition and diversity in improving these functions. Methodology/Principal Findings We used a replicated modular extensive (shallow growing- medium) green roof system planted with monocultures or mixtures containing one, three or five life-forms, to quantify two ecosystem services: summer roof cooling and water capture. We also measured the related ecosystem properties/processes of albedo, evapotranspiration, and the mean and temporal variability of aboveground biomass over four months. Mixtures containing three or five life-form groups, simultaneously optimized several green roof ecosystem functions, outperforming monocultures and single life-form groups, but there was much variation in performance depending on which life-forms were present in the three life-form mixtures. Some mixtures outperformed the best monocultures for water capture, evapotranspiration, and an index combining both water capture and temperature reductions. Combinations of tall forbs, grasses and succulents simultaneously optimized a range of ecosystem performance measures, thus the main benefit of including all three groups was not to maximize any single process but to perform a variety of functions well. Conclusions/Significance Ecosystem services from green roofs can be improved by planting certain life-form groups in combination, directly contributing to climate change mitigation and adaptation strategies. The strong performance by certain mixtures of life-forms, especially tall forbs, grasses and succulents, warrants further investigation into niche complementarity or facilitation as mechanisms

  11. Polymer containing functional end groups is base for new polymers

    NASA Technical Reports Server (NTRS)

    Hirshfield, S. M.

    1971-01-01

    Butadiene is polymerized with lithium-p-lithiophenoxide to produce linear polymer containing oxy-lithium group at one end and active carbon-lithium group at other end. Living polymers represent new approach to preparation of difunctional polymers in which structural features, molecular weight, type and number of end groups are controlled.

  12. Application of macrobenthos functional groups to estimate the ecosystem health in a semi-enclosed bay.

    PubMed

    Peng, Shitao; Zhou, Ran; Qin, Xuebo; Shi, Honghua; Ding, Dewen

    2013-09-15

    In this study, the functional group concept was first applied to evaluate the ecosystem health of Bohai Bay. Macrobenthos functional groups were defined according to feeding types and divided into five groups: a carnivorous group (CA), omnivorous group (OM), planktivorous group (PL), herbivorous group (HE), and detritivorous group (DE). Groups CA, DE, OM, and PL were identified, but the HE group was absent from Bohai Bay. Group DE was dominant during the study periods. The ecosystem health was assessed using a functional group evenness index. The functional group evenness values of most sampling stations were less than 0.40, indicating that the ecosystem health was deteriorated in Bohai Bay. Such deterioration could be attributed to land reclamation, industrial and sewage effluents, oil pollution, and hypersaline water discharge. This study demonstrates that the functional group concept can be applied to ecosystem health assessment in a semi-enclosed bay.

  13. Impact of Functional Group Modifications on Designer Phenethylamine Induced Hyperthermia.

    PubMed

    Grecco, Gregory G; Sprague, Jon E

    2016-05-16

    The popularity of designer phenethylamines such as synthetic cathinones ("bath salts") has led to increased reports of life-threatening hyperthermia. The diversity of chemical modifications has resulted in the toxicological profile of most synthetic cathinones being mostly uncharacterized. Here, we investigated the thermogenic effects of six recently identified designer phenethylamines (4-methylmethamphetamine, methylone, mephedrone, butylone, pentylone, and MDPV) and compared these effects to the established thermogenic agent 3,4-methylenedioxymethamphetamine (MDMA). Specifically, we determined the impact of a β-ketone, α-alkyl, or pyrrolidine functional group on core-body temperature changes. Sprague-Dawley rats (n = 5-6) were administered a dose (30 mg/kg, sc) of a designer phenethylamine or MDMA, and core body temperature measurements were recorded at 30 min intervals for 150 min post treatment. MDMA elicited the greatest maximum temperature change (ΔTmax), and this effect was significantly greater than that of its β-ketone analogue, methylone. Temperature-area under the curves (TAUCs) and ΔTmax were also significantly different between 4-methylmethamphetamine (4-MMA) and its β-ketone analogue mephedrone. Lengthening the α-alkyl chain of methylone to produce butylone and pentylone significantly attenuated the thermogenic response on both TAUCs and ΔTmax compared to those of methylone; however, butylone and pentylone were not different from each other. Pyrrolidine substitution on the N-terminus of pentylone produces 3,4-methylenedioxypyrovalerone (MDPV), which did not significantly alter core body temperature. Thermogenic comparisons of MDMA vs methylone and 4-MMA vs mephedrone indicate that oxidation at the benzylic position significantly attenuates the hyperthermic response. Furthermore, either extending the α-alkyl chain to ethyl and propyl (butylone and pentylone, respectively) or extending the α-alkyl chain and adding a pyrrolidine on the N

  14. Students' Perceptions of Classroom Group Work as a Function of Group Member Selection

    ERIC Educational Resources Information Center

    Myers, Scott A.

    2012-01-01

    The purpose of this assessment was to examine whether differences exist between students who self-select their classroom work group members and students who are randomly assigned to their classroom work groups in terms of their use of organizational citizenship behaviors with their work group members; their commitment to, trust in, and relational…

  15. Prediction of functional sites in proteins using conserved functional group analysis.

    PubMed

    Innis, C Axel; Anand, A Prem; Sowdhamini, R

    2004-04-01

    A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects. PMID:15033369

  16. Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

    2014-01-01

    To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

  17. Assessing nitrogen transformation processes in a trickling filter under hydraulic loading rate constraints using nitrogen functional gene abundances.

    PubMed

    Wang, Honglei; Ji, Guodong; Bai, Xueyuan; He, Chunguang

    2015-02-01

    A study was conducted of treatment performance and nitrogen transformation processes in a trickling filter (TF) used to treat micro-polluted source water under variable hydraulic loading rates (HLRs), ranging from 1.0 to 3.0 m(3)/m(2) d. The TF achieved high and stable COD (97.7-99.3%) and NH4(+)-N (67.3-92.7%) removal efficiencies. Nitrification and anaerobic ammonium oxidation were the dominant nitrogen removal processes in the TF. Path analysis indicated that amoA/anammox and amoA/(narG+napA) were the two key functional gene groups driving the major processes for NH4(+)-N and NO2(-)-N, respectively. The analysis also revealed that anammox/amoA and nxrA/(nirK+nirS) were the two key functional gene groups affecting processes associated with the NO3(-)-N transformation rate. The direct and indirect effect of functional gene groups further confirmed that nitrogen transformation processes are coupled at the molecular level, resulting in a mutual contribution to nitrogen removal in the TF.

  18. Millimeter-scale variations of stable isotope abundances in carbonates from banded iron-formations in the Hamersley Group of Western Australia.

    PubMed

    Baur, M E; Hayes, J M; Studley, S A; Walter, M R

    1985-01-01

    Several diamond drill cores from formations within the Hamersley Group of Western Australia have been studied for evidence of short-range variations in the isotopic compositions of the carbonates. For a set of 32 adjacent microbands analyzed in a specimen from the Marra Mamba Iron Formation, carbon isotope compositions of individual microbands ranged from -2.8 to -19.8 per mil compared to PDB and oxygen isotope compositions ranged from 10.2 to 20.8 per mil compared to SMOW. A pattern of alternating abundances was present, with the average isotopic contrasts between adjacent microbands being 3.0 per mil for carbon and 3.1 per mil for oxygen. Similar results were obtained for a suite of 34 microbands (in four groups) from the Bruno's Band unit of the Mount Sylvia Formation. Difficulties were experienced in preparing samples of single microbands from the Dales Gorge Member of the Brockman Iron Formation, but overall isotopic compositions were in good agreement with values reported by previous authors. Chemical analyses showed that isotopically light carbon and oxygen were correlated with increased concentrations of iron. The preservation of these millimeter-scale variations in isotopic abundances is interpreted as inconsistent with a metamorphic origin for the isotopically light carbon in the BIF carbonates. A biological origin is favored for the correlated variations in 13C and Fe, and it is suggested that the 13C-depleted carbonates may derive either from fermentative metabolism or from anaerobic respiration. A model is presented in which these processes occur near the sediment-water interface and are coupled with an initial oxidative precipitation of the iron. PMID:11539027

  19. Millimeter-scale variations of stable isotope abundances in carbonates from banded iron-formations in the Hamersley Group of Western Australia

    NASA Technical Reports Server (NTRS)

    Baur, M. E.; Hayes, J. M.; Studley, S. A.; Walter, M. R.

    1985-01-01

    Several diamond drill cores from formations within the Hamersley Group of Western Australia have been studied for evidence of short-range variations in the isotopic compositions of the carbonates. For a set of 32 adjacent microbands analyzed in a specimen from the Marra Mamba Iron Formation, carbon isotope compositions of individual microbands ranged from -2.8 to -19.8 per mil compared to PDB and oxygen isotope compositions ranged from 10.2 to 20.8 per mil compared to SMOW. A pattern of alternating abundances was present, with the average isotopic contrasts between adjacent microbands being 3.0 per mil for carbon and 3.1 per mil for oxygen. Similar results were obtained for a suite of 34 microbands (in four groups) from the Bruno's Band unit of the Mount Sylvia Formation. Difficulties were experienced in preparing samples of single microbands from the Dales Gorge Member of the Brockman Iron Formation, but overall isotopic compositions were in good agreement with values reported by previous authors. Chemical analyses showed that isotopically light carbon and oxygen were correlated with increased concentrations of iron. The preservation of these millimeter-scale variations in isotopic abundances is interpreted as inconsistent with a metamorphic origin for the isotopically light carbon in the BIF carbonates. A biological origin is favored for the correlated variations in 13C and Fe, and it is suggested that the 13C-depleted carbonates may derive either from fermentative metabolism or from anaerobic respiration. A model is presented in which these processes occur near the sediment-water interface and are coupled with an initial oxidative precipitation of the iron.

  20. Perceptual Visual Grouping under Inattention: Electrophysiological Functional Imaging

    ERIC Educational Resources Information Center

    Razpurker-Apfeld, Irene; Pratt, Hillel

    2008-01-01

    Two types of perceptual visual grouping, differing in complexity of shape formation, were examined under inattention. Fourteen participants performed a similarity judgment task concerning two successive briefly presented central targets surrounded by task-irrelevant simple and complex grouping patterns. Event-related potentials (ERPs) were…

  1. Regulation of metabolic health and adipose tissue function by group 2 innate lymphoid cells.

    PubMed

    Cautivo, Kelly M; Molofsky, Ari B

    2016-06-01

    Adipose tissue (AT) is home to an abundance of immune cells. With chronic obesity, inflammatory immune cells accumulate and promote insulin resistance and the progression to type 2 diabetes mellitus. In contrast, recent studies have highlighted the regulation and function of immune cells in lean, healthy AT, including those associated with type 2 or "allergic" immunity. Although traditionally activated by infection with multicellular helminthes, AT type 2 immunity is active independently of infection, and promotes tissue homeostasis, AT "browning," and systemic insulin sensitivity, protecting against obesity-induced metabolic dysfunction and type 2 diabetes mellitus. In particular, group 2 innate lymphoid cells (ILC2s) are integral regulators of AT type 2 immunity, producing the cytokines interleukin-5 and IL-13, promoting eosinophils and alternatively activated macrophages, and cooperating with and promoting AT regulatory T (Treg) cells. In this review, we focus on the recent developments in our understanding of group 2 innate lymphoid cell cells and type 2 immunity in AT metabolism and homeostasis.

  2. Pex11a deficiency is associated with a reduced abundance of functional peroxisomes and aggravated renal interstitial lesions.

    PubMed

    Weng, Huachun; Ji, Xu; Endo, Kosuke; Iwai, Naoharu

    2014-11-01

    Although proteinuria is known to be associated with the deterioration of chronic kidney disease, the molecular basis of this mechanism is not fully understood. We previously found that Pex11a deficiency was associated with a reduction of functional peroxisomes and impaired fatty acid metabolism in hepatocytes and resulted in steatosis. Proximal tubule cells are rich in peroxisomes. We assessed whether Pex11a deficiency might result in the derangement of peroxisome systems in proximal tubule cells and the aggravation of tubulointerstitial lesions in chronic kidney disease. Histological analyses showed that the number of functional peroxisomes in proximal tubule cells was reduced in Pex11a knockout (Pex11a(-/-)) mice. To clarify whether a decrease in the number of tubular peroxisomes might aggravate interstitial lesions, we assessed 2 models in which proximal tubule cells are overloaded with fatty acids (ie, deoxycorticosterone acetate and salt hypertension and the overload of fatty acid-bound albumin). Deoxycorticosterone acetate -salt-treated Pex11a(-/-) mice exhibited greater interstitial lesions than deoxycorticosterone acetate-salt-treated wild-type mice in terms of tubular lipid accumulation, blood pressure, urinary albumin, urinary N-acetyl-β-d-glucosaminidase, urinary 8-iso-prostane, and the histological evaluation of fibrosis and inflammation. An overload of fatty acid-bound albumin also resulted in more severe tubulointerstitial lesions in Pex11a(-/-) mice than in wild-type mice. Fenofibrate, a peroxisome proliferator-activated receptor-α agonist, restored the abundance of peroxisomes and reduced the tubulointerstitial lesions induced by deoxycorticosterone acetate-salt hypertension. In conclusion, our results indicate that proximal tubule peroxisomes play an important role in proteinuria-induced interstitial lesions. The activation of tubular peroxisomes might be an excellent therapeutic strategy against chronic kidney disease.

  3. Solar Wind Helium Abundance as a Function of Speed and Heliographic Latitude: Variation through a Solar Cycle

    NASA Technical Reports Server (NTRS)

    Kasper, J. C.; Stenens, M. L.; Stevens, M. L.; Lazarus, A. J.; Steinberg, J. T.; Ogilvie, Keith W.

    2006-01-01

    We present a study of the variation of the relative abundance of helium to hydrogen in the solar wind as a function of solar wind speed and heliographic latitude over the previous solar cycle. The average values of A(sub He), the ratio of helium to hydrogen number densities, are calculated in 25 speed intervals over 27-day Carrington rotations using Faraday Cup observations from the Wind spacecraft between 1995 and 2005. The higher speed and time resolution of this study compared to an earlier work with the Wind observations has led to the discovery of three new aspects of A(sub He), modulation during solar minimum from mid-1995 to mid-1997. First, we find that for solar wind speeds between 350 and 415 km/s, A(sub He), varies with a clear six-month periodicity, with a minimum value at the heliographic equatorial plane and a typical gradient of 0.01 per degree in latitude. For the slow wind this is a 30% effect. We suggest that the latitudinal gradient may be due to an additional dependence of coronal proton flux on coronal field strength or the stability of coronal loops. Second, once the gradient is subtracted, we find that A(sub He), is a remarkably linear function of solar wind speed. Finally, we identify a vanishing speed, at which A(sub He), is zero, is 259 km/s and note that this speed corresponds to the minimum solar wind speed observed at one AU. The vanishing speed may be related to previous theoretical work in which enhancements of coronal helium lead to stagnation of the escaping proton flux. During solar maximum the A(sub He), dependences on speed and latitude disappear, and we interpret this as evidence of two source regions for slow solar wind in the ecliptic plane, one being the solar minimum streamer belt and the other likely being active regions.

  4. Hydrolysis of organonitrate functional groups in aerosol particles

    SciTech Connect

    Liu, Shang; Shilling, John E.; Song, Chen; Hiranuma, Naruki; Zaveri, Rahul A.; Russell, Lynn M.

    2012-10-19

    Organonitrate (ON) groups are important substituents in secondary organic aerosols. Model simulations and laboratory studies indicate a large fraction of ON groups in aerosol particles, but much lower quantities are observed in the atmosphere. Hydrolysis of ON groups in aerosol particles has been proposed recently. To test this hypothesis, we simulated formation of ON molecules in a reaction chamber under a wide range of relative humidity (0% to 90%). The mass fraction of ON groups (5% to 20% for high-NOx experiments) consistently decreased with increasing relative humidity, which was best explained by hydrolysis of ON groups at a rate of 4 day-1 (lifetime of 6 hours) for reactions under relative humidity greater than 20%. In addition, we found that secondary nitrogen-containing molecules absorb light, with greater absorption under dry and high-NOx conditions. This work provides the first evidence for particle-phase hydrolysis of ON groups, a process that could substantially reduce ON group concentration in the atmosphere.

  5. Variations of the relative abundances of He, (C,N,O) and Fe-group nuclei in solar cosmic rays and their relationship to solar particle acceleration

    NASA Technical Reports Server (NTRS)

    Bertsch, D. L.; Biswas, S.; Fichtel, C. E.; Pellerin, C. J.; Reames, D. V.

    1973-01-01

    Measurements of the flux of helium nuclei in the 24 January 1971 event and of helium and (C,N,O) nuclei in the 1 September 1971 event are combined with previous measurements to obtain the relative abundances of helium, (C,N,O), and Fe-group nuclei in these events. These data are then summarized together with previously reported results to show that, even when the same detector system using a dE/dx plus range technique is used, differences in the He/(C,N,O) value in the same energy/nucleon interval are observed in solar cosmic ray events. Further, when the He/(C,N,O) value is lower the He/(Fe-group nuclei) value is also systematically lower in these large events. When solar particle acceleration theory is analyzed, it is seen that the results suggest that, for large events, Coulomb energy loss probably does not play a major role in determining solar particle composition at higher energies (10 MeV). The variations in multicharged nuclei composition are more likely due to partial ionization during the acceleration phase.

  6. Use of morphological characteristics to define functional groups of predatory fishes in the Celtic Sea.

    PubMed

    Reecht, Y; Rochet, M-J; Trenkel, V M; Jennings, S; Pinnegar, J K

    2013-08-01

    An ecomorphological method was developed, with a focus on predation functions, to define functional groups in the Celtic Sea fish community. Eleven functional traits, measured for 930 individuals from 33 species, led to 11 functional groups. Membership of functional groups was linked to body size and taxonomy. For seven species, there were ontogenetic changes in group membership. When diet composition, expressed as the proportions of different prey types recorded in stomachs, was compared among functional groups, morphology-based predictions accounted for 28-56% of the interindividual variance in prey type. This was larger than the 12-24% of variance that could be explained solely on the basis of body size.

  7. Effects of stocking rates on functional group diversity and forage quality in rangeland of Qilian Mountain, China.

    PubMed

    Zhanq, Yan; Chen, Xianjiang; Cheng, Yunxiang; Chang, Shenghua; Hou, Fujiang

    2015-07-01

    The present study aimed at investigating a balance between environment and livestock grazing, through identifying appropriate stocking rate in rangeland with highest biodiversity and forage quality. The experiment was carried out to determine the effects of six stocking rates on Shannon Weiner index of functional group diversity and nutritive value and relationship between them in the edge of the Tibetan plateau of China. The results showed that abundance of functional group diversity indices were significantly influenced by stocking rates (p < 0.05) and the highest appeared in 2.5 and 2.6 animal month unit (AMU) ha(-1)'. There were significant differences in forage content of nitrogen (N), water-soluble carbohydrate (WSC), neutral detergent fiber (NDF) and acid detergent fiber (ADF) under stocking rates (p<0.05). There were higher N and WSC content but lower NDF and ADF content under 2.5 and 2.6 AMU ha(-1) than other stocking rates. Positive relationship was found between all functional group diversity indices and N and WSC content of community but negative relationship between all functional group diversity indices and NDF and ADF content of community. All the results represented that moderate control of stocking rates was an effective management measure to protect functional diversity, improve forage quality and sustain rangeland health. PMID:26387344

  8. Effects of stocking rates on functional group diversity and forage quality in rangeland of Qilian Mountain, China.

    PubMed

    Zhanq, Yan; Chen, Xianjiang; Cheng, Yunxiang; Chang, Shenghua; Hou, Fujiang

    2015-07-01

    The present study aimed at investigating a balance between environment and livestock grazing, through identifying appropriate stocking rate in rangeland with highest biodiversity and forage quality. The experiment was carried out to determine the effects of six stocking rates on Shannon Weiner index of functional group diversity and nutritive value and relationship between them in the edge of the Tibetan plateau of China. The results showed that abundance of functional group diversity indices were significantly influenced by stocking rates (p < 0.05) and the highest appeared in 2.5 and 2.6 animal month unit (AMU) ha(-1)'. There were significant differences in forage content of nitrogen (N), water-soluble carbohydrate (WSC), neutral detergent fiber (NDF) and acid detergent fiber (ADF) under stocking rates (p<0.05). There were higher N and WSC content but lower NDF and ADF content under 2.5 and 2.6 AMU ha(-1) than other stocking rates. Positive relationship was found between all functional group diversity indices and N and WSC content of community but negative relationship between all functional group diversity indices and NDF and ADF content of community. All the results represented that moderate control of stocking rates was an effective management measure to protect functional diversity, improve forage quality and sustain rangeland health.

  9. Effects of spatial grouping on the functional response of predators

    USGS Publications Warehouse

    Cosner, C.; DeAngelis, D.L.; Ault, J.S.; Olson, D.B.

    1999-01-01

    A unified mechanistic approach is given for the derivation of various forms of functional response in predator-prey models. The derivation is based on the principle-of-mass action but with the crucial refinement that the nature of the spatial distribution of predators and/or opportunities for predation are taken into account in an implicit way. If the predators are assumed to have a homogeneous spatial distribution, then the derived functional response is prey-dependent. If the predators are assumed to form a dense colony or school in a single (possibly moving) location, or if the region where predators can encounter prey is assumed to be of limited size, then the functional response depends on both predator and prey densities in a manner that reflects feeding interference between predators. Depending on the specific assumptions, the resulting functional response may be of Beddington-DeAngelis type, of Hassell-Varley type, or ratio-dependent.

  10. Application of the functionally generated path technique to restore mandibular molars in bilateral group function occlusion.

    PubMed

    DuVall, Nicholas B; Rogers, Paul M

    2013-04-01

    The functionally generated path (FGP) is a static representation of the opposing cusps' dynamic eccentric movements from a centric position to achieve optimal articulation and occlusal harmony. When understood and appreciated, use of the FGP technique is a straightforward and practical method to achieve harmonious occlusal anatomy of restorations with the anterior determinant/anterior guidance, the posterior determinant/condylar guidance, existing occlusal and cuspal anatomy, and the neuromuscular system. Although the FGP technique is normally used in the fabrication of maxillary posterior indirect restorations, it is described and applied here in the fabrication of mandibular posterior restorations that maintained the patient's bilateral group function occlusion while eliminating the nonworking side and protrusive interferences. This novel procedure involved the use of a stone crib to intraorally construct a stone core that captured the FGP recording while simultaneously indexing to the contralateral and ipsilateral mandibular dentition. This technique lends additional stability to the stone core to minimize error during the mounting process.

  11. Olive ridley sea turtle hatching success as a function of the microbial abundance in nest sand at Ostional, Costa Rica.

    PubMed

    Bézy, Vanessa S; Valverde, Roldán A; Plante, Craig J

    2015-01-01

    Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g(-1) nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g(-1) g(-1) nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest.

  12. Olive ridley sea turtle hatching success as a function of the microbial abundance in nest sand at Ostional, Costa Rica.

    PubMed

    Bézy, Vanessa S; Valverde, Roldán A; Plante, Craig J

    2015-01-01

    Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g(-1) nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g(-1) g(-1) nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest. PMID:25714355

  13. Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica

    PubMed Central

    Bézy, Vanessa S.; Valverde, Roldán A.; Plante, Craig J.

    2015-01-01

    Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g-1 nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g-1 g-1 nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest. PMID:25714355

  14. Assessing physiological responses of dune forest functional groups to changing water availability: from Tropics to Mediterranean.

    NASA Astrophysics Data System (ADS)

    Antunes, Cristina; Lo Cascio, Mauro; Correia, Otília; Vieira, Simone; Cruz Diaz Barradas, Maria; Zunzunegui, Maria; Ramos, Margarida; João Pereira, Maria; Máguas, Cristina

    2014-05-01

    Alterations in water availability are important to vegetation as can produce dramatic changes in plant communities, on physiological performance or survival of plant species. Particularly, groundwater lowering and surface water diversions will affect vulnerable coastal dune forests, ecosystems particularly sensitive to groundwater limitation. Reduction of water tables can prevent the plants from having access to one of their key water sources and inevitably affect groundwater-dependent species. The additional impact of drought due to climatic change on groundwater-dependent ecosystems has become of increasing concern since it aggravates groundwater reduction impacts with consequent uncertainties about how vegetation will respond over the short and long term. Sand dune plant communities encompass a diverse number of species that differ widely in root depth, tolerance to drought and capacity to shift between seasonal varying water sources. Plant functional groups may be affected by water distribution and availability differently. The high ecological diversity of sand dune forests, characterized by sandy soils, well or poorly drained, poor in nutrients and with different levels of salinity, can occur in different climatic regions of the globe. Such is the case of Tropical, Meso-mediterranean and Mediterranean areas, where future climate change is predicted to change water availability. Analyses of the relative natural abundances of stable isotopes of carbon (13C/12C) and oxygen (18O/16O) have been used across a wide range of scales, contributing to our understanding of plant ecology and interactions. This approach can show important temporal and spatial changes in utilization of different water sources by vegetation. Accordingly, the core idea of this work is to evaluate, along a climatic gradient, the responses and capacity of different coastal plant communities to adapt to changing water availability. This large-climatic-scale study, covering Brazil, Portugal and

  15. Functional-group specific aptamers indirectly recognizing compounds with alkyl amino group.

    PubMed

    Mei, Hongcheng; Bing, Tao; Yang, Xiaojuan; Qi, Cui; Chang, Tianjun; Liu, Xiangjun; Cao, Zehui; Shangguan, Dihua

    2012-09-01

    Aptamers are usually generated against a specific molecule. Their high selectivity makes them only suitable for studying specific targets. Since it is nearly impossible to generate aptamers for every molecule, it can be of great interest to select aptamers recognizing a common feature of a group of molecules in many applications. In this paper, we describe the selection of aptamers for indirect recognition of alkyl amino groups. Because amino groups are small and positive charged, we introduced a protection group, p-nitrobenzene sulfonyl (p-nosyl) to convert them into a form suitable for aptamer selection. Taking N(ε)-p-nosyl-L-lysine (PSL) as a target, we obtained a group of aptamers using the SELEX technique. Two optimized aptamers, M6b-M14 and M13a exhibit strong affinity to PSL with the K(d) values in the range of 2-5 μM. They also show strong affinity to other compounds containing p-nosyl-protected amino groups except those also possessing an α-carboxyl group. Both aptamers adopt an antiparallel G-quadruplex structure when binding to targets. An aptamer beacon based on M6b-M14 showed good selectivity toward the reaction mixture of p-nosyl-Cl and alkyl amino compounds, and could recognize lysine from amino acid mixtures indirectly, suggesting that aptamers against a common moiety of a certain type of molecules can potentially lead to many new applications. Through this study, we have demonstrated the ability to select aptamers for a specific part of an organic compound, and the chemical conversion approach may prove to be valuable for aptamer selection against molecules that are generally difficult for SELEX.

  16. Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species

    PubMed Central

    Herben, Tomáš; Suda, Jan; Klimešová, Jitka; Mihulka, Stanislav; Říha, Pavel; Šímová, Irena

    2012-01-01

    Background and Aims Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate. Methods Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis. Key Results Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R2 = 0·145) than for perennials (R2 = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance. Conclusions The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes. PMID:22628380

  17. Effects of Oxygen-Containing Functional Groups on Supercapacitor Performance

    SciTech Connect

    Kerisit, Sebastien N.; Schwenzer, Birgit; Vijayakumar, M.

    2014-07-03

    Molecular dynamics (MD) simulations of the interface between graphene and the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (BMIM OTf) were carried out to gain molecular-level insights into the performance of graphene-based supercapacitors and, in particular, determine the effects of the presence of oxygen-containing defects at the graphene surface on their integral capacitance. The MD simulations predict that increasing the surface coverage of hydroxyl groups negatively affects the integral capacitance, whereas the effect of the presence of epoxy groups is much less significant. The calculated variations in capacitance are found to be directly correlated to the interfacial structure. Indeed, hydrogen bonding between hydroxyl groups and SO3 anion moieties prevents BMIM+ and OTf- molecules from interacting favorably in the dense interfacial layer and restrains the orientation and mobility of OTf- ions, thereby reducing the permittivity of the ionic liquid at the interface. The results of the molecular simulations can facilitate the rational design of electrode materials for supercapacitors.

  18. Rectifying and negative differential resistance behaviors of a functionalized Tour wire: The position effects of functional groups

    NASA Astrophysics Data System (ADS)

    Kwong, Gordon; Zhang, Zhenhua; Pan, Jinbo

    2011-09-01

    Based on Tour wire, we construct four D-π-A molecular devices with different positional functional groups, in an attempt to explore the position effects of functional groups on their electronic transport properties and to show that some interesting physical phenomena can emerge by only varying the position of functional groups. The first-principles calculations demonstrate that the position of functional groups can affect the rectifying behaviors (rectification direction and ratio) significantly and determines whether or not the negative differential resistance (NDR) can be observed as well as the physical origin of the NDR phenomenon.

  19. Hydrated goethite (alpha-FeOOH) (100) interface structure: Ordered water and surface functional groups.

    SciTech Connect

    Ghose, S.K.; Waychunas, G.A.; Trainor, T.P.; Eng, P.J.

    2009-12-15

    Goethite({alpha}-FeOOH), an abundant and highly reactive iron oxyhydroxide mineral, has been the subject of numerous stud-ies of environmental interface reactivity. However, such studies have been hampered by the lack of experimental constraints on aqueous interface structure, and especially of the surface water molecular arrangements. Structural information of this type is crucial because reactivity is dictated by the nature of the surface functional groups and the structure or distribution of water and electrolyte at the solid-solution interface. In this study we have investigated the goethite(100) surface using surface diffraction techniques, and have determined the relaxed surface structure, the surface functional groups, and the three dimensional nature of two distinct sorbed water layers. The crystal truncation rod (CTR) results show that the interface structure consists of a double hydroxyl, double water terminated interface with significant atom relaxations. Further, the double hydroxyl terminated surface dominates with an 89% contribution having a chiral subdomain structure on the(100) cleavage faces. The proposed interface stoichiometry is ((H{sub 2}O)-(H{sub 2}O)-OH{sub 2}-OH-Fe-O-O-Fe-R) with two types of terminal hydroxyls; a bidentate (B-type) hydroxo group and a monodentate (A-type) aquo group. Using the bond-valence approach the protonation states of the terminal hydroxyls are predicted to be OH type (bidentate hydroxyl with oxygen coupled to two Fe{sup 3+} ions) and OH{sub 2} type (monodentate hydroxyl with oxygen tied to only one Fe{sup 3+}). A double layer three dimensional ordered water structure at the interface was determined from refinement of fits to the experimental data. Application of bond-valence constraints to the terminal hydroxyls with appropriate rotation of the water dipole moments allowed a plausible dipole orientation model as predicted. The structural results are discussed in terms of protonation and H-bonding at the interface

  20. [Duffy blood group antigens: structure, serological properties and function].

    PubMed

    Łukasik, Ewa; Waśniowska, Kazimiera

    2016-01-01

    Duffy (Fy) blood group antigens are located on seven-transmembrane glycoprotein expressed on erythrocytes and endothelial cells, which acts as atypical chemokine receptor (ACKR1) and malarial receptor. The biological role of the Duffy glycoprotein has not been explained yet. It is suggested that Duffy protein modulate the intensity of the inflammatory response. The Duffy blood group system consists of two major antigens, Fy(a) and Fy(b), encoded by two codominant alleles designated FY*A and FY*B which differ by a single nucleotide polymorphism (SNP) at position 125G>A of the FY gene that results in Gly42Asp amino acid change in the Fy(a) and Fy(b) antigens, respectively. The presence of antigen Fy(a) and/or Fy(b) on the erythrocytes determine three Duffy-positive phenotypes: Fy(a+b-), Fy(a-b+) and Fy(a+b+), identified in Caucasian population. The Duffy-negative phenotype Fy(a-b-), frequent in Africans, but very rare in Caucasians, is defined by the homozygous state of FY*B-33 alleles. The FY*B-33 allele is associated with a SNP -33T>C in the promoter region of the FY gene, which suppresses erythroid expression of this gene without affecting its expression in other tissues. The FY*X allele, found in Caucasians, is correlated with weak expression of Fy(b) antigen. Fy(x) antigen differs from the native Fy(b) by the Arg89Cys and Ala100Thr amino acid substitutions due to SNPs: 265C>T and 298G>A in FY*B allele. The frequency of the FY alleles shows marked geographic disparities, the FY*B-33 allele is predominant in Africans, the FY*B in Caucasians, while the FY*A allele is dominant in Asians and it is the most prevalent allele globally. PMID:26943312

  1. A Generalized Logistic Regression Procedure to Detect Differential Item Functioning among Multiple Groups

    ERIC Educational Resources Information Center

    Magis, David; Raiche, Gilles; Beland, Sebastien; Gerard, Paul

    2011-01-01

    We present an extension of the logistic regression procedure to identify dichotomous differential item functioning (DIF) in the presence of more than two groups of respondents. Starting from the usual framework of a single focal group, we propose a general approach to estimate the item response functions in each group and to test for the presence…

  2. Functional groups grafted nonwoven fabrics for blood filtration-The effects of functional groups and wettability on the adhesion of leukocyte and platelet

    NASA Astrophysics Data System (ADS)

    Yang, Chao; Cao, Ye; Sun, Kang; Liu, Jiaxin; Wang, Hong

    2011-01-01

    In this work, the effects of grafted functional groups and surface wettability on the adhesion of leukocyte and platelet were investigated by the method of blood filtration. The filter materials, poly(butylene terephthalate) nonwoven fabrics bearing different functional groups including hydroxyl (OH), carboxyl (COOH), sulfonic acid group (SO3H) and zwitterionic sulfobetaine group (⊕N((CH3)2)(CH2)3SO3⊖) with controllable wettability were prepared by UV radiation grafting vinyl monomers with these functional groups. Our results emphasized that both surface functional groups and surface wettability had significant effects on the adhesion of leukocyte and platelet. In the case of filter materials with the same wettability, leukocytes adhering to filter materials decreased in the order: the surface bearing OH only > the surface bearing both OH and COOH > the surface bearing sulfobetaine group > the surface bearing SO3H, while platelets adhering to filter materials decreased as the following order: the surface bearing SO3H > the surface bearing both OH and COOH > the surface bearing OH only > the surface bearing sulfobetaine group. As the wettability of filter materials increased, both leukocyte and platelet adhesion to filter materials declined, except that leukocyte adhesion to the surface bearing OH only remained unchanged.

  3. METALLICITY DISTRIBUTION FUNCTIONS OF FOUR LOCAL GROUP DWARF GALAXIES

    SciTech Connect

    Ross, Teresa L.; Holtzman, Jon; Saha, Abhijit; Anthony-Twarog, Barbara J. E-mail: holtz@nmsu.edu

    2015-06-15

    We present stellar metallicities in Leo I, Leo II, IC 1613, and Phoenix dwarf galaxies derived from medium (F390M) and broad (F555W, F814W) band photometry using the Wide Field Camera 3 instrument on board the Hubble Space Telescope. We measured metallicity distribution functions (MDFs) in two ways, (1) matching stars to isochrones in color–color diagrams and (2) solving for the best linear combination of synthetic populations to match the observed color–color diagram. The synthetic technique reduces the effect of photometric scatter and produces MDFs 30%–50% narrower than the MDFs produced from individually matched stars. We fit the synthetic and individual MDFs to analytical chemical evolution models (CEMs) to quantify the enrichment and the effect of gas flows within the galaxies. Additionally, we measure stellar metallicity gradients in Leo I and II. For IC 1613 and Phoenix our data do not have the radial extent to confirm a metallicity gradient for either galaxy. We find the MDF of Leo I (dwarf spheroidal) to be very peaked with a steep metal-rich cutoff and an extended metal-poor tail, while Leo II (dwarf spheroidal), Phoenix (dwarf transition), and IC 1613 (dwarf irregular) have wider, less peaked MDFs than Leo I. A simple CEM is not the best fit for any of our galaxies; therefore we also fit the “Best Accretion Model” of Lynden-Bell. For Leo II, IC 1613, and Phoenix we find similar accretion parameters for the CEM even though they all have different effective yields, masses, star formation histories, and morphologies. We suggest that the dynamical history of a galaxy is reflected in the MDF, where broad MDFs are seen in galaxies that have chemically evolved in relative isolation and narrowly peaked MDFs are seen in galaxies that have experienced more complicated dynamical interactions concurrent with their chemical evolution.

  4. Diversity in in-group bias: structural factors, situational features, and social functions.

    PubMed

    Scheepers, Daan; Spears, Russell; Doosje, Bertjan; Manstead, Antony S R

    2006-06-01

    Four experiments addressed the different forms and functions of in-group bias in different contexts. The authors proposed 2 functions: an identity-expressive function and an instrumental function (or promotion of positive social change). The authors manipulated status differentials, the stability of these differences, and the communication context (intra- vs. intergroup) and measured in-group bias and both functions. As predicted, identity expression via in-group bias on symbolic measures was most important for stable, high-status groups. By contrast, material in-group bias for instrumental motives was most prevalent in unstable, low-status groups but only when communicating with in-group members. This latter effect illustrates the strategic adaptation of group behavior to audience (i.e., displaying in-group bias may provoke the out-group and be counterproductive in instrumental terms). Stable, low-status groups displayed more extreme forms of in-group bias for instrumental reasons regardless of communication context (i.e., they had nothing to lose). Results are discussed in terms of a contextual-functional approach to in-group bias.

  5. Group structure and weighting function effects on neutron penetration through thick sodium-iron shields

    SciTech Connect

    Fu, C.Y.; Ingersoll, D.T.

    1987-01-01

    The effects of group structures and weighting functions on neutron penetration through a thick Na-Fe geometry are studied. The recommended broad-group (61-neutron/23-gamma-ray) and few-group (22-neutron/10-gamma-ray) structures are tailored to the sodium and iron resonances, windows, and capture gamma-ray spectra. The best weighting functions are shown to be fine-group fluxes selected from a few key locations in the geometry. These group structures and weighting functions, relative to existing group structures and conventional weighting functions, improve the accuracy of the computed 61-neutron-group Bonner ball responses by up to one hundred percent and of the computed 22-neutron-group results by up to six hundred percent.

  6. Intravascular pressure enhances the abundance of functional Kv1.5 channels at the surface of arterial smooth muscle cells.

    PubMed

    Kidd, Michael W; Leo, M Dennis; Bannister, John P; Jaggar, Jonathan H

    2015-08-18

    Voltage-dependent potassium (K(v)) channels are present in various cell types, including smooth muscle cells (myocytes) of resistance-sized arteries that control systemic blood pressure and regional organ blood flow. Intravascular pressure depolarizes arterial myocytes, stimulating calcium (Ca(2+)) influx through voltage-dependent Ca(2+) (Ca(v)) channels that results in vasoconstriction and also K(+) efflux through K(v) channels that oppose vasoconstriction. We hypothesized that pressure-induced depolarization may not only increase the open probability of plasma membrane-resident K(v) channels but also increase the abundance of these channels at the surface of arterial myocytes to limit vasoconstriction. We found that K(v)1.5 and K(v)2.1 proteins were abundant in the myocytes of resistance-sized mesenteric arteries. K(v)1.5, but not K(v)2.1, continuously recycled between the intracellular compartment and the plasma membrane in contractile arterial myocytes. Using ex vivo preparations of intact arteries, we showed that physiological intravascular pressure through membrane depolarization or membrane depolarization in the absence of pressure inhibited the degradation of internalized K(v)1.5 and increased recycling of K(v)1.5 to the plasma membrane. Accordingly, by stimulating the activity of Ca(v)1.2, membrane depolarization increased whole-cell K(v)1.5 current density in myocytes and K(v)1.5 channel activity in pressurized arteries. In contrast, the total amount and cell surface abundance of K(v)2.1 were independent of intravascular pressure or membrane potential. Thus, our data indicate that intravascular pressure-induced membrane depolarization selectively increased K(v)1.5 surface abundance to increase K(v) currents in arterial myocytes, which would limit vasoconstriction.

  7. Use of the Nosyl Group as a Functional Protecting Group in Applications of a Michael/Smiles Tandem Process.

    PubMed

    Coulibali, Siomenan; Godou, Timothé; Canesi, Sylvain

    2016-09-01

    Concise preparations of elaborated polycyclic and heterocyclic systems present in natural products were obtained using the nosyl group as a functional protecting group not only to mask the reactivity of a sensitive moiety but also to provide a structure desired in the final target. The group is transferred to the substrate during deprotection through a novel extension of the Truce-Smiles rearrangement in tandem with a 1,4-addition. This strategy provides access to a ring system laden with valuable functionalities for subsequent manipulations and can serve as a versatile building block for the construction of more complex molecular architectures such as indoles in a manner compatible with the concepts of green chemistry and atom economy. PMID:27513700

  8. The abundance of a single domain cyclophilin in Solanaceae is regulated as a function of organ type and high temperature and not by other environmental constraints.

    PubMed

    Kiełbowicz-Matuk, Agnieszka; Rey, Pascal; Rorat, Tadeusz

    2007-11-01

    The abundance of a single domain cyclophilin (CyP), designated as SsCyP, was investigated in Solanum sogarandinum and Solanum tuberosum plants during development and in response to various environmental constraints. We show that under control conditions, SsCyP is distributed throughout the plant but in an organ-specific manner. In both Solanum species, the highest protein levels are observed in transporting organs and in tubers, and substantial amounts are noticed in open flowers and in stamens. We also show that the SsCyP abundance in leaves strongly decreases with age. In in vitro-grown plantlets of S. sogarandinum, the SsCyP gene is induced by low temperature at the transcript level but not at the protein level, indicating that post-transcriptional mechanisms control SsCyP expression under cold conditions. In in vivo-grown Solanum plants, the organ-dependent SsCyP protein distribution and abundance are not modified by cold, drought, salinity and photooxidative treatments. In contrast, the protein abundance substantially decreases in all organs of Solanum plants subjected to heat shock. We conclude that the SsCyP protein acts mainly during development and does not belong to the group of stress-induced CyPs.

  9. Functional Groups Based on Leaf Physiology: Are they Spatially and Temporally Robust?

    NASA Technical Reports Server (NTRS)

    Foster, Tammy E.; Brooks, J. Renee; Quincy, Charles (Technical Monitor)

    2002-01-01

    The functional grouping hypothesis, which suggests that complexity in function can be simplified by grouping species with similar responses, was tested in the Florida scrub habitat. Functional groups were identified based on how species in fire maintained FL scrub function in terms of carbon, water and nitrogen dynamics. The suite of physiologic parameters measured to determine function included both instantaneous gas exchange measurements obtained from photosynthetic light response curves and integrated measures of function. Using cluster analysis, five distinct physiologically-based functional groups were identified. Using non-parametric multivariate analyses, it was determined that these five groupings were not altered by plot differences or by the three different management regimes; prescribed burn, mechanically treated and burn, and fire-suppressed. The physiological groupings also remained robust between the two years 1999 and 2000. In order for these groupings to be of use for scaling ecosystem processes, there needs to be an easy-to-measure morphological indicator of function. Life form classifications were able to depict the physiological groupings more adequately than either specific leaf area or leaf thickness. THe ability of life forms to depict the groupings was improved by separating the parasitic Ximenia americana from the shrub category.

  10. Structure and function studies on enzymes with a catalytic carboxyl group(s): from ribonuclease T1 to carboxyl peptidases

    PubMed Central

    TAKAHASHI, Kenji

    2013-01-01

    A group of enzymes, mostly hydrolases or certain transferases, utilize one or a few side-chain carboxyl groups of Asp and/or Glu as part of the catalytic machinery at their active sites. This review follows mainly the trail of studies performed by the author and his colleagues on the structure and function of such enzymes, starting from ribonuclease T1, then extending to three major types of carboxyl peptidases including aspartic peptidases, glutamic peptidases and serine-carboxyl peptidases. PMID:23759941

  11. Geometries of functional group interactions in enzyme-ligand complexes: guides for receptor modelling.

    PubMed

    Tintelnot, M; Andrews, P

    1989-03-01

    An approach is described which makes use of X-ray structural data from enzyme-ligand complexes in order to obtain information for application in receptor modelling. The atomic surroundings of five different ligand functional groups were determined for all complex structures recorded in the Brookhaven Protein Data Bank. These atomic surroundings were then superimposed with respect to the atoms of the functional groups of the ligands in order to obtain clouds of neighbouring atoms. General principles were sought to describe the orientation or favoured position of groups or atoms around those functional groups when bound to a macromolecule. Some simple conclusions and leads for further modelling were thus derived.

  12. The galaxy luminosity function in groups and clusters: the faint-end upturn and the connection to the field luminosity function

    NASA Astrophysics Data System (ADS)

    Lan, Ting-Wen; Ménard, Brice; Mo, Houjun

    2016-07-01

    We characterize the luminosity functions of galaxies residing in z ˜ 0 groups and clusters over the broadest ranges of luminosity and mass reachable by the Sloan Digital Sky Survey. Our measurements cover four orders of magnitude in luminosity, down to about Mr = -12 mag or L = 107 L⊙, and three orders of magnitude in halo mass, from 1012 to 1015 M⊙. We find a characteristic scale, Mr ˜ -18 mag or L ˜ 109 L⊙, below which the slope of the luminosity function becomes systematically steeper. This trend is present for all halo masses and originates mostly from red satellites. This ubiquitous faint-end upturn suggests that it is formation, rather than halo-specific environmental effect, that plays a major role in regulating the stellar masses of faint satellites. We show that the satellite luminosity functions can be described in a simple manner by a double Schechter function with amplitudes scaling with halo mass over the entire range of observables. Combining these conditional luminosity functions with the dark matter halo mass function, we accurately recover the entire field luminosity function over 10 visual magnitudes and reveal that satellite galaxies dominate the field luminosity function at magnitudes fainter than -17. We find that the luminosity functions of blue and red satellite galaxies show distinct shapes and we present estimates of the stellar mass fraction as a function of halo mass and galaxy type. Finally, using a simple model, we demonstrate that the abundances and the faint-end slopes of blue and red satellite galaxies can be interpreted in terms of their formation history, with two distinct modes separated by some characteristic time.

  13. Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins.

    PubMed

    Zhang, Yu-Juan; Yang, Chun-Lin; Hao, You-Jin; Li, Ying; Chen, Bin; Wen, Jian-Fan

    2014-01-25

    To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.

  14. Can functional gene abundance predict N-fluxes? Examples from a well-studied hydrological flow path in a forested watershed in SW China

    NASA Astrophysics Data System (ADS)

    Liu, Binbin; Muzammil, Bushra; Dörsch, Peter; Zhu, Jing; Mulder, Jan; Frostegård, Åsa

    2014-05-01

    Edaphic, climatic and management factors shape soil microbial communities taxonomically and functionally, resulting in spatial separation of nitrogen (N) oxidation and reduction processes along hydrological flowpaths. In a recent study, we investigated N-cycling processes and N2O emissions along a mesic hillslope (HS) and a hydrologically connected groundwater discharge zone (GDZ) in a forested headwater catchment dominated by acid soils (pH 4.0 - 4.5) in subtropical China (Chongqing). The watershed receives 50 kg N ha-1 a-1 through atmogenic deposition (2/3 as ammonium), most of which is removed before discharge. Surprisingly, N2O emissions were found to be greatest on the well-drained HS, whereas a drop of NO3- concentrations along the flow path indicated that N removal was highest in the moist GDZ. Nitrification was assumed to be none-limiting as the total flux of NO3- leaving the hill slope soils roughly equalled the input of NH4+. To understand watershed N-cycling and removal in more detail, we studied the abundance of functional genes involved in ammonium oxidation (amoA of AOB and AOA), nitrite oxidation (nxrB) and denitrification (nirK, nirS, nosZ) in top soils from 8 locations along the flow path spanning from the hilltop to the outlet of the GDZ. 16S rRNA gene abundance was assessed as a general marker for bacterial abundance. All genes showed highest abundance per gram soil in the heavily disturbed GDZ (formerly cultivated terraces), despite lower soil organic carbon content (1-4% w/w as opposed to 10-20% w/w in HS topsoil) and periodically stagnant conditions due to high water tables after monsoonal rainfalls. Ratios of nosZ/nirS+nirK, commonly used to predict denitrification product stoichiometry (N2O/N2), yielded counterintuitive results with higher values for HS than for GDZ. However, comparing nir gene with 16S rRNA gene abundance revealed that denitrifiers accounted for up to 10% of the bacterial community in the GDZ soils whereas this value was

  15. Does the source of carbon influence the abundance of nirK, nirS and nosZ functional genes in laboratory denitrification bioreactors?

    NASA Astrophysics Data System (ADS)

    Barrett, Maria; Fenton, Owen; Ibrahim, Tristan G.; O'Flaherty, Vincent; Healey, Mark G.

    2014-05-01

    Biological denitrification in soil is the main producer of nitrous oxide (N2O) emissions. Denitrifying soil microbes are capable of reducing nitrate (NO3-) to nitrite (NO2-) to N2O and di-nitrogen gas (N2). One third of these denitrifers possess a truncated functional gene pathway, which may lack the nosZ gene and emit N2O as a final emission product instead of the more benign N2. A carbon rich environment, specific to certain types of carbon sources, has been shown to foster an anaerobic environment, which positively impacts microbial denitrification rates. The present study examined the effect of varying carbon sources in laboratory-scale denitrification bioreactors on NO3- removal and also correlated performance with the abundance of the denitrifying microbial consortia possessing the denitrifying functional genes nirK, nirS and nosZ in each bioreactor. The bioreactors comprised either lodgepole pine woodchips (LPW), lodgepole pine needles (LPN), barley straw (BBS), or cardboard (CCB), each mixed with soil in a 1:1 ratio (by volume) and subject to sequentially increasing hydraulic loading rates of 3, 5 and 10 cm d-1 for a total operation period of up to 744 days. A reactor containing soil only (CSO) was used as the study control. The abundance of denitrifers was determined by targeting nirK, nirS, nosZ functional genes and the overall microbial population was determined by targeting bacterial and archaeal 16sRNA genes. Nitrate removal from all bioreactors was > 99.7%, but when pollution swapping was considered, this ranged from 67% for LPW to 95% for the CCB ; this was also mirrored in the average nirk/nirS/nosZ gene abundance (CCB, c. 94% (c. 108); LPN, 75% (c. 107); BBS, c. 74% (c. 106/107); LPW, 70% (c. 105). Bacterial 16sRNA gene abundance was similar in all reactors including the control (P=0.0362). The abundance of nosZ genes and the genetic potential for N2 emissions varied in all reactors in comparison to the control CSO, BBS (P=0.0051); CCB (P=0

  16. Variations in abundance, genome size, morphology, and functional role of the virioplankton in Lakes Annecy and Bourget over a 1-year period.

    PubMed

    Zhong, Xu; Ram, Angia Siram Pradeep; Colombet, Jonathan; Jacquet, Stéphan

    2014-01-01

    We sampled the surface waters (2-50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16 × 10(7) (January) and 2.08 × 10(8) part mL(-1) (May) in Lake Bourget and between 2.7 × 10(7) (June) and 8.39 × 10(7) part mL(-1) (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1% (June) and 33.2% (October) in Lake Bourget and between 7.4% (June) and 52.6% (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal "diversity" were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this

  17. Oxygenated organic functional groups and their sources in single and submicron organic particles in MILAGRO 2006 campaign

    NASA Astrophysics Data System (ADS)

    Liu, S.; Takahama, S.; Russell, L. M.; Gilardoni, S.; Baumgardner, D.

    2009-02-01

    Fourier Transform Infrared (FTIR) and X-ray Fluorescence (XRF) were used to measure organic functional groups and elements of submicron particles collected during MILAGRO in March 2006 on three platforms: the Mexico City urban area (SIMAT), the high altitude site at 4010 m (Altzomoni), and the NCAR C130 aircraft. Scanning transmission X-ray Microscopy (STXM) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were applied to single particle organic functional group abundance analysis of particles simultaneously collected at SIMAT and C130. Correlations of elemental concentrations showed different groups of source related elements at SIMAT, Altzomoni, and C130, suggesting different processes affecting the air masses sampled at the three platforms. Cluster analysis resulted in seven distinct Clusters of FTIR spectra, with the last three clusters consisting of spectra collected almost exclusively on the C130 platform, reflecting the variety of sources contributing to C130 samples. Positive Matrix Factorization (PMF) of NEXAFS-STXM spectra identified three main factors representing soot, secondary, and biomass burning type spectra. PMF of FTIR spectra resulted in three fossil fuel combustion type factors, one biomass burning factor, and one mixed or processed factor. The fossil fuel combustion type factors were found to have the largest contributions to OM, while the processed factor has the largest O/C among all factors. Alkane, carboxylic acid, and amine functional groups were mainly associated with combustion related sources, while alcohol groups were likely from atmospheric processing of mixed sources. While the processed factor has the highest O/C, half of the OM and O/C measured could be attributed directly to fossil fuel combustion sources. Both PMF of NEXAFS-STXM spectra and PMF of FTIR spectra indicate that the combustion type factors are more affected by fluctuations in local sources, while the processed factors are more consistent during the sampling

  18. Oxygenated organic functional groups and their sources in single and submicron organic particles in MILAGRO 2006 campaign

    NASA Astrophysics Data System (ADS)

    Liu, S.; Takahama, S.; Russell, L. M.; Gilardoni, S.; Baumgardner, D.

    2009-09-01

    Fourier Transform Infrared (FTIR) and X-ray Fluorescence (XRF) were used to measure organic functional groups and elements of submicron particles collected during MILAGRO in March 2006 on three platforms: the Mexico City urban area (SIMAT), the high altitude site at 4010 m (Altzomoni), and the NCAR C130 aircraft. Scanning Transmission X-ray Microscopy (STXM) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were applied to single particle organic functional group abundance analysis of particles simultaneously collected at SIMAT and C130. Correlations of elemental concentrations showed different groups of source-related elements at SIMAT, Altzomoni, and C130, suggesting different processes affecting the air masses sampled at the three platforms. Cluster analysis resulted in seven distinct clusters of FTIR spectra, with the last three clusters consisting of spectra collected almost exclusively on the C130 platform, reflecting the variety of sources contributing to C130 samples. Positive Matrix Factorization (PMF) of STXM-NEXAFS spectra identified three main factors representing soot, secondary, and biomass burning type spectra. PMF of FTIR spectra resulted in two fossil fuel combustion factors and one biomass burning factor, the former representative of source regions to the northeast and southwest of SIMAT. Alkane, carboxylic acid, amine, and alcohol functional groups were mainly associated with combustion related sources, while non-acid carbonyl groups were likely from biomass burning events. The majority of OM and O/C was attributed to combustion sources, although no distinction between direct emissions and atmospherically processed OM could be identified.

  19. Characterization of Oxygen Containing Functional Groups on Carbon Materials with Oxygen K-edge X-ray Absorption Near Edge Structure Spectroscopy

    SciTech Connect

    K Kim; P Zhu; L Na; X Ma; Y Chen

    2011-12-31

    Surface functional groups on carbon materials are critical to their surface properties and related applications. Many characterization techniques have been used to identify and quantify the surface functional groups, but none is completely satisfactory especially for quantification. In this work, we used oxygen K-edge X-ray absorption near edge structure (XANES) spectroscopy to identify and quantify the oxygen containing surface functional groups on carbon materials. XANES spectra were collected in fluorescence yield mode to minimize charging effect due to poor sample conductivity which can potentially distort XANES spectra. The surface functional groups are grouped into three types, namely carboxyl-type, carbonyl-type, and hydroxyl-type. XANES spectra of the same type are very similar while spectra of different types are significantly different. Two activated carbon samples were analyzed by XANES. The total oxygen contents of the samples were estimated from the edge step of their XANES spectra, and the identity and abundance of different functional groups were determined by fitting of the sample XANES spectrum to a linear combination of spectra of the reference compounds. It is concluded that oxygen K-edge XANES spectroscopy is a reliable characterization technique for the identification and quantification of surface functional groups on carbon materials.

  20. Use of the Sequence Rule for Indexing Functional Groups in Organic Compounds

    ERIC Educational Resources Information Center

    Hudrlik, Paul F.

    1973-01-01

    A new method of indexing functional groups in organic compounds is described, utilizing the Cahn-Ingold-Prelog sequence rule. Functional carbon atoms are first classified by functionality, a measure of the oxidation state, then ordered by means of a modified sequence rule. Substructure searching and other applications are discussed. (30…

  1. Succession of phytoplankton functional groups regulated by monsoonal hydrology in a large canyon-shaped reservoir.

    PubMed

    Xiao, Li-Juan; Wang, Tian; Hu, Ren; Han, Bo-Ping; Wang, Sheng; Qian, Xin; Padisák, Judit

    2011-10-15

    Liuxihe reservoir is a deep, monomictic, oligo-mesotrophic canyon-reservoir in the subtropical monsoon climate region of southern China. Phytoplankton functional groups in the reservoir were investigated and a comparison made between the succession observed in 2008, an exceptionally wet year, and 2009, an average year. The reservoir shows strong annual fluctuations in water level caused by monsoon rains and artificial drawdown. Altogether 28 functional groups of phytoplankton were identified, including 79 genera. Twelve of the groups were analyzed in detail using redundancy analysis. Because of the oligo-mesotrophic and P-limited condition of the reservoir, the dominant functional groups were those tolerant of nutrient (phosphorus) deficiency. The predominant functional groups in the succession process were Groups A (Cyclotella with greatest axial linear dimension<10 μm), B (Cyclotella with greatest axial linear dimension>10 μm), LO (Peridinium), LM (Ceratium and Microcystis), E (Dinobryon and Mallomonas), F (Botryococcus), X1 (Ankistrodesmus, Ankyra, Chlorella and Monoraphidium) and X2 (Chlamydomonas and Chroomonas). The development of groups A, B and LO was remarkably seasonal. Group A was dominant during stratification, when characteristic small size and high surface/volume ratio morphology conferred an advantage. Group LO was dominant during dry stratification, when motility was advantageous. Group B plankton exhibited a high relative biomass during periods of reduced euphotic depth and isothermy. Groups LM, E, F, X1 and X2 occasionally exhibited high relative biomasses attributable to specific environmental events (e.g. drawdown, changes in zooplankton community). A greater diversity of phytoplankton functional groups was apparent during isothermy. This study underscores the usefulness of functional algal groups in studying succession in subtropical impoundments, in which phytoplankton succession can be significantly affected by external factors such as

  2. Abundance and Diversity of Bacterial Nitrifiers and Denitrifiers and Their Functional Genes in Tannery Wastewater Treatment Plants Revealed by High-Throughput Sequencing

    PubMed Central

    Wang, Zhu; Zhang, Xu-Xiang; Lu, Xin; Liu, Bo; Li, Yan; Long, Chao; Li, Aimin

    2014-01-01

    Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment. PMID:25420093

  3. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    PubMed

    Wang, Zhu; Zhang, Xu-Xiang; Lu, Xin; Liu, Bo; Li, Yan; Long, Chao; Li, Aimin

    2014-01-01

    Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment. PMID:25420093

  4. Abundances of platinum group elements in native sulfur condensates from the Niuatahi-Motutahi submarine volcano, Tonga rear arc: Implications for PGE mineralization in porphyry deposits

    NASA Astrophysics Data System (ADS)

    Park, Jung-Woo; Campbell, Ian H.; Kim, Jonguk

    2016-02-01

    Some porphyry Cu-Au deposits, which are enriched in Pd, are potentially an economic source of Pd. Magmatic volatile phases are thought to transport the platinum group elements (PGEs) from the porphyry source magma to the point of deposition. However, the compatibilities of the PGEs in magmatic volatile phases are poorly constrained. We report PGE and Re contents in native sulfur condensates and associated altered dacites from the Niuatahi-Motutahi submarine volcano, Tonga rear arc, in order to determine the compatibility of PGEs and Re in magmatic volatile phases, and their mobility during secondary hydrothermal alteration. The native sulfur we analyzed is the condensate of a magmatic volatile phase exsolved from the Niuatahi-Motutahi magma. The PGEs are moderately enriched in the sulfur condensates in comparison to the associated fresh dacite, with enrichment factors of 11-285, whereas Au, Cu and Re are strongly enriched with enrichment factors of ∼20,000, ∼5000 and ∼800 respectively. Although the PGEs are moderately compatible into magmatic volatile phases, their compatibility is significantly lower than that of Au, Cu and Re. Furthermore, the compatibility of PGEs decrease in the order: Ru > Pt > Ir > Pd. This trend is also observed in condensates and sublimates from other localities. PGE mineralization in porphyry Cu-Au deposits is characterized by substantially higher Pd/Pt (∼7-60) and Pd/Ir (∼100-10,500) than typical orthomagmatic sulfide deposits (e.g. Pd/Pt ∼0.6 and Pd/Ir ∼20 for the Bushveld). It has previously been suggested that the high mobility of Pd, relative to the other PGEs, may account for the preferential enrichment of Pd in porphyry Cu-Au deposits. However, the low compatibility of Pd in the volatile phase relative to the other PGEs, shown in this study, invalidates this explanation. We suggest that the PGE geochemistry of Pd-rich Cu-Au deposits is principally derived from the PGE characteristics of the magma from which the ore

  5. Renormalization group functions for two-dimensional phase transitions: To the problem of singular contributions

    SciTech Connect

    Pogorelov, A. A.; Suslov, I. M.

    2007-08-15

    According to the available publications, the field theoretical renormalization group approach in the two-dimensional case gives the critical exponents that differ from the known exact values. This property is associated with the existence of nonanalytic contributions in the renormalization group functions. The situation is analyzed in this work using a new algorithm for summing divergent series that makes it possible to determine the dependence of the results for the critical exponents on the expansion coefficients for the renormalization group functions. It has been shown that the exact values of all the exponents can be obtained with a reasonable form of the coefficient functions. These functions have small nonmonotonic sections or inflections, which are poorly reproduced in natural interpolations. It is not necessary to assume the existence of singular contributions in the renormalization group functions.

  6. Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology.

    PubMed

    Pendás, A Martín; Francisco, E; Blanco, M A

    2007-01-01

    We analyze the response of a quantum group within a molecule to charge transfer by using the interacting quantum atoms approach (IQA), an energy partitioning scheme within the quantum theory of atoms in molecules (QTAM). It is shown that this response lies at the core of the concept of the functional group. The manipulation of fractional electron populations is carried out by using distribution functions for the electron number within the quantum basins. Several test systems are studied to show that similar chemical potential groups are characterized by similar energetic behavior upon interaction with other groups. The origin of the empirical additivity rules for group energies in simple hydrocarbons is also investigated. It turns out to rest on the independent saturation of both the self-energies and the interaction energies of the groups as the size of the chain increases. We also show that our results are compatible with the standard group energies of the QTAM.

  7. Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis.

    PubMed

    Tourna, Maria; Maclean, Paul; Condron, Leo; O'Callaghan, Maureen; Wakelin, Steven A

    2014-06-01

    Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry.

  8. Hydrologic controls on nitrogen cycling processes and functional gene abundance in sediments of a groundwater flow-through lake

    USGS Publications Warehouse

    Stoliker, Deborah L.; Repert, Deborah A.; Smith, Richard L.; Song, Bongkeun; LeBlanc, Denis R.; McCobb, Timothy D.; Conaway, Christopher; Hyun, Sung Pil; Koh, Dong-Chan; Moon, Hee Sun; Kent, Douglas B.

    2016-01-01

    The fate and transport of inorganic nitrogen (N) is a critically important issue for human and aquatic ecosystem health because discharging N-contaminated groundwater can foul drinking water and cause algal blooms. Factors controlling N-processing were examined in sediments at three sites with contrasting hydrologic regimes at a lake on Cape Cod, MA. These factors included water chemistry, seepage rates and direction of groundwater flow, and the abundance and potential rates of activity of N-cycling microbial communities. Genes coding for denitrification, anaerobic ammonium oxidation (anammox), and nitrification were identified at all sites regardless of flow direction or groundwater dissolved oxygen concentrations. Flow direction was, however, a controlling factor in the potential for N-attenuation via denitrification in the sediments. Potential rates of denitrification varied from 6 to 4500 pmol N/g/h from the inflow to the outflow side of the lake, owing to fundamental differences in the supply of labile organic matter. The results of laboratory incubations suggested that when anoxia and limiting labile organic matter prevailed, the potential existed for concomitant anammox and denitrification. Where oxic lake water was downwelling, potential rates of nitrification at shallow depths were substantial (1640 pmol N/g/h). Rates of anammox, denitrification, and nitrification may be linked to rates of organic N-mineralization, serving to increase N-mobility and transport downgradient.

  9. Hydrologic Controls on Nitrogen Cycling Processes and Functional Gene Abundance in Sediments of a Groundwater Flow-Through Lake.

    PubMed

    Stoliker, Deborah L; Repert, Deborah A; Smith, Richard L; Song, Bongkeun; LeBlanc, Denis R; McCobb, Timothy D; Conaway, Christopher H; Hyun, Sung Pil; Koh, Dong-Chan; Moon, Hee Sun; Kent, Douglas B

    2016-04-01

    The fate and transport of inorganic nitrogen (N) is a critically important issue for human and aquatic ecosystem health because discharging N-contaminated groundwater can foul drinking water and cause algal blooms. Factors controlling N-processing were examined in sediments at three sites with contrasting hydrologic regimes at a lake on Cape Cod, MA. These factors included water chemistry, seepage rates and direction of groundwater flow, and the abundance and potential rates of activity of N-cycling microbial communities. Genes coding for denitrification, anaerobic ammonium oxidation (anammox), and nitrification were identified at all sites regardless of flow direction or groundwater dissolved oxygen concentrations. Flow direction was, however, a controlling factor in the potential for N-attenuation via denitrification in the sediments. Potential rates of denitrification varied from 6 to 4500 pmol N/g/h from the inflow to the outflow side of the lake, owing to fundamental differences in the supply of labile organic matter. The results of laboratory incubations suggested that when anoxia and limiting labile organic matter prevailed, the potential existed for concomitant anammox and denitrification. Where oxic lake water was downwelling, potential rates of nitrification at shallow depths were substantial (1640 pmol N/g/h). Rates of anammox, denitrification, and nitrification may be linked to rates of organic N-mineralization, serving to increase N-mobility and transport downgradient. PMID:26967929

  10. Better Alternatives to "Astronomical Silicate": Laboratory-based Optical Functions of Chondritic/Solar Abundance Glass with Application to HD 161796

    NASA Astrophysics Data System (ADS)

    Speck, A. K.; Pitman, K. M.; Hofmeister, A. M.

    2015-08-01

    “Astronomical” or “circumstellar” silicate optical functions (real and imaginary indices of refraction n(λ ) and k(λ )) have previously been derived from compositionally and structurally disparate samples; past values were compiled from different sources in the literature, and are essentially kluges of observational, laboratory, and extrapolated or interpolated values. These synthetic optical functions were created because astronomers lack the quantitative data on amorphous silicates at all wavelengths needed for radiative transfer modeling. This paper provides optical functions that (1) are created with a consistent methodology, (2) use the same sample across all wavelengths, and (3) minimize interpolation and extrapolation wherever possible. We present electronic data tables of optical functions derived from mid-ultraviolet to far-infrared (FIR) laboratory transmission spectra for two materials: iron-free glass with chondritic/solar atmospheric abundances, and metallic iron. We compare these optical functions to other popular n, k data used to model amorphous silicates (e.g., “astronomical” or “circumstellar” silicate), both directly and in application to a simple system: the dust shell of the post-AGB star HD 161796. Using the new optical functions, we find that the FIR profile of model spectral energy distributions are significantly affected by the ratio of glass to iron. Our case study on HD 161796 shows that in modeling with our new optical functions, the mineralogy is markedly different from that derived using synthetic optical functions and suggests a new scenario of crystalline silicate formation.

  11. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

    PubMed Central

    Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

    2015-01-01

    Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon – Simpson’s indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning. PMID:26396042

  12. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling.

    PubMed

    Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

    2015-09-23

    Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon - Simpson's indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning.

  13. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

    NASA Astrophysics Data System (ADS)

    Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

    2015-09-01

    Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon - Simpson’s indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning.

  14. Divergence of function in sequence-related groups of Escherichia coli proteins.

    PubMed

    Nahum, L A; Riley, M

    2001-08-01

    The most prominent mechanism of molecular evolution is believed to have been duplication and divergence of genes. Proteins that belong to sequence-related groups in any one organism are candidates to have emerged from such a process and to share a common ancestor. Groups of proteins in Escherichia coli having sequence similarity are mostly composed of proteins with closely related function, but some groups comprise proteins with unrelated functions. In order to understand how function can change while sequences remain similar, we have examined some of these groups in detail. The enzymes analyzed in this work include representatives of amidotransferases, phosphotransferases, decarboxylases, and others. Most sequence-related groups contain enzymes that are in the same classes of Enzyme Commission (EC) numbers. We have concentrated on groups that are heterogeneous in that respect, and also on groups containing more than one enzyme of any pathway. We find that although the EC number may differ, the reaction chemistry of these sequence-related proteins is the same or very similar. Some of these families illustrate how diversification has taken place in evolution, using common features of either reaction chemistry or ligand specificity, or both, to create catalysts for different kinds of biochemical reactions. This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function.

  15. Unique determination of the effective potential in terms of renormalization group functions

    SciTech Connect

    Chishtie, F. A.; Hanif, T.; McKeon, D. G. C.; Steele, T. G.

    2008-03-15

    The perturbative effective potential V in the massless {lambda}{phi}{sup 4} model with a global O(N) symmetry is uniquely determined to all orders by the renormalization group functions alone when the Coleman-Weinberg renormalization condition (d{sup 4}V/d{phi}{sup 4})|{sub {phi}}{sub ={mu}}={lambda} is used, where {mu} represents the renormalization scale. Systematic methods are developed to express the n-loop effective potential in the Coleman-Weinberg scheme in terms of the known n-loop minimal-subtraction (MS) renormalization group functions. Moreover, it also proves possible to sum the leading- and subsequent-to-leading-logarithm contributions to V. An essential element of this analysis is a conversion of the renormalization group functions in the Coleman-Weinberg scheme to the renormalization group functions in the MS scheme. As an example, the explicit five-loop effective potential is obtained from the known five-loop MS renormalization group functions and we explicitly sum the leading-logarithm, next-to-leading-logarithm, and further subleading-logarithm contributions to V. Extensions of these results to massless scalar QED are also presented. Because massless scalar QED has two couplings, conversion of the renormalization group functions from the MS scheme to the Coleman-Weinberg scheme requires the use of multiscale renormalization group methods.

  16. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function

    PubMed Central

    Krey, Jocelyn F.; Drummond, Meghan; Foster, Sarah; Porsov, Edward; Vijayakumar, Sarath; Choi, Dongseok; Friderici, Karen; Jones, Sherri M.; Nuttall, Alfred L.; Barr-Gillespie, Peter G.

    2016-01-01

    The phospholipid- and Ca2+-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, the inner ear’s sensory organelle. Using quantitative mass spectrometry, we estimated that ANXA5 accounts for ~15,000 copies per stereocilium, or ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were present at levels near ANXA5 in bundles and none were upregulated in stereocilia of Anxa5−/− mice. Annexins have been proposed to mediate Ca2+-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, mature Anxa5−/− mice not only have normal hearing and balance function, but following noise exposure, they are identical to wild-type mice in their temporary or permanent changes in hearing sensitivity. We suggest that despite the unusually high levels of ANXA5 in bundles, it does not play a role in the bundle’s key function, mechanotransduction, at least until after two months of age in the cochlea and six months of age in the vestibular system. These results reinforce the lack of correlation between abundance of a protein in a specific compartment or cellular structure and its functional significance. PMID:27251877

  17. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function.

    PubMed

    Krey, Jocelyn F; Drummond, Meghan; Foster, Sarah; Porsov, Edward; Vijayakumar, Sarath; Choi, Dongseok; Friderici, Karen; Jones, Sherri M; Nuttall, Alfred L; Barr-Gillespie, Peter G

    2016-01-01

    The phospholipid- and Ca(2+)-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, the inner ear's sensory organelle. Using quantitative mass spectrometry, we estimated that ANXA5 accounts for ~15,000 copies per stereocilium, or ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were present at levels near ANXA5 in bundles and none were upregulated in stereocilia of Anxa5(-/-) mice. Annexins have been proposed to mediate Ca(2+)-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, mature Anxa5(-/-) mice not only have normal hearing and balance function, but following noise exposure, they are identical to wild-type mice in their temporary or permanent changes in hearing sensitivity. We suggest that despite the unusually high levels of ANXA5 in bundles, it does not play a role in the bundle's key function, mechanotransduction, at least until after two months of age in the cochlea and six months of age in the vestibular system. These results reinforce the lack of correlation between abundance of a protein in a specific compartment or cellular structure and its functional significance.

  18. Functional Group Compositions of Carbonaceous Materials of Hayabusa-Returned Samples

    NASA Astrophysics Data System (ADS)

    Yabuta, H.; Uesugi, M.; Naraoka, H.; Ito, M.; Kilcoyne, D.; Sandford, S. A.; Kitajima, F.; Mita, H.; Takano, Y.; Yada, T.; Karouji, Y.; Ishibashi, Y.; Okada, T.; Abe, M.

    2014-09-01

    We have analyzed the functional group compositions of the carbonaceous materials of Hayabusa-returned samples by STXM-XANES, in order to identify whether the materials are terrestrial or extraterrestrial.

  19. Controlling surface functionality through generation of thiol groups in a self-assembled monolayer.

    SciTech Connect

    Lud, S. Q.; Neppl, S.; Richter, G.; Bruno, P.; Gruen, D. M.; Jordan, R.; Feulner, P.; Stutzmann, M.; Garrido, J. A.; Materials Science Division; Technische Univ. Munchen

    2010-01-01

    A lithographic method to generate reactive thiol groups on functionalized synthetic diamond for biosensor and molecular electronic applications is developed. We demonstrate that ultrananocrystalline diamond (UNCD) thin films covalently functionalized with surface-generated thiol groups allow controlled thiol-disulfide exchange surface hybridization processes. The generation of the thiol functional head groups was obtained by irradiating phenylsulfonic acid (PSA) monolayers on UNCD surfaces. The conversion of the functional headgroup of the self-assembled monolayer was verified by using X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and fluorescence microscopy. Our findings indicate the selective generation of reactive thiol surface groups. Furthermore, we demonstrate the grafting of yeast cytochrome c to the thiol-modified diamond surface and the electron transfer between protein and electrode.

  20. Production of Printed Indexes of Chemical Reactions. I. Analysis of Functional Group Interconversions

    ERIC Educational Resources Information Center

    Clinging, R.; Lynch, M. F.

    1973-01-01

    A program is described which identifies functional group interconversion reactions, hydrogenations, and dehydrogenations in a data base containing structures encoded as Wiswesser Line Notations. Production of the data base is briefly described. (17 references) (Authors)

  1. CNO abundances in H II regions of the Magellanic clouds and the galaxy with implications regarding the nucleosynthesis of the CNO element group

    NASA Technical Reports Server (NTRS)

    Dufour, R. J.; Shields, G. A.

    1982-01-01

    Final abundance results of IUE observations of the UV spectra of three H II regions in the Small Magellanic Cloud and four H II regions in the Large Magellanic Cloud are presented. Calculated yields of carbon and oxygen derived are y(C)=.00063 and y(O)=.0016. The nucleosynthetic origin of nitrogen was evaluated as being predominantly a secondary element produced from carbon as its seed. Plotting log N/C versus log C/H yielded the rather unexpected result that log N/C decreases with lo C/H over the SMC-LMC-Orion range. The cause of this relationship is discussed.

  2. Multiple-Group Noncompensatory Differential Item Functioning in Raju's Differential Functioning of Items and Tests

    ERIC Educational Resources Information Center

    Oshima, T. C.; Wright, Keith; White, Nick

    2015-01-01

    Raju, van der Linden, and Fleer (1995) introduced a framework for differential functioning of items and tests (DFIT) for unidimensional dichotomous models. Since then, DFIT has been shown to be a quite versatile framework as it can handle polytomous as well as multidimensional models both at the item and test levels. However, DFIT is still limited…

  3. Evaluation of Assertive Training and Homosexual Guidance Service Groups Designed to Improve Homosexual Functioning

    ERIC Educational Resources Information Center

    Russell, A.; Winkler, R.

    1977-01-01

    It is proposed that clinicians should develop research-based assertiveness training procedures for homosexuals that are designed to facilitate homosexual functioning. Subjects (N=27) were assigned to a behaviorally oriented assertive training group or a non-directive group run by a homosexual guidance service. Self-report measures indicated…

  4. The Use of Language Functions in Mathematical Group Games. Teacher Insights.

    ERIC Educational Resources Information Center

    Black, Carolyn; Huerta, Maria G.

    1994-01-01

    Six group games were introduced into a second-grade bilingual classroom. Children's talk during each game was classified using a modification of Dyson's five language functions (representational, directive, heuristic, personal, and interactional). Group games provided many communication opportunities. Some children tried new communication styles.…

  5. Characteristics of Interactional Management Functions in Group Oral by Japanese Learners of English

    ERIC Educational Resources Information Center

    Negishi, Junko

    2010-01-01

    This study attempted to investigate the characteristics of interaction dynamics in a group oral interaction carried out by Japanese learners of English. The relationship between the participants' language development and interactional management functions (IMFs) was also explored. Oral performance tests in a paired or a small group have recently…

  6. Aggressive and Prosocial Peer Group Functioning: Effects on Children's Social, School, and Psychological Adjustment

    ERIC Educational Resources Information Center

    Chung-Hall, Janet; Chen, Xinyin

    2010-01-01

    This study examined the effects of aggressive and prosocial contexts of peer groups on children's socioemotional and school adjustment. Data on informal peer groups, social functioning, and different aspects of adjustment were collected from multiple sources in a sample of elementary school children (149 boys, 181 girls; M age = 10 years).…

  7. Identification of Differential Item Functioning in Multiple-Group Settings: A Multivariate Outlier Detection Approach

    ERIC Educational Resources Information Center

    Magis, David; De Boeck, Paul

    2011-01-01

    We focus on the identification of differential item functioning (DIF) when more than two groups of examinees are considered. We propose to consider items as elements of a multivariate space, where DIF items are outlying elements. Following this approach, the situation of multiple groups is a quite natural case. A robust statistics technique is…

  8. Functional Groups Based on Leaf Physiology: Are they Spatially and Temporally Robust?

    NASA Technical Reports Server (NTRS)

    Foster, Tammy E.; Brooks, J. Renee

    2004-01-01

    The functional grouping hypothesis, which suggests that complexity in ecosystem function can be simplified by grouping species with similar responses, was tested in the Florida scrub habitat. Functional groups were identified based on how species in fire maintained Florida scrub regulate exchange of carbon and water with the atmosphere as indicated by both instantaneous gas exchange measurements and integrated measures of function (%N, delta C-13, delta N-15, C-N ratio). Using cluster analysis, five distinct physiologically-based functional groups were identified in the fire maintained scrub. These functional groups were tested to determine if they were robust spatially, temporally, and with management regime. Analysis of Similarities (ANOSIM), a non-parametric multivariate analysis, indicated that these five physiologically-based groupings were not altered by plot differences (R = -0.115, p = 0.893) or by the three different management regimes; prescribed burn, mechanically treated and burn, and fire-suppressed (R = 0.018, p = 0.349). The physiological groupings also remained robust between the two climatically different years 1999 and 2000 (R = -0.027, p = 0.725). Easy-to-measure morphological characteristics indicating functional groups would be more practical for scaling and modeling ecosystem processes than detailed gas-exchange measurements, therefore we tested a variety of morphological characteristics as functional indicators. A combination of non-parametric multivariate techniques (Hierarchical cluster analysis, non-metric Multi-Dimensional Scaling, and ANOSIM) were used to compare the ability of life form, leaf thickness, and specific leaf area classifications to identify the physiologically-based functional groups. Life form classifications (ANOSIM; R = 0.629, p 0.001) were able to depict the physiological groupings more adequately than either specific leaf area (ANOSIM; R = 0.426, p = 0.001) or leaf thickness (ANOSIM; R 0.344, p 0.001). The ability of

  9. Percolation galaxy groups and clusters in the sdss redshift survey: identification, catalogs, and the multiplicity function

    SciTech Connect

    Berlind, Andreas A.; Frieman, Joshua A.; Weinberg, David H.; Blanton, Michael R.; Warren, Michael S.; Abazajian, Kevork; Scranton, Ryan; Hogg, David W.; Scoccimarro, Roman; Bahcall, Neta A.; Brinkmann, J.; Gott, J.Richard, III; Kleinman, S.J.; Krzesinski, J.; Lee, Brian C.; Miller, Christopher J.; Nitta, Atsuko; Schneider, Donald P.; Tucker, Douglas L.; Zehavi, Idit; /CCPP, New York /Chicago U., Astron. Astrophys. Ctr. /Ohio State U., Dept. Astron. /Los Alamos /Pittsburgh U. /Princeton U. /Subaru Telescope /Apache Point Observ. /Mt. Suhora Observ., Cracow /LBL, Berkeley /Cerro-Tololo InterAmerican Obs. /Penn State U., Astron. Astrophys. /Fermilab /Arizona U., Astron. Dept. - Steward Observ. /Case Western Reserve U.

    2006-01-01

    We identify galaxy groups and clusters in volume-limited samples of the SDSS redshift survey, using a redshift-space friends-of-friends algorithm. We optimize the friends-of-friends linking lengths to recover galaxy systems that occupy the same dark matter halos, using a set of mock catalogs created by populating halos of N-body simulations with galaxies. Extensive tests with these mock catalogs show that no combination of perpendicular and line-of-sight linking lengths is able to yield groups and clusters that simultaneously recover the true halo multiplicity function, projected size distribution, and velocity dispersion. We adopt a linking length combination that yields, for galaxy groups with ten or more members: a group multiplicity function that is unbiased with respect to the true halo multiplicity function; an unbiased median relation between the multiplicities of groups and their associated halos; a spurious group fraction of less than {approx}1%; a halo completeness of more than {approx}97%; the correct projected size distribution as a function of multiplicity; and a velocity dispersion distribution that is {approx}20% too low at all multiplicities. These results hold over a range of mock catalogs that use different input recipes of populating halos with galaxies. We apply our group-finding algorithm to the SDSS data and obtain three group and cluster catalogs for three volume-limited samples that cover 3495.1 square degrees on the sky. We correct for incompleteness caused by fiber collisions and survey edges, and obtain measurements of the group multiplicity function, with errors calculated from realistic mock catalogs. These multiplicity function measurements provide a key constraint on the relation between galaxy populations and dark matter halos.

  10. Stabilization and strengthening effects of functional groups in two-dimensional titanium carbide

    NASA Astrophysics Data System (ADS)

    Fu, Z. H.; Zhang, Q. F.; Legut, D.; Si, C.; Germann, T. C.; Lookman, T.; Du, S. Y.; Francisco, J. S.; Zhang, R. F.

    2016-09-01

    Two-dimensional (2D) materials have attracted considerable interest due to their remarkable properties and potential applications for nanoelectronics, electrodes, energy storage devices, among others. However, many well-studied 2D materials lack appreciable conductivity and tunable mechanical strength, limiting their applications in flexible devices. Newly developed MXenes open up the opportunity to design novel flexible conductive electronic materials. Here, using density functional theory (DFT), we investigate systematically the effects of several functional groups on the stabilization, mechanical properties, and electronic structures of a representative MXene. It is found that oxygen possesses the largest adsorption energy as compared to other functional groups, indicating its good thermodynamic stabilization. In comparison with bare and other functionalized titanium carbides, the oxygen functionalized one exhibits the most superior ideal strength; however, the premature softening of the long-wave phonon modes might limit the intrinsic strength for T i3C2O2 . Furthermore, the introduction of functional groups can induce a strong anisotropy under tensile loading. By analyzing the deformation paths and the electronic instability under various loadings, we demonstrate that the unique strengthening by oxygen functional groups is attributed to a significant charge transfer from inner bonds to outer surface ones after functionalization. Our results shed a novel view into exploring a variety of MXenes for their potential applications in flexible electronic and energy storage devices.

  11. Psychosocial functioning in a group of Swedish adults with Asperger syndrome or high-functioning autism.

    PubMed

    Engström, I; Ekström, L; Emilsson, B

    2003-03-01

    This study reports on psychosocial functioning in Swedish adults with Asperger syndrome (AS) or high-functioning autism (HFA). A systematically selected sample of patients and relatives was interviewed concerning their psychosocial situation. The majority was living independently. All persons but one were unemployed. None was married and none had children. Only a few had some kind of partner. Most persons needed a high level of public and/or private support. The overall adjustment was rated good in 12 percent, fair in 75 percent and poor in 12 percent. Adult persons with AS/HFA have extensive need for support from their families and/or society. This information is important in order to provide adequate interventions that are in accordance with the expressed needs of the individuals themselves.

  12. The electrokinetic characterization of gold nanoparticles, functionalized with cationic functional groups, and its' interaction with DNA.

    PubMed

    Lazarus, Geraldine Genevive; Revaprasadu, Neerish; López-Viota, Julián; Singh, Moganavelli

    2014-09-01

    Gold nanoparticles have attracted strong biomedical interest for drug delivery due to their low toxic nature, surface plasmon resonance and capability of increasing the stability of the payload. However, gene transfection represents another important biological application. Considering that cellular barriers keep enclosed their secret to deliver genes using nanoparticles, an important step can be achieved by studying the functionalization of nanoparticles with DNA. In the present contribution the synthesis of nanoparticles consisting of a gold core coated with one or more layers of amino acid (l-lysine), and cationic polyelectrolytes (poly-ethyleneimine and poly-l-lysine) is reported. All nanoparticles were subjected to dynamic light scattering, electrophoretic mobility measurements, UV-vis optical spectrophotometry analysis and transmission electron microscopy imaging. In addition, the adsorption of DNA plasmid (pSGS) with linear and supercoiled configurations was studied for those gold nanoparticles under the most suitable surface modifications. Preliminary results showed that the gold nanoparticles functionalized with poly-ethyleneimine and poly-l-lysine, respectively, and bound to linear DNA configurations, present in absolute value a higher electrophoretic mobility irrespective of the pH of the media, compared to the supercoiled and nicked configuration. The findings from this study suggest that poly-ethyleneimine and poly-l-lysine functionalized gold nanoparticles are biocompatible and may be promising in the chemical design and future optimization of nanostructures for biomedical applications such as gene and drug delivery.

  13. The impact of functional group on the electronic structure of coordination center

    NASA Astrophysics Data System (ADS)

    Hooshmand Gharehbagh, Zahra; L, Duy; Rahman, Talat S.

    While 9, 10 dicyano-anthracene (DCA) forms a coordination network on Cu(111) surface with Cu adatom coordinated by three DCA molecules, its isomers, 9,10-diisocyano-anthracene forms, surprisingly, molecular rows on the same surface. To understand the impact of functional groups on the electronic structure of the coordination center, we have carried out density functional theory based calculations of the electronic structure of a set of naphthalene molecules with different functional groups (N, CN, NC, NH2, COH, COOH) adsorbed on Cu(111), with and without a Cu adatom. Our results show that while the interaction between the naphthalene backbone and the Cu(111) surface is dominated by van der Waals (vdW) forces, in all cases considered the functional group forms a covalent bond with the Cu (ad)atom (on) of the surface. The calculated differential charge redistribution shows that the strongest covalent bond is formed by the NC group, which differs remarkably from that formed by the CN group, while the vdW interaction is very similar in both cases. These results provide insights into the different surface coordination behavior of molecules with above-mentioned functional groups. Work support in part by NSF Grant CHE-1310327.

  14. Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.

    PubMed

    Kolker, Natali; Higdon, Roger; Broomall, William; Stanberry, Larissa; Welch, Dean; Lu, Wei; Haynes, Winston; Barga, Roger; Kolker, Eugene

    2011-01-01

    To address the monumental challenge of assigning function to millions of sequenced proteins, we completed the first of a kind all-versus-all sequence alignments using BLAST for 9.9 million proteins in the UniRef100 database. Microsoft Windows Azure produced over 3 billion filtered records in 6 days using 475 eight-core virtual machines. Protein classification into functional groups was then performed using Hive and custom jars implemented on top of Apache Hadoop utilizing the MapReduce paradigm. First, using the Clusters of Orthologous Genes (COG) database, a length normalized bit score (LNBS) was determined to be the best similarity measure for classification of proteins. LNBS achieved sensitivity and specificity of 98% each. Second, out of 5.1 million bacterial proteins, about two-thirds were assigned to significantly extended COG groups, encompassing 30 times more assigned proteins. Third, the remaining proteins were classified into protein functional groups using an innovative implementation of a single-linkage algorithm on an in-house Hadoop compute cluster. This implementation significantly reduces the run time for nonindexed queries and optimizes efficient clustering on a large scale. The performance was also verified on Amazon Elastic MapReduce. This clustering assigned nearly 2 million proteins to approximately half a million different functional groups. A similar approach was applied to classify 2.8 million eukaryotic sequences resulting in over 1 million proteins being assign to existing KOG groups and the remainder clustered into 100,000 functional groups. PMID:21809957

  15. Interrogating Surface Functional Group Heterogeneity of Activated Thermoplastics Using Super-Resolution Fluorescence Microscopy.

    PubMed

    ONeil, Colleen E; Jackson, Joshua M; Shim, Sang-Hee; Soper, Steven A

    2016-04-01

    We present a novel approach for characterizing surfaces utilizing super-resolution fluorescence microscopy with subdiffraction limit spatial resolution. Thermoplastic surfaces were activated by UV/O3 or O2 plasma treatment under various conditions to generate pendant surface-confined carboxylic acids (-COOH). These surface functional groups were then labeled with a photoswitchable dye and interrogated using single-molecule, localization-based, super-resolution fluorescence microscopy to elucidate the surface heterogeneity of these functional groups across the activated surface. Data indicated nonuniform distributions of these functional groups for both COC and PMMA thermoplastics with the degree of heterogeneity being dose dependent. In addition, COC demonstrated relative higher surface density of functional groups compared to PMMA for both UV/O3 and O2 plasma treatment. The spatial distribution of -COOH groups secured from super-resolution imaging were used to simulate nonuniform patterns of electroosmotic flow in thermoplastic nanochannels. Simulations were compared to single-particle tracking of fluorescent nanoparticles within thermoplastic nanoslits to demonstrate the effects of surface functional group heterogeneity on the electrokinetic transport process.

  16. GPU-based parallel group ICA for functional magnetic resonance data.

    PubMed

    Jing, Yanshan; Zeng, Weiming; Wang, Nizhuan; Ren, Tianlong; Shi, Yingchao; Yin, Jun; Xu, Qi

    2015-04-01

    The goal of our study is to develop a fast parallel implementation of group independent component analysis (ICA) for functional magnetic resonance imaging (fMRI) data using graphics processing units (GPU). Though ICA has become a standard method to identify brain functional connectivity of the fMRI data, it is computationally intensive, especially has a huge cost for the group data analysis. GPU with higher parallel computation power and lower cost are used for general purpose computing, which could contribute to fMRI data analysis significantly. In this study, a parallel group ICA (PGICA) on GPU, mainly consisting of GPU-based PCA using SVD and Infomax-ICA, is presented. In comparison to the serial group ICA, the proposed method demonstrated both significant speedup with 6-11 times and comparable accuracy of functional networks in our experiments. This proposed method is expected to perform the real-time post-processing for fMRI data analysis.

  17. Identifying organic aerosol sources by comparing functional group composition in chamber and atmospheric particles.

    PubMed

    Russell, Lynn M; Bahadur, Ranjit; Ziemann, Paul J

    2011-03-01

    Measurements of submicron particles by Fourier transform infrared spectroscopy in 14 campaigns in North America, Asia, South America, and Europe were used to identify characteristic organic functional group compositions of fuel combustion, terrestrial vegetation, and ocean bubble bursting sources, each of which often accounts for more than a third of organic mass (OM), and some of which is secondary organic aerosol (SOA) from gas-phase precursors. The majority of the OM consists of alkane, carboxylic acid, hydroxyl, and carbonyl groups. The organic functional groups formed from combustion and vegetation emissions are similar to the secondary products identified in chamber studies. The near absence of carbonyl groups in the observed SOA associated with combustion is consistent with alkane rather than aromatic precursors, and the absence of organonitrate groups can be explained by their hydrolysis in humid ambient conditions. The remote forest observations have ratios of carboxylic acid, organic hydroxyl, and nonacid carbonyl groups similar to those observed for isoprene and monoterpene chamber studies, but in biogenic aerosols transported downwind of urban areas the formation of esters replaces the acid and hydroxyl groups and leaves only nonacid carbonyl groups. The carbonyl groups in SOA associated with vegetation emissions provides striking evidence for the mechanism of esterification as the pathway for possible oligomerization reactions in the atmosphere. Forest fires include biogenic emissions that produce SOA with organic components similar to isoprene and monoterpene chamber studies, also resulting in nonacid carbonyl groups in SOA.

  18. Identifying organic aerosol sources by comparing functional group composition in chamber and atmospheric particles

    PubMed Central

    Russell, Lynn M.; Bahadur, Ranjit; Ziemann, Paul J.

    2011-01-01

    Measurements of submicron particles by Fourier transform infrared spectroscopy in 14 campaigns in North America, Asia, South America, and Europe were used to identify characteristic organic functional group compositions of fuel combustion, terrestrial vegetation, and ocean bubble bursting sources, each of which often accounts for more than a third of organic mass (OM), and some of which is secondary organic aerosol (SOA) from gas-phase precursors. The majority of the OM consists of alkane, carboxylic acid, hydroxyl, and carbonyl groups. The organic functional groups formed from combustion and vegetation emissions are similar to the secondary products identified in chamber studies. The near absence of carbonyl groups in the observed SOA associated with combustion is consistent with alkane rather than aromatic precursors, and the absence of organonitrate groups can be explained by their hydrolysis in humid ambient conditions. The remote forest observations have ratios of carboxylic acid, organic hydroxyl, and nonacid carbonyl groups similar to those observed for isoprene and monoterpene chamber studies, but in biogenic aerosols transported downwind of urban areas the formation of esters replaces the acid and hydroxyl groups and leaves only nonacid carbonyl groups. The carbonyl groups in SOA associated with vegetation emissions provides striking evidence for the mechanism of esterification as the pathway for possible oligomerization reactions in the atmosphere. Forest fires include biogenic emissions that produce SOA with organic components similar to isoprene and monoterpene chamber studies, also resulting in nonacid carbonyl groups in SOA. PMID:21317360

  19. Binding sites for abundant nuclear factors modulate RNA polymerase I-dependent enhancer function in Saccharomyces cerevisiae.

    PubMed

    Kang, J J; Yokoi, T J; Holland, M J

    1995-12-01

    The 190-base pair (bp) rDNA enhancer within the intergenic spacer sequences of Saccharomyces cerevisiae rRNA cistrons activates synthesis of the 35S-rRNA precursor about 20-fold in vivo (Mestel,, R., Yip, M., Holland, J. P., Wang, E., Kang, J., and Holland, M. J. (1989) Mol. Cell. Biol. 9, 1243-1254). We now report identification and analysis of transcriptional activities mediated by three cis-acting sites within a 90-bp portion of the rDNA enhancer designated the modulator region. In vivo, these sequences mediated termination of transcription by RNA polymerase I and potentiated the activity of the rDNA enhancer element. Two trans-acting factors, REB1 and REB2, bind independently to sites within the modulator region (Morrow, B. E., Johnson, S. P., and Warner, J. R. (1989) J. Biol. Chem. 264, 9061-9068). We show that REB2 is identical to the ABF1 protien. Site-directed mutagenesis of REB1 and ABF1 binding sites demonstrated uncoupling of RNA polymerase I-dependent termination from transcriptional activation in vivo. We conclude that REB1 and ABF1 are required for RNA polymerase I-dependent termination and enhancer function, respectively, Since REB1 and ABF1 proteins also regulate expression of class II genes and other nuclear functions, our results suggest further similarities between RNA polymerase I and II regulatory mechanisms. Two rDNA enhancers flanking a rDNA minigene stimulated RNA polymerase I transcription in a "multiplicative" fashion. Deletion mapping analysis showed that similar cis-acting sequences were required for enhancer function when positioned upstream or downstream from a rDNA minigene.

  20. The effect of heavy metal concentration and soil pH on the abundance of selected microbial groups within ArcelorMittal Poland steelworks in Cracow.

    PubMed

    Lenart, Anna; Wolny-Koładka, Katarzyna

    2013-01-01

    The present study aimed to identify the effect of heavy metal concentration and soil pH on the abundance of the selected soil microorganisms within ArcelorMittal Poland steelworks, Cracow. The analysis included 20 soil samples, where the concentration of Fe, Zn, Cd, Pb, Ni, Cu, Mn, Cr and soil pH were evaluated together with the number of mesophilic bacteria, fungi, Actinomycetes and Azotobacter spp. In the majority of samples soil pH was alkaline. The limits of heavy metals exceeded in eight samples and in one sample, the concentration of Zn exceeded 31-fold. Chromium was the element which most significantly limited the number of bacteria and Actinomycetes.

  1. Subtle cytotoxicity and genotoxicity differences in superparamagnetic iron oxide nanoparticles coated with various functional groups

    PubMed Central

    Hong, Seong Cheol; Lee, Jong Ho; Lee, Jaewook; Kim, Hyeon Yong; Park, Jung Youn; Cho, Johann; Lee, Jaebeom; Han, Dong-Wook

    2011-01-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) have been widely utilized for the diagnosis and therapy of specific diseases, as magnetic resonance imaging (MRI) contrast agents and drug-delivery carriers, due to their easy transportation to targeted areas by an external magnetic field. For such biomedical applications, SPIONs must have multifunctional characteristics, including optimized size and modified surface. However, the biofunctionality and biocompatibility of SPIONs with various surface functional groups of different sizes have yet to be elucidated clearly. Therefore, it is important to carefully monitor the cytotoxicity and genotoxicity of SPIONs that are surfaced-modified with various functional groups of different sizes. In this study, we evaluated SPIONs with diameters of approximately 10 nm and 100~150 nm, containing different surface functional groups. SPIONs were covered with −O− groups, so-called bare SPIONs. Following this, they were modified with three different functional groups – hydroxyl (−OH), carboxylic (−COOH), and amine (−NH2) groups – by coating their surfaces with tetraethyl orthosilicate (TEOS), (3-aminopropyl)trimethoxysilane (APTMS), TEOS-APTMS, or citrate, which imparted different surface charges and sizes to the particles. The effects of SPIONs coated with these functional groups on mitochondrial activity, intracellular accumulation of reactive oxygen species, membrane integrity, and DNA stability in L-929 fibroblasts were determined by water-soluble tetrazolium, 2′,7′-dichlorodihydrofluorescein, lactate dehydrogenase, and comet assays, respectively. Our toxicological observations suggest that the functional groups and sizes of SPIONs are critical determinants of cellular responses, degrees of cytotoxicity and genotoxicity, and potential mechanisms of toxicity. Nanoparticles with various surface modifications and of different sizes induced slight, but possibly meaningful, changes in cell cytotoxicity and

  2. On the psychological function of flags and logos: Group identity symbols increase perceived entitativity.

    PubMed

    Callahan, Shannon P; Ledgerwood, Alison

    2016-04-01

    Group identity symbols such as flags and logos have been widely used across time and cultures, yet researchers know very little about the psychological functions that such symbols can serve. The present research tested the hypotheses that (a) simply having a symbol leads collections of individuals to seem more like real, unified groups, (b) this increased psychological realness leads groups to seem more threatening and effective to others, and (c) group members therefore strategically emphasize symbols when they want their group to appear unified and intimidating. In Studies 1a-1c, participants perceived various task groups as more entitative when they happened to have a symbol. In Study 2, symbols not only helped groups make up for lacking a physical characteristic associated with entitativity (physical similarity), but also led groups to seem more threatening. Study 3 examined the processes underlying this effect and found that group symbols increase entitativity by increasing perceived cohesiveness. Study 4 extended our results to show that symbols not only shape the impressions people form of novel groups, but also change people's existing impressions of more familiar and real-world social groups, making them seem more entitative and competent but also less warm. Finally, Studies 5a and 5b further expand our understanding of the psychological function of symbols by showing that group members strategically display symbols when they are motivated to convey an impression of their group as unified and threatening (vs. inclusive and cooperative). We discuss implications for understanding how group members navigate their social identities. PMID:27078507

  3. Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

    PubMed

    Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

    2016-01-01

    In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon.

  4. Local and Regional Determinants of an Uncommon Functional Group in Freshwater Lakes and Ponds

    PubMed Central

    McCann, Michael James

    2015-01-01

    A combination of local and regional factors and stochastic forces is expected to determine the occurrence of species and the structure of communities. However, in most cases, our understanding is incomplete, with large amounts of unexplained variation. Using functional groups rather than individual species may help explain the relationship between community composition and conditions. In this study, I used survey data from freshwater lakes and ponds to understand factors that determine the presence of the floating plant functional group in the northeast United States. Of the 176 water bodies surveyed, 104 (59.1%) did not contain any floating plant species. The occurrence of this functional group was largely determined by local abiotic conditions, which were spatially autocorrelated across the region. A model predicting the presence of the floating plant functional group performed similarly to the best species-specific models. Using a permutation test, I also found that the observed prevalence of floating plants is no different than expected by random assembly from a species pool of its size. These results suggest that the size of the species pool interacts with local conditions in determining the presence of a functional group. Nevertheless, a large amount of unexplained variation remains, attributable to either stochastic species occurrence or incomplete predictive models. The simple permutation approach in this study can be extended to test alternative models of community assembly. PMID:26121636

  5. Energies of the adsorption of functional groups to calcium carbonate polymorphs: the importance of -OH and -COOH groups.

    PubMed

    Okhrimenko, D V; Nissenbaum, J; Andersson, M P; Olsson, M H M; Stipp, S L S

    2013-09-01

    The adsorption behavior of calcium carbonate is an important factor in many processes in nature, industry, and biological systems. We determined and compared the adsorption energies for a series of small molecules of different sizes and polarities (i.e., water, several alcohols, and acetic acid) on three synthetic CaCO3 polymorphs (calcite, aragonite, and vaterite). We measured isosteric heats of adsorption from vapor adsorption isotherms for 273 < T < 293 K, and we used XRD and SEM to confirm that samples did not change phase during the experiments. Density functional calculations and molecular dynamics simulations complemented the experimental results and aided interpretation. Alcohols with molecular mass greater than that of methanol bind more strongly to the calcium carbonate polymorphs than water and acetic acid. The adsorption energies for the alcohols are typical of chemisorption and indicate alcohol displacement of water from calcium carbonate surfaces. This explains why organisms favor biomolecules that contain alcohol functional groups (-OH) to control which polymorph they use, the crystal face and orientation, and the particle shape and size in biomineralization processes. This new insight is also very useful in understanding organic molecule adsorption mechanisms in soils, sediments, and rocks, which is important for predicting the behavior of mineral-fluid interactions when the challenge is to remediate contaminated groundwater aquifers or to produce oil and gas from reservoirs.

  6. Linking of Sensor Molecules with Amino Groups to Amino-Functionalized AFM Tips

    PubMed Central

    2011-01-01

    The measuring tip of an atomic force microscope (AFM) can be upgraded to a specific biosensor by attaching one or a few biomolecules to the apex of the tip. The biofunctionalized tip is then used to map cognate target molecules on a sample surface or to study biophysical parameters of interaction with the target molecules. The functionality of tip-bound sensor molecules is greatly enhanced if they are linked via a thin, flexible polymer chain. In a typical scheme of tip functionalization, reactive groups are first generated on the tip surface, a bifunctional cross-linker is then attached with one of its two reactive ends, and finally the probe molecule of interest is coupled to the free end of the cross-linker. Unfortunately, the most popular functional group generated on the tip surface is the amino group, while at the same time, the only useful coupling functions of many biomolecules (such as antibodies) are also NH2 groups. In the past, various tricks or detours were applied to minimize the undesired bivalent reaction of bifunctional linkers with adjacent NH2 groups on the tip surface. In the present study, an uncompromising solution to this problem was found with the help of a new cross-linker (“acetal-PEG-NHS”) which possesses one activated carboxyl group and one acetal-protected benzaldehyde function. The activated carboxyl ensures rapid unilateral attachment to the amino-functionalized tip, and only then is the terminal acetal group converted into the amino-reactive benzaldehyde function by mild treatment (1% citric acid, 1–10 min) which does not harm the AFM tip. As an exception, AFM tips with magnetic coating become demagnetized in 1% citric acid. This problem was solved by deprotecting the acetal group before coupling the PEG linker to the AFM tip. Bivalent binding of the corresponding linker (“aldehyde-PEG-NHS”) to adjacent NH2 groups on the tip was largely suppressed by high linker concentrations. In this way, magnetic AFM tips could be

  7. Experimental Manipulation of Soil Moisture Regime Impacts Soil Microbial Community Abundance, Diversity, and Function in a Semi-Arid Sagebrush Steppe

    NASA Astrophysics Data System (ADS)

    Sorensen, P. O.; Feris, K. P.; Germino, M. J.

    2010-12-01

    Rising global temperatures are predicted to alter regional climate regimes, including the spatial and temporal distribution of precipitation. In water-limited (e.g. arid and semi-arid) ecosystems annual precipitation is low and shows a high degree of variability. In these environments, soil microbes occupy a pivotal seat coupling the effects of water availability and plant productivity to biogeochemical cycling and ecosystem function. Using a long running ecological field experiment (>15 years) sited in Idaho’s sagebrush steppe, effects of experimentally manipulated precipitation regime on microbial diversity, abundance, and terrestrial carbon cycling are being explored. Soils were sampled in January (winter) of 2009. Replicate cores collected at 15-20cm and 95-100cm, were taken from field plots planted with native vegetation under three different precipitation amendments; Ambient, Summer (+200mm in June), or Fall/Spring (+200mm in April or October). Bacterial and Fungal community structure was analyzed by high-resolution 454 pyrosequencing. Edaphic properties (soil moisture, pH, total C, total N, organic C, inorganic N, ortho P) were measured and used as factors for general linear modeling of Bacterial and Fungal community structure against field treatments. Labile soil carbon pools were measured as C mineralization rates by gas chromatography using long term soil incubations. Pyrosequencing analysis of soil Bacterial communities has revealed greater Bacterial community abundance and diversity across all treatments relative to Archaeal and Fungal communities. General linear modeling of sequences obtained from 454 pyrosequencing showed significant interactions of phyla-level Bacterial and Fungal abundance with experimental precipitation regime and depth of sampling. Edaphic properties such as soil moisture and pH also showed significant interactions with phyla-level Bacterial and Fungal abundance. Long-term soil incubation studies revealed treatment effects on

  8. Carboxyl group (-CO2 H) functionalized coordination polymer nanoparticles as efficient platforms for drug delivery.

    PubMed

    Novio, Fernando; Lorenzo, Julia; Nador, Fabiana; Wnuk, Karolina; Ruiz-Molina, Daniel

    2014-11-17

    Functionalization of nanoparticles can significantly influence their properties and potential applications. Although researchers can now functionalize metal, metal oxide, and organic polymer nanoparticles with a high degree of precision, controlled surface functionalization of nanoscale coordination polymer particles (CPPs) has remained a significant challenge. The lack of methodology is perhaps one of the greatest roadblocks to the advancement of CPPs into high added-value drug delivery applications. Here, we report having achieved this goal through a stepwise formation and functionalization protocol. We fabricated robust nanoparticles with enhanced thermal and colloidal stabilities by incorporation of carboxyl groups and these surface carboxyl groups could be subsequently functionalized through well-known peptide coupling reactions. The set of chemistries that we employed as proof-of-concept enabled a plethora of new functional improvements for the application of CPPs as drug delivery carriers, including enhanced colloidal stabilities and the incorporation of additional functional groups such as polyethylene glycol (PEG) or fluorescent dyes that enabled tracking of their cellular uptake. Finally, we ascertained the cytotoxicity of the new CPP nanoparticles loaded with camptothecin to human breast adenocarcinoma (MCF-7). Efflux measurements show that the encapsulation of camptothecin enhances the potency of the drug 6.5-fold and increases the drug retention within the cell. PMID:25284328

  9. Carboxyl group (-CO2 H) functionalized coordination polymer nanoparticles as efficient platforms for drug delivery.

    PubMed

    Novio, Fernando; Lorenzo, Julia; Nador, Fabiana; Wnuk, Karolina; Ruiz-Molina, Daniel

    2014-11-17

    Functionalization of nanoparticles can significantly influence their properties and potential applications. Although researchers can now functionalize metal, metal oxide, and organic polymer nanoparticles with a high degree of precision, controlled surface functionalization of nanoscale coordination polymer particles (CPPs) has remained a significant challenge. The lack of methodology is perhaps one of the greatest roadblocks to the advancement of CPPs into high added-value drug delivery applications. Here, we report having achieved this goal through a stepwise formation and functionalization protocol. We fabricated robust nanoparticles with enhanced thermal and colloidal stabilities by incorporation of carboxyl groups and these surface carboxyl groups could be subsequently functionalized through well-known peptide coupling reactions. The set of chemistries that we employed as proof-of-concept enabled a plethora of new functional improvements for the application of CPPs as drug delivery carriers, including enhanced colloidal stabilities and the incorporation of additional functional groups such as polyethylene glycol (PEG) or fluorescent dyes that enabled tracking of their cellular uptake. Finally, we ascertained the cytotoxicity of the new CPP nanoparticles loaded with camptothecin to human breast adenocarcinoma (MCF-7). Efflux measurements show that the encapsulation of camptothecin enhances the potency of the drug 6.5-fold and increases the drug retention within the cell.

  10. Assessment of female sexual function in a group of uncircumcised obese Egyptian women.

    PubMed

    Elnashar, A R M; Ibrahim, N H; Ahmed, H-Eh; Hassanin, A M; Elgawady, M A

    2015-01-01

    The aim of the present study was to assess female sexual function in an obese group (250 women) and to compare it with a control group (100 women), among 25-35-year-old uncircumcised Egyptian women, using female sexual function index (FSFI) score. FSFI total score of ⩽ 26.55 was considered diagnostic of Female Sexual Dysfunction (FSD). The percentage of FSD in the obese group was 73.6% while it was 71% in the control group, which was statistically insignificant (P > 0.05). The difference between both groups regarding the total (FSFI) score was insignificant (P > 0.05), but arousal and satisfaction domains scores were significantly lower in the obese group. In the obese group, a strong negative correlation between body mass index and arousal, orgasm and the total FSFI score was found. Women with excessive obesity had the lowest total FSFI score. In the obese group, college graduates had the highest total scores and all domain scores of FSFI followed by high school graduates while the least educated women had the lowest scores and when these subgroups were compared, significant differences were found among them. We conclude that in uncircumcised 25-35-year-old Egyptian women, obesity is not a major detrimental factor for FSD, but it may affect some sexual domains such as arousal and satisfaction, although excessive obesity is associated with FSD. Also, educational and cultural factors may have an impact on perception of sex and pleasure. PMID:26155831

  11. Wigner functions for noncommutative quantum mechanics: A group representation based construction

    SciTech Connect

    Chowdhury, S. Hasibul Hassan; Ali, S. Twareque

    2015-12-15

    This paper is devoted to the construction and analysis of the Wigner functions for noncommutative quantum mechanics, their marginal distributions, and star-products, following a technique developed earlier, viz, using the unitary irreducible representations of the group G{sub NC}, which is the three fold central extension of the Abelian group of ℝ{sup 4}. These representations have been exhaustively studied in earlier papers. The group G{sub NC} is identified with the kinematical symmetry group of noncommutative quantum mechanics of a system with two degrees of freedom. The Wigner functions studied here reflect different levels of non-commutativity—both the operators of position and those of momentum not commuting, the position operators not commuting and finally, the case of standard quantum mechanics, obeying the canonical commutation relations only.

  12. Porous polymer monoliths with large surface area and functional groups prepared via copolymerization of protected functional monomers and hypercrosslinking.

    PubMed

    Maya, Fernando; Svec, Frantisek

    2013-11-22

    A new approach to the preparation of porous polymer monoliths possessing both large surface area and functional groups has been developed. The chloromethyl groups of poly(styrene-co-4-acetoxystyrene-co-vinylbenzyl chloride-co-divinylbenzene) monolith enable post-polymerization hypercrosslinking catalyzed by ferric chloride in dichloroethane leading to a multitude of small pores thus enhancing the surface area. The acetoxy functionalities are easily deprotected using hydrazine to produce polar phenolic hydroxyl groups, which would be difficult to obtain by direct copolymerization of hydroxyl-containing monomers. The hypercrosslinking and deprotection reactions as well as their sequence were studied in detail with bulk polymer monoliths containing up to 50% 4-acetoxystyrene and its progress monitored by infrared spectrometry and nitrogen adsorption/desorption measurements. No significant difference was found for both possible successions. All monoliths were also prepared in a capillary column format, then deprotected and hypercrosslinked. Capillary columns were tested for the separation of small molecules using reversed phase and normal phase chromatographic modes. For polymer monoliths containing 50% deprotected 4-acetoxystyrene, column efficiencies of 40,000 plates/m for benzene in reversed phase mode and 31,800 plates/m for nitrobenzene in normal phase mode, were obtained. The percentage of hydroxyl groups in the monoliths enables modulation of polarity of the stationary phase. They also represent functionalities that are potentially suitable for further modifications and formation of new types of stationary phases for liquid chromatography.

  13. Functional grouping and cortical–subcortical interactions in emotion: A meta-analysis of neuroimaging studies

    PubMed Central

    Kober, Hedy; Barrett, Lisa Feldman; Joseph, Josh; Bliss-Moreau, Eliza; Lindquist, Kristen; Wager, Tor D.

    2009-01-01

    We performed an updated quantitative meta-analysis of 162 neuroimaging studies of emotion using a novel multi-level kernel-based approach, focusing on locating brain regions consistently activated in emotional tasks and their functional organization into distributed functional groups, independent of semantically defined emotion category labels (e.g., “anger,” “fear”). Such brain-based analyses are critical if our ways of labeling emotions are to be evaluated and revised based on consistency with brain data. Consistent activations were limited to specific cortical sub-regions, including multiple functional areas within medial, orbital, and inferior lateral frontal cortices. Consistent with a wealth of animal literature, multiple subcortical activations were identified, including amygdala, ventral striatum, thalamus, hypothalamus, and periaqueductal gray. We used multivariate parcellation and clustering techniques to identify groups of co-activated brain regions across studies. These analyses identified six distributed functional groups, including medial and lateral frontal groups, two posterior cortical groups, and paralimbic and core limbic/brainstem groups. These functional groups provide information on potential organization of brain regions into large-scale networks. Specific follow-up analyses focused on amygdala, periaqueductal gray (PAG), and hypothalamic (Hy) activations, and identified frontal cortical areas co-activated with these core limbic structures. While multiple areas of frontal cortex co-activated with amygdala sub-regions, a specific region of dorsomedial prefrontal cortex (dmPFC, Brodmann’s Area 9/32) was the only area co-activated with both PAG and Hy. Subsequent mediation analyses were consistent with a pathway from dmPFC through PAG to Hy. These results suggest that medial frontal areas are more closely associated with core limbic activation than their lateral counterparts, and that dmPFC may play a particularly important role in the

  14. Plant diversity and functional groups affect Si and Ca pools in aboveground biomass of grassland systems.

    PubMed

    Schaller, Jörg; Roscher, Christiane; Hillebrand, Helmut; Weigelt, Alexandra; Oelmann, Yvonne; Wilcke, Wolfgang; Ebeling, Anne; Weisser, Wolfgang W

    2016-09-01

    Plant diversity is an important driver of nitrogen and phosphorus stocks in aboveground plant biomass of grassland ecosystems, but plant diversity effects on other elements also important for plant growth are less understood. We tested whether plant species richness, functional group richness or the presence/absence of particular plant functional groups influences the Si and Ca concentrations (mmol g(-1)) and stocks (mmol m(-2)) in aboveground plant biomass in a large grassland biodiversity experiment (Jena Experiment). In the experiment including 60 temperate grassland species, plant diversity was manipulated as sown species richness (1, 2, 4, 8, 16) and richness and identity of plant functional groups (1-4; grasses, small herbs, tall herbs, legumes). We found positive species richness effects on Si as well as Ca stocks that were attributable to increased biomass production. The presence of particular functional groups was the most important factor explaining variation in aboveground Si and Ca stocks (mmol m(-2)). Grass presence increased the Si stocks by 140 % and legume presence increased the Ca stock by 230 %. Both the presence of specific plant functional groups and species diversity altered Si and Ca stocks, whereas Si and Ca concentration were affected mostly by the presence of specific plant functional groups. However, we found a negative effect of species diversity on Si and Ca accumulation, by calculating the deviation between mixtures and mixture biomass proportions, but in monoculture concentrations. These changes may in turn affect ecosystem processes such as plant litter decomposition and nutrient cycling in grasslands.

  15. Functional network organizations of two contrasting temperament groups in dimensions of novelty seeking and harm avoidance.

    PubMed

    Kyeong, Sunghyon; Kim, Eunjoo; Park, Hae-Jeong; Hwang, Dong-Uk

    2014-08-01

    Novelty seeking (NS) and harm avoidance (HA) are two major dimensions of temperament in Cloninger׳s neurobiological model of personality. Previous neurofunctional and biological studies on temperament dimensions of HA and NS suggested that the temperamental traits have significant correlations with cortical and subcortical brain regions. However, no study to date has investigated the functional network modular organization as a function of the temperament dimension. The temperament dimensions were originally proposed to be independent of one another. However, a meta-analysis based on 16 published articles found a significant negative correlation between HA and NS (Miettunen et al., 2008). Based on this negative correlation, the current study revealed the whole-brain connectivity modular architecture for two contrasting temperament groups. The k-means clustering algorithm, with the temperamental traits of HA and NS as an input, was applied to divide the 40 subjects into two temperament groups: 'high HA and low NS' versus 'low HA and high NS'. Using the graph theoretical framework, we found a functional segregation of whole brain network architectures derived from resting-state functional MRI. In the 'high HA and low NS' group, the regulatory brain regions, such as the prefrontal cortex (PFC), are clustered together with the limbic system. In the 'low HA and high NS' group, however, brain regions lying on the dopaminergic pathways, such as the PFC and basal ganglia, are partitioned together. These findings suggest that the neural basis of inhibited, passive, and inactive behaviors in the 'high HA and low NS' group was derived from the increased network associations between the PFC and limbic clusters. In addition, supporting evidence of topological differences between the two temperament groups was found by analyzing the functional connectivity density and gray matter volume, and by computing the relationships between the morphometry and function of the brain.

  16. Plant diversity and functional groups affect Si and Ca pools in aboveground biomass of grassland systems.

    PubMed

    Schaller, Jörg; Roscher, Christiane; Hillebrand, Helmut; Weigelt, Alexandra; Oelmann, Yvonne; Wilcke, Wolfgang; Ebeling, Anne; Weisser, Wolfgang W

    2016-09-01

    Plant diversity is an important driver of nitrogen and phosphorus stocks in aboveground plant biomass of grassland ecosystems, but plant diversity effects on other elements also important for plant growth are less understood. We tested whether plant species richness, functional group richness or the presence/absence of particular plant functional groups influences the Si and Ca concentrations (mmol g(-1)) and stocks (mmol m(-2)) in aboveground plant biomass in a large grassland biodiversity experiment (Jena Experiment). In the experiment including 60 temperate grassland species, plant diversity was manipulated as sown species richness (1, 2, 4, 8, 16) and richness and identity of plant functional groups (1-4; grasses, small herbs, tall herbs, legumes). We found positive species richness effects on Si as well as Ca stocks that were attributable to increased biomass production. The presence of particular functional groups was the most important factor explaining variation in aboveground Si and Ca stocks (mmol m(-2)). Grass presence increased the Si stocks by 140 % and legume presence increased the Ca stock by 230 %. Both the presence of specific plant functional groups and species diversity altered Si and Ca stocks, whereas Si and Ca concentration were affected mostly by the presence of specific plant functional groups. However, we found a negative effect of species diversity on Si and Ca accumulation, by calculating the deviation between mixtures and mixture biomass proportions, but in monoculture concentrations. These changes may in turn affect ecosystem processes such as plant litter decomposition and nutrient cycling in grasslands. PMID:27164912

  17. A Simple and Versatile Amide Directing Group for C-H Functionalizations.

    PubMed

    Zhu, Ru-Yi; Farmer, Marcus E; Chen, Yan-Qiao; Yu, Jin-Quan

    2016-08-26

    Achieving selective C-H activation at a single and strategic site in the presence of multiple C-H bonds can provide a powerful and generally useful retrosynthetic disconnection. In this context, a directing group serves as a compass to guide the transition metal to C-H bonds by using distance and geometry as powerful recognition parameters to distinguish between proximal and distal C-H bonds. However, the installation and removal of directing groups is a practical drawback. To improve the utility of this approach, one can seek solutions in three directions: 1) Simplifying the directing group, 2) using common functional groups or protecting groups as directing groups, and 3) attaching the directing group to substrates via a transient covalent bond to render the directing group catalytic. This Review describes the rational development of an extremely simple and yet broadly applicable directing group for Pd(II) , Rh(III) , and Ru(II) catalysts, namely the N-methoxy amide (CONHOMe) moiety. Through collective efforts in the community, a wide range of C-H activation transformations using this type of simple directing group have been developed. PMID:27479708

  18. Pyrrolic tripodal receptors for carbohydrates. Role of functional groups and binding geometry on carbohydrate recognition.

    PubMed

    Cacciarini, Martina; Nativi, Cristina; Norcini, Martina; Staderini, Samuele; Francesconi, Oscar; Roelens, Stefano

    2011-02-21

    The contribution from several H-bonding groups and the impact of geometric requirements on the binding ability of benzene-based tripodal receptors toward carbohydrates have been investigated by measuring the affinity of a set of structures toward octyl β-D-glucopyranoside, selected as a representative monosaccharide. The results reported in the present study demonstrate that a judicious choice of correct geometry and appropriate functional groups is critical to achieve the complementary hydrogen bonding interactions required for an effective carbohydrate recognition.

  19. Designed nitrogen doping of few-layer graphene functionalized by selective oxygenic groups

    PubMed Central

    2014-01-01

    Few-layer nitrogen doped graphene was synthesized originating from graphene oxide functionalized by selective oxygenic functional groups (hydroxyl, carbonyl, carboxyl etc.) under hydrothermal conditions, respectively. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) observation evidenced few-layer feature of the graphene oxide. X-ray diffraction (XRD) pattern confirmed phase structure of the graphene oxide and reduced graphene oxide. Nitrogen doping content and bonding configuration of the graphene was determined by X-ray photoelectron spectroscopy (XPS), which indicated that different oxygenic functional groups were evidently different in affecting the nitrogen doping process. Compared with other oxygenic groups, carboxyl group played a crucial role in the initial stage of nitrogen doping while hydroxyls exhibited more evident contribution to the doping process in the late stage of the reaction. Formation of graphitic-like nitrogen species was controlled by a synergistic effect of the involved oxygenic groups (e.g., -COOH, -OH, C-O-C, etc.). The doping mechanism of nitrogen in the graphene was scrutinized. The research in this work may not only contribute to the fundamental understandings of nitrogen doping within graphene but promote the development of producing novel graphene-based devices with designed surface functionalization. PMID:25520594

  20. The Effect of Functional Groups in Bio-Derived Fuel Candidates.

    PubMed

    Jenkins, Rhodri W; Moore, Cameron M; Semelsberger, Troy A; Chuck, Christopher J; Gordon, John C; Sutton, Andrew D

    2016-05-10

    Interest in developing renewable fuels is continuing to grow and biomass represents a viable source of renewable carbon with which to replace fossil-based components in transportation fuels. During our own work, we noticed that chemists think in terms of functional groups whereas fuel engineers think in terms of physical fuel properties. In this Concept article, we discuss the effect of carbon and oxygen functional groups on potential fuel properties. This serves as a way of informing our own thinking and provides us with a basis with which to design and synthesize molecules from biomass that could provide useful transportation fuels. PMID:27099975

  1. In Vivo Models to Address the Function of Polycomb Group Proteins.

    PubMed

    Bantignies, Frédéric

    2016-01-01

    Initially discovered as repressors of homeotic gene expression in Drosophila, Polycomb group (PcG) proteins have now been shown to be involved in a plethora of biological processes. Indeed, by repressing a large number of target genes, including specific lineage genes, these chromatin factors play major roles in a multitude of cellular functions, such as pluripotency, differentiation, reprogramming, tissue regeneration, and nuclear organization. In this book chapter are presented in vivo approaches and technologies, which have been used in both mammalian and Drosophila systems to study the cellular functions of Polycomb group proteins. PMID:27659991

  2. Effects of surface functional groups on the formation of nanoparticle-protein corona

    NASA Astrophysics Data System (ADS)

    Podila, R.; Chen, R.; Ke, P. C.; Brown, J. M.; Rao, A. M.

    2012-12-01

    Herein, we examined the dependence of protein adsorption on the nanoparticle surface in the presence of functional groups. Our UV-visible spectrophotometry, transmission electron microscopy, infrared spectroscopy, and dynamic light scattering measurements evidently suggested that the functional groups play an important role in the formation of nanoparticle-protein corona. We found that uncoated and surfactant-free silver nanoparticles derived from a laser ablation process promoted a maximum protein (bovine serum albumin) coating due to increased changes in entropy. On the other hand, bovine serum albumin displayed a relatively lower affinity for electrostatically stabilized nanoparticles due to the constrained entropy changes.

  3. [Responses of ground arthropod functional groups to the enclosure of grazing grassland in desert steppe].

    PubMed

    Liu, Ren-tao; Li, Xue-bin; Xin, Ming; Ma, Lin; Liu, Kai

    2011-08-01

    With the support of the National Resources Monitoring Station in Yanchi County of Ningxia, an investigation was conducted on the ground arthropods, vegetations, and soil properties in the enclosed and un-enclosed grazing grassland in desert steppe. In the meantime, the functional groups of ground arthropods were classified according to their feeding habits. The ground arthropods in the desert steppe could be classified into four functional groups, i.e., predatory, phytophagous, saprophagous, and omnivorous, among which, predatory and phytophagous groups were dominant in quantity, and phytophagous and saprophagous groups were predominant in biomass, implying that the ground arthropod in desert steppe was mainly characterized by phytophagous arthropods. Enclosure increased the individual and group number of predatory, phytophagous, and omnivorous arthropods as well as the biomass of predatory and omnivorous arthropods, and enhanced the biodiversity of predatory and phytophagous arthropods, which was closely correlated with the vegetation recovery and soil environment improvement, and demonstrated that the enclosure of grazing grassland increased the diversity and complexity of ground arthropod functional groups in desert steppe. Nevertheless, the individual number and biomass of saprophagous arthropods decreased after the enclosure, reflecting the dependence of these arthropods on grazing grassland.

  4. Mechanisms of Innovation Diffusion under Information Abundance and Information Scarcity--On the Contribution of Social Networks in Group vs. Individual Extension Approaches in Semi-Arid Kenya

    ERIC Educational Resources Information Center

    Darr, Dietrich; Pretzsch, Jurgen

    2008-01-01

    Purpose: The objective of this paper is to assess the effectiveness of innovation diffusion under group-oriented and individual-oriented extension. Current theoretical notions of innovation diffusion in social networks shall be briefly reviewed, and the concepts of "search" and "innovation" vis-a-vis "transfer" and "imitation" mechanisms (Hansen,…

  5. Changes of Nitrogen Transformation Rates and Related Functional Genes Abundance under Different Dissolved Oxygen Levels in sediments form an Urban River

    NASA Astrophysics Data System (ADS)

    Zhang, Y.

    2015-12-01

    In the nitrogen rich urban river sediments, we investigated the nitrogen transformation rates and nitrogen-cycling genes in response to different dissolved oxygen (DO) supply levels (saturation, DO > 8.00 mg L-1; aerobic, 2.50 mg L-1 abundance by an order, but its influence on anammox (hzsB) was insignificant. Four quantitative response relationships between nitrogen transformation rates, nitrogen functional genes abundances, and nitrogen concentrations were established by stepwise linear regression analysis. These relationships confirmed that different nitrogen transformation processes were coupled at the molecular level (functional genes), especially for the coupling of ammonium oxidation and anammox.

  6. Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

    PubMed

    Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

    2015-01-13

    Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

  7. Effect of Duration of Disease on Ventilatory Function in an Ethnic Saudi Group of Diabetic Patients

    PubMed Central

    Meo, Sultan A.; Al Drees, Abdul Majeed; Ahmed, Jehangeer; Ahmed Shah, Sayed Fayaz; Al-Regaiey, Khalid; Husain, Ashraf; Al-Rubean, Khalid

    2007-01-01

    Background Diabetes mellitus is a leading cause of illness and death across the world and is responsible for a growing proportion of global health care expenditures. The present study was designed to observe the effect of diabetes mellitus on lung function in patients with diabetes belonging to a specific ethnic group, namely Saudis. Method In this study, a group of 47 apparently healthy volunteer male Saudi patients with diabetes was randomly selected. Their ages ranged from 20 to 70 years. The patients were matched with another group of 50 healthy male control subjects in terms of age, height, weight, ethnicity, and socioeconomic status. Both groups met exclusion criteria as per standard. Spirometry was performed with an electronic spirometer (Schiller AT-2 Plus, Switzerland), and results were compared by a Student's t test. Results Subjects with diabetes showed a significant reduction in forced vital capacity (FVC) and forced expiratory volume in the first second (FEV1) relative to their matched controls. However, there were no significant differences in the forced expiratory ratio (FEV1/FVC%) and the middle half of the FVC (FEF25–75%) between the groups. We observed a significantly negative correlation between duration of disease and pulmonary function, as measured by FEV1 (r = 0.258, p = 0.04), FVC (r = 0.282, p = 0.28), and the middle half of the FVC (FEF25–75%) (r = 0.321, p = 0.014). Conclusions Pulmonary function in a specific ethnic group of patients with diabetes was impaired as evidenced by a decrease in FVC and FEV1 compared to pulmonary function in matched controls. Stratification of results by years of disease revealed a significant correlation between duration of disease and a decline in pulmonary function. PMID:19885139

  8. Isolation and Characterization of Functional Tripartite Group II Introns Using a Tn5-Based Genetic Screen

    PubMed Central

    Ritlop, Christine; Monat, Caroline; Cousineau, Benoit

    2012-01-01

    Background Group II introns are RNA enzymes that splice themselves from pre-mRNA transcripts. Most bacterial group II introns harbour an open reading frame (ORF), coding for a protein with reverse transcriptase, maturase and occasionally DNA binding and endonuclease activities. Some ORF-containing group II introns were shown to be mobile retroelements that invade new DNA target sites. From an evolutionary perspective, group II introns are hypothesized to be the ancestors of the spliceosome-dependent nuclear introns and the small nuclear RNAs (snRNAs – U1, U2, U4, U5 and U6) that are important functional elements of the spliceosome machinery. The ability of some group II introns fragmented in two or three pieces to assemble and undergo splicing in trans supports the theory that spliceosomal snRNAs evolved from portions of group II introns. Methodology/Principal Findings We used a transposon-based genetic screen to explore the ability of the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis to be fragmented into three pieces in vivo. Trans-splicing tripartite variants of Ll.LtrB were selected using a highly efficient and sensitive trans-splicing/conjugation screen. We report that numerous fragmentation sites located throughout Ll.LtrB support tripartite trans-splicing, showing that this intron is remarkably tolerant to fragmentation. Conclusions/Significance This work unveils the great versatility of group II intron fragments to assemble and accurately trans-splice their flanking exons in vivo. The selected introns represent the first evidence of functional tripartite group II introns in bacteria and provide experimental support for the proposed evolutionary relationship between group II introns and snRNAs. PMID:22876289

  9. Abundance of jackfruit (Artocarpus heterophyllus) affects group characteristics and use of space by golden-headed lion tamarins (Leontopithecus chrysomelas) in Cabruca agroforest.

    PubMed

    Oliveira, Leonardo C; Neves, Leonardo G; Raboy, Becky E; Dietz, James M

    2011-08-01

    Cabruca is an agroforest of cacao trees shaded by native forest trees. It is the predominant vegetation type throughout eastern part of the range of the golden-headed lion tamarins, Leontopithecus chrysomelas, an endangered primate endemic to Atlantic Forest. Understanding how lion tamarins use this agroforest is a conservation priority. To address this question, we documented the diet, home range size, group sizes and composition, density, number of litters and body condition of lion tamarins living in cabruca, and other habitats. Jackfruit, Artocarpus heterophyllus, was the most used species used by lion tamarins in cabruca and was widely available and used throughout the year. In cabruca, home range size was the smallest (22-28 ha) and density of lion tamarins was the highest (1.7 ind/ha) reported for the species. Group size averaged 7.4 individuals and was not significantly different among the vegetation types. In cabruca, groups produced one or two litters a year, and all litters were twins. Adult males in cabruca were significantly heavier than males in primary forest. Our study is the first to demonstrate that breeding groups of golden-headed lion tamarins can survive and reproduce entirely within cabruca agroforest. Jackfruit proved to be a keystone resource for lion tamarins in cabruca, and bromeliads were important as an animal prey foraging microhabitat. In cases where cabruca contains concentrated resources, such as jackfruit and bromeliads, lion tamarins may not only survive and reproduce but may fare better than in other forest types, at least for body condition and reproduction.

  10. Abundance of jackfruit (Artocarpus heterophyllus) affects group characteristics and use of space by golden-headed lion tamarins (Leontopithecus chrysomelas) in Cabruca agroforest.

    PubMed

    Oliveira, Leonardo C; Neves, Leonardo G; Raboy, Becky E; Dietz, James M

    2011-08-01

    Cabruca is an agroforest of cacao trees shaded by native forest trees. It is the predominant vegetation type throughout eastern part of the range of the golden-headed lion tamarins, Leontopithecus chrysomelas, an endangered primate endemic to Atlantic Forest. Understanding how lion tamarins use this agroforest is a conservation priority. To address this question, we documented the diet, home range size, group sizes and composition, density, number of litters and body condition of lion tamarins living in cabruca, and other habitats. Jackfruit, Artocarpus heterophyllus, was the most used species used by lion tamarins in cabruca and was widely available and used throughout the year. In cabruca, home range size was the smallest (22-28 ha) and density of lion tamarins was the highest (1.7 ind/ha) reported for the species. Group size averaged 7.4 individuals and was not significantly different among the vegetation types. In cabruca, groups produced one or two litters a year, and all litters were twins. Adult males in cabruca were significantly heavier than males in primary forest. Our study is the first to demonstrate that breeding groups of golden-headed lion tamarins can survive and reproduce entirely within cabruca agroforest. Jackfruit proved to be a keystone resource for lion tamarins in cabruca, and bromeliads were important as an animal prey foraging microhabitat. In cases where cabruca contains concentrated resources, such as jackfruit and bromeliads, lion tamarins may not only survive and reproduce but may fare better than in other forest types, at least for body condition and reproduction. PMID:21079956

  11. Abundance of Jackfruit ( Artocarpus heterophyllus) Affects Group Characteristics and Use of Space by Golden-Headed Lion Tamarins ( Leontopithecus chrysomelas) in Cabruca Agroforest

    NASA Astrophysics Data System (ADS)

    Oliveira, Leonardo C.; Neves, Leonardo G.; Raboy, Becky E.; Dietz, James M.

    2011-08-01

    Cabruca is an agroforest of cacao trees shaded by native forest trees. It is the predominant vegetation type throughout eastern part of the range of the golden-headed lion tamarins, Leontopithecus chrysomelas, an endangered primate endemic to Atlantic Forest. Understanding how lion tamarins use this agroforest is a conservation priority. To address this question, we documented the diet, home range size, group sizes and composition, density, number of litters and body condition of lion tamarins living in cabruca, and other habitats. Jackfruit, Artocarpus heterophyllus, was the most used species used by lion tamarins in cabruca and was widely available and used throughout the year. In cabruca, home range size was the smallest (22-28 ha) and density of lion tamarins was the highest (1.7 ind/ha) reported for the species. Group size averaged 7.4 individuals and was not significantly different among the vegetation types. In cabruca, groups produced one or two litters a year, and all litters were twins. Adult males in cabruca were significantly heavier than males in primary forest. Our study is the first to demonstrate that breeding groups of golden-headed lion tamarins can survive and reproduce entirely within cabruca agroforest. Jackfruit proved to be a keystone resource for lion tamarins in cabruca, and bromeliads were important as an animal prey foraging microhabitat. In cases where cabruca contains concentrated resources, such as jackfruit and bromeliads, lion tamarins may not only survive and reproduce but may fare better than in other forest types, at least for body condition and reproduction.

  12. Attachment theory and group processes: the association between attachment style and group-related representations, goals, memories, and functioning.

    PubMed

    Rom, Eldad; Mikulincer, Mario

    2003-06-01

    Four studies examined attachment-style differences in group-related cognitions and behaviors. In Studies 1-2, participants completed scales on group-related cognitions and emotions. In Studies 3-4, participants were divided into small groups, and their performance in group tasks as well as the cohesion of their group were assessed. Both attachment anxiety and avoidance in close relationships were associated with negative group-related cognitions and emotions. Anxiety was also related to the pursuit of closeness goals and impaired instrumental performance in group tasks. Avoidance was related to the pursuit of distance goals and deficits in socioemotional and instrumental performance. Group cohesion significantly moderated the effects of attachment anxiety. The discussion emphasizes the relevance of attachment theory within group contexts. PMID:12793586

  13. Attachment theory and group processes: the association between attachment style and group-related representations, goals, memories, and functioning.

    PubMed

    Rom, Eldad; Mikulincer, Mario

    2003-06-01

    Four studies examined attachment-style differences in group-related cognitions and behaviors. In Studies 1-2, participants completed scales on group-related cognitions and emotions. In Studies 3-4, participants were divided into small groups, and their performance in group tasks as well as the cohesion of their group were assessed. Both attachment anxiety and avoidance in close relationships were associated with negative group-related cognitions and emotions. Anxiety was also related to the pursuit of closeness goals and impaired instrumental performance in group tasks. Avoidance was related to the pursuit of distance goals and deficits in socioemotional and instrumental performance. Group cohesion significantly moderated the effects of attachment anxiety. The discussion emphasizes the relevance of attachment theory within group contexts.

  14. 14 CFR 10 - Functional Classification-Operating Expenses of Group I Air Carriers

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 4 2012-01-01 2012-01-01 false Functional Classification-Operating Expenses of Group I Air Carriers Section 10 Section Section 10 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) ECONOMIC REGULATIONS UNIFORM SYSTEM OF ACCOUNTS AND REPORTS FOR LARGE CERTIFICATED AIR...

  15. Review of Social Skills Training Groups for Youth with Asperger Syndrome and High Functioning Autism

    ERIC Educational Resources Information Center

    Cappadocia, M. Catherine; Weiss, Jonathan A.

    2011-01-01

    Although social skills deficits represent core symptoms of Asperger Syndrome and High Functioning Autism, there is limited research investigating the empirical validity of social skills interventions currently being used with these populations. This literature review compares three types of social skills training groups: traditional, cognitive…

  16. Attraction to a Group as a Function of Attitude Similarity and Geographic Distance.

    ERIC Educational Resources Information Center

    Davis, John M.

    1984-01-01

    Investigated attraction toward a group as a function of attitude similarity and perceived geographic distance in students (N=60). Results showed that effects of attitude similarity were strongly significant and that distance had no signficant effect on attraction and limited effect on evaluations. (LLL)

  17. An Epistemological Inquiry into Organic Chemistry Education: Exploration of Undergraduate Students' Conceptual Understanding of Functional Groups

    ERIC Educational Resources Information Center

    Akkuzu, Nalan; Uyulgan, Melis Arzu

    2016-01-01

    This study sought to determine the levels of conceptual understanding of undergraduate students regarding organic compounds within different functional groups. A total of 60 students who were enrolled in the Department of Secondary Science and Mathematics Education of a Faculty of Education at a state university in Turkey and who had followed an…

  18. A FUNCTIONAL GROUP CHARACTERIZATION OF ORGANIC PM 2.5 EXPOSURE: RESULTS FROM THE RIOPA STUDY

    EPA Science Inventory

    The functional group (FG) composition of urban residential outdoor, indoor, and personal fine particle (PM2.5) samples is presented and used to provide insights relevant to organic PM2.5 exposure. PM2.5 samples (48 h) were collected during the Rel...

  19. Social Resources and Change in Functional Health: Comparing Three Age Groups

    ERIC Educational Resources Information Center

    Randall, G. Kevin; Martin, Peter; Bishop, Alex J.; Johnson, Mary Ann; Poon, Leonard W.

    2012-01-01

    This study examined the mediating and moderating role of social resources on the association between age and change in functional health for three age groups of older adults. Data were provided by those in their 60s, 80s, and 100s who participated in the first two phases of the Georgia Centenarian study. Analyses confirmed the study's hypothesis…

  20. Chemkarta: A Card Game for Teaching Functional Groups in Undergraduate Organic Chemistry

    ERIC Educational Resources Information Center

    Knudtson, Christopher A.

    2015-01-01

    Students in undergraduate organic chemistry courses are frequently overwhelmed by the volume and complexity of information they are expected to learn. To aid in students' learning of organic functional groups, a novel card game "ChemKarta" is reported that can serve as a useful alternative to flashcards. This pedagogy is a simple…

  1. Detecting Native Language Group Differences at the Subskills Level of Reading: A Differential Skill Functioning Approach

    ERIC Educational Resources Information Center

    Li, Hongli; Suen, Hoi K.

    2013-01-01

    Differential skill functioning (DSF) exists when examinees from different groups have different probabilities of successful performance in a certain subskill underlying the measured construct, given that they have the same ability on the overall construct. Using a DSF approach, this study examined the differences between two native language…

  2. Urinary Cortisol Circadian Rhythm in a Group of High-Functioning Children with Autism.

    ERIC Educational Resources Information Center

    Richdale, Amanda L.; Prior, Margot R.

    1992-01-01

    This study found no evidence for abnormal temporal placement of the basal urinary cortisol circadian rhythm in a group of 18 high-functioning children (ages 4-14) with autism. There was a tendency toward cortisol hypersecretion during the day, predominantly in autistic children who were integrated into the normal school system. (Author/JDD)

  3. Group-Specific Effects of Matching Subtest Contamination on the Identification of Differential Item Functioning

    ERIC Educational Resources Information Center

    Keiffer, Elizabeth Ann

    2011-01-01

    A differential item functioning (DIF) simulation study was conducted to explore the type and level of impact that contamination had on type I error and power rates in DIF analyses when the suspect item favored the same or opposite group as the DIF items in the matching subtest. Type I error and power rates were displayed separately for the…

  4. Magnetic iron oxide nanoparticle functionalization: isocyanate moiety as a suitable monodentate anchoring group.

    PubMed

    Carrara, Claudio; Sala, Maria C; Caneva, Enrico; Cauteruccio, Silvia; Licandro, Emanuela

    2014-01-17

    A new strategy for anchoring organic molecules onto superparamagnetic iron oxide nanoparticles (SPIONs) using isocyanate containing linkers has been realized. This functional group easily and efficiently reacts with the hydroxyl residues of the nanoparticle surface, leading to the formation of a stable carbamate bond, as confirmed by means of spectroscopic and analytical data.

  5. Youth in group home care: youth characteristics and predictors of later functioning.

    PubMed

    Chow, Wai-Ying; Mettrick, Jennifer E; Stephan, Sharon H; Von Waldner, Christina A

    2014-10-01

    This paper presents the findings of an exploratory research study of foster care youth residing in group homes in a mid-Atlantic state in the USA. The aims of the present study were to (1) describe youth characteristics, (2) explore whether baseline functioning differed by gender or ethnicity, (3) explore predictors of cross-time differences in psychosocial functioning, and (4) explore predictors of later functioning, specifically age, gender, and length of stay. Psychosocial functioning at two time points (i.e., T1 = admission into group home; T2 = current or discharge) in 180 charts from 29 randomly selected group homes were reviewed. Youth were on average 14.86 years of age, predominantly male (71%; n = 128), and predominantly African American (79%). Findings suggest that group home placement may benefit some youth but not others, particularly girls and younger children with lower initial level of need. Findings underscore the potential complexity of intervention impact in the context of unique youth, family, and environment factors. PMID:22529035

  6. Class-Wide Function-Related Intervention Teams: Effects of Group Contingency Programs in Urban Classrooms

    ERIC Educational Resources Information Center

    Kamps, Debra; Wills, Howard P.; Heitzman-Powell, Linda; Laylin, Jeff; Szoke, Carolyn; Petrillo, Tai; Culey, Amy

    2011-01-01

    The purpose of the study was to determine the effectiveness of the Class-Wide Function-related Intervention Teams (CW-FIT) program, a group contingency intervention for whole classes, and for students with disruptive behaviors who are at risk for emotional/behavioral disorders (EBD). The CW-FIT program includes four elements designed from…

  7. Neuropsychological Functioning in Specific Learning Disorders--Reading, Writing and Mixed Groups

    ERIC Educational Resources Information Center

    Kohli, Adarsh; Kaur, Manreet; Mohanty, Manju; Malhotra, Savita

    2006-01-01

    Aim: The study compared the pattern of deficits, intelligence and neuropsychological functioning in subcategories of learning disorders. Methods: Forty-six children (16 with reading disorders, 11 with writing disorders and 19 with both reading and writing disorders--mixed group) in the age range of 7-14 years were assessed using the NIMHANS Index…

  8. Minerals and functional groups present in the jackfruit seed: a spectroscopic investigation.

    PubMed

    Barua, A Gohain; Boruah, B R

    2004-09-01

    In this work, emission and Fourier transform infrared spectra of the jackfruit seed, in powdered form, are recorded. Analysis of the emission spectrum confirms the presence of two hitherto undetected elements, manganese and magnesium. The Fourier transform infrared spectrum reveals the presence of some specific functional groups, attributed to the different bands present in the spectrum.

  9. IMPORTANCE OF ACTIVATED CARBON'S OXYGEN SURFACE FUNCTIONAL GROUPS ON ELEMENTAL MERCURY ADSORPTION

    EPA Science Inventory

    The effect of varying physical and chemical properties of activated carbons on adsorption of elemental mercury [Hg(0)] was studied by treating two activated carbons to modify their surface functional groups and pore structures. Heat treatment (1200 K) in nitrogen (N2), air oxidat...

  10. Functional group analysis in coal and on coal surfaces by NMR spectroscopy

    SciTech Connect

    Verkade, J.G.

    1990-01-01

    An accurate knowledge of the oxygen-bearing labile hydrogen functional groups (e.g., carboxylic acids, phenols and alcohols) in coal is required for today's increasingly sophisticated coal cleaning and beneficiation processes. Phospholanes (compounds having the general structure -POCH{sub 2}CH{sub 2}O (1)) are being investigated as reagents for the tagging of liable hydrogen functional groups in coal materials with the NMR-active {sup 31}P nucleus. Of twelve such reagents investigated so far, 2 (2-chloro-1,3-dioxaphospholane, ClPOCH{sub 2}CH{sub 2}O) and 8 (2-chloro-1,3-dithiaphospholane, ClPSCH{sub 2}CH{sub 2}S) have been found to be useful in identifying and quantitating, by {sup 31}P NMR spectroscopy, labile hydrogen functional groups in an Illinois No. 6 coal condensate. Reagent 2 has also been used to quantitate moisture in pyridine extracts of Argonne Premium Coal Samples. Preliminary {sup 119}Sn NMR spectroscopic results on model compounds with the new reagent CF{sub 3}C(O)NHSnMe{sub 3} (N-trimethylstannyltrifluoroacetamide, 14) suggest that labile hydrogen functional groups in coal materials may be more precisely identified with 14 than with phospholanes. 14 refs., 2 figs., 2 tabs.

  11. Organic functional group transformations in water at elevated temperature and pressure: Reversibility, reactivity, and mechanisms

    NASA Astrophysics Data System (ADS)

    Shipp, Jessie; Gould, Ian R.; Herckes, Pierre; Shock, Everett L.; Williams, Lynda B.; Hartnett, Hilairy E.

    2013-03-01

    Many transformation reactions involving hydrocarbons occur in the presence of H2O in hydrothermal systems and deep sedimentary systems. We investigate these reactions using laboratory-based organic chemistry experiments at high temperature and pressure (300 °C and 100 MPa). Organic functional group transformation reactions using model organic compounds based on cyclohexane with one or two methyl groups provided regio- and stereochemical markers that yield information about reversibility and reaction mechanisms. We found rapidly reversible interconversion between alkanes, alkenes, dienes, alcohols, ketones, and enones. The alkane-to-ketone reactions were not only completely reversible, but also exhibited such extensive reversibility that any of the functional groups along the reaction path (alcohol, ketone, and even the diene) could be used as the reactant and form all the other groups as products. There was also a propensity for these ring-based structures to dehydrogenate; presumably from the alkene, through a diene, to an aromatic ring. The product suites provide strong evidence that water behaved as a reactant and the various functional groups showed differing degrees of reactivity. Mechanistically-revealing products indicated reaction mechanisms that involve carbon-centered cation intermediates. This work therefore demonstrates that a wide range of organic compound types can be generated by abiotic reactions at hydrothermal conditions.

  12. A meta-analysis of functional group responses to forest recovery outside of the tropics.

    PubMed

    Spake, Rebecca; Ezard, Thomas H G; Martin, Philip A; Newton, Adrian C; Doncaster, C Patrick

    2015-12-01

    Both active and passive forest restoration schemes are used in degraded landscapes across the world to enhance biodiversity and ecosystem service provision. Restoration is increasingly also being implemented in biodiversity offset schemes as compensation for loss of natural habitat to anthropogenic development. This has raised concerns about the value of replacing old-growth forest with plantations, motivating research on biodiversity recovery as forest stands age. Functional diversity is now advocated as a key metric for restoration success, yet it has received little analytical attention to date. We conducted a meta-analysis of 90 studies that measured differences in species richness for functional groups of fungi, lichens, and beetles between old-growth control and planted or secondary treatment forests in temperate, boreal, and Mediterranean regions. We identified functional-group-specific relationships in the response of species richness to stand age after forest disturbance. Ectomycorrhizal fungi averaged 90 years for recovery to old-growth values (between 45 years and unrecoverable at 95% prediction limits), and epiphytic lichens took 180 years to reach 90% of old-growth values (between 140 years and never for recovery to old-growth values at 95% prediction limits). Non-saproxylic beetle richness, in contrast, decreased as stand age of broadleaved forests increased. The slow recovery by some functional groups essential to ecosystem functioning makes old-growth forest an effectively irreplaceable biodiversity resource that should be exempt from biodiversity offsetting initiatives. PMID:26040756

  13. A meta-analysis of functional group responses to forest recovery outside of the tropics.

    PubMed

    Spake, Rebecca; Ezard, Thomas H G; Martin, Philip A; Newton, Adrian C; Doncaster, C Patrick

    2015-12-01

    Both active and passive forest restoration schemes are used in degraded landscapes across the world to enhance biodiversity and ecosystem service provision. Restoration is increasingly also being implemented in biodiversity offset schemes as compensation for loss of natural habitat to anthropogenic development. This has raised concerns about the value of replacing old-growth forest with plantations, motivating research on biodiversity recovery as forest stands age. Functional diversity is now advocated as a key metric for restoration success, yet it has received little analytical attention to date. We conducted a meta-analysis of 90 studies that measured differences in species richness for functional groups of fungi, lichens, and beetles between old-growth control and planted or secondary treatment forests in temperate, boreal, and Mediterranean regions. We identified functional-group-specific relationships in the response of species richness to stand age after forest disturbance. Ectomycorrhizal fungi averaged 90 years for recovery to old-growth values (between 45 years and unrecoverable at 95% prediction limits), and epiphytic lichens took 180 years to reach 90% of old-growth values (between 140 years and never for recovery to old-growth values at 95% prediction limits). Non-saproxylic beetle richness, in contrast, decreased as stand age of broadleaved forests increased. The slow recovery by some functional groups essential to ecosystem functioning makes old-growth forest an effectively irreplaceable biodiversity resource that should be exempt from biodiversity offsetting initiatives.

  14. Development of Acid Functional Groups and Lactones During the Thermal Degradation of Wood and Wood Components

    USGS Publications Warehouse

    Rutherford, David W.; Wershaw, Robert L.; Reeves, James B.

    2008-01-01

    Black carbon (pyrogenic materials including chars) in soils has been recognized as a substantial portion of soil organic matter, and has been shown to play a vital role in nutrient cycling; however, little is known concerning the properties of this material. Previous studies have largely been concerned with the creation of high-surface-area materials for use as sorbents. These materials have been manufactured at high temperature and have often been activated. Chars occurring in the environment can be formed over a wide range of temperature. Because it is extremely difficult to isolate black carbon once it has been incorporated in soils, chars produced in the laboratory under controlled conditions can be used to investigate the range of properties possible for natural chars. This report shows that charring conditions (temperature and time) have substantial impact on the acid functional group and lactone content of chars. Low temperatures (250?C) and long charring times (greater than 72 hours) produce chars with the highest acid functional group and lactone content. The charring of cellulose appears to be responsible for the creation of the acid functional group and lactones. The significance of this study is that low-temperature chars can have acid functional group contents comparable to humic materials (as high as 8.8 milliequivalents per gram). Acid functional group and lactone content decreases as charring temperature increases. The variation in formation conditions expected under natural fire conditions will result in a wide range of sorption properties for natural chars which are an important component of soil organic matter. By controlling the temperature and duration of charring, it is possible to tailor the sorption properties of chars, which may be used as soil amendments.

  15. Advances in the development of catalytic tethering directing groups for C-H functionalization reactions.

    PubMed

    Sun, Huan; Guimond, Nicolas; Huang, Yong

    2016-09-28

    Transition metal-catalyzed C-H bond insertion is one of the most straightforward strategies to introduce functionalities within a hydrocarbon microenvironment. For the past two decades, selective activation and functionalization of certain inert C-H bonds have been made possible with the help of directing groups (DGs). Despite the enormous advances in the field, an overwhelming majority of systems require two extra steps from their simple precursors: installation and removal of the DGs. Recently, traceless and multitasking groups were invented as a partial solution to DG release. However, installation remains largely unsolved. Ideally, a transient, catalytic DG would circumvent this problem and increase the step- and atom-economy of C-H functionalization processes. In this review, we summarize the recent development of the transient tethering strategy for C-H activation reactions. PMID:27506568

  16. Selective functionalization of hollow nanospheres with Acid and base groups for cascade reactions.

    PubMed

    Gao, Jinsuo; Zhang, Xueying; Lu, Yong; Liu, Shaomin; Liu, Jian

    2015-05-11

    The inner-surface functionalization of hollow silica spheres has rarely been reported and is still a challenging topic. Herein, we report a deacetalization-Henry cascade reaction catalyzed by dual-functionalized mesoporous silica hollow nanospheres with basic amine groups (NH2 ) on the internal shell and carboxylic acid groups (COOH) on the external shell. The selective functionalization has been realized by a combination of "step-by-step post-grafting" and "cationic surfactant-assisted selective etching" strategy. Compared to unisolated catalyst, the selectively isolated acidic and basic dual catalyst provides excellent catalytic performance for the deacetalization-Henry cascade reaction in terms of both activity (>99 %) and selectivity (95 %).

  17. Wetting properties of model interphases coated with defined organic functional groups

    NASA Astrophysics Data System (ADS)

    Woche, Susanne K.; Goebel, Marc-O.; Guggenberger, Georg; Tunega, Daniel; Bachmann, Joerg

    2013-04-01

    Surface properties of soil particles are of particular interest regarding transport of water and sorption of solutes, especially hazardous xenobiotic species. Wetting properties (e.g. determined by contact angle, CA), governed by the functional groups exposed, are crucial to understand sorption processes in water repellent soils as well as for the geometry of water films sustaining microbial processes on the pore scale. Natural soil particle surfaces are characterized by a wide variety of mineralogical and chemical compounds. Their composition is almost impossible to identify in full. Hence, in order to get a better understanding about surface properties, an option is the usage of defined model surfaces, whereas the created surface should be comparable to natural soil interphases. We exposed smooth glass surfaces to different silane compounds, resulting in a coating covalently bound to the surface and exhibiting defined organic functional groups towards the pore space. The wetting properties as evaluated by CA and the surface free energy (SFE), calculated according to the Acid-Base Theory, were found to be a function of the specific functional group. Specifically, the treated surfaces showed a large variation of CA and SFE as function of chain length and polarity of the organic functional group. The study of wetting properties was accompanied by XPS analysis for selective detection of chemical compounds of the interphase. As the reaction mechanism of the coating process is known, the resulting interphase structure can be modeled based on energetic considerations. A next step is to use same coatings for the defined modification of the pore surfaces of porous media to study transport and sorption processes in complex three phase systems.

  18. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    PubMed

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further.

  19. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    PubMed

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. PMID:25862282

  20. Zooplankton functional groups on the continental shelf of the yellow sea

    NASA Astrophysics Data System (ADS)

    Sun, Song; Huo, Yuanzi; Yang, Bo

    2010-06-01

    Zooplankton plays a vital role in marine ecosystems. Variations in the zooplankton species composition, biomass, and secondary production will change the structure and function of the ecosystem. How to describe this process and make it easier to be modeled in the Yellow Sea ecosystem is the main purpose of this paper. The zooplankton functional groups approach, which is considered a good method of linking the structure of food webs and the energy flow in the ecosystems, is used to describe the main contributors of secondary produciton of the Yellow Sea ecosystem. The zooplankton can be classified into six functional groups: giant crustaceans, large copepods, small copepods, chaetognaths, medusae, and salps. The giant crustaceans, large copepods, and small copepods groups, which are the main food resources for fish, are defined depending on the size spectrum. Medusae and chaetognaths are the two gelatinous carnivorous groups, which compete with fish for food. The salps group, acting as passive filter-feeders, competes with other species feeding on phytoplankton, but their energy could not be efficiently transferred to higher trophic levels. From the viewpoint of biomass, which is the basis of the food web, and feeding activities, the contributions of each functional group to the ecosystem were evaluated; the seasonal variations, geographical distribution patterns, and species composition of each functional group were analyzed. The average zooplankton biomass was 2.1 g dry wt m -2 in spring, to which the giant crustaceans, large copepods, and small copepods contributed 19, 44, and 26%, respectively. High biomasses of the large copepods and small copepods were distributed at the coastal waters, while the giant crustaceans were mainly located at offshore area. In summer, the mean biomass was 3.1 g dry wt m -2, which was mostly contributed by the giant crustaceans (73%), and high biomasses of the giant crustaceans, large copepods, and small copepods were all distributed

  1. Functionalization of carbon nanotubes with -CH(n), -NH(n) fragments, -COOH and -OH groups.

    PubMed

    Milowska, Karolina Z; Majewski, Jacek A

    2013-05-21

    We present results of extensive theoretical studies concerning stability, morphology, and band structure of single wall carbon nanotubes (CNTs) covalently functionalized by -CH(n) (for n = 2,3,4), -NH(n) (for n = 1,2,3,4), -COOH, and -OH groups. These studies are based on ab initio calculations in the framework of the density functional theory. For functionalized systems, we determine the dependence of the binding energies on the concentration of the adsorbed molecules, critical densities of adsorbed molecules, global and local changes in the morphology, and electronic structure paying particular attention to the functionalization induced changes of the band gaps. These studies reveal physical mechanisms that determine stability and electronic structure of functionalized systems and also provide valuable theoretical predictions relevant for application. In particular, we observe that functionalization of CNTs causes generally their elongation and locally sp(2) to sp(3) rehybridization in the neighborhood of chemisorbed molecules. For adsorbants making particularly strong covalent bonds with the CNTs, such as the -CH2 fragments, we observe formation of the characteristic pentagon/heptagon (5/7) defects. In systems functionalized with the -CH2, -NH4, and -OH groups, we determine critical density of molecules that could be covalently bound to the lateral surface of CNTs. Our studies show that functionalization of CNTs can be utilized for band gap engineering. Functionalization of CNTs can also lead to changes in their metallic/semiconductor character. In semiconducting CNTs, functionalizing molecules such as -CH3, -NH2, -OH, -COOH, and both -OH and -COOH, introduce "impurity" bands in the band gap of pristine CNTs. In the case of -CH3, -NH2 molecules, the induced band gaps are typically smaller than in the pure CNT and depend strongly on the concentration of adsorbants. However, functionalization of semiconducting CNTs with hydroxyl groups leads to the metallization

  2. Tumor-suppressor effects of chemical functional groups in an in vitro co-culture system

    NASA Astrophysics Data System (ADS)

    Xu, Su-Ju; Cui, Fu-Zhai; Kong, Xiang-Dong

    2014-06-01

    Liver normal cells and cancer cells co-cultured on surfaces modified by different chemical functional groups, including mercapto (-SH), hydroxyl (-OH) and methyl (-CH3) groups. The results showed that different cells exhibited changes in response to different surfaces. Normal cells on -SH surface exhibited the smallest contact area with mostly rounded morphology, which led to the death of cancer cells, while cancer cells could not grow on -CH3 groups, which also died. In the co-culture system, the -CH3 group exhibited its unique effect that could trigger the death of cancer cells and had no effects on normal cells. Our findings provide useful information on strategies for the design of efficient and safe regenerative medicine materials.

  3. Kelvin-probe force microscopy of the pH-dependent charge of functional groups

    NASA Astrophysics Data System (ADS)

    Stone, Alexander D. D.; Mesquida, Patrick

    2016-06-01

    Kelvin-probe Force Microscopy (KFM) is an established method to map surface potentials or surface charges at high, spatial resolution. However, KFM does not work in water, which restricts its applicability considerably, especially when considering common, functional chemical groups in biophysics such as amine or carboxy groups, whose charge depends on pH. Here, we demonstrate that the KFM signal of such groups taken in air after exposure to water correlates qualitatively with their expected charge in water for a wide range of pH values. The correlation was tested with microcontact-printed thiols exposing amine and carboxy groups. Furthermore, it was shown that collagen fibrils, as an example of a biological material, exhibit a particular, pH-sensitive surface charge pattern, which could be caused by the particular arrangement of ionizable residues on the collagen fibril surface.

  4. Hydrogen-bond acidic functionalized carbon nanotubes (CNTs) with covalently-bound hexafluoroisopropanol groups

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

    Fluorinated hydrogen-bond acidic groups are directly attached to the backbone of single walled carbon nanotubes (SWCNTs) without the introduction of intermediate electron donating surface groups. Hexafluoroalcohol functional groups are exceptionally strong hydrogen bond acids, and are added to the nanotube surface using the aryl diazonium approach to create hydrogen-bond acidic carbon nanotube (CNT) surfaces. These groups can promote strong hydrogen-bonding interactions with matrix materials in composites or with molecular species to be concentrated and sensed. In the latter case, this newly developed material is expected to find useful application in chemical sensors and in CNT-based preconcentrator devices for the detection of pesticides, chemical warfare agents and explosives.

  5. Effects of Trehalose Polycation End-group Functionalization on Plasmid DNA Uptake and Transfection

    PubMed Central

    Anderson, Kevin; Sizovs, Antons; Cortez, Mallory; Waldron, Chris; Haddleton, D.M.; Reineke, Theresa M.

    2012-01-01

    In this study, we have synthesized six analogs of a trehalose-pentaethylenehexamine glycopolymer (Tr4) that contain (1A) adamantane, (1B) carboxy, (1C) alkynyl-oligoethyleneamine, (1D) azido trehalose, (1E) octyl, or (1F) oligoethyleneamine end groups and evaluated the effects of polymer end group chemistry on the ability of these systems to bind, compact, and deliver pDNA in cultured HeLa cells. The polymers were synthesized in one-pot azide-alkyne cycloaddition reactions with an adaptation of the Carothers equation for step-growth polymerization to produce a series of polymers with similar degrees of polymerization. An excess of end-capping monomer was added at the end of the polymerizations to maximize functionalization efficiency, which was evaluated with GPC, NMR and MALDI-TOF. The polymers were all found to bind and compact pDNA at similarly low N/P ratios and form polyplexes with plasmid DNA. The effects of the different end group structures were most evident in the polyplex internalization and transfection assays completed in the presence of serum, as determined by flow cytometry and luciferase gene expression respectively. The Tr4 polymers end-capped with carboxyl groups (1B) (N/P = 7), octyne (1E) (N/P = 7), and oligoethyleneamine (1F) (N/P = 7), were taken into cells as polyplex and exhibited the highest levels of fluorescence, resulting from labeled reporter plasmid. Similarly, the polymers end-functionalized with the carboxyl groups (1E at N/P = 7), octyl groups (1E at N/P = 15) and, in particular, the oligoethyleneamine groups (F at N/P = 15) yielded dramatically higher reporter gene expression in the presence of serum. This study yields insight into how very subtle structural changes in the polymer chemistry such as end groups can yield very significant differences in the biological delivery efficiency and transgene expression of polymers used for pDNA delivery. PMID:22616977

  6. Effects of trehalose polycation end-group functionalization on plasmid DNA uptake and transfection.

    PubMed

    Anderson, Kevin; Sizovs, Antons; Cortez, Mallory; Waldron, Chris; Haddleton, D M; Reineke, Theresa M

    2012-08-13

    In this study, we have synthesized six analogs of a trehalose-pentaethylenehexamine glycopolymer (Tr4) that contain (1A) adamantane, (1B) carboxy, (1C) alkynyl-oligoethyleneamine, (1D) azido trehalose, (1E) octyl, or (1F) oligoethyleneamine end groups and evaluated the effects of polymer end group chemistry on the ability of these systems to bind, compact, and deliver pDNA to cultured HeLa cells. The polymers were synthesized in one-pot azide-alkyne cycloaddition reactions with an adaptation of the Carothers equation for step-growth polymerization to produce a series of polymers with similar degrees of polymerization. An excess of end-capping monomer was added at the end of the polymerizations to maximize functionalization efficiency, which was evaluated with GPC, NMR, and MALDI-TOF. The polymers were all found to bind and compact pDNA at similarly low N/P ratios and form polyplexes with plasmid DNA. The effects of the different end group structures were most evident in the polyplex internalization and transfection assays in the presence of serum as determined by flow cytometry and luciferase gene expression, respectively. The Tr4 polymers end-capped with carboxyl groups (1B) (N/P = 7), octyne (1E) (N/P = 7), and oligoethyleneamine (1F) (N/P = 7), were taken into cells as polyplex and exhibited the highest levels of fluorescence, resulting from labeled plasmid. Similarly, the polymers end-functionalized with carboxyl groups (1E at N/P = 7), octyl groups (1E at N/P = 15), and in particular oligoethyleneamine groups (1F at N/P = 15) yielded dramatically higher reporter gene expression in the presence of serum. This study yields insight into how very subtle structural changes in polymer chemistry, such as end groups can yield very significant differences in the biological delivery efficiency and transgene expression of polymers used for pDNA delivery.

  7. Refinements to the structure of graphite oxide: absolute quantification of functional groups via selective labelling

    NASA Astrophysics Data System (ADS)

    Eng, Alex Yong Sheng; Chua, Chun Kiang; Pumera, Martin

    2015-11-01

    Chemical modification and functionalization of inherent functional groups within graphite oxide (GO) are essential aspects of graphene-based nano-materials used in wide-ranging applications. Despite extensive research, there remains some discrepancy in its structure, with current knowledge limited primarily to spectroscopic data from XPS, NMR and vibrational spectroscopies. We report herein an innovative electrochemistry-based approach. Four electroactive labels are chosen to selectively functionalize groups in GO, and quantification of each group is achieved by voltammetric analysis. This allows for the first time quantification of absolute amounts of each group, with a further advantage of distinguishing various carbonyl species: namely ortho- and para-quinones from aliphatic ketones. Intrinsic variations in the compositions of permanganate versus chlorate-oxidized GOs were thus observed. Principal differences include permanganate-GO exhibiting substantial quinonyl content, in comparison to chlorate-GO with the vast majority of its carbonyls as isolated ketones. The results confirm that carboxylic groups are rare in actuality, and are in fact entirely absent from chlorate-GO. These observations refine and advance our understanding of GO structure by addressing certain disparities in past models resulting from employment of different oxidation routes, with the vital implication that GO production methods cannot be used interchangeably in the manufacture of graphene-based devices.Chemical modification and functionalization of inherent functional groups within graphite oxide (GO) are essential aspects of graphene-based nano-materials used in wide-ranging applications. Despite extensive research, there remains some discrepancy in its structure, with current knowledge limited primarily to spectroscopic data from XPS, NMR and vibrational spectroscopies. We report herein an innovative electrochemistry-based approach. Four electroactive labels are chosen to selectively

  8. Tunable Oxygen Functional Groups as Electrocatalysts on Graphite Felt Surfaces for All-Vanadium Flow Batteries.

    PubMed

    Estevez, Luis; Reed, David; Nie, Zimin; Schwarz, Ashleigh M; Nandasiri, Manjula I; Kizewski, James P; Wang, Wei; Thomsen, Edwin; Liu, Jun; Zhang, Ji-Guang; Sprenkle, Vincent; Li, Bin

    2016-06-22

    A dual oxidative approach using O2 plasma followed by treatment with H2 O2 to impart oxygen functional groups onto the surface of a graphite felt electrode. When used as electrodes for an all-vanadium redox flow battery (VRB) system, the energy efficiency of the cell is enhanced by 8.2 % at a current density of 150 mA cm(-2) compared with one oxidized by thermal treatment in air. More importantly, by varying the oxidative techniques, the amount and type of oxygen groups was tailored and their effects were elucidated. It was found that O-C=O groups improve the cells performance whereas the C-O and C=O groups degrade it. The reason for the increased performance was found to be a reduction in the cell overpotential after functionalization of the graphite felt electrode. This work reveals a route for functionalizing carbon electrodes to improve the performance of VRB cells. This approach can lower the cost of VRB cells and pave the way for more commercially viable stationary energy storage systems that can be used for intermittent renewable energy storage. PMID:27184225

  9. Quantity of Hydrophobic Functional CH-Groups - Decisive for Soil Water Repellency Caused by Digestate Amendment

    NASA Astrophysics Data System (ADS)

    Voelkner, Amrei; Holthusen, Dörthe; Ellerbrock, Ruth H.; Horn, Rainer

    2015-04-01

    Anaerobic digestates are used as organic fertilizers; however, they are suspected to interfere negatively with soils. To investigate the relevance of the anaerobic digestates composition on potential wettability and contact angle of the soil, we mixed in a laboratory experiment 30 m³ ha-1 of anaerobic digestates derived from mechanically pre-treated substrates from maize and sugar beet with a homogenized Cambic Luvisol. Fourier transform infrared-spectra and diffuse reflectance infrared Fourier transform-spectra of particle intact and finely ground soilanaerobic digestates-mixtures were analyzed to determine the quantities of hydrophobic functional groups in the soil-anaerobic digestates-mixtures that are used here as an indicator for the potential hydrophobicity. The anaerobic digestates application increased the amount of hydrophobic functional groups of the mixtures and reduced the wettability of the soil. However, for intact particle samples an up to threefold higher amount of hydrophobic groups was found as compared to the finely ground ones, indicating a dilution effect of mechanical grinding on the effectivity of the organic matter that is presumably located as a coating on mineral soil particles. For the particle intact samples, the intensity of hydrophobic functional groups bands denoting hydrophobic brickstones in organic matter is indicative for the actual wettability of the soil-anaerobic digestates-mixtures.

  10. Tunable Oxygen Functional Groups as Electrocatalysts on Graphite Felt Surfaces for All-Vanadium Flow Batteries.

    PubMed

    Estevez, Luis; Reed, David; Nie, Zimin; Schwarz, Ashleigh M; Nandasiri, Manjula I; Kizewski, James P; Wang, Wei; Thomsen, Edwin; Liu, Jun; Zhang, Ji-Guang; Sprenkle, Vincent; Li, Bin

    2016-06-22

    A dual oxidative approach using O2 plasma followed by treatment with H2 O2 to impart oxygen functional groups onto the surface of a graphite felt electrode. When used as electrodes for an all-vanadium redox flow battery (VRB) system, the energy efficiency of the cell is enhanced by 8.2 % at a current density of 150 mA cm(-2) compared with one oxidized by thermal treatment in air. More importantly, by varying the oxidative techniques, the amount and type of oxygen groups was tailored and their effects were elucidated. It was found that O-C=O groups improve the cells performance whereas the C-O and C=O groups degrade it. The reason for the increased performance was found to be a reduction in the cell overpotential after functionalization of the graphite felt electrode. This work reveals a route for functionalizing carbon electrodes to improve the performance of VRB cells. This approach can lower the cost of VRB cells and pave the way for more commercially viable stationary energy storage systems that can be used for intermittent renewable energy storage.

  11. Functional characterization and phylogenetic analysis of acquired and intrinsic macrolide phosphotransferases in the Bacillus cereus group.

    PubMed

    Wang, Chao; Sui, Zhihai; Leclercq, Sébastien Olivier; Zhang, Gang; Zhao, Meilin; Chen, Weiqi; Feng, Jie

    2015-05-01

    The Bacillus cereus group is composed of Gram-positive spore-forming bacteria of clinical and ecological importance. More than 200 B. cereus group isolates have been sequenced. However, there are few reports of B. cereus group antibiotic resistance genes. This study identified two functional classes of macrolide phosphotransferases (Mphs) in the B. cereus group. Cluster A Mphs inactivate 14- and 15-membered macrolides while Cluster B Mphs inactivate 14-, 15- and 16-membered compounds. The genomic region surrounding the Cluster B Mph gene is related to various plasmid sequences, suggesting that this gene is an acquired resistance gene. In contrast, the Cluster A Mph gene is located in a chromosomal region conserved among all B. cereus group isolates, and data indicated that it was acquired early in the evolution of the group. Therefore, the Cluster A gene can be considered an intrinsic resistance gene. However, the gene itself is not present in all strains and our comparative genomics analyses showed that it is exchanged among strains of the B. cereus group by the mean of homologous recombination. These results provide an alternative mechanism to intrinsic resistance.

  12. Biofuel purification in zeolitic imidazolate frameworks: the significant role of functional groups.

    PubMed

    Zhang, Kang; Nalaparaju, Anjaiah; Chen, Yifei; Jiang, Jianwen

    2014-05-28

    A molecular simulation study is reported for biofuel purification in six zeolitic imidazolate frameworks (ZIF-8, -25, -71, -90, -96 and -97) with different functional groups. For pure ethanol and water, the predicted adsorption isotherms agree fairly well with experimental data. Hydrogen bonding has an important effect on the adsorption of ethanol and water. In hydrophilic ZIFs (ZIF-90, -96 and -97) with polar groups, adsorption capacities are higher than in hydrophobic counterparts (ZIF-8, -25 and -71). The atomic charges in symmetrically functionalized ZIF-8, -25, and -71 are found to have an indiscernible effect on adsorption, in remarkable contrast to asymmetrically functionalized ZIF-90, -96 and -97. For ethanol-water mixtures representing the biofuel, the selectivity of ethanol-water drops with increasing ethanol in mixtures. It is revealed that the selectivity is determined primarily by framework hydrophobicity as well as the cage size. Among the six ZIFs, ZIF-8 exhibits the highest selectivity. This simulation study provides a microscopic insight into the adsorption of ethanol and water in various ZIFs, reveals the significant role of functional groups in governing biofuel purification, and would facilitate the development of new nanoporous materials for high-efficacy liquid separation.

  13. Nanomechanical characterization of chemical interaction between gold nanoparticles and chemical functional groups

    PubMed Central

    2012-01-01

    We report on how to quantify the binding affinity between a nanoparticle and chemical functional group using various experimental methods such as cantilever assay, PeakForce quantitative nanomechanical property mapping, and lateral force microscopy. For the immobilization of Au nanoparticles (AuNPs) onto a microscale silicon substrate, we have considered two different chemical functional molecules of amine and catecholamine (here, dopamine was used). It is found that catecholamine-modified surface is more effective for the functionalization of AuNPs onto the surface than the amine-modified surface, which has been shown from our various experiments. The dimensionless parameter (i.e., ratio of binding affinity) introduced in this work from such experiments is useful in quantitatively depicting such binding affinity, indicating that the binding affinity and stability between AuNPs and catecholamine is approximately 1.5 times stronger than that between amine and AuNPs. Our study sheds light on the experiment-based quantitative characterization of the binding affinity between nanomaterial and chemical groups, which will eventually provide an insight into how to effectively design the functional material using chemical groups. PMID:23113991

  14. Linking avian communities and avian influenza ecology in southern Africa using epidemiological functional groups.

    PubMed

    Caron, Alexandre; de Garine-Wichatitsky, Michel; Ndlovu, Mduduzi; Cumming, Graeme S

    2012-01-01

    The ecology of pathogens, and particularly their emergence in multi-host systems, is complex. New approaches are needed to reduce superficial complexities to a level that still allows scientists to analyse underlying and more fundamental processes. One promising approach for simplification is to use an epidemiological-function classification to describe ecological diversity in a way that relates directly to pathogen dynamics. In this article, we develop and apply the epidemiological functional group (EFG) concept to explore the relationships between wild bird communities and avian influenza virus (AIV) in three ecosystems in southern Africa. Using a two year dataset that combined bird counts and bimonthly sampling for AIV, we allocated each bird species to a set of EFGs that captured two overarching epidemiological functions: the capacity of species to maintain AIV in the system, and their potential to introduce the virus. Comparing AIV prevalence between EFGs suggested that the hypothesis that anseriforms (ducks) and charadriiforms (waders) drive AIV epidemiology cannot entirely explain the high prevalence observed in some EFGs. If anseriforms do play an important role in AIV dynamics in each of the three ecosystems, the role of other species in the local maintenance of AIV cannot be ruled out. The EFG concept thus helped us to identify gaps in knowledge and to highlight understudied bird groups that might play a role in AIV epidemiology. In general, the use of EFGs has potential for generating a range of valuable insights in epidemiology, just as functional group approaches have done in ecology. PMID:23101696

  15. The central role of ketones in reversible and irreversible hydrothermal organic functional group transformations

    NASA Astrophysics Data System (ADS)

    Yang, Ziming; Gould, Ian R.; Williams, Lynda B.; Hartnett, Hilairy E.; Shock, Everett L.

    2012-12-01

    Studies of hydrothermal reactions involving organic compounds suggest complex, possibly reversible, reaction pathways that link functional groups from reduced alkanes all the way to oxidized carboxylic acids. Ketones represent a critical functional group because they occupy a central position in the reaction pathway, at the point where Csbnd C bond cleavage is required for the formation of the more oxidized carboxylic acids. The mechanisms for the critical bond cleavage reactions in ketones, and how they compete with other reactions are the focus of this experimental study. We studied a model ketone, dibenzylketone (DBK), in H2O at 300 °C and 70 MPa for up to 528 h. Product analysis was performed as a function of time at low DBK conversions to reveal the primary reaction pathways. Reversible interconversion between ketone, alcohol, alkene and alkane functional groups is observed in addition to formation of radical coupling products derived from irreversible Csbnd C and Csbnd H homolytic bond cleavage. The product distributions are time-dependent but the bond cleavage products dominate. The major products that accumulate at longer reaction times are toluene and larger, dehydrogenated structures that are initially formed by radical coupling. The hydrogen atoms generated by dehydrogenation of the coupling products are predominantly consumed in the formation of toluene. Even though bond cleavage products dominate, no carboxylic acids were observed on the timescale of the reactions under the chosen experimental conditions.

  16. First-principles study of the effect of functional groups on polyaniline backbone

    PubMed Central

    Chen, X. P.; Jiang, J. K.; Liang, Q. H.; Yang, N.; Ye, H. Y.; Cai, M.; Shen, L.; Yang, D. G.; Ren, T. L.

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

  17. Wetland macroinvertebrates of Prentiss Bay, Lake Huron, Michigan: diversity and functional group composition

    USGS Publications Warehouse

    Merritt, R.W.; Benbow, M.E.; Hudson, P.L.

    2002-01-01

    The Great Lakes support many fish and waterbirds that depend directly or indirectly on coastal wetlands during some portion of their life cycle. It is known that macroinvertebrates make up an important part of wetland food webs and ecosystem function; however, our understanding of species distribution within and among wetlands has only recently received attention. We investigated the macroinvertebrates of a freshwater marsh (Prentiss Bay) in the Les Chenaux Island Area of Northern Lake Huron, Michigan. Macroinvertebrate taxa diversity and functional feeding group composition were compared between two habitats. A shallow depositional habitat with higher vegetation diversity and little wave action was compared to a deeper erosional habitat with fewer plant species and more wave action. A total of 83 taxa were collected over the summer of 1996, representing two phyla (Arthropoda and Mollusca) and five classes (Arachnida, Bivalvia, Malacostraca, Gastropoda and Insecta). A total of 79 genera were identified, with 92% being insects (39 families composed of at least 73 genera). Of the total, 42 insect genera were common to both habitats,while relatively fewer were collected exclusively from the erosional compared the depositional habitat. When habitats were pooled, predators comprised about 50% of the functional group taxa, while gathering collectors and shredders each were about 20%. Filtering collectors and scrapers each represented < 10%. When comparing habitats, there was a relatively higher percentage of predators and shredders in the depositional habitat, while all other functional groups were lower. These data suggest that vegetation diversity, depth and wave action affect taxa composition and functional group organization of the Prentiss Bay marsh.

  18. Control of oxo-group functionalization and reduction of the uranyl ion.

    PubMed

    Arnold, Polly L; Pécharman, Anne-Frédérique; Lord, Rianne M; Jones, Guy M; Hollis, Emmalina; Nichol, Gary S; Maron, Laurent; Fang, Jian; Davin, Thomas; Love, Jason B

    2015-04-01

    Uranyl complexes of a large, compartmental N8-macrocycle adopt a rigid, "Pacman" geometry that stabilizes the U(V) oxidation state and promotes chemistry at a single uranyl oxo-group. We present here new and straightforward routes to singly reduced and oxo-silylated uranyl Pacman complexes and propose mechanisms that account for the product formation, and the byproduct distributions that are formed using alternative reagents. Uranyl(VI) Pacman complexes in which one oxo-group is functionalized by a single metal cation are activated toward single-electron reduction. As such, the addition of a second equivalent of a Lewis acidic metal complex such as MgN″2 (N″ = N(SiMe3)2) forms a uranyl(V) complex in which both oxo-groups are Mg functionalized as a result of Mg-N bond homolysis. In contrast, reactions with the less Lewis acidic complex [Zn(N″)Cl] favor the formation of weaker U-O-Zn dative interactions, leading to reductive silylation of the uranyl oxo-group in preference to metalation. Spectroscopic, crystallographic, and computational analysis of these reactions and of oxo-metalated products isolated by other routes have allowed us to propose mechanisms that account for pathways to metalation or silylation of the exo-oxo-group.

  19. Functionality of In vitro Reconstituted Group II Intron RmInt1-Derived Ribonucleoprotein Particles

    PubMed Central

    Molina-Sánchez, Maria D.; García-Rodríguez, Fernando M.; Toro, Nicolás

    2016-01-01

    The functional unit of mobile group II introns is a ribonucleoprotein particle (RNP) consisting of the intron-encoded protein (IEP) and the excised intron RNA. The IEP has reverse transcriptase activity but also promotes RNA splicing, and the RNA-protein complex triggers site-specific DNA insertion by reverse splicing, in a process called retrohoming. In vitro reconstituted ribonucleoprotein complexes from the Lactococcus lactis group II intron Ll.LtrB, which produce a double strand break, have recently been studied as a means of developing group II intron-based gene targeting methods for higher organisms. The Sinorhizobium meliloti group II intron RmInt1 is an efficient mobile retroelement, the dispersal of which appears to be linked to transient single-stranded DNA during replication. The RmInt1IEP lacks the endonuclease domain (En) and cannot cut the bottom strand to generate the 3′ end to initiate reverse transcription. We used an Escherichia coli expression system to produce soluble and active RmInt1 IEP and reconstituted RNPs with purified components in vitro. The RNPs generated were functional and reverse-spliced into a single-stranded DNA target. This work constitutes the starting point for the use of group II introns lacking DNA endonuclease domain-derived RNPs for highly specific gene targeting methods. PMID:27730127

  20. Unification of [FeFe]-hydrogenases into three structural and functional groups

    DOE PAGES

    Poudel, Saroj; Tokmina-Lukaszewska, Monika; Colman, Daniel R.; Refai, Mohammed; Schut, Gerrit J.; King, Paul W.; Maness, Pin-Ching; Adams, Michael W. W.; Peters, John W.; Bothner, Brian; et al

    2016-05-27

    [FeFe]-hydrogenases (Hyd) are structurally diverse enzymes that catalyze the reversible oxidation of hydrogen (H2). Recent biochemical data demonstrate new functional roles for these enzymes, including those that function in electron bifurcation where an exergonic reaction is coupled with an endergonic reaction to drive the reversible oxidation/production of H2. To identify the structural determinants that underpin differences in enzyme functionality, a total of 714 homologous sequences of the catalytic subunit, HydA, were compiled. Bioinformatics approaches informed by biochemical data were then used to characterize differences in inferred quaternary structure, HydA active site protein environment, accessory iron-sulfur clusters in HydA, and regulatorymore » proteins encoded in HydA gene neighborhoods. HydA homologs were clustered into one of three classification groups, Group 1 (G1), Group 2 (G2), and Group 3 (G3). G1 enzymes were predicted to be monomeric while those in G2 and G3 were predicted to be multimeric and include HydB, HydC (G2/G3) and HydD (G3) subunits. Variation in the HydA active site and accessory iron-sulfur clusters did not vary by group type. Group-specific regulatory genes were identified in the gene neighborhoods of both G2 and G3 Hyd. Analyses of purified G2 and G3 enzymes by mass spectrometry strongly suggests that they are post-translationally modified by phosphorylation. In conclusion, these results suggest that bifurcation capability is dictated primarily by the presence of both HydB and HydC in Hyd complexes, rather than by variation in HydA.« less

  1. Compatibility of functional groups in K[sup ow]-based QSARs: Application to nitro compounds

    SciTech Connect

    Banerjee, S.; Williams, C.L. )

    1993-10-01

    Nitro compounds are particular difficult to handle in simple K[sup ow]-based QSARs, owing to differences in their lipid-phase activity coefficients. These differences can be corrected, in part, through inclusion of a term in octanol solubility. A procedure for identifying potentially incompatible groups in a given QSAR is suggested. The quality of a QSAR is best if the interactions of the functional groups involved with octanol fall within a narrow range. These interactions are easily calculated by the UNIFAC method.

  2. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  3. Impact of Nanotopography and/or Functional Groups on Periodontal Ligament Cell Growth

    NASA Astrophysics Data System (ADS)

    Şaşmazel, Hilal Türkoğlu; Manolache, S.; Gümüşderelİoğlu, M.

    The main purpose of this contribution was to obtain COOH functionalities and/or nanotopographic changes on the surface of 3D, non-woven polyester fabric (NWPF) discs (12.5 mm in diameter) by using low pressure water/O2 plasma assisted treatments. The prepared discs were characterized by various methods after the plasma treatment. Periodontal ligament (PDL) fibroblasts were used in cell culture studies. The cell culture results showed that plasma treated 3D NWPF discs are favorable for PDL cell spreading, growth and viability due to the presence of functional groups and/or the nanotopography of their surfaces.

  4. On the stabilization mechanisms of organic functional groups on ZnO surfaces.

    PubMed

    Moreira, Ney Henrique; Domıinguez, Adriel; Frauenheim, Thomas; da Rosa, Andreia Luisa

    2012-11-28

    Density functional theory (DFT) calculations have been employed to investigate the interaction between ZnO-(101[combining macron]0) and (12[combining macron]10) surfaces and organic functional groups. We analyze the influence of the surface coverage on the geometries and binding energies under a dry environment. Our calculations show that coverages θ = 1 ML are favored under ligand-rich conditions and a dry environment. However, based on thermodynamic considerations we suggest that these ligands may not be stable against adsorption of liquid water and water vapor. PMID:23073244

  5. Platinum-group element abundances and Re-Os isotopic systematics of the upper continental crust through time: Evidence from glacial diamictites

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Walker, Richard J.; Rudnick, Roberta L.; Gao, Shan; Gaschnig, Richard M.; Puchtel, Igor S.; Tang, Ming; Hu, Zhao-Chu

    2016-10-01

    The fine-grained matrix of glacial diamictites, deposited periodically by continental ice sheets over much of Earth history, provides insights into the average composition and chemical evolution of the upper continental crust (UCC) (Gaschnig et al., 2016, and references therein). The concentrations of platinum-group elements (PGEs, including Os, Ir, Ru, Pt and Pd) and the geochemically related Re, as well as 187Re/188Os and 187Os/188Os ratios, are reported here for globally-distributed glacial diamictites that were deposited during the Mesoarchean, Paleoproterozoic, Neoproterozoic and Paleozoic eras. The medians and averages of PGE concentrations of these diamictite composites decrease from the Mesoarchean to the Neoproterozoic, mimicking decreases in the concentrations of first-row transition elements (Sc, V, Cr, Co and Ni). By contrast, Re concentrations are highly variable with no discernable trend, owing to its high solubility. Assuming these diamictites are representative of average UCC through time, the new data are fully consistent with the previous inference that the Archean UCC contained a greater proportion of mafic-ultramafic rocks relative to younger UCC. Linear regressions of PGEs versus Cr and Ni concentrations in all the diamictite composites from the four time periods are used to estimate the following concentrations of the PGEs in the present-day UCC: 0.059 ± 0.016 ng/g Os, 0.036 ± 0.008 ng/g Ir, 0.079 ± 0.026 ng/g Ru, 0.80 ± 0.22 ng/g Pt and 0.80 ± 0.26 ng/g Pd (2σ of 10,000 bootstrapping regression results). These PGE estimates are slightly higher than the estimates obtained from loess samples. We suggest this probably results from loess preferentially sampling younger UCC rocks that have lower PGE concentrations, or PGEs being fractionated during loess formation. A Re concentration of 0.25 ± 0.12 ng/g (2σ) is obtained from a regression of Re versus Mo. From this, time-integrated 187Re/188Os and 187Os/188Os ratios for the UCC are

  6. Approaching many-body localization from disordered Luttinger liquids via the functional renormalization group

    NASA Astrophysics Data System (ADS)

    Karrasch, C.; Moore, J. E.

    2015-09-01

    We study the interplay of interactions and disorder in a one-dimensional fermion lattice coupled adiabatically to infinite reservoirs. We employ both the functional renormalization group (FRG) as well as matrix product state techniques, which serve as an accurate benchmark for small systems. Using the FRG, we compute the length- and temperature-dependence of the conductance averaged over 104 samples for lattices as large as 105 sites. We identify regimes in which non-Ohmic power law behavior can be observed and demonstrate that the corresponding exponents can be understood by adapting earlier predictions obtained perturbatively for disordered Luttinger liquids. In the presence of both disorder and isolated impurities, the conductance has a universal single-parameter scaling form. This lays the groundwork for an application of the functional renormalization group to the realm of many-body localization.

  7. Amination of activated carbon for enhancing phenol adsorption: Effect of nitrogen-containing functional groups

    NASA Astrophysics Data System (ADS)

    Yang, Guo; Chen, Honglin; Qin, Hangdao; Feng, Yujun

    2014-02-01

    To study the contribution of different nitrogen-containing functional groups to enhancement of phenol adsorption, the aminated activated carbons (AC) were characterized by N2 adsorption/desorption, XPS, Boehm titration, and pH drift method and tested for adsorption behaviors of phenol. Adsorption isotherm fitting revealed that the Langmuir model was preferred for the aminated ACs. The adsorption capacity per unit surface area (qm/SSABET) was linearly correlated with the amount of pyridinic and pyrrolic N, which suggested that these two functional groups played a critical role in phenol adsorption. The enhancement of adsorption capacity was attributed to the strengthened π-π dispersion between phenol and basal plane of AC by pyridinic, pyrrolic N. The adsorption kinetics was found to follow the pseudo-second-order kinetic model, and intraparticle diffusion was one of the rate-controlling steps in the adsorption process.

  8. Effects of acidic functional groups on dielectric properties of sodium alginates and carrageenans in water.

    PubMed

    Tsubaki, Shuntaro; Hiraoka, Masanori; Hadano, Shingo; Okamura, Kei; Ueda, Tadaharu; Nishimura, Hiroshi; Kashimura, Keiichiro; Mitani, Tomohiko

    2015-01-22

    This study investigated the dielectric properties of sodium alginates and carrageenans in water at frequencies between 100 MHz and 20 GHz in regard to water-hydrocolloid interactions via acidic functional groups. Both sodium alginates and carrageenans showed conduction loss at lower frequencies and dielectric loss at higher frequencies. Reduction and desulfation of sodium alginates and carrageenans, which decreased the numbers of acidic functional groups, decreased their conduction loss. In addition, H(+)-form carrageenans showed the highest ionic conduction. Correlational analysis of dielectric properties and related physical parameters showed that the loss tangent (tanδ) of the hydrocolloid solution was determined by the conductivity of the aqueous solution. Especially at pH below 2, strong H(+) conduction was associated with high tanδ probably due to the Grotthuss mechanism. The molecular dynamics of free water and H(+), viscosity conditions were also suggested to be associated with dielectric property of water-hydrocolloid system. PMID:25439871

  9. Synthesis and physicochemical properties of polysiloxane functionalized with aminoacetic acid groups

    NASA Astrophysics Data System (ADS)

    Lakiza, N. V.; Neudachina, L. K.

    2016-07-01

    Polysiloxane functionalized with aminoacetic acid groups was synthesized using sol-gel technology. Elemental analysis and FTIR spectroscopy were used to determine the composition of the polysiloxane show that it is a mesoporous material with a developed surface (109.4 m2/g). It was found that the selective properties of carboxymethylated polysiloxane towards transition metal ions simultaneously present in an ammonium acetate solution change in the order Zn < Cu > Ni > Co > Pb > Cd. It was shown that the sorption of copper(II) ions by carboxymethylated aminopropylpolysiloxane with particle sizes of 50-71 μm reaches its maximum level within 2 h; the rate-limiting step of the process is the chemical reaction between the ions and the polysiloxane functional groups; and the pseudo-second-order model is the best way of describing sorption.

  10. Group Forces in Instruction: Relationship to Learning. A Student and Teacher Training Program in Small Group Learning Functions.

    ERIC Educational Resources Information Center

    Mack, Richard G.; And Others

    The project's objectives were to increase achievement in mathematics, alter behavior in mathematics classes, and alter attitudes toward small-group work through training in small-group dynamics. The subjects were 85 10th grade geometry students assigned to one of two class periods (morning or afternoon). Within each class period, the students were…

  11. Determination of arterial input function in dynamic susceptibility contrast MRI using group independent component analysis technique

    NASA Astrophysics Data System (ADS)

    Chen, Sharon; Liu, Ho-Ling; Yang, Yihong; Hsu, Yuan-Yu; Chuang, Keh-Shih

    2006-12-01

    Quantification of cerebral blood flow (CBF) with dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) requires the determination of the arterial input function (AIF). The segmentation of surrounding tissue by manual selection is error-prone due to the partial volume artifacts. Independent component analysis (ICA) has the advantage in automatically decomposing the signals into interpretable components. Recently group ICA technique has been applied to fMRI study and showed reduced variance caused by motion artifact and noise. In this work, we investigated the feasibility and efficacy of the use of group ICA technique to extract the AIF. Both simulated and in vivo data were analyzed in this study. The simulation data of eight phantoms were generated using randomized lesion locations and time activity curves. The clinical data were obtained from spin-echo EPI MR scans performed in seven normal subjects. Group ICA technique was applied to analyze data through concatenating across seven subjects. The AIFs were calculated from the weighted average of the signals in the region selected by ICA. Preliminary results of this study showed that group ICA technique could not extract accurate AIF information from regions around the vessel. The mismatched location of vessels within the group reduced the benefits of group study.

  12. Preconversion catalytic deoxygenation of phenolic functional groups. Quarterly report, January 1--March 30, 1996

    SciTech Connect

    Kubiak, C.P.

    1996-12-31

    Over the course of the studies on catalytic deoxygenation of phenolic residues in coal by carbon monoxide, the author performed preliminary investigations into the removal of other heteroatom groups. This report describes the attempted carbonylation of phenyl amido complexes. These studies resulted in the surprisingly facile formation of amidines. The amidine group is the nitrogen analog of carboxylic acids and esters. This functional group combines the properties of an azomethane-like C=N double bond with an amide-like C-N single bond. This group, like the related allyl (C-C-C), aza-allyl (C-N-C), and carboxylato (O-C-O) groups, form a number of transition metal derivatives, with both early and late transition metals. Various bonding modes of the amidino group have been reported. However, most isolated complexes have the amidino ligand as a chelating ligand or bridging two metals. This is due to the preference of amidines to bond via the nitrogen lone pairs, in contrast to the {eta}3 bonding observed in metal-allyl complexes. The experimental section of the paper describes the synthesis of platinum complexes, X-ray diffraction data for one Pt complex, and its reaction with carbon monoxide. Results are presented on the crystal and molecular structure of a platinum complex.

  13. Temporal lobe contribution to perceptual function: A tale of three patient groups.

    PubMed

    Behrmann, M; Lee, A C H; Geskin, J Z; Graham, K S; Barense, M D

    2016-09-01

    There has been growing recognition of the contribution of medial and anterior temporal lobe structures to non-mnemonic functions, such as perception. To evaluate the nature of this contribution, we contrast the perceptual performance of three patient groups, all of whom have a perturbation of these temporal lobe structures. Specifically, we compare the profile of patients with focal hippocampal (HC) lesions, those with more extensive lesions to the medial temporal lobe (MTL) that include HC and perirhinal cortex (PrC), and those with congenital prosopagnosia (CP), whose deficit has been attributed to the disconnection of the anterior temporal lobe from more posterior structures. All participants completed a range of'oddity' tasks in which, on each trial, they determined which of four visual stimuli in a display was the'odd-one-out'. There were five stimulus categories including faces, scenes, objects (high and low ambiguity) and squares of different sizes. Comparisons were conducted separately for the HC, MTL and CP groups against their matched control groups and then the group data were compared to each other directly. The group profiles were easily differentiable. Whereas the HC group stood out for its difficulty in discriminating scenes and the CP group stood out for its disproportionate difficulty in discriminating faces with milder effects for scenes and high ambiguity objects, the MTL group evinced a more general discrimination deficit for faces, scenes and high ambiguity objects. The group differences highlight distinct profiles for each of the three groups and distinguish the signature perceptual impairments following more extended temporal lobe alterations. In the recent reconsideration of the role of the hippocampus and neocortex, Moscovitch and colleagues (Moscovitch et al., 2016) note that the medial temporal lobe structures play a role in non-mnemonic functions, such as perception, problem solving, decision-making and language. Here, we address this

  14. Sum-Rule Conserving Spectral Functions from the Numerical Renormalization Group

    NASA Astrophysics Data System (ADS)

    Weichselbaum, Andreas; von Delft, Jan

    2007-08-01

    We show how spectral functions for quantum impurity models can be calculated very accurately using a complete set of discarded numerical renormalization group eigenstates, recently introduced by Anders and Schiller. The only approximation is to judiciously exploit energy scale separation. Our derivation avoids both the overcounting ambiguities and the single-shell approximation for the equilibrium density matrix prevalent in current methods, ensuring that relevant sum rules hold rigorously and spectral features at energies below the temperature can be described accurately.

  15. β-Diversity of Functional Groups of Woody Plants in a Tropical Dry Forest in Yucatan

    PubMed Central

    López-Martínez, Jorge Omar; Sanaphre-Villanueva, Lucía; Dupuy, Juan Manuel; Hernández-Stefanoni, José Luis; Meave, Jorge Arturo; Gallardo-Cruz, José Alberto

    2013-01-01

    Two main theories have attempted to explain variation in plant species composition (β-diversity). Niche theory proposes that most of the variation is related to environment (environmental filtering), whereas neutral theory posits that dispersal limitation is the main driver of β-diversity. In this study, we first explored how α- and β-diversity of plant functional groups defined by growth form (trees, shrubs and lianas, which represent different strategies of resource partitioning), and dispersal syndrome (autochory, anemochory and zoochory, which represent differences in dispersal limitation) vary with successional age and topographic position in a tropical dry forest. Second, we examined the effects of environmental, spatial, and spatially-structured environmental factors on β-diversity of functional groups; we used the spatial structure of sampling sites as a proxy for dispersal limitation, and elevation, soil properties and forest stand age as indicators of environmental filtering. We recorded 200 species and 22,245 individuals in 276 plots; 120 species were trees, 41 shrubs and 39 lianas. We found that β-diversity was highest for shrubs, intermediate for lianas and lowest for trees, and was slightly higher for zoochorous than for autochorous and anemochorous species. All three dispersal syndromes, trees and shrubs varied in composition among vegetation classes (successional age and topographic position), whilst lianas did not. β-diversity was influenced mostly by proxies of environmental filtering, except for shrubs, for which the influence of dispersal limitation was more important. Stand age and topography significantly influenced α-diversity across functional groups, but showed a low influence on β-diversity –possibly due to the counterbalancing effect of resprouting on plant distribution and composition. Our results show that considering different plant functional groups reveals important differences in both α- and β-diversity patterns and

  16. Two group I ribozymes with different functions in a nuclear rDNA intron.

    PubMed Central

    Decatur, W A; Einvik, C; Johansen, S; Vogt, V M

    1995-01-01

    DiSSU1, a mobile intron in the nuclear rRNA gene of Didymium iridis, was previously reported to contain two independent catalytic RNA elements. We have found that both catalytic elements, renamed GIR1 and GIR2, are group I ribozymes, but with differing functionality. GIR2 carries out the several reactions associated with self-splicing. GIR1 carries out a hydrolysis reaction at an internal processing site (IPS-1). These conclusions are based on the catalytic properties of RNAs transcribed in vitro. Mutation of the P7 pairing segment of GIR2 abrogated self-splicing, while mutation of P7 in GIR1 abrogated hydrolysis at the IPS-1. Much of the P2 stem and all of the associated loop could be deleted without effect on self-splicing. These results are accounted for by a secondary structure model, in which a long P2 pairing segment brings the 5' splice site to the GIR2 catalytic core. GIR1 is the smallest natural group I ribozyme yet reported and is the first example of a group I ribozyme whose presumptive biological function is hydrolysis. We hypothesize that GIR1-mediated cleavage of the excised intron RNA functions in the generation and expression of the mRNA for the intron-encoded endonuclease I-DirI. Images PMID:7556099

  17. Prediction of cloud condensation nuclei activity for organic compounds using functional group contribution methods

    DOE PAGES

    Petters, M. D.; Kreidenweis, S. M.; Ziemann, P. J.

    2016-01-19

    A wealth of recent laboratory and field experiments demonstrate that organic aerosol composition evolves with time in the atmosphere, leading to changes in the influence of the organic fraction to cloud condensation nuclei (CCN) spectra. There is a need for tools that can realistically represent the evolution of CCN activity to better predict indirect effects of organic aerosol on clouds and climate. This work describes a model to predict the CCN activity of organic compounds from functional group composition. Following previous methods in the literature, we test the ability of semi-empirical group contribution methods in Köhler theory to predict themore » effective hygroscopicity parameter, kappa. However, in our approach we also account for liquid–liquid phase boundaries to simulate phase-limited activation behavior. Model evaluation against a selected database of published laboratory measurements demonstrates that kappa can be predicted within a factor of 2. Simulation of homologous series is used to identify the relative effectiveness of different functional groups in increasing the CCN activity of weakly functionalized organic compounds. Hydroxyl, carboxyl, aldehyde, hydroperoxide, carbonyl, and ether moieties promote CCN activity while methylene and nitrate moieties inhibit CCN activity. The model can be incorporated into scale-bridging test beds such as the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) to evaluate the evolution of kappa for a complex mix of organic compounds and to develop suitable parameterizations of CCN evolution for larger-scale models.« less

  18. Surface modification influencing adsorption of red wine constituents: The role of functional groups

    NASA Astrophysics Data System (ADS)

    Mierczynska-Vasilev, Agnieszka; Smith, Paul A.

    2016-11-01

    The adsorption of wine constituents at solid surfaces is important in applications such as filtration and membrane fouling, binding to tanks and fittings and interactions with processing aids such as bentonite. The interaction of wine constituents with surfaces is mediated through adsorbed wine components, where the type of constituents, amount, orientation, and conformation are of consequence for the surface response. This study examines the effect of surface chemical functionalities on the adsorption of red wine constituents. Plasma-polymerized films rich in amine, carboxyl, hydroxyl, formyl and methyl functional groups were generated on solid substrates whereas, glycidyltrimethylammonium chloride was covalently attached to allylamine plasma-polymer modified surface and poly(sodium styrenesulfonate) was electrostatically adsorbed to an amine plasma-polymerized surface. The surface chemical functionalities were characterized by X-ray photoelectron spectroscopy. The ability of different substrates to adsorb red wine constituents was evaluated by quartz crystal microbalance and atomic force microscopy. The results showed that substrates modified with -SO3H and -COOH groups can adsorb more of the wine nitrogen-containing compounds whereas -NH2 and -NR3 groups encourage carbon-containing compounds adsorption. Red wine constituents after filtration were adsorbed in higher extend on -NR3 and -CHO surfaces. The -OH modified surfaces had the lowest ability to absorb wine components.

  19. Microstructures and functional groups of Nannochloropsis sp. cells with arsenic adsorption and lipid accumulation.

    PubMed

    Sun, Jing; Cheng, Jun; Yang, Zongbo; Li, Ke; Zhou, Junhu; Cen, Kefa

    2015-10-01

    The pore structures and surface morphological characteristics of Nannochloropsis sp. cells with arsenic adsorption were initially investigated by N2-adsorption analysis and scanning electronic microscopy. Functional groups of cells were analysed by Fourier-transform infrared spectrometry and X-ray photoelectron spectroscopy. Total surface area of microalgal cells increased from 0.54 m(2)/g to 1.80 m(2)/g upon arsenic adsorption. The external cell surface area increased. More wrinkles and measles-like granules formed on the surfaces as a result of arsenic toxicity. Arsenic ions blocked cell pores and decreased the average pore diameter and total pore volume. Ether cross-linked structures in the algaenan layer of cell walls were disrupted as the percentage of C-O functional groups decreased. These functional groups underwent complexation reactions with arsenic ions. Accumulation of polyunsaturated fatty acids decreased because of oxidative stresses induced by arsenic. The increase in generation of short-chain saturated fatty acids was favourable for the production of quality biodiesel. PMID:26210144

  20. Aspartyl Oxidation Catalysts That Dial In Functional Group Selectivity, along with Regio- and Stereoselectivity

    PubMed Central

    2016-01-01

    A remarkable aspect of enzyme evolution is the portability of catalytic mechanisms for fundamentally different chemical reactions. For example, aspartyl proteases, which contain two active site carboxylic acid groups, catalyze the hydrolysis of amide bonds, while glycosyltransferases (and glycosyl hydrolases), which often also contain two active site carboxylates, have evolved to form (or break) glycosidic bonds. However, neither catalyst exhibits cross-reactivity in the intracellular environment. The large, macromolecular architectures of these biocatalysts tailor their active sites to their precise, divergent functions. The analogous portability of a small-molecule catalyst for truly orthogonal chemical reactivity is rare. Herein, we report aspartic acid containing peptides that can be directed to different sectors of a substrate for which the danger of cross-reactivity looms large. A transiently formed aspartyl peracid catalyst can participate either as an electrophilic oxidant to catalyze alkene epoxidation or as a nucleophilic oxidant to mediate the Baeyer–Villiger oxidation (BVO) of ketones. We show in this study that an appended peptide sequence can dictate the mode of reactivity for this conserved catalytic functional group within a substrate that has the potential to undergo both alkene epoxidation and BVO; in both cases the additional aspects of chemical selectivity (regio- and stereoselectivity) are high. This sequence-dependent tuning of a common catalytic moiety for functional group selective reactions constitutes a biomimetic strategy that may impact late-stage diversification of complex polyfunctional molecules. PMID:27800556

  1. Interpersonal distance regulates functional grouping tendencies of agents in team sports.

    PubMed

    Passos, Pedro; Milho, João; Fonseca, Sofia; Borges, João; Araújo, Duarte; Davids, Keith

    2011-01-01

    The authors examined whether, similar to collective agent behaviors in complex, biological systems (e.g., schools of fish and colonies of ants), performers in team sports displayed functional coordination tendencies, based on local interaction rules during performance. To investigate this issue, they used videogrammetry and digitizing procedures to observe interpersonal interactions in common 4 versus 2 + 2 subphases of the team sport of rugby union, involving 16 participants aged between 16 and 17 years of age. They observed pattern-forming dynamics in attacking subunits (n = 4 players) attempting to penetrate 2 defensive lines (n = 2 players in each). Data showed that within each attacking subunit, the 4 players displayed emergent functional grouping tendencies that differed between the 2 defensive lines. Results confirmed that grouping tendencies in attacking subunits of team games are sensitive to different task constraints, such as relative positioning to nearest defenders. It was concluded that running correlations were particularly useful for measuring the level of interpersonal coordination in functional grouping tendencies within attacking subunits.

  2. Life span and structure of ephemeral root modules of different functional groups from a desert system.

    PubMed

    Liu, Bo; He, Junxia; Zeng, Fanjiang; Lei, Jiaqiang; Arndt, Stefan K

    2016-07-01

    The terminal branch orders of plant root systems have been proposed as short-lived 'ephemeral' modules specialized for resource absorption. The occurrence of ephemeral root modules has so far only been reported for a temperate tree species and it is unclear if the concept also applies to other woody (shrub, tree) and herb species. Fine roots of 12 perennial dicotyledonous herb, shrub and tree species were monitored for two growing seasons using a branch-order classification, sequential sampling and rhizotrons in the Taklamakan desert. Two root modules existed in all three plant functional groups. Among the first five branch orders, the first two (perennial herbs, shrubs) or three (trees) root orders were ephemeral and had a primary anatomical structure, high nitrogen (N) concentrations, high respiration rates and very short life spans of 1-4 months, whereas the last two branch orders in all functional groups were perennial, with thicker diameters, no or collapsed cortex, distinct secondary growth, low N concentrations, low respiration rates, but much longer life spans. Ephemeral, short-lived root modules and long-lived, persistent root modules seem to be a general feature across many plant functional groups and could represent a basic root system design.

  3. Prediction of cloud condensation nuclei activity for organic compounds using functional group contribution methods

    NASA Astrophysics Data System (ADS)

    Petters, M. D.; Kreidenweis, S. M.; Ziemann, P. J.

    2016-01-01

    A wealth of recent laboratory and field experiments demonstrate that organic aerosol composition evolves with time in the atmosphere, leading to changes in the influence of the organic fraction to cloud condensation nuclei (CCN) spectra. There is a need for tools that can realistically represent the evolution of CCN activity to better predict indirect effects of organic aerosol on clouds and climate. This work describes a model to predict the CCN activity of organic compounds from functional group composition. Following previous methods in the literature, we test the ability of semi-empirical group contribution methods in Köhler theory to predict the effective hygroscopicity parameter, kappa. However, in our approach we also account for liquid-liquid phase boundaries to simulate phase-limited activation behavior. Model evaluation against a selected database of published laboratory measurements demonstrates that kappa can be predicted within a factor of 2. Simulation of homologous series is used to identify the relative effectiveness of different functional groups in increasing the CCN activity of weakly functionalized organic compounds. Hydroxyl, carboxyl, aldehyde, hydroperoxide, carbonyl, and ether moieties promote CCN activity while methylene and nitrate moieties inhibit CCN activity. The model can be incorporated into scale-bridging test beds such as the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) to evaluate the evolution of kappa for a complex mix of organic compounds and to develop suitable parameterizations of CCN evolution for larger-scale models.

  4. Magneto-Sensitive Adsorbents Modified by Functional Nitrogen-Containing Groups

    NASA Astrophysics Data System (ADS)

    Melnyk, Inna V.; Gdula, Karolina; Dąbrowski, Andrzej; Zub, Yuriy L.

    2016-02-01

    In order to obtain amino-functionalized silica materials with magnetic core, one-step synthesis was carried out. Several materials, differ in number and structure of amino groups, were synthesized on the basis of sol-gel method. The synthesized materials were examined by several analytical techniques. The presence and content of amino groups were measured by using Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectroscopy and acid-base titration, respectively. Specific surface areas were measured by nitrogen/adsorption desorption isotherms. It was proved that sol-gel approach leads to obtain materials with high content of amino groups built into their surfaces (in the range 1.6-2.7 mmol/g). As-obtained materials were tested as potential adsorbents for copper(II) ions. The received maximum adsorption capacities were in the range 0.4-0.7 mmol/g.

  5. Magneto-Sensitive Adsorbents Modified by Functional Nitrogen-Containing Groups.

    PubMed

    Melnyk, Inna V; Gdula, Karolina; Dąbrowski, Andrzej; Zub, Yuriy L

    2016-12-01

    In order to obtain amino-functionalized silica materials with magnetic core, one-step synthesis was carried out. Several materials, differ in number and structure of amino groups, were synthesized on the basis of sol-gel method. The synthesized materials were examined by several analytical techniques. The presence and content of amino groups were measured by using Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectroscopy and acid-base titration, respectively. Specific surface areas were measured by nitrogen/adsorption desorption isotherms. It was proved that sol-gel approach leads to obtain materials with high content of amino groups built into their surfaces (in the range 1.6-2.7 mmol/g). As-obtained materials were tested as potential adsorbents for copper(II) ions. The received maximum adsorption capacities were in the range 0.4-0.7 mmol/g. PMID:26842794

  6. Synthesis and characterization of bifunctional surfaces with tunable functional group pairs

    NASA Astrophysics Data System (ADS)

    Galloway, John M.; Kung, Mayfair; Kung, Harold H.

    2016-06-01

    Grafting of pairs of functional groups onto a silica surface was demonstrated by tethering both terminals of an organochlorosilane precursor molecule, Cl2(CH3)Si(CH2)4(CO)(OSi(i-Pr)2)(CH2)2Si(CH3)Cl2, that possess a cleavable silyl ester bond, onto a silica surface. Hydrolytic cleavage of the silyl ester bond of the grafted molecule resulted in the generation of organized pairs of carboxylic acid and organosilanol groups. This organosilanol moiety was easily transformed into other functional groups through condensation reactions to form, together with the neighboring acid group, pairs such as carboxylic acid/secondary amine, carboxylic acid/pyridine, and carboxylic acid/phosphine. In the case of carboxylic acid/amine pairing, there was evidence of the formation of amide. A sample grafted with amine-carboxylic acid pairs was three times more active (per free amine) than a sample without such pairs for the nitroaldol condensation of 4-nitrobenzaldehyde and nitromethane.

  7. Sulfhydryl-group modifications of Torpedo Californica acetylcholine receptor: subunit localization and effects on function

    SciTech Connect

    McNamee, M.G.; Yee, A.S.

    1986-05-01

    The effects of thiol-group modification on acetylcholine receptor (ACHR) function were measured using purified Torpedo ACHR reconstituted into soybean lipid vesicles. N-Phenyl-maleimide (NPM) was used to modify sulfhydryl groups in ACHR in the absence of any prior reduction by dithiotheitol. Modification by NPM led to the inhibition of ion channel activity without a detectable effect on ligand binding. The ion flux inhibition by NPM primarily affected channel activation, since the initial rates of activation decreased over a wide range of carbamylcholine concentrations. The /sup 3/H-NPM subunit labelling pattern of ACHR (a multisubunit membrane protein with ..cap alpha../sub 2/..beta gamma..delta stoichiometry) revealed preferential labelling of the ..gamma.. subunit. At high NPM concentration, the number of sulfhydryl groups on the ..gamma.. subunit that could be modified with NPM was two. Detergent was required during labelling for functionally relevant thiol group modifications, and most of the label was protected from protease digestion in the reconstituted membranes. These results are consistent with the presence of the NPM modification in a bilayer and/or cytoplasmic domain. Analysis of cyanogen bromide and trypsin fragments indicates that the labeled cysteines may be located in the postulated amphipathic helix region of the ..gamma.. subunit.

  8. Molecular weight distribution and functional group profiles of TEMPO-oxidized lyocell fibers.

    PubMed

    Milanovic, Jovana; Schiehser, Sonja; Milanovic, Predrag; Potthast, Antje; Kostic, Mirjana

    2013-10-15

    The effects of TEMPO-mediated oxidation, performed with NaClO, a catalytic amount of NaBr, and 2,2',6,6'-tetramethylpiperidine-1-oxy radical (TEMPO), were studied on lyocell fibers by means of GPC using multiple detection and group-selective fluorescence labeling according to the CCOA and FDAM methodology. The applied method determines functional group content as a sum parameter, as well as functional group profiles in relation to the molecular weight of the cellulose fibers. Both the CHO and COOH profiles, as well as molecular weight alterations, were analyzed. A significant decrease in the average molecular weight was obtained during the first hour of TEMPO-mediated oxidation, but prolonged oxidation time resulted in no strong additional chain scission. Significant amounts of COOH groups were introduced in the high molecular weight fractions by the oxidation with higher concentrations of NaClO (2.42-9.67 mmol NaClO/g fiber) after modification times of 1h or longer.

  9. Click chemistry: a new facile and efficient strategy for the preparation of Fe3O4 nanoparticles covalently functionalized with IDA-Cu and their application in the depletion of abundant protein in blood samples

    NASA Astrophysics Data System (ADS)

    Jian, Guiqin; Liu, Yuxing; He, Xiwen; Chen, Langxing; Zhang, Yukui

    2012-09-01

    In this study, we report a novel method to synthesize core-shell structured Fe3O4 nanoparticles (NPs) covalently functionalized with iminodiacetic acid (IDA) via click chemistry between the azide and alkyne groups and charged with Cu2+. Firstly, the Fe3O4@SiO2 NPs were obtained using tetraethoxysilane (TEOS) to form a silica shell on the surface of the Fe3O4 core. The azide group-modified Fe3O4@SiO2 NPs were obtained by a sol-gel process using 3-azidopropyltriethoxysilane (AzPTES) as the silane agent. Fe3O4@SiO2-N3 was directly reacted with N-propargyl iminodiacetic via click chemistry, in the presence of a Cu(I) catalyst, to acquire the IDA-modified Fe3O4 NPs. Finally, through the addition of Cu2+, the Fe3O4@SiO2-IDA-Cu NP product was obtained. The morphology, structure and composition of the NPs were characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The resulting NPs showed a strong magnetic response to an externally applied magnetic field, a high adsorption capacity and excellent specificity towards hemoglobin (Hb). In addition, the Fe3O4@SiO2-IDA-Cu NPs can be used for the selective removal of abundant Hb protein in bovine and human blood samples.

  10. Analysis of functional groups in atmospheric aerosols by infrared spectroscopy: sparse methods for statistical selection of relevant absorption bands

    NASA Astrophysics Data System (ADS)

    Takahama, Satoshi; Ruggeri, Giulia; Dillner, Ann M.

    2016-07-01

    Various vibrational modes present in molecular mixtures of laboratory and atmospheric aerosols give rise to complex Fourier transform infrared (FT-IR) absorption spectra. Such spectra can be chemically informative, but they often require sophisticated algorithms for quantitative characterization of aerosol composition. Naïve statistical calibration models developed for quantification employ the full suite of wavenumbers available from a set of spectra, leading to loss of mechanistic interpretation between chemical composition and the resulting changes in absorption patterns that underpin their predictive capability. Using sparse representations of the same set of spectra, alternative calibration models can be built in which only a select group of absorption bands are used to make quantitative prediction of various aerosol properties. Such models are desirable as they allow us to relate predicted properties to their underlying molecular structure. In this work, we present an evaluation of four algorithms for achieving sparsity in FT-IR spectroscopy calibration models. Sparse calibration models exclude unnecessary wavenumbers from infrared spectra during the model building process, permitting identification and evaluation of the most relevant vibrational modes of molecules in complex aerosol mixtures required to make quantitative predictions of various measures of aerosol composition. We study two types of models: one which predicts alcohol COH, carboxylic COH, alkane CH, and carbonyl CO functional group (FG) abundances in ambient samples based on laboratory calibration standards and another which predicts thermal optical reflectance (TOR) organic carbon (OC) and elemental carbon (EC) mass in new ambient samples by direct calibration of infrared spectra to a set of ambient samples reserved for calibration. We describe the development and selection of each calibration model and evaluate the effect of sparsity on prediction performance. Finally, we ascribe

  11. Ecology of Ephemeroptera, Plecoptera and Trichoptera (Insecta) in Rivers of the Gunung Jerai Forest Reserve: Diversity and Distribution of Functional Feeding Groups

    PubMed Central

    Hamid, Suhaila Ab; Md Rawi, Che Salmah

    2014-01-01

    A field study was performed to describe the functional feeding groups (FFGs) of Ephemeroptera, Plecoptera and Trichoptera (EPT) in the Tupah, Batu Hampar and Teroi Rivers in the Gunung Jerai Forest Reserve (GJFR), Kedah, Malaysia. Twenty-nine genera belonging to 19 families were identified. The EPTs were classified into five FFGs: collector-gatherers (CG), collector-filterers (CF), shredders (SH), scrapers (SC) and predators (P). In this study, CG and CF were the dominant groups inhabiting all three rivers. Ephemeroptera dominated these rivers due to their high abundance, and they were also the CG (90.6%). SC were the lowest in abundance among all groups. Based on the FFGs, the Teroi River was suitable for CG, whereas the Tupah and Batu Hampar Rivers were suitable for CG and CF. The distribution of FFGs differed among the rivers (CG, χ2 = 23.6, p = 0.00; SH, χ2 = 10.02, p = 0.007; P, χ2 = 25.54, p = 0.00; CF, χ2 = 21.95, p = 0.00; SC, χ2 = 9.31, p = 0.01). These findings indicated that the FFGs found in rivers of the GJFR represent high river quality. PMID:25210588

  12. Functional group composition of organic aerosol from combustion emissions and secondary processes at two contrasted urban environments

    NASA Astrophysics Data System (ADS)

    El Haddad, Imad; Marchand, Nicolas; D'Anna, Barbara; Jaffrezo, Jean Luc; Wortham, Henri

    2013-08-01

    The quantification of major functional groups in atmospheric organic aerosol (OA) provides a constraint on the types of compounds emitted and formed in atmospheric conditions. This paper presents functional group composition of organic aerosol from two contrasted urban environments: Marseille during summer and Grenoble during winter. Functional groups were determined using a tandem mass spectrometry approach, enabling the quantification of carboxylic (RCOOH), carbonyl (RCOR‧), and nitro (RNO2) functional groups. Using a multiple regression analysis, absolute concentrations of functional groups were combined with those of organic carbon derived from different sources in order to infer the functional group contents of different organic aerosol fractions. These fractions include fossil fuel combustion emissions, biomass burning emissions and secondary organic aerosol (SOA). Results clearly highlight the differences between functional group fingerprints of primary and secondary OA fractions. OA emitted from primary sources is found to be moderately functionalized, as about 20 carbons per 1000 bear one of the functional groups determined here, whereas SOA is much more functionalized, as in average 94 carbons per 1000 bear a functional group under study. Aging processes appear to increase both RCOOH and RCOR‧ functional group contents by nearly one order of magnitude. Conversely, RNO2 content is found to decrease with photochemical processes. Finally, our results also suggest that other functional groups significantly contribute to biomass smoke and SOA. In particular, for SOA, the overall oxygen content, assessed using aerosol mass spectrometer measurements by an O:C ratio of 0.63, is significantly higher than the apparent O:C* ratio of 0.17 estimated based on functional groups measured here. A thorough examination of our data suggests that this remaining unexplained oxygen content can be most probably assigned to alcohol (ROH), organic peroxides (ROOH

  13. Rates of N2 production and diversity and abundance of functional genes associated with denitrification and anaerobic ammonium oxidation in the sediment of the Amundsen Sea Polynya, Antarctica

    NASA Astrophysics Data System (ADS)

    Choi, Ayeon; Cho, Hyeyoun; Kim, Sung-Han; Thamdrup, Bo; Lee, SangHoon; Hyun, Jung-Ho

    2016-01-01

    A combination of molecular microbiological analyses and metabolic rate measurements was conducted to elucidate the diversity and abundance of denitrifying and anaerobic ammonium oxidation (anammox) bacteria and the nitrogen gas (N2) production rates in sediment underlying the highly productive polynya (Stns. 10 and 17) and the sea-ice zone on the outer shelf (Stn. 83) of the Amundsen Sea, Antarctica. Despite the high water column productivity, the N2 production rates by denitrification (0.04-0.31 nmol N cm-3sed. h-1) and anammox (0.13-0.26 nmol N cm-3 sed. h-1) were lower than those measured in other polar regions. In contrast, gene copy number (106-107 copies cm-3 of nirS and nosZ genes targeting denitirifiers and 105-107 copies cm-3 of 16S rRNA genes related to anammox bacteria) of the two bacterial groups at Stn. 17 was similar compared to those of other organic-rich environments. The majority of the nirS sequences were affiliated with Gammaproteobacteria (54% and 61% of the total nirS gene at Stns. 17 and 83, respectively), which were closely related to Pseudomonas aeruginosa. Most nosZ sequences (92% and 72% of the total nosZ genes at Stns. 17 and 83, respectively) were related to the Alphaproteobacteria, which were closely related to Ruegeria pomeroyi and Roseobacter denitrificans. Most (98%) of the sequences related to anammox bacteria were affiliated with Candidatus Scalindua at Stn. 17. Consequently, despite the low metabolic activity, the abundance and composition of most denitrifying and anammox bacteria detected from the ASP were similar to those reported from a variety of marine environments. Our results further imply that increased labile organic matter production resulting from a shift of the phytoplankton community from Phaeocystis to diatoms in response to rapid melting of sea ice stimulates metabolic activities of the denitrifying and anammox bacteria, thereby enhancing the N removal process in the ASP.

  14. A meta‐analysis of functional group responses to forest recovery outside of the tropics

    PubMed Central

    Ezard, Thomas H. G.; Martin, Philip A.; Newton, Adrian C.; Doncaster, C. Patrick

    2015-01-01

    Abstract Both active and passive forest restoration schemes are used in degraded landscapes across the world to enhance biodiversity and ecosystem service provision. Restoration is increasingly also being implemented in biodiversity offset schemes as compensation for loss of natural habitat to anthropogenic development. This has raised concerns about the value of replacing old‐growth forest with plantations, motivating research on biodiversity recovery as forest stands age. Functional diversity is now advocated as a key metric for restoration success, yet it has received little analytical attention to date. We conducted a meta‐analysis of 90 studies that measured differences in species richness for functional groups of fungi, lichens, and beetles between old‐growth control and planted or secondary treatment forests in temperate, boreal, and Mediterranean regions. We identified functional‐group–specific relationships in the response of species richness to stand age after forest disturbance. Ectomycorrhizal fungi averaged 90 years for recovery to old‐growth values (between 45 years and unrecoverable at 95% prediction limits), and epiphytic lichens took 180 years to reach 90% of old‐growth values (between 140 years and never for recovery to old‐growth values at 95% prediction limits). Non‐saproxylic beetle richness, in contrast, decreased as stand age of broadleaved forests increased. The slow recovery by some functional groups essential to ecosystem functioning makes old‐growth forest an effectively irreplaceable biodiversity resource that should be exempt from biodiversity offsetting initiatives. PMID:26040756

  15. Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides

    PubMed Central

    Prentice, Boone M.; Gilbert, Joshua D.; Stutzman, John R.; Forrest, William P.; McLuckey, Scott A.

    2012-01-01

    Gas-phase modification of carboxylic acid functionalities is performed via ion/ion reactions with carbodiimide reagents [N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide (CMC) and [3-(3-Ethylcarbodiimide-1-yl)propyl]trimethylaminium (ECPT). Gas-phase ion/ion covalent chemistry requires the formation of a long-lived complex. In this instance, the complex is stabilized by an electrostatic interaction between the fixed charge quaternary ammonium group of the carbodiimide reagent cation and the analyte dianion. Subsequent activation results in characteristic loss of an isocyanate derivative from one side of the carbodiimide functionality, a signature for this covalent chemistry. The resulting amide bond is formed on the analyte at the site of the original carboxylic acid. Reactions involving analytes that do not contain available carboxylic acid groups (e.g., they have been converted to sodium salts) or reagents that do not have the carbodiimide functionality do not undergo a covalent reaction. This chemistry is demonstrated using PAMAM generation 0.5 dendrimer, ethylenediaminetetraacetic acid (EDTA), and the model peptide DGAILDGAILD. This work demonstrates the selective gas-phase covalent modification of carboxylic acid functionalities. PMID:23208744

  16. Various fates of neuronal progenitor cells observed on several different chemical functional groups

    NASA Astrophysics Data System (ADS)

    Liu, Xi; Wang, Ying; He, Jin; Wang, Xiu-Mei; Cui, Fu-Zhai; Xu, Quan-Yuan

    2011-12-01

    Neuronal progenitor cells cultured on gold-coated glass surfaces modified by different chemical functional groups, including hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), bromo (-Br), mercapto (-SH), - Phenyl and methyl (-CH3), were studied here to investigate the influence of surface chemistry on the cells' adhesion, morphology, proliferation and functional gene expression. Focal adhesion staining indicated in the initial culture stage cells exhibited morphological changes in response to different chemical functional groups. Cells cultured on -NH2 grafted surface displayed focal adhesion plaque and flattened morphology and had the largest contact area. However, their counter parts on -CH3 grafted surface displayed no focal adhesion and rounded morphology and had the smallest contact area. After 6 days culture, the proliferation trend was as follows: -NH2 > -SH> -COOH> - Phenyl > - Br > -OH> -CH3. To determine the neural functional properties of the cells affected by surface chemistry, the expression of glutamate decarboxylase (GAD67), nerve growth factor (NGF) and brainderived neurotrophic factor (BDNF) were characterized. An increase of GAD67 expression was observed on -NH2, -COOH and -SH grafted surfaces, while no increase in NGF and BDNF expression was observed on any chemical surfaces. These results highlight the importance of surface chemistry in the fate determination of neuronal progenitor cells, and suggest that surface chemistry must be considered in the design of biomaterials for neural tissue engineering.

  17. 14 CFR Section 11 - Functional Classification-Operating Expenses of Group II and Group III Air Carriers

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... operations and the maintenance and repair of property and equipment of all types and classes, regardless of... periodic maintenance operations and the maintenance and repair of property and equipment of all types and... in function 5400 Maintenance, or function 6400 Aircraft and Traffic Servicing. 5400Maintenance....

  18. Galaxies in ΛCDM with Halo Abundance Matching: Luminosity-Velocity Relation, Baryonic Mass-Velocity Relation, Velocity Function, and Clustering

    NASA Astrophysics Data System (ADS)

    Trujillo-Gomez, Sebastian; Klypin, Anatoly; Primack, Joel; Romanowsky, Aaron J.

    2011-11-01

    It has long been regarded as difficult if not impossible for a cosmological model to account simultaneously for the galaxy luminosity, mass, and velocity distributions. We revisit this issue using a modern compilation of observational data along with the best available large-scale cosmological simulation of dark matter (DM). We find that the standard cosmological model, used in conjunction with halo abundance matching (HAM) and simple dynamical corrections, fits—at least on average—all basic statistics of galaxies with circular velocities V circ > 80 km s-1 calculated at a radius of ~10 kpc. Our primary observational constraint is the luminosity-velocity (LV) relation—which generalizes the Tully-Fisher and Faber-Jackson relations in allowing all types of galaxies to be included, and provides a fundamental benchmark to be reproduced by any theory of galaxy formation. We have compiled data for a variety of galaxies ranging from dwarf irregulars to giant ellipticals. The data present a clear monotonic LV relation from ~50 km s-1 to ~500 km s-1, with a bend below ~80 km s-1 and a systematic offset between late- and early-type galaxies. For comparison to theory, we employ our new ΛCDM "Bolshoi" simulation of DM, which has unprecedented mass and force resolution over a large cosmological volume, while using an up-to-date set of cosmological parameters. We use HAM to assign rank-ordered galaxy luminosities to the DM halos, a procedure that automatically fits the empirical luminosity function and provides a predicted LV relation that can be checked against observations. The adiabatic contraction of DM halos in response to the infall of the baryons is included as an optional model ingredient. The resulting predictions for the LV relation are in excellent agreement with the available data on both early-type and late-type galaxies for the luminosity range from Mr = -14 to Mr = -22. We also compare our predictions for the "cold" baryon mass (i.e., stars and cold gas) of

  19. Renormalization group improved computation of correlation functions in theories with nontrivial phase diagram

    NASA Astrophysics Data System (ADS)

    Codello, Alessandro; Tonero, Alberto

    2016-07-01

    We present a simple and consistent way to compute correlation functions in interacting theories with nontrivial phase diagram. As an example we show how to consistently compute the four-point function in three dimensional Z2 -scalar theories. The idea is to perform the path integral by weighting the momentum modes that contribute to it according to their renormalization group (RG) relevance, i.e. we weight each mode according to the value of the running couplings at that scale. In this way, we are able to encode in a loop computation the information regarding the RG trajectory along which we are integrating. We show that depending on the initial condition, or initial point in the phase diagram, we obtain different behaviors of the four-point function at the endpoint of the flow.

  20. Sequential Linker Installation: Precise Placement of Functional Groups in Multivariate Metal-Organic Frameworks

    SciTech Connect

    Yuan, S; Lu, WG; Chen, YP; Zhang, Q; Liu, TF; Feng, DW; Wang, X; Qin, JS; Zhou, HC

    2015-03-11

    A unique strategy, sequential linker installation (SLI), has been developed to construct multivariate MOFs with functional groups precisely positioned. PCN-700, a Zr-MOF with eight-connected Zr6O4(OH)(8)(H2O)(4) clusters, has been judiciously designed; the Zr-6 clusters in this MOF are arranged in such a fashion that, by replacement of terminal OH-/H2O ligands, subsequent insertion of linear dicarboxylate linkers is achieved. We demonstrate that linkers with distinct lengths and functionalities can be sequentially installed into PCN-700. Single-crystal to single-crystal transformation is realized so that the positions of the subsequently installed linkers are pinpointed via single-crystal X-ray diffraction analyses. This methodology provides a powerful tool to construct multivariate MOFs with precisely positioned functionalities in the desired proximity, which would otherwise be difficult to achieve.

  1. C-H Coupling Reactions Directed by Sulfoxides: Teaching an Old Functional Group New Tricks.

    PubMed

    Pulis, Alexander P; Procter, David J

    2016-08-16

    Sulfoxides are classical functional groups for directing the stoichiometric metalation and functionalization of C-H bonds. In recent times, sulfoxides have been given a new lease on life owing to the development of modern synthetic methods that have arisen because of their unique reactivity. They have recently been used in catalytic C-H activation proceeding via coordination of an internal sulfoxide to a metal or through the action of an external sulfoxide ligand. Furthermore, sulfoxides are able to capture nucleophiles and electrophiles to give sulfonium salts, which subsequently enable the formation of C-C bonds at the expense of C-H bonds. This Review summarizes a renaissance period in the application of sulfoxides arising from their versatility in directing C-H functionalization. PMID:27409984

  2. Star Formation as a Function of Neutral Hydrogen Gas Density in Local Group Galaxies

    NASA Astrophysics Data System (ADS)

    Carlson, Erika K.; Madore, Barry F.; Freedman, Wendy L.

    2016-06-01

    We present a study of the efficiency and timescales of star formation as a function of local neutral hydrogen gas density in four Local Group galaxies: M33, NGC 6822, the LMC, and the SMC. In this work, we conceptualize the process of star formation as a cycle of two major phases - (1) a gas dynamics phase in which neutral hydrogen gas coalesces into clouds, and (2) a stellar phase in which stars have formed and interrupt further gas coalescence during their active lifetimes. By examining the spatial distribution and number densities of stars on maps of neutral hydrogen, we estimate the timescale of the gas coalescence phase relative to the timescale of the stellar phase and infer an efficiency of star formation as a function of neutral hydrogen gas density. From these timescales and efficiencies, we will calculate star formation rates as a function of neutral hydrogen gas density in these galaxies.

  3. Knock-down of transcript abundance of a family of Kunitz proteinase inhibitor genes in white clover (Trifolium repens) reveals a redundancy and diversity of gene function.

    PubMed

    Islam, Afsana; Leung, Susanna; Burgess, Elisabeth P J; Laing, William A; Richardson, Kim A; Hofmann, Rainer W; Dijkwel, Paul P; McManus, Michael T

    2015-12-01

    The transcriptional regulation of four phylogenetically distinct members of a family of Kunitz proteinase inhibitor (KPI) genes isolated from white clover (Trifolium repens; designated Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5) has been investigated to determine their wider functional role. The four genes displayed differential transcription during seed germination, and in different tissues of the mature plant, and transcription was also ontogenetically regulated. Heterologous over-expression of Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5 in Nicotiana tabacum retarded larval growth of the herbivore Spodoptera litura, and an increase in the transcription of the pathogenesis-related genes PR1 and PR4 was observed in the Tr-KPI1 and Tr-KPI4 over-expressing lines. RNA interference (RNAi) knock-down lines in white clover displayed significantly altered vegetative growth phenotypes with inhibition of shoot growth and a stimulation of root growth, while knock-down of Tr-KPI1, Tr-KPI2 and Tr-KPI5 transcript abundance also retarded larval growth of S. litura. Examination of these RNAi lines revealed constitutive stress-associated phenotypes as well as altered transcription of cellular signalling genes. These results reveal a functional redundancy across members of the KPI gene family. Further, the regulation of transcription of at least one member of the family, Tr-KPI2, may occupy a central role in the maintenance of a cellular homeostasis.

  4. Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid

    PubMed Central

    Wei, Wen-Hua; Guo, Yunfei; Kindt, Alida S.D.; Merriman, Tony R.; Semple, Colin A.; Wang, Kai; Haley, Chris S.

    2014-01-01

    Human serum uric acid concentration (SUA) is a complex trait. A recent meta-analysis of multiple genome-wide association studies (GWAS) identified 28 loci associated with SUA jointly explaining only 7.7% of the SUA variance, with 3.4% explained by two major loci (SLC2A9 and ABCG2). Here we examined whether gene–gene interactions had any roles in regulating SUA using two large GWAS cohorts included in the meta-analysis [the Atherosclerosis Risk in Communities study cohort (ARIC) and the Framingham Heart Study cohort (FHS)]. We found abundant genome-wide significant local interactions in ARIC in the 4p16.1 region located mostly in an intergenic area near SLC2A9 that were not driven by linkage disequilibrium and were replicated in FHS. Taking the forward selection approach, we constructed a model of five SNPs with marginal effects and three epistatic SNP pairs in ARIC—three marginal SNPs were located within SLC2A9 and the remaining SNPs were all located in the nearby intergenic area. The full model explained 1.5% more SUA variance than that explained by the lead SNP alone, but only 0.3% was contributed by the marginal and epistatic effects of the SNPs in the intergenic area. Functional analysis revealed strong evidence that the epistatically interacting SNPs in the intergenic area were unusually enriched at enhancers active in ENCODE hepatic (HepG2, P = 4.7E−05) and precursor red blood (K562, P = 5.0E−06) cells, putatively regulating transcription of WDR1 and SLC2A9. These results suggest that exploring epistatic interactions is valuable in uncovering the complex functional mechanisms underlying the 4p16.1 region. PMID:24821702

  5. Functionalized quantum dots induce proinflammatory responses in vitro: the role of terminal functional group-associated endocytic pathways

    NASA Astrophysics Data System (ADS)

    Zhang, Yijuan; Pan, Hong; Zhang, Pengfei; Gao, Ningning; Lin, Yi; Luo, Zichao; Li, Ping; Wang, Ce; Liu, Lanlan; Pang, Daiwen; Cai, Lintao; Ma, Yifan

    2013-06-01

    PEGylation has been applied as an effective strategy of surface functionalization to improve the stability and reduce non-specific binding of quantum dots (QDs). However, its effects on the proinflammatory properties of QDs and the underlying mechanism have not been well elucidated yet. Herein, the proinflammatory effects of PEGylated CdSe/ZnS QDs with an amphiphilic polymer coating (PEG-pQDs) were investigated in human pulmonary epithelial cells and macrophages by evaluating the cytokine/chemokine production. The results showed that the proinflammatory effects of PEG-pQDs were strongly associated with the functional groups (-COOH, -NH2, -OH, and -OCH3) at the end of PEG chain. COOH-PEG-pQDs demonstrated the most proinflammatory effects followed by NH2-PEG-pQDs and HO-PEG-pQDs with CH3O-PEG-pQDs exhibiting the least proinflammatory effects. The proinflammatory effects of PEG-pQDs relied on lipid raft- and class A scavenger receptor (SRA)-dependent endocytic pathways as well as the downstream NF-κB and MAPK signaling cascades. COOH-PEG-pQDs were selectively internalized by lipid raft- and SRA-mediated endocytosis, which consequently activated NF-κB signaling pathway. On the other hand, NH2-PEG-pQDs and HO-PEG-pQDs were mostly internalized via lipid raft-mediated endocytosis, thereby activating p38 MAPK/AP-1 signaling cascades. These data revealed a critical role of terminal functional group-associated endocytic pathways in the proinflammatory responses induced by PEGylated QDs in human pulmonary epithelial cells and macrophages.PEGylation has been applied as an effective strategy of surface functionalization to improve the stability and reduce non-specific binding of quantum dots (QDs). However, its effects on the proinflammatory properties of QDs and the underlying mechanism have not been well elucidated yet. Herein, the proinflammatory effects of PEGylated CdSe/ZnS QDs with an amphiphilic polymer coating (PEG-pQDs) were investigated in human pulmonary epithelial

  6. Late embryogenesis abundant proteins

    PubMed Central

    Olvera-Carrillo, Yadira; Reyes, José Luis

    2011-01-01

    Late Embryogenesis Abundant (LEA) proteins accumulate at the onset of seed desiccation and in response to water deficit in vegetative plant tissues. The typical LEA proteins are highly hydrophilic and intrinsically unstructured. They have been classified in different families, each one showing distinctive conserved motifs. In this manuscript we present and discuss some of the recent findings regarding their role in plant adaptation to water deficit, as well as those concerning to their possible function, and how it can be related to their intrinsic structural flexibility. PMID:21447997

  7. Water Desalination through Zeolitic Imidazolate Framework Membranes: Significant Role of Functional Groups.

    PubMed

    Gupta, Krishna M; Zhang, Kang; Jiang, Jianwen

    2015-12-01

    A molecular simulation study is reported for water desalination through five zeolitic imidazolate framework (ZIF) membranes, namely ZIF-25, -71, -93, -96, and -97. The five ZIFs possess identical rho-topology but differ in functional groups. The rejection of salt (NaCl) is found to be around 97% in ZIF-25, and 100% in the other four ZIFs. The permeance ranges from 27 to 710 kg/(m(2)·h·bar), about one∼two orders of magnitude higher compared with commercial reverse osmosis membranes. Due to a larger aperture size da, ZIF-25, -71, and -96 exhibit a much higher water flux than ZIF-93 and -97; however, the flux in ZIF-25, -71, and -96 is governed by the polarity of functional group rather than da. With the hydrophobic CH3 group, ZIF-25 has the highest flux despite the smallest da among ZIF-25, -71, and -96. The lifetime of hydrogen bonding in ZIF-25 is shorter than that in ZIF-71 and -96. Furthermore, water molecules undergo a fast flushing motion in ZIF-25, but frequent jumping in ZIF-96 and particularly in ZIF-97. An Arrhenius-type relationship is found between water flux in ZIF-25 and temperature, and the activation energy is predicted to be 6.5 kJ/mol. This simulation study provides a microscopic insight into water desalination in a series of ZIFs, reveals the key factors (aperture size and polarity of functional group) governing water flux, and suggests that ZIF-25 might be an interesting reverse osmosis membrane for high-performance water desalination.

  8. Comparison of statistical tests for group differences in brain functional networks.

    PubMed

    Kim, Junghi; Wozniak, Jeffrey R; Mueller, Bryon A; Shen, Xiaotong; Pan, Wei

    2014-11-01

    Brain functional connectivity has been studied by analyzing time series correlations in regional brain activities based on resting-state fMRI data. Brain functional connectivity can be depicted as a network or graph defined as a set of nodes linked by edges. Nodes represent brain regions and an edge measures the strength of functional correlation between two regions. Most of existing work focuses on estimation of such a network. A key but inadequately addressed question is how to test for possible differences of the networks between two subject groups, say between healthy controls and patients. Here we illustrate and compare the performance of several state-of-the-art statistical tests drawn from the neuroimaging, genetics, ecology and high-dimensional data literatures. Both real and simulated data were used to evaluate the methods. We found that Network Based Statistic (NBS) performed well in many but not all situations, and its performance critically depends on the choice of its threshold parameter, which is unknown and difficult to choose in practice. Importantly, two adaptive statistical tests called adaptive sum of powered score (aSPU) and its weighted version (aSPUw) are easy to use and complementary to NBS, being higher powered than NBS in some situations. The aSPU and aSPUw tests can also be applied to adjust for covariates. Between the aSPU and aSPUw tests, they often, but not always, performed similarly with neither one as a uniform winner. On the other hand, Multivariate Matrix Distance Regression (MDMR) has been applied to detect group differences for brain connectivity; with the usual choice of the Euclidean distance, MDMR is a special case of the aSPU test. Consequently NBS, aSPU and aSPUw tests are recommended to test for group differences in functional connectivity. PMID:25086298

  9. Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology.

    PubMed

    Isabelle, Boulangeat; Pauline, Philippe; Sylvain, Abdulhak; Roland, Douzet; Luc, Garraud; Sébastien, Lavergne; Sandra, Lavorel; Jérémie, Van Es; Pascal, Vittoz; Wilfried, Thuiller

    2012-11-01

    The pace of on-going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid-DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process-based models, are able to involve an intermediate number of well-chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid-DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid-DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling. PMID:24403847

  10. Tree Diametric Increment and Litterfall Production in an Eastern Amazonian Forest: the Role of Functional Groups

    NASA Astrophysics Data System (ADS)

    Camargo, P. B. D.; Ferreira, M. L.; Oliveira Junior, R. C.; Saleska, S. R.

    2014-12-01

    Tree growth is a biotic variable of great importance in understanding the dynamics of tree communities and may be used as a tool in studies of biological or climate modeling. Some climate models predict more recurrent climate anomalies in this century, which may alter the functioning of tropical forests with serious structural and demographic implications. The present study aimed to evaluate the profile of tree growth and litterfall production in an eastern Amazon forest, which has suffered recent climatic disturbances. We contrasted different functional groups based on wood density (stem with 0.55; 0.56-0.7; >0.7 g cm-3), light availability (crown illumination index; high illuminated crown - IIC1 until shaded crown - IIC5), and, size class (trees 10-22.5; 22.6-35; 35.1-55; 55,1-90; >90 cm dbh). Tree diameter increment was monthly measured from November 2011 to September 2013 by using dendrometer bands installed on 850 individuals from different families. Litterfall was collected in 64 circular traps, oven dried and weighed, separated into leaves, twigs, reproductive parts and miscellaneous. During the rainy season the sampled trees had the highest rates of tree diametric increment. When analyzing the data by functional groups, large trees had faster growth, but when grouped by wood density, trees with wood density up to 0.55 and between 0.56 and 0.7 g cm-3 had the fastest rates of growth. When grouped by crown illumination index, trees exposed to higher levels of light grew more in comparison to partially shaded trees. Maximum daily air temperature and precipitation were the most important environmental variables in determining the diametric increment profile of the trees. Litterfall production was estimated to be 7.1 Mg ha-1.year-1 and showed a strong seasonal pattern, with dry season production being higher than in the rainy season. Leaves formed the largest fraction of the litterfall, followed by twigs, reproductive parts, and finally miscellaneous. These

  11. Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications

    PubMed Central

    Wang, Wei; Qin, Jiang-Jiang; Voruganti, Sukesh; Nag, Subhasree; Zhou, Jianwei; Zhang, Ruiwen

    2016-01-01

    Polycomb group (PcG) proteins are transcriptional repressors that regulate several crucial developmental and physiological processes in the cell. More recently, they have been found to play important roles in human carcinogenesis and cancer development and progression. The deregulation and dysfunction of PcG proteins often lead to blocking or inappropriate activation of developmental pathways, enhancing cellular proliferation, inhibiting apoptosis, and increasing the cancer stem cell population. Genetic and molecular investigations of PcG proteins have long been focused on their PcG functions. However, PcG proteins have recently been shown to exert non-polycomb functions, contributing to the regulation of diverse cellular functions. We and others have demonstrated that PcG proteins regulate the expression and function of several oncogenes and tumor suppressor genes in a PcG-independent manner, and PcG proteins are associated with the survival of patients with cancer. In this review, we summarize the recent advances in the research on PcG proteins, including both the polycomb-repressive and non-polycomb functions. We specifically focus on the mechanisms by which PcG proteins play roles in cancer initiation, development, and progression. Finally, we discuss the potential value of PcG proteins as molecular biomarkers for the diagnosis and prognosis of cancer, and as molecular targets for cancer therapy. PMID:26227500

  12. Toward a standardized structural-functional group connectome in MNI space.

    PubMed

    Horn, Andreas; Blankenburg, Felix

    2016-01-01

    The analysis of the structural architecture of the human brain in terms of connectivity between its subregions has provided profound insights into its underlying functional organization and has coined the concept of the "connectome", a structural description of the elements forming the human brain and the connections among them. Here, as a proof of concept, we introduce a novel group connectome in standard space based on a large sample of 169 subjects from the Enhanced Nathan Kline Institute-Rockland Sample (eNKI-RS). Whole brain structural connectomes of each subject were estimated with a global tracking approach, and the resulting fiber tracts were warped into standard stereotactic (MNI) space using DARTEL. Employing this group connectome, the results of published tracking studies (i.e., the JHU white matter and Oxford thalamic connectivity atlas) could be largely reproduced directly within MNI space. In a second analysis, a study that examined structural connectivity between regions of a functional network, namely the default mode network, was reproduced. Voxel-wise structural centrality was then calculated and compared to others' findings. Furthermore, including additional resting-state fMRI data from the same subjects, structural and functional connectivity matrices between approximately forty thousand nodes of the brain were calculated. This was done to estimate structure-function agreement indices of voxel-wise whole brain connectivity. Taken together, the combination of a novel whole brain fiber tracking approach and an advanced normalization method led to a group connectome that allowed (at least heuristically) performing fiber tracking directly within MNI space. Such an approach may be used for various purposes like the analysis of structural connectivity and modeling experiments that aim at studying the structure-function relationship of the human connectome. Moreover, it may even represent a first step toward a standard DTI template of the human brain

  13. Impact of dendrimer surface functional groups on the release of doxorubicin from dendrimer carriers.

    PubMed

    Zhang, Mengen; Guo, Rui; Kéri, Mónika; Bányai, István; Zheng, Yun; Cao, Mian; Cao, Xueyan; Shi, Xiangyang

    2014-02-13

    Generation 5 (G5) poly(amidoamine) dendrimers with acetyl (G5.NHAc), glycidol hydroxyl (G5.NGlyOH), and succinamic acid (G5.SAH) terminal groups were used to physically encapsulate an anticancer drug doxorubicin (DOX). Both UV-vis spectroscopy and multiple NMR techniques including one-dimensional NMR and two-dimensional NMR were applied to investigate the interactions between different dendrimers and DOX. The influence of the surface functional groups of G5 dendrimers on the DOX encapsulation, release kinetics, and cancer cell inhibition effect was investigated. We show that all three types of dendrimers are able to effectively encapsulate DOX and display therapeutic inhibition effect to cancer cells, which is solely associated with the loaded DOX. The relatively stronger interactions of G5.NHAc or G5.NGlyOH dendrimers with DOX than that of G5.SAH dendrimers with DOX demonstrated by NMR techniques correlate well with the slow release rate of DOX from G5.NHAc/DOX or G5.NGlyOH/DOX complexes. In contrast, the demonstrated weak interaction between G5.SAH and DOX causes a fast release of DOX, suggesting that the G5.SAH/DOX complex may not be a proper option for further in vivo research. Our findings suggest that the dendrimer surface functional groups are crucial for further design of multifunctional dendrimer-based drug delivery systems for various biomedical applications.

  14. Differences in menstrual bleeding characteristics, functional status, and attitudes toward menstruation in three groups of women.

    PubMed

    Geller, S E; Harlow, S D; Bernstein, S J

    1999-05-01

    This report examines differences in bleeding characteristics, functional status, and attitudes toward menstruation among three groups of women: (1) women who complain of abnormal uterine bleeding (AUB), (2) women who have similar menstrual patterns as those complaining of AUB but who do not perceive themselves to have abnormal bleeding, and (3) women without evidence of prolonged or excessive bleeding. Women who complain of AUB and women with heavy bleeding but not complaining of AUB, although similar on two important menstrual symptoms (very heavy bleeding or episodes of unusually heavy bleeding) differ on a number of other menstrual characteristics, including the frequency of short cycles, the probability of having an abnormally long period, and reporting of unusually heavy bleeding lasting longer than 1 day. Whether women reported concerns with menstruation or not, the majority of women in this analysis had fairly negative attitudes toward menstruation. However, this negativity toward menstruation did not translate into women wanting a hysterectomy, even for those with heavy bleeding. The major difference among the three groups of women was the strong negative effect of AUB on functional status. A majority of women complaining of AUB reported that the bleeding interfered significantly with their daily routine, making them unable to function at work and at home. These results suggest that although the main complaint of women with AUB is very heavy bleeding, a number of other specific menstrual characteristics differentiate women with AUB from other women with very heavy bleeding who do not perceive the bleeding to be problematic. The complaint of AUB appears to be related to how significantly bleeding affects daily functioning. Therefore, an important factor to assess when considering treatment of AUB is the extent to which bleeding symptoms significantly affect functional status.

  15. Group 2 innate lymphoid cells express functional NKp30 receptor inducing type 2 cytokine production1

    PubMed Central

    Salimi, Maryam; Xue, Luzheng; Jolin, Helen; Hardman, Clare; Cousins, David J.; McKenzie, Andrew N.J.; Ogg, Graham S.

    2016-01-01

    Group 2 innate lymphoid cells (ILC2) are important in effector functions for eliciting allergic inflammation, parasite defence, epithelial repair and lipid homeostasis. ILC2 lack rearranged antigen-specific receptors, and while many soluble factors such as cytokines and lipid mediators can influence ILC2, direct interaction of these cells with microenvironment and other cells has been less explored. Natural cytotoxicity receptors are expressed by subsets of ILC1 and ILC3 and thought to be important for their effector function, but have not been shown to be expressed by ILC2. Therefore, we sought to investigate the expression and functional properties of the natural cytotoxicity receptor NKp30 on human group 2 innate lymphoid cells. A subset of ex vivo and cultured ILC2 express NKp30 that upon interaction with its cognate activatory ligand B7-H6 induces rapid production of type 2 cytokines. This interaction can be blocked by NKp30 blocking antibody and an inhibitory ligand, galectin-3. Higher expression of B7-H6 was observed in lesional skin biopsies of patients with atopic dermatitis; and incubation of keratinocytes with pro-inflammatory and type 2 cytokines upregulated B7-H6 leading to increased ILC2 cytokine production. NKp30-B7-H6 interaction is a novel cell contact mechanism that mediates activation of ILC2 and identifies a potential target for the development of novel therapeutics for atopic dermatitis and other atopic diseases. PMID:26582946

  16. The synthesis of desired functional groups on PEI microgel particles for biomedical and environmental applications

    NASA Astrophysics Data System (ADS)

    Sahiner, Nurettin; Demirci, Sahin; Sahiner, Mehtap; Al-Lohedan, Hamad

    2015-11-01

    Polyethyleneimine (PEI) microgels were synthesized by micro emulsion polymerization technique and converted to positively charged forms by chemical treatments with various modifying agents with different functional groups, such as 2-bromoethanol (-OH), 4-bromobutyronitrile (-CN), 2-bromoethylamine hydrobromide (-NH2), and glycidol (-OH). The functionalization of PEI microgels was confirmed by FT-IR, TGA and zeta potential measurements. Furthermore, a second modification of the modified PEI microgels was induced on 4-bromo butyronitrile-modified PEI microgels (PEI-CN) by amidoximation, to generate new functional groups on the modified PEI microgels. The PEI and modified PEI microgels were also tested for their antimicrobial effects against various bacteria such as Bacillus subtilis ATCC 6633, Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 25323. Moreover, the PEI-based particles were used for removal of organic dyes such as methyl orange (MO) and congo red (CR). The absorption capacity of PEI-based microgels increased with modification from 101.8 mg/g to 218.8 mg/g with 2-bromoethylamine, 216.2 m/g with 1-bromoethanol, and 224.5 mg/g with 4-bromobutyronitrile for MO. The increase in absorption for CR dyes was from 347.3 mg/g to 390.4 mg/g with 1-bromoethanol, 399.6 mg/g with glycidol, and 349.9 mg/g with 4-bromobutyronitrile.

  17. Abundance of field galaxies

    NASA Astrophysics Data System (ADS)

    Klypin, Anatoly; Karachentsev, Igor; Makarov, Dmitry; Nasonova, Olga

    2015-12-01

    We present new measurements of the abundance of galaxies with a given circular velocity in the Local Volume: a region centred on the Milky Way Galaxy and extending to distance ˜10 Mpc. The sample of ˜750 mostly dwarf galaxies provides a unique opportunity to study the abundance and properties of galaxies down to absolute magnitudes MB ≈ -10 and virial masses M_vir= 109{ M_{⊙}}. We find that the standard Λ cold dark matter (ΛCDM) model gives remarkably accurate estimates for the velocity function of galaxies with circular velocities V ≳ 70 kms-1 and corresponding virial masses M_vir≳ 5× 10^{10}{ M_{⊙}}, but it badly fails by overpredicting ˜5 times the abundance of large dwarfs with velocities V = 30-40 kms-1. The warm dark matter (WDM) models cannot explain the data either, regardless of mass of WDM particle. Just as in previous observational studies, we find a shallow asymptotic slope dN/dlog V ∝ Vα, α ≈ -1 of the velocity function, which is inconsistent with the standard ΛCDM model that predicts the slope α = -3. Though reminiscent to the known overabundance of satellite problem, the overabundance of field galaxies is a much more difficult problem. For the standard ΛCDM model to survive, in the 10 Mpc radius of the Milky Way there should be 1000 not yet detected galaxies with virial mass M_vir≈ 10^{10}{ M_{⊙}}, extremely low surface brightness and no detectable H I gas. So far none of this type of galaxies have been discovered.

  18. Detecting Functional Groups of Arabidopsis Mutants by Metabolic Profiling and Evaluation of Pleiotropic Responses

    PubMed Central

    Hofmann, Jörg; Börnke, Frederik; Schmiedl, Alfred; Kleine, Tatjana; Sonnewald, Uwe

    2011-01-01

    Metabolic profiles and fingerprints of Arabidopsis thaliana plants with various defects in plastidic sugar metabolism or photosynthesis were analyzed to elucidate if the genetic mutations can be traced by comparing their metabolic status. Using a platform of chromatographic and spectrometric tools data from untargeted full MS scans as well as from selected metabolites including major carbohydrates, phosphorylated intermediates, carboxylates, free amino acids, major antioxidants, and plastidic pigments were evaluated. Our key observations are that by multivariate statistical analysis each mutant can be separated by a unique metabolic signature. Closely related mutants come close. Thus metabolic profiles of sugar mutants are different but more similar than those of photosynthesis mutants. All mutants show pleiotropic responses mirrored in their metabolic status. These pleiotropic responses are typical and can be used for separating and grouping of the mutants. Our findings show that metabolite fingerprints can be taken to classify mutants and hence may be used to sort genes into functional groups. PMID:22639613

  19. Biomass Vanillin-Derived Polymeric Microspheres Containing Functional Aldehyde Groups: Preparation, Characterization, and Application as Adsorbent.

    PubMed

    Zhang, Huanyu; Yong, Xueyong; Zhou, Jinyong; Deng, Jianping; Wu, Youping

    2016-02-01

    The contribution reports the first polymeric microspheres derived from a biomass, vanillin. It reacted with methacryloyl chloride, providing monomer vanillin methacrylate (VMA), which underwent suspension polymerization in aqueous media and yielded microspheres in high yield (>90 wt %). By controlling the N2 bubbling mode and by optimizing the cosolvent for dissolving the solid monomer, the microspheres were endowed with surface pores, demonstrated by SEM images and mercury intrusion porosimetry measurement. Taking advantage of the reactive aldehyde groups, the microspheres further reacted with glycine, thereby leading to a novel type of Schiff-base chelating material. The functionalized microspheres demonstrated remarkable adsorption toward Cu(2+) (maximum, 135 mg/g) which was taken as representative for metal ions. The present study provides an unprecedented class of biobased polymeric microspheres showing large potentials as adsorbents in wastewater treatment. Also importantly, the reactive aldehyde groups may enable the microspheres to be used as novel materials for immobilizing biomacromolecules, e.g. enzymes. PMID:26752344

  20. Biomass Vanillin-Derived Polymeric Microspheres Containing Functional Aldehyde Groups: Preparation, Characterization, and Application as Adsorbent.

    PubMed

    Zhang, Huanyu; Yong, Xueyong; Zhou, Jinyong; Deng, Jianping; Wu, Youping

    2016-02-01

    The contribution reports the first polymeric microspheres derived from a biomass, vanillin. It reacted with methacryloyl chloride, providing monomer vanillin methacrylate (VMA), which underwent suspension polymerization in aqueous media and yielded microspheres in high yield (>90 wt %). By controlling the N2 bubbling mode and by optimizing the cosolvent for dissolving the solid monomer, the microspheres were endowed with surface pores, demonstrated by SEM images and mercury intrusion porosimetry measurement. Taking advantage of the reactive aldehyde groups, the microspheres further reacted with glycine, thereby leading to a novel type of Schiff-base chelating material. The functionalized microspheres demonstrated remarkable adsorption toward Cu(2+) (maximum, 135 mg/g) which was taken as representative for metal ions. The present study provides an unprecedented class of biobased polymeric microspheres showing large potentials as adsorbents in wastewater treatment. Also importantly, the reactive aldehyde groups may enable the microspheres to be used as novel materials for immobilizing biomacromolecules, e.g. enzymes.

  1. Multi-Walled Carbon Nanotube Functionalization by Radical Addition Using Hydroxymethylene Groups.

    PubMed

    Rodríguez-Jiménez, Rubén; Alonso-Núñez, Gabriel; Paraguay-Delgado, Francisco; Espinoza-Gómez, Heriberto; Vélez-López, Ernesto; Rogel-Hernández, Eduardo

    2016-01-01

    Synthetic methodology and characterization of multi-walled carbon nanotubes (MWCNTs) function- alized with hydroxymethylene groups are reported. The MWCNTs were synthesized by the spray pyrolysis technique using toluene as carbon source and ferrocene as catalyst. Hydroxymethylation of MWCNTs was carried out by methanol using benzoyl peroxide (BPO) at different quantities (300 to 900 mg); the optimum BPO quantity was 300 mg. The resulting materials were characterized by FT-IR, Raman Spectroscopy, Thermal Gravimetric Analysis (TGA) and Transmission Electron Microscopy (TEM). The presence of the hydroxymethylene group on the MWCNTs surface was demonstrated by FT-IR, Raman Spectroscopy, TGA, EDS, TEM and Mass Spectrometry. The func- tionalized MWCNTs were not damaged by this methodology. PMID:27398563

  2. Acidity of the amidoxime functional group in aqueous solution. A combined experimental and computational study

    DOE PAGES

    Mehio, Nada; Lashely, Mark A.; Nugent, Joseph W.; Tucker, Lyndsay; Correia, Bruna; Do-Thanh, Chi-Linh; Dai, Sheng; Hancock, Robert D.; Bryantsev, Vyacheslav S.

    2015-01-26

    Poly(acrylamidoxime) adsorbents are often invoked in discussions of mining uranium from seawater. It has been demonstrated repeatedly in the literature that the success of these materials is due to the amidoxime functional group. While the amidoxime-uranyl chelation mode has been established, a number of essential binding constants remain unclear. This is largely due to the wide range of conflicting pKa values that have been reported for the amidoxime functional group in the literature. To resolve this existing controversy we investigated the pKa values of the amidoxime functional group using a combination of experimental and computational methods. Experimentally, we used spectroscopicmore » titrations to measure the pKa values of representative amidoximes, acetamidoxime and benzamidoxime. Computationally, we report on the performance of several protocols for predicting the pKa values of aqueous oxoacids. Calculations carried out at the MP2 or M06-2X levels of theory combined with solvent effects calculated using the SMD model provide the best overall performance with a mean absolute error of 0.33 pKa units and 0.35 pKa units, respectively, and a root mean square deviation of 0.46 pKa units and 0.45 pKa units, respectively. Finally, we employ our two best methods to predict the pKa values of promising, uncharacterized amidoxime ligands. Hence, our study provides a convenient means for screening suitable amidoxime monomers for future generations of poly(acrylamidoxime) adsorbents used to mine uranium from seawater.« less

  3. Acidity of the amidoxime functional group in aqueous solution. A combined experimental and computational study

    SciTech Connect

    Mehio, Nada; Lashely, Mark A.; Nugent, Joseph W.; Tucker, Lyndsay; Correia, Bruna; Do-Thanh, Chi-Linh; Dai, Sheng; Hancock, Robert D.; Bryantsev, Vyacheslav S.

    2015-01-26

    Poly(acrylamidoxime) adsorbents are often invoked in discussions of mining uranium from seawater. It has been demonstrated repeatedly in the literature that the success of these materials is due to the amidoxime functional group. While the amidoxime-uranyl chelation mode has been established, a number of essential binding constants remain unclear. This is largely due to the wide range of conflicting pKa values that have been reported for the amidoxime functional group in the literature. To resolve this existing controversy we investigated the pKa values of the amidoxime functional group using a combination of experimental and computational methods. Experimentally, we used spectroscopic titrations to measure the pKa values of representative amidoximes, acetamidoxime and benzamidoxime. Computationally, we report on the performance of several protocols for predicting the pKa values of aqueous oxoacids. Calculations carried out at the MP2 or M06-2X levels of theory combined with solvent effects calculated using the SMD model provide the best overall performance with a mean absolute error of 0.33 pKa units and 0.35 pKa units, respectively, and a root mean square deviation of 0.46 pKa units and 0.45 pKa units, respectively. Finally, we employ our two best methods to predict the pKa values of promising, uncharacterized amidoxime ligands. Hence, our study provides a convenient means for screening suitable amidoxime monomers for future generations of poly(acrylamidoxime) adsorbents used to mine uranium from seawater.

  4. Ecological Significance of a Geomorphic Stream Classification: Species and Functional Group Composition of Riparian Plant Communities

    NASA Astrophysics Data System (ADS)

    Shaw, J. R.; Cooper, D. J.

    2014-12-01

    We tested the ecological significance of a geomorphic classification of Sonoran Desert ephemeral stream channels based on channel plan-form, degree of lateral confinement, and boundary material composition. This typology has been shown to discriminate among channel geometry and hydraulic characteristics for bedrock, bedrock with alluvium, incised alluvium, braided, and piedmont headwater channels. We examined stream reach-scale relationships of geomorphic stream types to the relative cover and density of perennial plant species and functional groups, and identified the dominant fluvial drivers, within riparian communities at 101 ephemeral stream reaches on the U.S. Army Yuma Proving Ground and Barry M. Goldwater Air Force Range in southwestern Arizona, USA. Nonparametric multivariate analysis of variance showed that species and functional group composition differed significantly among geomorphic stream types, both in terms of relative cover and density. Partitioning of among-site multivariate dissimilarity revealed that species compositional differences between stream types were caused largely by variation in the cover and density of the most common members of the regional flora. Distinctive functional group composition among reach types resulted from differences in the cover and density of drought-deciduous shrubs and subshrubs, evergreen trees and shrubs, and photosynthetic-stemmed trees. Comparison of environmental and biotic dissimilarity matrices highlighted the role of channel gradient as the dominant abiotic driver of riparian plant community composition, with stream channel elevation and width:depth providing additional explanatory power. Distinctive riparian plant community composition among the geomorphic stream types demonstrates the ecological significance of this a priori channel classification, and indicates its potential utility in understanding spatial patterns of ecological dynamics, sample stratification for process-based studies, and reference

  5. Algorithmic derivation of functional renormalization group equations and Dyson-Schwinger equations

    NASA Astrophysics Data System (ADS)

    Huber, Markus Q.; Braun, Jens

    2012-06-01

    We present the Mathematica application DoFun which allows to derive Dyson-Schwinger equations and renormalization group flow equations for n-point functions in a simple manner. DoFun offers several tools which considerably simplify the derivation of these equations from a given physical action. We discuss the application of DoFun by means of two different types of quantum field theories, namely a bosonic O(N) theory and the Gross-Neveu model. Program summaryProgram title:DoFun Catalogue identifier: AELN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 506 No. of bytes in distributed program, including test data, etc.: 571 837 Distribution format: tar.gz Programming language: Mathematica 7 and higher Computer: PCs and workstations Operating system: All on which Mathematica is available (Windows, Unix, MacOS) Classification: 11.1, 11.4, 11.5, 11.6 Nature of problem: Derivation of functional renormalization group equations and Dyson-Schwinger equations from the action of a given theory. Solution method: Implementation of an algorithm to derive functional renormalization group and Dyson-Schwinger equations. Unusual features: The results can be plotted as Feynman diagrams in Mathematica. The output is compatible with the syntax of many other programs and is therefore suitable for further (algebraic) computations. Running time: Seconds to minutes

  6. Functional gene group analysis indicates no role for heterotrimeric G proteins in cognitive ability.

    PubMed

    Hill, W David; de Leeuw, Christiaan; Davies, Gail; Liewald, David Cherry McLachlan; Payton, Anthony; Craig, Leone C A; Whalley, Lawrence J; Horan, Mike; Ollier, William; Starr, John M; Pendleton, Neil; Posthuma, Danielle; Bates, Timothy C; Deary, Ian J

    2014-01-01

    Previous functional gene group analyses implicated common single nucleotide polymorphisms (SNPs) in heterotrimeric G protein coding genes as being associated with differences in human intelligence. Here, we sought to replicate this finding using five independent cohorts of older adults including current IQ and childhood IQ, and using both gene- and SNP-based analytic strategies. No significant associations were found between variation in heterotrimeric G protein genes and intelligence in any cohort at either of the two time points. These results indicate that, whereas G protein systems are important in cognition, common genetic variation in these genes is unlikely to be a substantial influence on human intelligence differences. PMID:24626473

  7. Importance of minor groove functional groups for the stability of DNA duplexes.

    PubMed

    Sun, Zhenhua; Chen, Dongli; Lan, Tao; McLaughlin, Larry W

    2002-11-01

    Eight oligonucleotide duplexes have been prepared with four pairs of selected complementary pairs of native/analogue heterocyclic bases incorporated at a selected test site. The base pairs vary in the nature of their functionality in the minor groove. Each pair has a minor groove purine amino group present or absent, and correspondingly has a minor grove pyrimidine carbonyl present or absent. Loss of duplex stability is most notable when the minor groove pyrimidine carbonyl is absent although in other respects normal Watson-Crick hydrogen bonding is maintained in these sequences. These differences in stability are discussed in terms of possible variations in minor groove hydration.

  8. Effects of Functional Groups and Sugar Composition of Quercetin Derivatives on Their Radical Scavenging Properties.

    PubMed

    Kato, Komei; Ninomiya, Masayuki; Tanaka, Kaori; Koketsu, Mamoru

    2016-07-22

    Quercetin derivatives are widespread in the plant kingdom and exhibit various biological actions. The aim of this study was to investigate the structure-activity relationships of quercetin derivatives, with a focus on the influence of functional groups and sugar composition on their antioxidant capacity. A series of quercetin derivatives were therefore prepared and assessed for their DPPH radical scavenging properties. Isoquercetin O-gallates were more potent radical scavengers than quercetin. The systematic analysis highlights the importance of the distribution of hydroxy substituents in isoquercetin O-gallates to their potency. PMID:27314621

  9. Function of Integrin-Linked Kinase in Modulating the Stemness of IL-6-Abundant Breast Cancer Cells by Regulating γ-Secretase-Mediated Notch1 Activation in Caveolae.

    PubMed

    Hsu, En-Chi; Kulp, Samuel K; Huang, Han-Li; Tu, Huang-Ju; Salunke, Santosh B; Sullivan, Nicholas J; Sun, Duxin; Wicha, Max S; Shapiro, Charles L; Chen, Ching-Shih

    2015-06-01

    Interleukin-6 (IL-6) and Notch signaling are important regulators of breast cancer stem cells (CSCs), which drive the malignant phenotype through self-renewal, differentiation, and development of therapeutic resistance. We investigated the role of integrin-linked kinase (ILK) in regulating IL-6-driven Notch1 activation and the ability to target breast CSCs through ILK inhibition. Ectopic expression/short hairpin RNA-mediated knockdown of ILK, pharmacological inhibition of ILK with the small molecule T315, Western blot analysis, immunofluorescence, and luciferase reporter assays were used to evaluate the regulation of IL-6-driven Notch1 activation by ILK in IL-6-producing triple-negative breast cancer cell lines (MDA-MB-231, SUM-159) and in MCF-7 and MCF-7(IL-6) cells. The effects of ILK on γ-secretase complex assembly and cellular localization were determined by immunofluorescence, Western blots of membrane fractions, and immunoprecipitation. In vivo effects of T315-induced ILK inhibition on CSCs in SUM-159 xenograft models were assessed by mammosphere assays, flow cytometry, and tumorigenicity assays. Results show that the genetic knockdown or pharmacological inhibition of ILK suppressed Notch1 activation and the abundance of the γ-secretase components presenilin-1, nicastrin, and presenilin enhancer 2 at the posttranscriptional level via inhibition of caveolin-1-dependent membrane assembly of the γ-secretase complex. Accordingly, knockdown of ILK inhibited breast CSC-like properties in vitro and the breast CSC subpopulation in vivo in xenograft tumor models. Based on these findings, we propose a novel function of ILK in regulating γ-secretase-mediated Notch1 activation, which suggests the targeting of ILK as a therapeutic approach to suppress IL-6-induced breast CSCs.

  10. Myeloid-derived suppressor cell function is reduced by Withaferin A, a potent and abundant component of Withania somnifera root extract.

    PubMed

    Sinha, Pratima; Ostrand-Rosenberg, Suzanne

    2013-11-01

    Myeloid cells play a crucial role in tumor progression. The most common tumor-infiltrating myeloid cells are myeloid-derived suppressor cells (MDSC) and tumor-associated macrophages (TAMs). These cells promote tumor growth by their inherent immune suppressive activity which is enhanced by their cross-talk. The root extract of the plant Withania somnifera (Ashwagandha) (WRE) has been reported to reduce tumor growth. HPLC analysis identified Withaferin A (WA) as the most abundant constituent of WRE and led us to determine whether the anti-tumor effects of WRE and WA involve modulating MDSC and TAM activity. A prominent effect of MDSC is their production of IL-10 which increases upon cross-talk with macrophages, thus polarizing immunity to a pro-tumor type 2 phenotype. In vitro treatment with WA decreased MDSC production of IL-10 and prevented additional MDSC production of IL-10 generated by MDSC-macrophage cross-talk. Macrophage secretion of IL-6 and TNFα, cytokines that increase MDSC accumulation and function, was also reduced by in vitro treatment with WA. Much of the T-cell suppressive activity of MDSC is due to MDSC production of reactive oxygen species (ROS), and WA significantly reduced MDSC production of ROS through a STAT3-dependent mechanism. In vivo treatment of tumor-bearing mice with WA decreased tumor weight, reduced the quantity of granulocytic MDSC, and reduced the ability of MDSC to suppress antigen-driven activation of CD4+ and CD8+ T cells. Thus, adjunctive treatment with WA reduced myeloid cell-mediated immune suppression, polarized immunity toward a tumor-rejecting type 1 phenotype, and may facilitate the development of anti-tumor immunity.

  11. Nonperturbative renormalization group and momentum dependence of n-point functions. I

    SciTech Connect

    Blaizot, Jean-Paul; Mendez-Galain, Ramon; Wschebor, Nicolas

    2006-11-15

    We present an approximation scheme to solve the nonperturbative renormalization group equations and obtain the full momentum dependence of the n-point functions. It is based on an iterative procedure where, in a first step, an initial ansatz for the n-point functions is constructed by solving approximate flow equations derived from well motivated approximations. These approximations exploit the derivative expansion and the decoupling of high momentum modes. The method is applied to the O(N) model. In leading order, the self-energy is already accurate both in the perturbative and the scaling regimes. A stringent test is provided by the calculation of the shift {delta}T{sub c} in the transition temperature of the weakly repulsive Bose gas, a quantity which is particularly sensitive to all momentum scales. The leading order result is in agreement with lattice calculations, albeit with a theoretical uncertainty of about 25%.

  12. Functional groups in a single pteridosperm species: Variability and circumscription (Pennsylvanian, Nova Scotia, Canada)

    USGS Publications Warehouse

    Zodrow, E.L.; Mastalerz, Maria

    2007-01-01

    Multiple foliar specimens of the Late Pennsylvanian fossil pteridosperm [gymnosperm] Alethopteris zeilleri (Ragot) Wagner were collected from one restricted stratigraphical horizon in the Canadian Sydney Coalfield. Variability of functional-group distribution using FTIR technique was studied in compressions, adaxial versus abaxial cuticles, and in unseparated cuticles as a function of maceration time from 48 to 168??h. The results obtained document spectral variability that could be expected within specimens of one species. For example, CH2/CH3 and Al/ox ratios can differ by as much as 20% of the values. Moreover, the experiments performed confirm that by using a previously established maceration protocol, long maceration periods do not bias FTIR spectra in terms of oxygenation overprinting. The inference that this cuticle is robust, under the given diagenetic level, probably reflects a reassuring degree of chemical fidelity of the Pennsylvanian plant to support Carboniferous chemotaxonomic observations. ?? 2006 Elsevier B.V. All rights reserved.

  13. Functional correlations of spatial quantitative EEG and intelligences in a nonalphabetical language group.

    PubMed

    Yang, Chih-Chien; Yang, Chih-Chiang; Chaou, Wun-Tsong

    2005-01-01

    This study investigated any functional correlations between intelligences and spatially recorded quantitative electroencephalograms (QEEGs) in a nonalphabetical language group. Participants, between 6 and 8 years old, were sampled in a teaching hospital located at the central Taiwan region. The Chinese Wechsler Intelligence Scale for Children-III (WISC-III) intelligence test and quantitative electroencephalograph recording procedures were both administrated to collect data. Intelligences were divided into two categories, verbal and performance intelligences, for statistical investigations. Statistical analyses of the noncontaminated QEEG dataset investigated the differentiability of each frequency on a single cortical region and coherence between cortical regions. Low QEEG frequencies were found to have a significant correlation with intelligences on some cortical regions. Coherence between symmetric cortical regions was found to be an important factor in predicting intelligences. Results showed the feasibility of functional brain mapping in the particular language population.

  14. Functional renormalization group approach to the Yang-Lee edge singularity

    NASA Astrophysics Data System (ADS)

    An, X.; Mesterházy, D.; Stephanov, M. A.

    2016-07-01

    We determine the scaling properties of the Yang-Lee edge singularity as described by a one-component scalar field theory with imaginary cubic coupling, using the nonperturbative functional renormalization group in 3 ≤ d ≤ 6 Euclidean dimensions. We find very good agreement with high-temperature series data in d = 3 dimensions and compare our results to recent estimates of critical exponents obtained with the four-loop ɛ = 6 - d expansion and the conformal bootstrap. The relevance of operator insertions at the corresponding fixed point of the RG β functions is discussed and we estimate the error associated with O({partial}^4) truncations of the scale-dependent effective action.

  15. Chiral dynamics in a magnetic field from the functional renormalization group

    NASA Astrophysics Data System (ADS)

    Kamikado, Kazuhiko; Kanazawa, Takuya

    2014-03-01

    We investigate the quark-meson model in a magnetic field using the functional renormalization group equation beyond the local-potential approximation. Our truncation of the effective action involves anisotropic wave function renormalization for mesons, which allows us to investigate how the magnetic field distorts the propagation of neutral mesons. Solving the flow equation numerically, we find that the transverse velocity of mesons decreases with the magnetic field at all temperatures, which is most prominent at zero temperature. The meson screening masses and the pion decay constants are also computed. The constituent quark mass is found to increase with magnetic field at all temperatures, resulting in the crossover temperature that increases monotonically with the magnetic field. This tendency is consistent with most model calculations but not with the lattice simulation performed at the physical point. Our work suggests that the strong anisotropy of meson propagation may not be the fundamental origin of the inverse magnetic catalysis.

  16. Effects of the peer group on the development of social functioning and academic achievement: a longitudinal study in Chinese children.

    PubMed

    Chen, Xinyin; Chang, Lei; Liu, Hongyun; He, Yunfeng

    2008-01-01

    This longitudinal study examined, in a sample of Chinese children (initial mean ages = 9.5 and 12.7 years, N = 505), how the peer group contributed to social functioning and academic achievement and their associations. Data on informal peer groups, social functioning, and academic achievement were collected from multiple sources. Multilevel structural equation modeling revealed that group academic performance made direct contributions to children's social development. Group academic performance also moderated the individual-level relations between academic performance and later social functioning. Whereas high-achieving groups strengthened the positive relations between academic achievement and social competence, low-achieving groups facilitated the negative relations between academic achievement and social problems. The results indicate the significance of the peer group for social functioning from a developmental perspective.

  17. A comparison of fish communities of subtidal seagrass beds and sandy seabeds in 13 marine embayments of a Caribbean island, based on species, families, size distribution and functional groups

    NASA Astrophysics Data System (ADS)

    Nagelkerken, I.; van der Velde, G.

    2004-08-01

    Differences in fish community structure between different estuaries, lagoons and bays can be very large, and generalisations are complicated by the use of a wide variety of sampling methods. In the present study, fish communities of subtidal seagrass beds and sandy seabeds in 13 marine embayments of a single Caribbean island were therefore sampled using a uniform method. The objective of the study was to determine whether the seagrass and sandy seabed habitats of various embayments are characterised by typical fish assemblages which differ in terms of taxa (species, families), size classes (life stages) and functional groups (ecological species groups, feeding time and diet). This was linked to the hypothesis that differences in fish assemblages between habitats in different embayments are larger at taxonomic levels than at the level of functional groups. A second objective was to determine the most useful discriminating features between the two habitat types. The above hypothesis was rejected, since differences in fish assemblages from different seagrass and sandy seabed sites did not increase from functional to taxonomic level, but from size class to diet/species to family/feeding time to ecological species group. However, the seagrass and sandy seabed habitats could each be characterised by typical fish assemblages which differed in taxonomical and functional group composition, irrespective of differences in environmental and biotic variables between the embayments in which these habitats were situated. The two habitat types could be best characterised on the basis of fish family, ecological species group, feeding time and size distribution. Seagrass beds mainly harboured nocturnally active nursery species (Haemulidae, Lutjanidae, etc.), whose relative abundance was related to vegetation (mainly seagrass) cover. Sandy seabeds mainly harboured diurnally active bay species (Gerreidae, etc.) whose relative abundance was related to cover of bare sand. Similarities

  18. Control of Surface Functional Groups on Pertechntate Sorption on Activated Carbon

    SciTech Connect

    Y. Wang; H. Gao; R. Yeredla; H. Xu; M. Abrecht; G.D. Stasio

    2006-07-05

    {sup 99}Tc is highly soluble and poorly adsorbed by natural materials under oxidizing conditions, thus being of particular concern for radioactive waste disposal. Activated carbon can potentially be used as an adsorbent for removing Tc from aqueous solutions. We have tested six commercial activated carbon materials for their capabilities for sorption of pertechnetate (TcO{sub 4}{sup -}). The tested materials can be grouped into two distinct types: Type I materials have high sorption capabilities with the distribution coefficients (K{sub d}) varying from 9.5 x 10{sup 5} to 3.2 x 10{sup 3} mL/g as the pH changes from 4.5 to 9.5, whereas type II materials have relatively low sorption capabilities with K{sub d} remaining more or less constant (1.1 x 10{sup 3} - 1.8 x 10{sup 3} mL/g) over a similar pH range. The difference in sorption behavior between the two types of materials is attributed to the distribution of surface functional groups. The predominant surface groups are identified to be carboxylic and phenolic groups. The carboxylic group can be further divided into three subgroups A, B, and C in the order of increasing acidity. The high sorption capabilities of type I materials are found to be caused by the presence of a large fraction of carboxylic subgroups A and B, while the low sorption capabilities of type II materials are due to the exclusive presence of phenolic and carboxylic subgroup C. Therefore, the performance of activated carbon for removing TcO{sub 4}{sup -} can be improved by enhancing the formation of carboxylic subgroups A and B during material processing.

  19. Control of pertechnetate sorption on activated carbon by surface functional groups.

    PubMed

    Wang, Yifeng; Gao, Huizhen; Yeredla, Rakesh; Xu, Huifang; Abrecht, Mike

    2007-01-15

    The isotope 99Tc is highly soluble and poorly adsorbed by natural materials under oxidizing conditions, thus being of particular concern for radioactive waste disposal. Activated carbon can potentially be used as an adsorbent for removing Tc from aqueous solutions. We have tested six commercial activated carbon materials for their capabilities for sorption of pertechnetate (TcO4-). The tested materials can be grouped into two distinct types: Type I materials have high sorption capabilities with the distribution coefficients (Kd) varying from 9.5 x 10(5) to 3.2 x 10(3) ml/g as the pH changes from 4.5 to 9.5, whereas type II materials have relatively low sorption capabilities with Kd remaining more or less constant (1.1 x 10(3)-1.8 x 10(3) ml/g) over a similar pH range. The difference in sorption behavior between the two types of materials is attributed to the distribution of surface functional groups. The predominant surface groups are identified as carboxylic and phenolic groups. The carboxylic group can be further divided into three subgroups, A, B, and C, in the order of increasing acidity. The high sorption capabilities of type I materials are found to be caused by the presence of a large fraction of carboxylic subgroups A and B, while the low sorption capabilities of type II materials are due to the exclusive presence of phenolic and carboxylic subgroup C. Therefore, the performance of activated carbon for removing TcO4- can be improved by enhancing the formation of carboxylic subgroups A and B during materials processing.

  20. Trophic links between functional groups of arable plants and beetles are stable at a national scale.

    PubMed

    Brooks, David R; Storkey, Jonathan; Clark, Suzanne J; Firbank, Les G; Petit, Sandrine; Woiwod, Ian P

    2012-01-01

    1. There is an urgent need to accurately model how environmental change affects the wide-scale functioning of ecosystems, but advances are hindered by a lack of knowledge of how trophic levels are linked across space. It is unclear which theoretical approach to take to improve modelling of such interactions, but evidence is gathering that linking species responses to their functional traits can increase understanding of ecosystem dynamics. Currently, there are no quantitative studies testing how this approach might improve models of multiple, trophically interacting species, at wide spatial scales. 2. Arable weeds play a foundational role in linking food webs, providing resources for many taxa, including carabid beetles that feed on their seeds and weed-associated invertebrate prey. Here, we model associations between weeds and carabids across farmland in Great Britain (GB), to test the hypothesis that wide-scale trophic links between these groups are structured by their species functional traits. 3. A network of c. 250 arable fields, covering four crops and most lowland areas of GB, was sampled for weed, carabid and invertebrate taxa over 3 years. Data sets of these groups were closely matched in time and space, and each contained numerous species with a range of eco-physiological traits. The consistency of trophic linkages between multiple taxa sharing functional traits was tested within multivariate and log-linear models. 4. Robust links were established between the functional traits of taxa and their trophic interactions. Autumn-germinating, small-seeded weeds were associated with smaller, spring-breeding carabids, more specialised in seed feeding, whereas spring-germinating, large-seeded weeds were associated with a range of larger, autumn-breeding omnivorous carabids. These relationships were strong and dynamic, being independent of changes in invertebrate food resources and consistent across sample dates, crops and regions of GB. 5. We conclude that, in at

  1. Functional Identification of Ligands for a Catalytic Metal Ion in Group I Introns†

    PubMed Central

    Forconi, Marcello; Lee, Jihee; Lee, Jungjoon K.; Piccirilli, Joseph A.; Herschlag, Daniel

    2009-01-01

    Many enzymes use metal ions within their active sites to achieve enormous rate acceleration. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). The three-dimensional arrangement determined by X-ray crystallography provides a powerful starting point for identifying ground state interactions, but only functional studies can establish and interrogate transition state interactions. The Tetrahymena group I ribozyme is a paradigm for the study of RNA catalysis, and previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified catalytic metal ions making five contacts with the substrate atoms. Here, we have combined atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to establish transition state ligands on the ribozyme for one of the catalytic metal ions, referred to as MA. We identified the pro-S P oxygen atoms at nucleotides C208, A304, and A306 as ground state ligands for Ma, verifying interactions suggested by the Azoarcus crystal structures. We further established that these interactions are present in the chemical transition state, a conclusion that requires functional studies, such as those carried out herein. Elucidating these active site connections is a crucial step toward an in-depth understanding of how specific structural features of the group I intron lead to catalysis. PMID:18517225

  2. Synthesis, algal inhibition activities and QSAR studies of novel gramine compounds containing ester functional groups

    NASA Astrophysics Data System (ADS)

    Li, Xia; Yu, Liangmin; Jiang, Xiaohui; Xia, Shuwei; Zhao, Haizhou

    2009-05-01

    2,5,6-Tribromo-1-methylgramine (TBG), isolated from bryozoan Zoobotryon pellucidum was shown to be very efficient in preventing recruitment of larval settlement. In order to improve the compatibility of TBG and its analogues with other ingredients in antifouling paints, structural modification of TBG was focused mainly on halogen substitution and N-substitution. Two halogen-substitute gramines and their derivatives which contain ester functional groups at N-position of gramines were synthesized. Algal inhibition activities of the synthesized compounds against algae Nitzschia closterium were evaluated and the Median Effective Concentration (EC50) range was 1.06-6.74 μg ml-1. Compounds that had a long chain ester group exhibited extremely high antifouling activity. Quantitive Structure Activity Relationship (QSAR) studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors and biological activity of the synthesized compounds. The results show that the toxicity (log (1/EC50)) is correlated well with the partition coefficient log P. Thus, these products have potential function as antifouling agents.

  3. Photoluminescence of oxygen vacancies and hydroxyl group surface functionalized SnO2 nanoparticles.

    PubMed

    Bonu, Venkataramana; Das, Arindam; Amirthapandian, S; Dhara, Sandip; Tyagi, Ashok Kumar

    2015-04-21

    We report, for the first time, the luminescence property of the hydroxyl group surface functionalized quantum dots (QDs) and nanoparticles (NPs) of SnO2 using low energy excitations of 2.54 eV (488 nm) and 2.42 eV (514.5 nm). This luminescence is in addition to generally observed luminescence from 'O' defects. The as-prepared SnO2 QDs are annealed at different temperatures under ambient conditions to create NPs with varying sizes. Subsequently, the average size of the NPs is calculated from the acoustic vibrations observed at low frequencies in the Raman spectra and by the transmission electron microscopy measurements. Detailed photoluminescence studies with 3.815 eV (325 nm) excitation reveal the nature of in-plane and bridging 'O' vacancies as well as adsorption and desorption occurring at different annealing temperatures. X-ray photoelectron spectroscopy studies also support this observation. The defect level related to the surface -OH functional groups shows a broad luminescence peak at around 1.96 eV in SnO2 NPs which is elaborated using temperature dependent studies. PMID:25774472

  4. Solubility and crystallizability: facile access to functionalized π-conjugated compounds with chlorendylimide protecting groups.

    PubMed

    Gebers, Jan; Rolland, Damien; Marty, Roman; Suàrez, Stéphane; Cervini, Luca; Scopelliti, Rosario; Brauer, Jan Cornelius; Frauenrath, Holger

    2015-01-19

    Functional π-conjugated molecules are relevant for the preparation of new organic electronic materials with improved performance. However, their synthesis is often rendered difficult by their inherently low solubility, and the permanent attachment of solubilizing groups may change the properties of the material. Here, we introduced the chlorendylimidyl moiety as a new temporary protecting group for the straightforward large-scale synthesis of protected quarter-, sexi-, octathiophene, and perylene bisimide diamine and dicarboxylic acid derivatives. The obtained chlorendylimides and chlorendylimidyl active esters were highly soluble in organic solvents, and optical spectroscopy confirmed the low tendency of the compounds to aggregate in solution. At the same time, they could be conveniently purified by recrystallization or precipitation. Single-crystal X-ray structures obtained for most compounds showed supramolecular motifs highlighting the role of the rigid, polychlorinated chlorendyl moieties in their crystallization. The obtained protected diamine and dicarboxylic acid derivatives were easily deprotected and converted into various amide-substituted oligothiophenes and perylene bisimides that are of interest as new functional materials for organic electronic thin film or nanowire devices. PMID:25427947

  5. Existence of ultrafine crevices and functional groups along the edge surfaces of graphitized thermal carbon black.

    PubMed

    Zeng, Yonghong; Do, D D; Nicholson, D

    2015-04-14

    Adsorption of different gases on graphitized thermal carbon black (GTCB) has been studied with a new molecular model to examine the consequences of micropore crevices and functional groups at the junctions between adjacent basal planes. Adsorption was simulated in the Grand Canonical Monte Carlo ensemble and the theoretical Henry constants were calculated by Monte Carlo volume integration over the Boltzmann factor of the solid-fluid potential. The simulation results are in good agreement with high-resolution experimental isotherms for argon on mineralogical graphite measured by Lopez-Gonzalez et al.1 From detailed inspection of the argon isotherms at extremely low coverages, we find two distinct Henry law regions, separated by a plateau (suggesting saturation of the stronger sites) that spans over a few decades of pressure. The first Henry law region is attributed to adsorption in the ultrafine crevices at the junctions between two adjacent basal planes, and the second region corresponds to adsorption on the basal plane, as confirmed by the theoretical Henry constant. The simulated isosteric heat and snapshots of molecular configurations show that argon adsorbs preferentially in the ultrafine crevices where there is a deep potential well due to overlap from the opposite pore walls. Similar behavior was found for other nonassociating fluids (Ar, N2, and CO2); however, for associating fluids (NH3 and H2O), the strong sites for adsorption and nucleation come from the combined effects of functional groups and ultrafine crevices, since the latter cannot alone account for the observed adsorption. PMID:25797845

  6. Response of herbivore functional groups to sequential perturbations in Moorea, French Polynesia

    NASA Astrophysics Data System (ADS)

    Han, Xueying; Adam, Thomas C.; Schmitt, Russell J.; Brooks, Andrew J.; Holbrook, Sally J.

    2016-09-01

    The reefs surrounding the island of Moorea, French Polynesia, experienced two large pulse perturbations between 2008 and 2010, an outbreak of the crown-of-thorns seastar ( Acanthaster planci) followed by a cyclone, that resulted in the reduction in live coral cover on the fore reef from ~40 to <5 %. Live coral cover in back reef and fringing reef habitats initially remained relatively stable, but began a gradual decline around 2010. We assessed the changes in the functional composition of the herbivorous fish community following the pulse perturbations and during the time of gradual coral decline on the back reef and fringing reef. Forty-nine species of herbivorous fishes quantified in yearly surveys between 2006 and 2014 were assigned to six functional groups: browser, detritivore, excavator, farmer, grazer/detritivore, and scraper. Non-metric multidimensional scaling analyses revealed that despite unique functional assemblages initially existing among the fringing reef, back reef, and fore reef habitats, the herbivorous fish communities in all three habitats responded in a qualitatively similar fashion to coral decline by moving toward functional communities characterized by an increased representation of excavators and scrapers. Island-wide scraper biomass increased by ~sevenfold in the post-disturbance time period, while excavator biomass increased by nearly threefold. The biomass of detritivores and grazers/detritivores also increased over the same time period, but to a much lesser degree, while the biomass of browsers and farmers remained essentially unchanged. Macroalgae remained a relatively minor space holder (<10 % cover) in lagoon habitats and on the fore reef through 2014, enabling recruitment of juvenile coral and initiating coral recovery on the fore reef. Results suggest that a functional community with a substantial biomass of herbivores and the capacity for the biomass of scrapers and excavators to increase rapidly in response to landscape

  7. Functional renormalization group approach to electronic structure calculations for systems without translational symmetry

    NASA Astrophysics Data System (ADS)

    Seiler, Christian; Evers, Ferdinand

    2016-10-01

    A formalism for electronic-structure calculations is presented that is based on the functional renormalization group (FRG). The traditional FRG has been formulated for systems that exhibit a translational symmetry with an associated Fermi surface, which can provide the organization principle for the renormalization group (RG) procedure. We here advance an alternative formulation, where the RG flow is organized in the energy-domain rather than in k space. This has the advantage that it can also be applied to inhomogeneous matter lacking a band structure, such as disordered metals or molecules. The energy-domain FRG (ɛ FRG) presented here accounts for Fermi-liquid corrections to quasiparticle energies and particle-hole excitations. It goes beyond the state of the art G W -BSE , because in ɛ FRG the Bethe-Salpeter equation (BSE) is solved in a self-consistent manner. An efficient implementation of the approach that has been tested against exact diagonalization calculations and calculations based on the density matrix renormalization group is presented. Similar to the conventional FRG, also the ɛ FRG is able to signalize the vicinity of an instability of the Fermi-liquid fixed point via runaway flow of the corresponding interaction vertex. Embarking upon this fact, in an application of ɛ FRG to the spinless disordered Hubbard model we calculate its phase boundary in the plane spanned by the interaction and disorder strength. Finally, an extension of the approach to finite temperatures and spin S =1 /2 is also given.

  8. A guide to the selection of switchable functional groups for CO2-switchable compounds.

    PubMed

    Alshamrani, A K; Vanderveen, J R; Jessop, P G

    2016-07-28

    Many CO2-responsive species, including many of the CO2-switchable surfactants, solvents, solutes, gels, colloids, and surfaces, rely on the ability of CO2 to lower the pH of water. Uncharged basic groups on the CO2-responsive species are therefore converted from a neutral state to a protonated cationic state (a bicarbonate salt), which causes dramatic and useful changes to the properties of the species. However, this switching process only works correctly if a basic group of appropriate basicity has been selected. This article presents a comprehensive guide to the selection of basic groups for CO2-switchable species for use in water. The appropriate basicity, as measured by the pKaH (the pKa of the protonated compound), is a function of the concentration of the switchable species, the temperature, the pressure of CO2, the presence or absence of an organic liquid phase, and the solubility of the neutral form of the compound. PMID:27373897

  9. Tailoring the mass distribution and functional group density of dimethylsiloxane-based films by thermal evaporation

    NASA Astrophysics Data System (ADS)

    Töpper, Tino; Lörcher, Samuel; Weiss, Florian; Müller, Bert

    2016-05-01

    The tailoring of molecular weight distribution and the functional group density of vinyl-terminated polydimethylsiloxane (PDMS) by molecular beam deposition is demonstrated herein. Thermally evaporated PDMS and its residue are characterized using gel permeation chromatography and nuclear magnetic resonance. Thermal fragmentation of vinyl groups occurs for evaporation temperatures above 487 K (214 °C). At a background pressure of 10-6 mbar, the maximum molecular weight distribution is adjusted from (700 ± 100) g/mol to (6100 ± 100) g/mol with a polydispersity index of 1.06 ± 0.02. The content of vinyl-termination per repeating unit of PDMS is tailored from (2.8 ± 0.2)% to (5.6 ± 0.1)%. Molecular weights of vinyl-terminated PDMS evaporated at temperatures above 388 K (115 °C) correspond to those attributed to trimethyl-terminated PDMS. Side groups of linear PDMS dominate intermolecular interactions and vapor pressure.

  10. Grafting of phosphorylcholine functional groups on polycarbonate urethane surface for resisting platelet adhesion.

    PubMed

    Gao, Bin; Feng, Yakai; Lu, Jian; Zhang, Li; Zhao, Miao; Shi, Changcan; Khan, Musammir; Guo, Jintang

    2013-07-01

    In order to improve the resistance of platelet adhesion on material surface, 2-methacryloyloxyethyl phosphorylcholine (MPC) was grafted onto polycarbonate urethane (PCU) surface via Michael reaction to create biomimetic structure. After introducing primary amine groups via coupling tris(2-aminoethyl)amine (TAEA) onto the polymer surface, the double bond of MPC reacted with the amino group to obtain MPC modified PCU. The modified surface was characterized by Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The results verified that MPC was grafted onto PCU surface by Michael reaction method. The MPC grafted PCU surface had a low water contact angle and a high water uptake. This means that the hydrophilic PC functional groups improved the surface hydrophilicity significantly. In addition, surface morphology of MPC grafted PCU film was imaged by atomic force microscope (AFM). The results showed that the grafted surface was rougher than the blank PCU surface. In addition, platelet adhesion study was evaluated by scanning electron microscopy (SEM) observation. The PCU films after treated with platelet-rich plasma demonstrated that much fewer platelets adhered to the MPC-grafted PCU surface than to the blank PCU surface. The antithrombogenicity of the MPC-grafted PCU surface was determined by the activated partial thromboplastin time (APTT). The result suggested that the MPC modified PCU may have potential application as biomaterials in blood-contacting and some subcutaneously implanted devices.

  11. Image registration algorithm using Mexican hat function-based operator and grouped feature matching strategy.

    PubMed

    Jin, Feng; Feng, Dazheng

    2014-01-01

    Feature detection and matching are crucial for robust and reliable image registration. Although many methods have been developed, they commonly focus on only one class of image features. The methods that combine two or more classes of features are still novel and significant. In this work, methods for feature detection and matching are proposed. A Mexican hat function-based operator is used for image feature detection, including the local area detection and the feature point detection. For the local area detection, we use the Mexican hat operator for image filtering, and then the zero-crossing points are extracted and merged into the area borders. For the feature point detection, the Mexican hat operator is performed in scale space to get the key points. After the feature detection, an image registration is achieved by using the two classes of image features. The feature points are grouped according to a standardized region that contains correspondence to the local area, precise registration is achieved eventually by the grouped points. An image transformation matrix is estimated by the feature points in a region and then the best one is chosen through competition of a set of the transformation matrices. This strategy has been named the Grouped Sample Consensus (GCS). The GCS has also ability for removing the outliers effectively. The experimental results show that the proposed algorithm has high registration accuracy and small computational volume. PMID:24752223

  12. Effects of the Peer Group on the Development of Social Functioning and Academic Achievement: A Longitudinal Study in Chinese Children

    ERIC Educational Resources Information Center

    Chen, Xinyin; Chang, Lei; Liu, Hongyun; He, Yunfeng

    2008-01-01

    This longitudinal study examined, in a sample of Chinese children (initial mean ages = 9.5 and 12.7 years, N = 505), how the peer group contributed to social functioning and academic achievement and their associations. Data on informal peer groups, social functioning, and academic achievement were collected from multiple sources. Multilevel…

  13. Meta-selective C-H functionalization using a nitrile-based directing group and cleavable Si-tether.

    PubMed

    Lee, Sunggi; Lee, Hyelee; Tan, Kian L

    2013-12-18

    A nitrile-based template that enables meta-selective C-H bond functionalization was developed. The template is applicable to a range of substituted arenes and tolerates a variety of functional groups. The directing group uses a silicon atom for attachment, allowing for a facile introduction/deprotection strategy increasing the synthetic practicality of this template.

  14. In situ synchrotron IR study relating temperature and heating rate to surface functional group changes in biomass.

    PubMed

    Kirtania, Kawnish; Tanner, Joanne; Kabir, Kazi Bayzid; Rajendran, Sharmen; Bhattacharya, Sankar

    2014-01-01

    Three types of woody biomass were investigated under pyrolysis condition to observe the change in the surface functional groups by Fourier transform infrared (FTIR) technique with increasing temperature under two different (5 and 150°C/min) heating rates. The experiments were carried out in situ in the infrared microscopy beamline (IRM) of the Australian Synchrotron. The capability of the beamline made it possible to focus on single particles to obtain low noise measurements without mixing with KBr. At lower heating rate, the surface functional groups were completely removed by 550°C. In case of higher heating rate, a delay was observed in losing the functional groups. Even at a high temperature, significant number of functional groups was retained after the higher heating rate experiments. This implies that at considerably high heating rates typical of industrial reactors, more functional groups will remain on the surface.

  15. [The establishment, development and application of classification approach of freshwater phytoplankton based on the functional group: a review].

    PubMed

    Yang, Wen; Zhu, Jin-Yong; Lu, Kai-Hong; Wan, Li; Mao, Xiao-Hua

    2014-06-01

    Appropriate schemes for classification of freshwater phytoplankton are prerequisites and important tools for revealing phytoplanktonic succession and studying freshwater ecosystems. An alternative approach, functional group of freshwater phytoplankton, has been proposed and developed due to the deficiencies of Linnaean and molecular identification in ecological applications. The functional group of phytoplankton is a classification scheme based on autoecology. In this study, the theoretical basis and classification criterion of functional group (FG), morpho-functional group (MFG) and morphology-based functional group (MBFG) were summarized, as well as their merits and demerits. FG was considered as the optimal classification approach for the aquatic ecology research and aquatic environment evaluation. The application status of FG was introduced, with the evaluation standards and problems of two approaches to assess water quality on the basis of FG, index methods of Q and QR, being briefly discussed.

  16. Multistimulation group therapy in Alzheimer's disease promotes changes in brain functioning.

    PubMed

    Baglio, Francesca; Griffanti, Ludovica; Saibene, Francesca Lea; Ricci, Cristian; Alberoni, Margherita; Critelli, Raffaella; Villanelli, Fabiana; Fioravanti, Raffaella; Mantovani, Federica; D'amico, Alessandra; Cabinio, Monia; Preti, Maria Giulia; Nemni, Raffaello; Farina, Elisabetta

    2015-01-01

    Background. The growing social emergency represented by Alzheimer's disease (AD) and the lack of medical treatments able to modify the disease course have kindled the interest in nonpharmacological therapies. Objective. We introduced a novel nonpharmacological approach for people with AD (PWA) named Multidimensional Stimulation group Therapy (MST) to improve PWA condition in different disease domains: cognition, behavior, and motor functioning. Methods. Enrolling 60 PWA in a mild to moderate stage of the disease, we evaluated the efficacy of MST with a randomized-controlled study. Neuropsychological and neurobehavioral measures and functional magnetic resonance imaging (fMRI) data were considered as outcome measures. Results. The following significant intervention-related changes were observed: reduction in Neuropsychiatric Inventory scale score, improvement in language and memory subscales of Alzheimer's Disease Assessment Scale-Cognitive subscale, and increased fMRI activations in temporal brain areas, right insular cortex, and thalamus. Conclusions. Cognitive-behavioral and fMRI results support the notion that MST has significant effects in improving PWA cognitive-behavioral status by restoring neural functioning.

  17. IL-12 drives functional plasticity of human group 2 innate lymphoid cells.

    PubMed

    Lim, Ai Ing; Menegatti, Silvia; Bustamante, Jacinta; Le Bourhis, Lionel; Allez, Matthieu; Rogge, Lars; Casanova, Jean-Laurent; Yssel, Hans; Di Santo, James P

    2016-04-01

    Group 2 innate lymphoid cells (ILC2) include IL-5- and IL-13-producing CRTh2(+)CD127(+)cells that are implicated in early protective immunity at mucosal surfaces. Whereas functional plasticity has been demonstrated for both human and mouse ILC3 subsets that can reversibly give rise to IFN-γ-producing ILC1, plasticity of human or mouse ILC2 has not been shown. Here, we analyze the phenotypic and functional heterogeneity of human peripheral blood ILC2. Although subsets of human CRTh2(+)ILC2 differentially express CD117 (c-kit receptor), some ILC2 surface phenotypes are unstable and can be modulated in vitro. Surprisingly, human IL-13(+)ILC2 can acquire the capacity to produce IFN-γ, thereby generating plastic ILC2. ILC2 cultures demonstrated that IFN-γ(+)ILC2 clones could be derived and were stably associated with increased T-BET expression. The inductive mechanism for ILC2 plasticity was mapped to the IL-12-IL-12R signaling pathway and was confirmed through analysis of patients with Mendelian susceptibility to mycobacterial disease due to IL-12Rβ1 deficiencies that failed to generate plastic ILC2. We also detected IL-13(+)IFN-γ(+)ILC2 ex vivo in intestinal samples from Crohn's disease patients. These results demonstrate cytokine production plasticity for human ILC2 and further suggest that environmental cues can dictate ILC phenotype and function for these tissue-resident innate effector cells.

  18. Data-driven visualization and group analysis of multichannel EEG coherence with functional units.

    PubMed

    ten Caat, Michael; Maurits, Natasha M; Roerdink, Jos B T M

    2008-01-01

    A typical data-driven visualization of electroencephalography (EEG) coherence is a graph layout, with vertices representing electrodes and edges representing significant coherences between electrode signals. A drawback of this layout is its visual clutter for multichannel EEG. To reduce clutter, we define a functional unit (FU) as a data-driven region of interest (ROI). An FU is a spatially connected set of electrodes recording pairwise significantly coherent signals, represented in the coherence graph by a spatially connected clique. Earlier we presented two methods to detect FUs: a maximal clique based (MCB) method (time complexity O(3n/3), with n being the number of vertices) and a more efficient watershed based (WB) method (time complexity O (n2 log n)). To reduce the potential over-segmentation of the WB method, we introduce here an improved WB (IWB) method (time complexity O(n2 log n)). The IWB method merges basins representing FUs during the segmentation if they are spatially connected and if their union is a clique. The WB and IWB methods are both up to a factor of 100,000 faster than the MCB method for a typical multichannel setting with 128 EEG channels, thus making interactive visualization of multichannel EEG coherence possible. Results show that considering the MCB method as the gold standard, the difference between IWB and MCB FU maps is smaller than between WB and MCB FU maps. We also introduce two novel group maps for data-driven group analysis as extensions of the IWB method. First, the group mean coherence map preserves dominant features from a collection of individual FU maps. Second, the group FU size map visualizes the average FU size per electrode across a collection of individual FU maps. Finally, we employ an extensive case study to evaluate the IWB FU map and the two new group maps for data-driven group analysis. Results, in accordance with the conventional findings, indicate differences in EEG coherence between younger and older adults

  19. Expansion and Functional Divergence of AP2 Group Genes in Spermatophytes Determined by Molecular Evolution and Arabidopsis Mutant Analysis

    PubMed Central

    Wang, Pengkai; Cheng, Tielong; Lu, Mengzhu; Liu, Guangxin; Li, Meiping; Shi, Jisen; Lu, Ye; Laux, Thomas; Chen, Jinhui

    2016-01-01

    The APETALA2 (AP2) genes represent the AP2 group within a large group of DNA-binding proteins called AP2/EREBP. The AP2 gene is functional and necessary for flower development, stem cell maintenance, and seed development, whereas the other members of AP2 group redundantly affect flowering time. Here we study the phylogeny of AP2 group genes in spermatophytes. Spermatophyte AP2 group genes can be classified into AP2 and TOE types, six clades, and we found that the AP2 group homologs in gymnosperms belong to the AP2 type, whereas TOE types are absent, which indicates the AP2 type gene are more ancient and TOE type was split out of AP2 type and losing the major function. In Brassicaceae, the expansion of AP2 and TOE type lead to the gene number of AP2 group were up to six. Purifying selection appears to have been the primary driving force of spermatophyte AP2 group evolution, although positive selection occurred in the AP2 clade. The transition from exon to intron of AtAP2 in Arabidopsis mutant leads to the loss of gene function and the same situation was found in AtTOE2. Combining this evolutionary analysis and published research, the results suggest that typical AP2 group genes may first appear in gymnosperms and diverged in angiosperms, following expansion of group members and functional differentiation. In angiosperms, AP2 genes (AP2 clade) inherited key functions from ancestors and other genes of AP2 group lost most function but just remained flowering time controlling in gene formation. In this study, the phylogenies of AP2 group genes in spermatophytes was analyzed, which supported the evidence for the research of gene functional evolution of AP2 group. PMID:27703459

  20. Abundances in Sagittarius Stars

    NASA Astrophysics Data System (ADS)

    Bonifacio, P.; Zaggia, S.; Sbordone, L.; Santin, P.; Monaco, L.; Monai, S.; Molaro, P.; Marconi, G.; Girardi, L.; Ferraro, F.; di Marcantonio, P.; Caffau, E.; Bellazzini, M.

    The Sagittarius dwarf spheroidal is a very complex galaxy, which has undergone prolonged star formation. From the very first high resolution chemical analysis of Sgr stars, conducted using spectra obtained during the commissioning of UVES at VLT, it was clear that the star had undergone a high level of chemical processing, at variance with most of the other Local Group dwarf spheroidals. Thanks to FLAMES at VLT we now have accurate metallicities and abundances of alpha-chain elements for about 150 stars, which provide the first reliable metallicity distribution for this galaxy. Besides the already known high metallicity tail the existence of a metal-poor population has also been highlighted, although an assessment of the fraction of Sgr stars which belong to this population requires a larger sample. From our data it is also obvious that Sagittarius is a nucleated galaxy and that the centre of the nucleus coincides with M54, as already shown by Monaco et al.

  1. Functional renormalization group analysis of the soft mode at the QCD critical point

    NASA Astrophysics Data System (ADS)

    Yokota, Takeru; Kunihiro, Teiji; Morita, Kenji

    2016-07-01

    We make an intensive investigation of the soft mode at the quantum chromodynamics (QCD) critical point on the basis of the functional renormalization group (FRG) method in the local potential approximation. We calculate the spectral functions ρ_{σ, π}(ω, p) in the scalar (σ) and pseudoscalar (π) channels beyond the random phase approximation in the quark-meson model. At finite baryon chemical potential μ with a finite quark mass, the baryon-number fluctuation is coupled to the scalar channel and the spectral function in the σ channel has a support not only in the time-like (ω > p) but also in the space-like (ω < p) regions, which correspond to the mesonic and the particle-hole phonon excitations, respectively. We find that the energy of the peak position of the latter becomes vanishingly small with the height being enhanced as the system approaches the QCD critical point, which is a manifestation of the fact that the phonon mode is the soft mode associated with the second-order transition at the QCD critical point, as has been suggested by some authors. Moreover, our extensive calculation of the spectral function in the (ω, p) plane enables us to see that the mesonic and phonon modes have the respective definite dispersion relations ω_{σ.ph}(p), and it turns out that ω_{σ}(p) crosses the light-cone line into the space-like region, and then eventually merges into the phonon mode as the system approaches the critical point more closely. This implies that the sigma-mesonic mode also becomes soft at the critical point. We also provide numerical stability conditions that are necessary for obtaining the accurate effective potential from the flow equation.

  2. Evolution of long-lived globular cluster stars. II. Sodium abundance variations on the asymptotic giant branch as a function of globular cluster age and metallicity

    NASA Astrophysics Data System (ADS)

    Charbonnel, Corinne; Chantereau, William

    2016-02-01

    Context. Long-lived stars in globular clusters exhibit chemical peculiarities with respect to their halo counterparts. In particular, sodium-enriched stars are identified as belonging to a second stellar population born from cluster material contaminated by the hydrogen-burning ashes of a first stellar population. Their presence and numbers in different locations of the colour-magnitude diagram provide important constraints on the self-enrichment scenarios. In particular, the ratio of Na-poor to Na-rich stars on the asymptotic giant branch (AGB) has recently been found to vary strongly from cluster to cluster (NGC 6752, 47 Tuc, and NGC 2808), while it is relatively constant on the red giant branch (RGB). Aims: We investigate the impact of both age and metallicity on the theoretical sodium spread along the AGB within the framework of the fast rotating massive star (FRMS) scenario for globular cluster self-enrichment. Methods: We computed evolution models of low-mass stars for four different metallicities ([Fe/H] = -2.2, -1.75, -1.15, -0.5) assuming the initial helium-sodium abundance correlation for second population stars derived from the FRMS models and using mass loss prescriptions on the RGB with two realistic values of the free parameter in the Rei